U.S. patent application number 14/020054 was filed with the patent office on 2014-11-06 for novel fungal enzymes.
This patent application is currently assigned to DYADIC INTERNATIONAL, INC.. The applicant listed for this patent is DYADIC INTERNATIONAL, INC.. Invention is credited to Mark A. EMARLFARB, Mark Gosink, Alexander Vasilievich Gusakov, Sandra Wihelmina Agnes Hinz, Zhijie Jiang, Peter J. Punt, Arkady Panteleimonovich Sinitsyn, Jan Cornelis Verdoes, Elena Vlasenko.
Application Number | 20140329292 14/020054 |
Document ID | / |
Family ID | 40429719 |
Filed Date | 2014-11-06 |
United States Patent
Application |
20140329292 |
Kind Code |
A1 |
EMARLFARB; Mark A. ; et
al. |
November 6, 2014 |
NOVEL FUNGAL ENZYMES
Abstract
This invention relates to novel enzymes and novel methods for
producing the same. More specifically this invention relates to a
variety of fungal enzymes. Nucleic acid molecules encoding such
enzymes, compositions, recombinant and genetically modified host
cells, and methods of use are described. The invention also relates
to a method to convert lignocellulosic biomass to fermentable
sugars with enzymes that degrade the lignocellulosic material and
novel combinations of enzymes, including those that provide a
synergistic release of sugars from plant biomass. The invention
also relates to a method to release cellular content by degradation
of cell walls. The invention also relates to methods to use the
novel enzymes and compositions of such enzymes in a variety of
other processes, including washing of clothing, detergent
processes, biorefining, deinking and biobleaching of paper and
pulp, and treatment of waste streams.
Inventors: |
EMARLFARB; Mark A.;
(Jupiter, FL) ; Gusakov; Alexander Vasilievich;
(Moscow, RU) ; Punt; Peter J.; (Houten, NL)
; Verdoes; Jan Cornelis; (Bennekom, NL) ;
Sinitsyn; Arkady Panteleimonovich; (Moscow, RU) ;
Vlasenko; Elena; (Davis, CA) ; Hinz; Sandra Wihelmina
Agnes; (Wageningen, NL) ; Gosink; Mark;
(Wellington, FL) ; Jiang; Zhijie; (West Palm
Beach, FL) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
DYADIC INTERNATIONAL, INC. |
Jupiter |
FL |
US |
|
|
Assignee: |
DYADIC INTERNATIONAL, INC.
Jupiter
FL
|
Family ID: |
40429719 |
Appl. No.: |
14/020054 |
Filed: |
September 6, 2013 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
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12205694 |
Sep 5, 2008 |
8551751 |
|
|
14020054 |
|
|
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60970876 |
Sep 7, 2007 |
|
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Current U.S.
Class: |
435/198 ;
435/197; 435/209; 435/252.3; 435/254.11; 435/254.3; 435/254.5;
435/254.6; 435/254.7; 435/254.8; 435/257.2; 435/320.1; 435/419;
536/23.2 |
Current CPC
Class: |
C12N 9/248 20130101;
C12Y 302/01023 20130101; Y02E 50/10 20130101; C12N 9/2434 20130101;
C12Y 302/01151 20130101; C12N 9/2471 20130101; C12Y 302/01037
20130101; C12Y 302/01139 20130101; C07H 21/00 20130101; C12N 9/2402
20130101; Y02E 50/17 20130101; Y02E 50/16 20130101; C12N 9/2408
20130101; C12Y 302/01055 20130101; C12Y 301/01072 20130101; C12Y
302/01155 20130101; A61P 29/00 20180101 |
Class at
Publication: |
435/198 ;
536/23.2; 435/320.1; 435/254.11; 435/419; 435/257.2; 435/252.3;
435/254.5; 435/254.8; 435/254.7; 435/254.3; 435/254.6; 435/209;
435/197 |
International
Class: |
C12N 9/24 20060101
C12N009/24; C12N 9/42 20060101 C12N009/42; C12N 9/26 20060101
C12N009/26 |
Claims
1. An isolated nucleic acid molecule comprising a nucleic acid
sequence selected from the group consisting of: (a) a nucleic acid
sequence encoding a polypeptide comprising an amino acid sequence
selected from the group consisting of: SEQ ID NO: 2, SEQ ID NO: 5,
SEQ ID NO: 8, SEQ ID NO: 11, SEQ ID NO: 14, SEQ ID NO: 17, SEQ ID
NO: 20, SEQ ID NO: 23, SEQ ID NO: 26, SEQ ID NO: 29, SEQ ID NO: 32,
SEQ ID NO: 35, SEQ ID NO: 38, SEQ ID NO: 41, SEQ ID NO: 44, SEQ ID
NO: 47, SEQ ID NO: 50, SEQ ID NO: 53, SEQ ID NO: 56, SEQ ID NO: 59,
SEQ ID NO: 62, SEQ ID NO: 65, SEQ ID NO: 68, SEQ ID NO: 71, SEQ ID
NO: 74, SEQ ID NO: 77, SEQ ID NO: 80, SEQ ID NO: 83, SEQ ID NO: 86,
SEQ ID NO: 89, SEQ ID NO: 92, SEQ ID NO: 95, SEQ ID NO: 98, SEQ ID
NO: 101, SEQ ID NO: 104, SEQ ID NO: 107, SEQ ID NO: 110, SEQ ID NO:
113, SEQ ID NO: 116, SEQ ID NO: 119, SEQ ID NO: 122, SEQ ID NO:
125, SEQ ID NO: 128, SEQ ID NO: 131, SEQ ID NO: 134, SEQ ID NO:
137, SEQ ID NO: 140, SEQ ID NO: 143, SEQ ID NO: 146, SEQ ID NO:
149, SEQ ID NO: 152, SEQ ID NO: 155, SEQ ID NO: 158, SEQ ID NO:
161, SEQ ID NO: 164, SEQ ID NO: 167, SEQ ID NO: 170, SEQ ID NO:
173, SEQ ID NO: 176, SEQ ID NO: 179, SEQ ID NO: 182, SEQ ID NO:
185, SEQ ID NO: 188, SEQ ID NO: 191, SEQ ID NO: 194, SEQ ID NO:
197, SEQ ID NO: 200, SEQ ID NO: 203, SEQ ID NO: 206, SEQ ID NO:
209, SEQ ID NO: 212, SEQ ID NO: 215, SEQ ID NO: 218, SEQ ID NO:
221, SEQ ID NO: 224, SEQ ID NO: 227, SEQ ID NO: 230, and SEQ ID NO:
233. (b) a nucleic acid sequence encoding a fragment of a
polypeptide specified in (a), wherein the fragment retains at least
one biological activity said polypeptide; and (c) a nucleic acid
sequence encoding an amino acid sequence that is at least about 70%
identical to a polypeptide specified in (a) and retains at least
one biological activity of said polypeptide.
2. The isolated nucleic acid molecule of claim 1, wherein said
nucleic acid sequence comprises a nucleic acid sequence selected
from the group consisting of: SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID
NO: 4, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 10, SEQ
ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO:
18, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 24, SEQ
ID NO: 25, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO:
31, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 37, SEQ
ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO:
45, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 51, SEQ
ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO:
58, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 63, SEQ ID NO: 64, SEQ
ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO:
72, SEQ ID NO: 73, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 78, SEQ
ID NO: 79, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 84, SEQ ID NO:
85, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 91, SEQ
ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 96, SEQ ID NO: 97, SEQ ID NO:
99, SEQ ID NO: 100, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 105,
SEQ ID NO: 106, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 111, SEQ
ID NO: 112, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID
NO: 118, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 123, SEQ ID NO:
124, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 129, SEQ ID NO:
130, SEQ ID NO: 132, SEQ ID NO: 133, SEQ ID NO: 135, SEQ ID NO:
136, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 141, SEQ ID NO:
142, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 147, SEQ ID NO:
148, SEQ ID NO: 150, SEQ ID NO: 151, SEQ ID NO: 153, SEQ ID NO:
154, SEQ ID NO: 156, SEQ ID NO: 157, SEQ ID NO: 159, SEQ ID NO:
160, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 165, SEQ ID NO:
166, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 171, SEQ ID NO:
172, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 177, SEQ ID NO:
178, SEQ ID NO: 180, SEQ ID NO: 181, SEQ ID NO: 183, SEQ ID NO:
184, SEQ ID NO: 186, SEQ ID NO: 187, SEQ ID NO: 189, SEQ ID NO:
190, SEQ ID NO: 192, SEQ ID NO: 193, SEQ ID NO: 195, SEQ ID NO:
196, SEQ ID NO: 198, SEQ ID NO: 199, SEQ ID NO: 201, SEQ ID NO:
202, SEQ ID NO: 204, SEQ ID NO: 205, SEQ ID NO: 207, SEQ ID NO:
208, SEQ ID NO: 210, SEQ ID NO: 211, SEQ ID NO: 213, SEQ ID NO:
214, SEQ ID NO: 216, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO:
220, SEQ ID NO: 222, SEQ ID NO: 223, SEQ ID NO: 225, SEQ ID NO:
226, SEQ ID NO: 228, SEQ ID NO: 229, SEQ ID NO: 231, SEQ ID NO:
232, and SEQ ID NO: 234.
3. A vector comprising the nucleic acid of claim 1.
4. A vector comprising the nucleic acid of claim 1, wherein said
nucleic acid is operably-linked to a promoter.
5. A modified cell comprising the nucleic acid of claim 1.
6. The modified cell of claim 5, wherein said nucleic acid is
operably-linked to a promoter functional in said cell.
7. The modified cell of claim 6, wherein said cell is selected from
the group consisting of: a fungal cell, a plant cell, an algal
cell, and a bacterial cell.
8. The modified cell of claim 7, wherein said cell is a fungal cell
selected from the group consisting of: a yeast cell, a mushroom
cell, and a filamentous fungus cell.
9. The modified cell of claim 8, wherein said filamentous fungus
cell is from a genus selected from the group consisting of:
Chrysosporium, Thielavia, Neurospora, Aureobasidium, Filibasidium,
Piromyces, Corynascus, Cryplococcus, Acremonium, Tolypocladium,
Scytalidium, Schizophyllum, Sporotrichum, Penicillium, Gibberella,
Myceliophthora, Mucor, Aspergillus, Fusarium, Humicola, and
Trichoderma, and anamorphs and teleomorphs thereof.
10. The modified cell of claim 9, wherein said cell comprises at
least one additional nucleic acid encoding at least one additional
polypeptide, wherein said additional nucleic acid is
operably-linked to a promoter functional in said cell.
11. The modified cell of claim 10, wherein said additional
polypeptide is an enzyme selected from the group consisting of:
cellulase, glucosidase, xylanase, xylosidase, ligninase,
glucuronidase, arabinofuranosidase, arabinase, arabinogalactanase,
ferulic acid esterase, lipase, pectinase, glucomannase, amylase,
laminarinase, xyloglucanase, galactanase, galactosidase,
glucoamylase, pectate lyase, chitosanases,
exo-.beta.-D-glucosaminidase, cellobiose dehydrogenase, and
acetylxylan esterase.
12. A method of preparing a composition comprising one or more
polypeptides obtained from the modified cell of claim 6,
comprising: (a) growing said modified cell in a medium; (b)
preparing a cell-free medium; and (c) concentrating and/or
purifying one or more polypeptides from said cell-free medium.
13. A composition comprising one or more polypeptides isolated from
a modified cell of claim 11.
14. The composition of claim 13, further comprising at least one
additional polypeptide for degrading a lignocellulosic material or
a fragment thereof that retains biological activity of said
additional polypeptide.
15. The enzyme composition of claim 14, wherein said composition
comprises at least one cellobiohydrolase, at least one xylanase, at
least one endoglucanase, at least one .beta.-glucosidase, at least
one .beta.-xylosidase, and at least one accessory enzyme.
16. The enzyme composition of claim 14, wherein between about 50%
and about 70% of the enzymes in the composition are
cellobiohydrolases.
17. The enzyme composition of claim 14, wherein between about 10%
and about 30% of the enzymes in the composition are xylanases.
18. The enzyme composition of claim 14, wherein between about 5%
and about 15% of the enzymes in the composition are
endoglucanases.
19. The enzyme composition of claim 14, wherein between about 1%
and about 5% of the enzymes in the composition are
.beta.-glucosidases.
20. The enzyme composition of claim 14, wherein between about 1%
and about 3% of the enzymes in the composition are
.beta.-xylosidases.
21. The enzyme composition of claim 14, wherein the composition
comprises about 60% cellobiohydrolases, about 20% xylanases, about
10% endoglucanases, about 3% .beta.-glucosidases, about 2%
xylosidases, and about 5% accessory enzymes.
22. The enzyme composition of claim 21, wherein the xylanases are
selected from the group consisting of: endoxylanases, exoxylanases,
and .beta.-xylosidases.
23. The enzyme composition of claim 21, wherein the accessory
enzymes include an enzyme selected from the group consisting of:
cellulase, glucosidase, xylanase, xylosidase, ligninase,
glucuronidase, arabinofuranosidase, arabinase, arabinogalactanase,
ferulic acid esterase, lipase, pectinase, glucomannase, amylase,
laminarinase, xyloglucanase, galactanase, galactosidase,
glucoamylase, pectate lyase, chitosanases,
exo-.beta.-D-glucosaminidase, cellobiose dehydrogenase, and
acetylxylan esterase.
24. The composition of claim 13, wherein the multi-enzyme
composition comprises at least one hemicellulase.
25. The composition of claim 24, wherein the hemicellulase is
selected from the group consisting of a xylanase, an
arabinofuranosidase, an acetyl xylan esterase, a glucuronidase, and
endo-galactanase, a mannanase, an endo arabinase, an exo arabinase,
an exo-galactanase, a ferulic acid esterase, a galactomannanase, a
xylogluconase, and mixtures thereof.
26. The composition of claim 25, wherein the xylanase is selected
from the group consisting of endoxylanases, exoxylanase, and
.beta.-xylosidase.
27. The composition of claim 13, wherein the multi-enzyme
composition comprises at least one cellulase.
28. The composition of claim 13, wherein the composition is a crude
fermentation product.
29. The composition of claim 13, wherein the composition is a crude
fermentation product that has been subjected to a purification
step.
30. The composition of claim 13, further comprising one or more
accessory enzymes.
31. The composition of claim 30, wherein the accessory enzymes
includes at least one enzyme selected from the group consisting of:
cellulase, glucosidase, xylanase, xylosidase, ligninase,
glucuronidase, arabinofuranosidase, arabinase, arabinogalactanase,
ferulic acid esterase, lipase, pectinase, glucomannase, amylase,
laminarinase, xyloglucanase, galactanase, galactosidase,
glucoamylase, pectate lyase, chitosanases,
exo-.beta.-D-glucosaminidase, cellobiose dehydrogenase, and
acetylxylan esterase.
32. The composition of claim 30, wherein the accessory enzyme is
selected from the group consisting of a glucoamylase, a pectinase,
and a ligninase.
33. The composition of claim 30, wherein the accessory enzyme is a
glucoamylase.
34. The composition of claim 30, wherein the accessory enzyme is
added as a crude or a semi-purified enzyme mixture.
35. The composition of claim 30, wherein the accessory enzyme is
produced by culturing at least one organism on a substrate to
produce the enzyme.
36. An composition comprising at least one polypeptide of claim 13,
and at least one additional polypeptide for degrading an
arabinoxylan-containing material or a fragment thereof that has
biological activity.
37. The composition of claim 36, wherein the composition comprises
at least one endoxylanase, at least one .beta.-xylosidase, and at
least one arabinofuranosidase.
38. The composition of claim 36, wherein the at least one
arabinofuranosidase comprises an arabinofuranosidase with
specificity towards single substituted xylose residues, an
arabinofuranosidase with specificity towards double substituted
xylose residues, or a combination thereof.
39. A purified polypeptide comprising an amino acid sequence
encoded by the nucleic acid molecule of claim 1.
40. A purified polypeptide comprising an amino acid sequence
encoded by the nucleic acid molecule of claim 2.
Description
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit of priority under 35
U.S.C. .sctn.119(e) of U.S. Provisional Application No. 60/970,876,
filed on Sep. 7, 2007, and also claims benefit under 35 U.S.C.
.sctn.120 to U.S. application Ser. No. U.S. Ser. No. 12/205,694,
filed Sep. 5, 2008 both of which are herein incorporated by
reference in its entirety.
INCORPORATION-BY-REFERENCE OF A SEQUENCE LISTING
[0002] This application contains a Sequence Listing submitted as an
electronic text file named "124702.sub.--0278_D2_ST25.txt", having
a size in bytes of 1,034,075 bytes, created on Sep. 5, 2013, and
modified on Sep. 5, 2013. The information contained in this
electronic file is hereby incorporated by reference in its entirety
pursuant to 37 CFR .sctn.1.52(e)(5).
FIELD OF THE INVENTION
[0003] This invention relates to novel enzymes and novel methods
for producing the same. More specifically this invention relates to
enzymes produced by fungi. The invention also relates to a method
to convert lignocellulosic biomass to fermentable sugars with
enzymes that degrade the lignocellulosic material and novel
combinations of enzymes, including those that provide a synergistic
release of sugars from plant biomass. The invention also relates to
a method to release cellular contents by effecting degradation of
the cell walls. The invention also relates to methods to use the
novel enzymes and compositions of such enzymes in a variety of
other processes, such as washing of clothing, detergent processes,
animal feed, food, beverage, biorefining, deinking and biobleaching
of paper and pulp, and treatment of air waste streams.
BACKGROUND OF THE INVENTION
[0004] Large amounts of carbohydrates in plant biomass provide a
plentiful source of potential energy in the form of sugars (both
five carbon and six carbon sugars) that can be utilized for
numerous industrial and agricultural processes. However, the
enormous energy potential of these carbohydrates is currently
under-utilized because the sugars are locked in complex polymers,
and hence are not readily accessible for fermentation. These
complex polymers are often referred to collectively as
lignocellulose. Sugars generated from degradation of plant biomass
potentially represent plentiful, economically competitive
feedstocks for fermentation into chemicals, plastics, and fuels,
including ethanol as a substitute for petroleum.
[0005] For example, distillers' dried grains (DDG) are
lignocellulosic byproducts of the corn dry milling process. Milled
whole corn kernels are treated with amylases to liquefy the starch
within the kernels and hydrolyze it to glucose. The glucose so
produced is then fermented in a second step to ethanol. The
residual solids after the ethanol fermentation and distillation are
centrifuged and dried, and the resulting product is DDG, which is
used as an animal feed stock. Although DDG composition can vary, a
typical composition for DDG is: about 32% hemicellulose, 22%
cellulose, 30% protein, 10% lipids, 4% residual starch, and 4%
inorganics. In theory, the cellulose and hemicellulose fractions,
comprising about 54% of the weight of the DDG, can be efficiently
hydrolyzed to fermentable sugars by enzymes; however, it has been
found that the carbohydrates comprising lignocellulosic materials
in DDG are more difficult to digest. To date, the efficiency of
hydrolysis of these (hemi) cellulosic polymers by enzymes is much
lower than the hydrolytic efficiency of starch, due to the more
complex and recalcitrant nature of these substrates. Accordingly,
the cost of producing the requisite enzymes is higher than the cost
of producing amylases for starch hydrolysis.
[0006] Major polysaccharides comprising lignocellulosic materials
include cellulose and hemicelluloses. The enzymatic hydrolysis of
these polysaccharides to soluble sugars (and finally to monomers
such as glucose, xylose and other hexoses and pentoses) is
catalyzed by several enzymes acting in concert. For example,
endo-1,4-.beta.-glucanases (EGs) and exo-cellobiohydrolases (CBHs)
catalyze the hydrolysis of insoluble cellulose to
cellooligosaccharides (with cellobiose the main product), while
.beta.-glucosidases (BGLs) convert the oligosaccharides to glucose.
Similarly, xylanases, together with other enzymes such as
.alpha.-L-arabinofuranosidases, ferulic and acetylxylan esterases
and .beta.-xylosidases, catalyze the hydrolysis of
hemicelluloses.
[0007] Regardless of the type of cellulosic feedstock, the cost and
hydrolytic efficiency of enzymes are major factors that restrict
the widespread use of biomass bioconversion processes. The
hydrolytic efficiency of a multi-enzyme complex in the process of
lignocellulosic saccharification depends both on properties of the
individual enzymes and the ratio of each enzyme within the
complex.
[0008] Enzymes useful for the hydrolysis of complex polysaccharides
are also highly useful in a variety of industrial textile
applications, as well as industrial paper and pulp applications,
and in the treatment of waste streams. For example, as an
alternative to the use of pumice in the stone washing process,
methods for treating cellulose-containing fabrics for clothing with
hydrolytic enzymes, such as cellulases, are known to improve the
softness or feel of such fabrics. Cellulases are also used in
detergent compositions, either for the purpose of enhancing the
cleaning ability of the composition or as a softening agent.
Cellulases are also used in combination with polymeric agents in
processes for providing a localized variation in the color density
of fibers. Such enzymes can also be used for the saccharification
of lignocellulosic biomass in waste streams, such as municipal
solid waste, for biobleaching of wood pulp, and for deinking of
recycled print paper. As with the hydrolysis of these
polysaccharides in lignocellulosic materials for use as feedstocks
described above, the cost and hydrolytic efficiency of the enzymes
are major factors that control the use of enzymes in these
processes.
[0009] Filamentous fungi are a source of cellulases and
hemicellulases, as well as other enzymes useful in the enzymatic
hydrolysis of major polysaccharides. In particular, strains of
Trichodenna sp., such as T. viride, T. reesei and T.
longibrachiatum, and Penicillium sp., and enzymes derived from
these strains, have previously been used to hydrolyze crystalline
cellulose. However, the costs associated with producing enzymes
from these fungi, as well as the presence of additional,
undesirable enzymes, remains a drawback. It is therefore desirable
to produce inexpensive enzymes and enzyme mixtures that efficiently
degrade cellulose and hemicellulose for use in a variety of
agricultural and industrial applications.
SUMMARY OF THE INVENTION
[0010] In one embodiment, the present invention comprises an
isolated nucleic acid molecule comprising a nucleic acid sequence
selected from the group consisting of:
[0011] a) a nucleic acid sequence encoding a protein comprising an
amino acid sequence selected from the group consisting of: SEQ ID
NO: 2, SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 11, SEQ ID NO: 14,
SEQ ID NO: 17, SEQ ID NO: 20, SEQ ID NO: 23, SEQ ID NO: 26, SEQ ID
NO: 29, SEQ ID NO: 32, SEQ ID NO: 35, SEQ ID NO: 38, SEQ ID NO: 41,
SEQ ID NO: 44, SEQ ID NO: 47, SEQ ID NO: 50, SEQ ID NO: 53, SEQ ID
NO: 56, SEQ ID NO: 59, SEQ ID NO: 62, SEQ ID NO: 65, SEQ ID NO: 68,
SEQ ID NO: 71, SEQ ID NO: 74, SEQ ID NO: 77, SEQ ID NO: 80, SEQ ID
NO: 83, SEQ ID NO: 86, SEQ ID NO: 89, SEQ ID NO: 92, SEQ ID NO: 95,
SEQ ID NO: 98, SEQ ID NO: 101, SEQ ID NO: 104, SEQ ID NO: 107, SEQ
ID NO: 110, SEQ ID NO: 113, SEQ ID NO: 116, SEQ ID NO: 119, SEQ ID
NO: 122, SEQ ID NO: 125, SEQ ID NO: 128, SEQ ID NO: 131, SEQ ID NO:
134, SEQ ID NO: 137, SEQ ID NO: 140, SEQ ID NO: 143, SEQ ID NO:
146, SEQ ID NO: 149, SEQ ID NO: 152, SEQ ID NO: 155, SEQ ID NO:
158, SEQ ID NO: 161, SEQ ID NO: 164, SEQ ID NO: 167, SEQ ID NO:
170, SEQ ID NO: 173, SEQ ID NO: 176, SEQ ID NO: 179, SEQ ID NO:
182, SEQ ID NO: 185, SEQ ID NO: 188, SEQ ID NO: 191, SEQ ID NO:
194, SEQ ID NO: 197, SEQ ID NO: 200, SEQ ID NO: 203, SEQ ID NO:
206, SEQ ID NO: 209, SEQ ID NO: 212, SEQ ID NO: 215, SEQ ID NO:
218, SEQ ID NO: 221, SEQ ID NO: 224, SEQ ID NO: 227, SEQ ID NO:
230, and SEQ ID NO: 233.
[0012] b) a nucleic acid sequence encoding a fragment of the
protein of (a), wherein the fragment has a biological activity of
the protein of (a); and
[0013] c) a nucleic acid sequence encoding an amino acid sequence
that is at least about 70% identical to an amino acid sequence of
(a) and has a biological activity of the protein comprising the
amino acid sequence.
[0014] In some embodiments, the nucleic acid sequence encodes an
amino acid sequence that is at least about 90%, at least about 95%,
at least about 97% or at least about 99% identical to the amino
acid sequence of (a) and has a biological activity of the protein
comprising the amino acid sequence.
[0015] In some embodiments, the nucleic acid sequence encodes a
protein comprising an amino acid sequence selected from the group
consisting of: SEQ ID NO: 2, SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO:
1, SEQ ID NO: 14, SEQ ID NO: 17, SEQ ID NO: 20, SEQ ID NO: 23, SEQ
ID NO: 26, SEQ ID NO: 29, SEQ ID NO: 32, SEQ ID NO: 35, SEQ ID NO:
38, SEQ ID NO: 41, SEQ ID NO: 44, SEQ ID NO: 47, SEQ ID NO: 50, SEQ
ID NO: 53, SEQ ID NO: 56, SEQ ID NO: 59, SEQ ID NO: 62, SEQ ID NO:
65, SEQ ID NO: 68, SEQ ID NO: 71, SEQ ID NO: 74, SEQ ID NO: 77, SEQ
ID NO: 80, SEQ ID NO: 83, SEQ ID NO: 86, SEQ ID NO: 89, SEQ ID NO:
92, SEQ ID NO: 95, SEQ ID NO: 98, SEQ ID NO: 101, SEQ ID NO: 104,
SEQ ID NO: 107, SEQ ID NO: 110, SEQ ID NO: 113, SEQ ID NO: 116, SEQ
ID NO: 119, SEQ ID NO: 122, SEQ ID NO: 125, SEQ ID NO: 128, SEQ ID
NO: 131, SEQ ID NO: 134, SEQ ID NO: 137, SEQ ID NO: 140, SEQ ID NO:
143, SEQ ID NO: 146, SEQ ID NO: 149, SEQ ID NO: 152, SEQ ID NO:
155, SEQ ID NO: 158, SEQ ID NO: 161, SEQ ID NO: 164, SEQ ID NO:
167, SEQ ID NO: 170, SEQ ID NO: 173, SEQ ID NO: 176, SEQ ID NO:
179, SEQ ID NO: 182, SEQ ID NO: 185, SEQ ID NO: 188, SEQ ID NO:
191, SEQ ID NO: 194, SEQ ID NO: 197, SEQ ID NO: 200, SEQ ID NO:
203, SEQ ID NO: 206, SEQ ID NO: 209, SEQ ID NO: 212, SEQ ID NO:
215, SEQ ID NO: 218, SEQ ID NO: 221, SEQ ID NO: 224, SEQ ID NO:
227, SEQ ID NO: 230, and SEQ ID NO: 233.
[0016] In some embodiments, the nucleic acid sequence comprises a
nucleic acid sequence selected from the group consisting of: SEQ ID
NO: 1, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 7, SEQ
ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO:
15, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 21, SEQ
ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 27, SEQ ID NO:
28, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 34, SEQ
ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO:
42, SEQ ID NO: 43, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 48, SEQ
ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO:
55, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 61, SEQ
ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO:
69, SEQ ID NO: 70, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 75, SEQ
ID NO: 76, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 81, SEQ ID NO:
82, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 87, SEQ ID NO: 88, SEQ
ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO:
96, SEQ ID NO: 97, SEQ ID NO: 99, SEQ ID NO: 100, SEQ ID NO: 102,
SEQ ID NO: 103, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 108, SEQ
ID NO: 109, SEQ ID NO: 101, SEQ ID NO: 112, SEQ ID NO: 114, SEQ ID
NO: 115, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 120, SEQ ID NO:
121, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 126, SEQ ID NO:
127, SEQ ID NO: 129, SEQ ID NO: 130, SEQ ID NO: 132, SEQ ID NO:
133, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 138, SEQ ID NO:
139, SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 144, SEQ ID NO:
145, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 150, SEQ ID NO:
151, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 156, SEQ ID NO:
157, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 162, SEQ ID NO:
163, SEQ ID NO: 165, SEQ ID NO: 166, SEQ ID NO: 168, SEQ ID NO:
169, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO: 174, SEQ ID NO:
175, SEQ ID NO: 177, SEQ ID NO: 178, SEQ ID NO: 180, SEQ ID NO:
181, SEQ ID NO: 183, SEQ ID NO: 184, SEQ ID NO: 186, SEQ ID NO:
187, SEQ ID NO: 189, SEQ ID NO: 190, SEQ ID NO: 192, SEQ ID NO:
193, SEQ ID NO: 195, SEQ ID NO: 196, SEQ ID NO: 198, SEQ ID NO:
199, SEQ ID NO: 201, SEQ ID NO: 202, SEQ ID NO: 204, SEQ ID NO:
205, SEQ ID NO: 207, SEQ ID NO: 208, SEQ ID NO: 210, SEQ ID NO:
211, SEQ ID NO: 213, SEQ ID NO: 214, SEQ ID NO: 216, SEQ ID NO:
217, SEQ ID NO: 219, SEQ ID NO: 220, SEQ ID NO: 222, SEQ ID NO:
223, SEQ ID NO: 225, SEQ ID NO: 226, SEQ ID NO: 228, SEQ ID NO:
229, SEQ ID NO: 231, SEQ ID NO: 232, and SEQ ID NO: 234.
[0017] In some embodiments, the nucleic acid sequence of (a)
encodes a protein comprising an amino acid sequence selected from
the group consisting of: SEQ ID NO: 29, SEQ ID NO: 32, SEQ ID NO:
35, SEQ ID NO: 38, SEQ ID NO: 41, SEQ ID NO: 44, SEQ ID NO: 47, SEQ
ID NO: 50, SEQ ID NO: 53, SEQ ID NO: 56, SEQ ID NO: 59, SEQ ID NO:
62, SEQ ID NO: 65, SEQ ID NO: 68, SEQ ID NO: 95, SEQ ID NO: 98, SEQ
ID NO: 101, SEQ ID NO: 104, and SEQ ID NO: 107, wherein the protein
has cellulolytic enhancing activity.
[0018] In some embodiments, the present invention comprises nucleic
acid sequences that are fully complementary to any of the nucleic
acid sequences described above.
[0019] In some embodiments, the present invention comprises an
isolated protein comprising an amino acid sequence encoded by any
of the nucleic acid molecules described above.
[0020] In some embodiments, the present invention comprises an
isolated fusion protein comprising an isolated protein of the
present invention fused to a protein comprising an amino acid
sequence that is heterologous to the isolated protein.
[0021] In some embodiments, the present invention comprises an
isolated antibody or antigen binding fragment thereof that
selectively binds to a protein of the present invention.
[0022] In some embodiments, the present invention comprises a kit
for degrading a lignocellulosic material to fermentable sugars
comprising at least one isolated protein of the present
invention.
[0023] In some embodiments, the present invention comprises a
detergent comprising at least one isolated protein of the present
invention.
[0024] In some embodiments, the present invention comprises a
composition for the degradation of a lignocellulosic material
comprising at least one isolated protein of the present
invention.
[0025] In some embodiments, the present invention comprises a
recombinant nucleic acid molecule comprising an isolated nucleic
acid molecule of the present invention, operatively linked to at
least one expression control sequence. In some embodiments, the
recombinant nucleic acid molecule comprises an expression vector.
In some embodiments, the recombinant nucleic acid molecule
comprises a targeting vector.
[0026] In some embodiments, the present invention comprises an
isolated host cell transfected with a nucleic acid molecule of the
present invention. In some embodiments, the host cell is a fungus.
In some embodiments, the host cell is a filamentous fungus. In some
embodiments, the filamentous fungus is from a genus selected from
the group consisting of: Chrysosporium, Thielavia, Neurospora,
Aureobasidium, Filibasidium, Piromyces, Corynascus, Cryplococcus,
Acremonium, Tolypocladium, Scytalidium, Schizophyllum,
Sporotrichum, Penicillium, Gibberella, Myceliophthora, Mucor,
Aspergillus, Fusarium, Humicola, and Trichoderma, and anamorphs and
teleomorphs thereof. In some embodiments, the host cell is a
bacterium.
[0027] In some embodiments, the present invention comprises an
oligonucleotide consisting essentially of at least 12 consecutive
nucleotides of a nucleic acid sequence selected from the group
consisting of: SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO:
6, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID
NO: 13, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 19,
SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID
NO: 27, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 33,
SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID
NO: 40, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 45, SEQ ID NO: 46,
SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID
NO: 54, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 60,
SEQ ID NO: 61, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID
NO: 67, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 72, SEQ ID NO: 73,
SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID
NO: 81, SEQ ID NO: 82, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 87,
SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID
NO: 94, SEQ ID NO: 96, SEQ ID NO: 97, SEQ ID NO: 99, SEQ ID NO:
100, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 105, SEQ ID NO:
106, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 111, SEQ ID NO:
112, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO:
118, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 123, SEQ ID NO:
124, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 129, SEQ ID NO:
130, SEQ ID NO: 132, SEQ ID NO: 133, SEQ ID NO: 135, SEQ ID NO:
136, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 141, SEQ ID NO:
142, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 147, SEQ ID NO:
148, SEQ ID NO: 150, SEQ ID NO: 151, SEQ ID NO: 153, SEQ ID NO:
154, SEQ ID NO: 156, SEQ ID NO: 157, SEQ ID NO: 159, SEQ ID NO:
160, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 165, SEQ ID NO:
166, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 171, SEQ ID NO:
172, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 177, SEQ ID NO:
178, SEQ ID NO: 180, SEQ ID NO: 181, SEQ ID NO: 183, SEQ ID NO:
184, SEQ ID NO: 186, SEQ ID NO: 187, SEQ ID NO: 189, SEQ ID NO:
190, SEQ ID NO: 192, SEQ ID NO: 193, SEQ ID NO: 195, SEQ ID NO:
196, SEQ ID NO: 198, SEQ ID NO: 199, SEQ ID NO: 201, SEQ ID NO:
202, SEQ ID NO: 204, SEQ ID NO: 205, SEQ ID NO: 207, SEQ ID NO:
208, SEQ ID NO: 210, SEQ ID NO: 211, SEQ ID NO: 213, SEQ ID NO:
214, SEQ ID NO: 216, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO:
220, SEQ ID NO: 222, SEQ ID NO: 223, SEQ ID NO: 225, SEQ ID NO:
226, SEQ ID NO: 228, SEQ ID NO: 229, SEQ ID NO: 231, SEQ ID NO:
232, and SEQ ID NO: 234 or the complement thereof.
[0028] In some embodiments, the present invention comprises a kit
comprising at least one oligonucleotide of the present
invention.
[0029] In some embodiments, the present invention comprises methods
for producing a protein of the present invention, comprising
culturing a cell that has been transfected with a nucleic acid
molecule comprising a nucleic acid sequence encoding the protein,
and expressing the protein with the transfected cell. In some
embodiments, the present invention further comprises recovering the
protein from the cell or from a culture comprising the cell.
[0030] In some embodiments, the present invention comprises a
genetically modified organism comprising components suitable for
degrading a lignocellulosic material to fermentable sugars, wherein
the organism has been genetically modified to express at least one
protein of the present invention.
[0031] In some embodiments, the genetically modified organism is a
plant, alga, fungus or bacterium. In some embodiments, the fungus
is yeast, mushroom or filamentous fungus. In some embodiments, the
filamentous fungus is from a genus selected from the group
consisting of: Chrysosporium, Thielavia, Neurospora, Aureobasidium,
Filibasidium, Piromyces, Corynascus, Cryplococcus, Acremonium,
Tolypocladium, Scytalidium, Schizophyllum, Sporotrichum,
Penicillium, Talaromyces, Gibberella, Myceliophthora, Mucor,
Aspergillus, Fusarium, Humicola, and Trichoderma. In some
embodiments, the filamentous fungus is selected from the group
consisting of: Trichoderma reesei, Chrysosporium lucknowense,
Aspergillus japonicus, Penicillium canescens, Penicillium solitum,
Penicillium funiculosum, and Talaromyces flavus.
[0032] In some embodiments, the genetically modified organism has
been genetically modified to express at least one additional
enzyme. In some embodiments, the additional enzyme is an accessory
enzyme selected from the group consisting of: cellulase,
glucosidase, xylanase, xylosidase, ligninase, glucuronidase,
arabinofuranosidase, arabinase, arabinogalactanase, ferulic acid
esterase, lipase, pectinase, glucomannase, amylase, laminarinase,
xyloglucanase, galactanase, galactosidase, glucoamylase, pectate
lyase, chitosanases, exo-.beta.-D-glucosaminidase, cellobiose
dehydrogenase, and acetylxylan esterase.
[0033] In some embodiments, the genetically modified organism is a
plant.
[0034] In some embodiments, the present invention comprises a
recombinant enzyme isolated from a genetically modified
microorganism of the present invention. In some embodiments the
recombinant enzyme has been subjected to a purification step.
[0035] In some embodiments, the present invention comprises a crude
fermentation product produced by culturing the cells from the
genetically modified organism of the present invention, wherein the
crude fermentation product contains at least one protein of the
present invention.
[0036] In some embodiments, the present invention comprises a
multi-enzyme composition comprising enzymes produced by a
genetically modified organism of the present invention, and
recovered therefrom.
[0037] In some embodiments, the present invention comprises a
multi-enzyme composition comprising at least one protein of the
present inventions, and at least one additional protein for
degrading a lignocellulosic material or a fragment thereof that has
biological activity.
[0038] In some embodiments, the multi-enzyme composition comprises
at least one cellobiohydrolase, at least one xylanase, at least one
endoglucanase, at least one .beta.-glucosidase, at least one
.beta.-xylosidase, and at least one accessory enzyme.
[0039] In some embodiments, between about 50% and about 70% of the
enzymes in the multi-enzyme composition are cellobiohydrolases. In
some embodiments, between about 10% and about 30% of the enzymes in
the composition are xylanases. In some embodiments, between about
5% and about 15% of the enzymes in the composition are
endoglucanases. In some embodiments, between about 1% and about 5%
of the enzymes in the composition are .beta.-glucosidases. In some
embodiments, between about 1% and about 3% of the enzymes in the
composition are .beta.-xylosidases.
[0040] In some embodiments, the multi-enzyme composition comprises
about 60% cellobiohydrolases, about 20% xylanases, about 10%
endoglucanases, about 3% .beta.-glucosidases, about 2%
.beta.-xylosidases, and about 5% accessory enzymes.
[0041] In some embodiments, the xylanases are selected from the
group consisting of: endoxylanases, exoxylanases, and
.beta.-xylosidases.
[0042] In some embodiments, the accessory enzymes include an enzyme
selected from the group consisting of: cellulase, glucosidase,
xylanase, xylosidase, ligninase, glucuronidase,
arabinofuranosidase, arabinase, arabinogalactanase, ferulic acid
esterase, lipase, pectinase, glucomannase, amylase, laminarinase,
xyloglucanase, galactanase, galactosidase, glucoamylase, pectate
lyase, chitosanase, exo-.beta.-D-glucosaminidase, cellobiose
dehydrogenase, and acetylxylan esterase.
[0043] In some embodiments, the multi-enzyme composition comprises
at least one hemicellulase. In some embodiments, the hemicellulase
is selected from the group consisting of a xylanase, an
arabinofuranosidase, an acetyl xylan esterase, a glucuronidase, and
endo-galactanase, a mannanase, an endo arabinase, an exo arabinase,
an exo-galactanase, a ferulic acid esterase, a galactomannanase, a
xylogluconase, and mixtures thereof. In some embodiments, the
xylanase is selected from the group consisting of endoxylanases,
exoxylanase, and .beta.-xylosidase.
[0044] In some embodiments, the multi-enzyme composition comprises
at least one cellulase.
[0045] In some embodiments, the composition is a crude fermentation
product. In some embodiments, the composition is a crude
fermentation product that has been subjected to a purification
step.
[0046] In some embodiments, the multi-enzyme composition further
comprises one or more accessory enzymes. In some embodiments, the
accessory enzymes include at least one enzyme selected from the
group consisting of: cellulase, glucosidase, xylanase, xylosidase,
ligninase, glucuronidase, arabinofuranosidase, arabinase,
arabinogalactanase, ferulic acid esterase, lipase, pectinase,
glucomannase, amylase, laminarinase, xyloglucanase, galactanase,
galactosidase, glucoamylase, pectate lyase, chitosanase,
exo-.beta.-D-glucosaminidase, cellobiose dehydrogenase, and
acetylxylan esterase. In some embodiments, the accessory enzyme is
selected from the group consisting of a glucoamylase, a pectinase,
and a ligninase. In some embodiments, the accessory enzyme is added
as a crude or a semi-purified enzyme mixture. In some embodiments,
the accessory enzyme is produced by culturing at least one organism
on a substrate to produce the enzyme.
[0047] In some embodiments, the multi-enzyme composition comprises
at least one protein of the present invention, and at least one
additional protein for degrading an arabinoxylan-containing
material or a fragment thereof that has biological activity.
[0048] In some embodiments, the composition comprises at least one
endoxylanase, at least one .beta.-xylosidase, and at least one
arabinofuranosidase. In some embodiments, the arabinofuranosidase
comprises an arabinofuranosidase with specificity towards single
substituted xylose residues, an arabinofuranosidase with
specificity towards double substituted xylose residues, or a
combination thereof.
[0049] In some embodiments, the present invention comprises methods
for degrading a lignocellulosic material to fermentable sugars,
comprising contacting the lignocellulosic material with at least
one isolated protein of the present invention.
[0050] In some embodiments, the methods of the present invention
further comprise contacting the lignocellulosic material with at
least one additional isolated protein comprising an amino acid
sequence that is at least about 95% identical to an amino acid
sequence selected from the group consisting of: SEQ ID NO: 29, SEQ
ID NO: 32, SEQ ID NO: 35, SEQ ID NO: 38, SEQ ID NO: 41, SEQ ID NO:
44, SEQ ID NO: 47, SEQ ID NO: 50, SEQ ID NO: 53, SEQ ID NO: 56, SEQ
ID NO: 59, SEQ ID NO: 62, SEQ ID NO: 65, SEQ ID NO: 68, SEQ ID NO:
95, SEQ ID NO: 98, SEQ ID NO: 101, SEQ ID NO: 104, and SEQ ID NO:
107, wherein the at least one additional protein has cellulolytic
enhancing activity.
[0051] In some embodiments, the additional isolated protein is part
of a multi-enzyme composition.
[0052] In some embodiments, the present invention comprises methods
for degrading a lignocellulosic material to fermentable sugars,
comprising contacting the lignocellulosic material with at least
one multi-enzyme composition of the present invention.
[0053] In some embodiments, the present invention comprises a
method for producing an organic substance, comprising:
[0054] a) saccharifying a lignocellulosic material with a
multi-enzyme composition of the present invention;
[0055] b) fermenting the saccharified lignocellulosic material
obtained with one or more fermenting microorganisms; and
[0056] c) recovering the organic substance from the
fermentation.
[0057] In some embodiments, the steps of saccharifying and
fermenting are performed simultaneously.
[0058] In some embodiments, the organic substance is an alcohol,
organic acid, ketone, amino acid, or gas. In some embodiments, the
alcohol is ethanol.
[0059] In some embodiments, the lignocellulosic material is
selected from the group consisting of herbaceous material,
agricultural residue, forestry residue, municipal solid waste,
waste paper, and pulp and paper mill residue.
[0060] In some embodiments, the lignocellulosic material is
distiller's dried grains (DDG) or DDG with solubles. In some
embodiments, the DDG or DDG with solubles is derived from corn.
[0061] In some embodiments, the present invention comprises a
method for degrading a lignocellulosic material consisting of DDG
or DDG with solubles to sugars, the method comprising contacting
the DDG or DDG with solubles with a multi-enzyme composition of the
present invention, whereby at least about 10% of the fermentable
sugars are liberated. In some embodiments, at least about 15%, at
least 20%, or at least about 23% of the sugars are liberated.
[0062] In some embodiments, the present invention further comprises
a pretreatment process for pretreating the lignocellulosic
material.
[0063] In some embodiments, the pretreatment process is selected
from the group consisting of physical treatment, metal ion,
ultraviolet light, ozone, organosolv treatment, steam explosion
treatment, lime impregnation with steam explosion treatment,
hydrogen peroxide treatment, hydrogen peroxide/ozone (peroxone)
treatment, acid treatment, dilute acid treatment, and base
treatment. In some embodiments, the pretreatment process is
selected from the group consisting of organosolv, steam explosion,
heat treatment and AFEX. In some embodiments, the heat treatment
comprises heating the lignocellulosic material to 121.degree. C.
for 15 minutes.
[0064] In some embodiments, the present invention further comprises
detoxifying the lignocellulosic material.
[0065] In some embodiments, the present invention further comprises
recovering the fermentable sugar.
[0066] In some embodiments, the sugar is selected from the group
consisting of glucose, xylose, arabinose, galactose, mannose,
rhamnose, sucrose and fructose.
[0067] In some embodiments, the present invention further comprises
recovering the contacted lignocellulosic material after the
fermentable sugars are degraded.
[0068] In some embodiments, the present invention comprises a feed
additive comprising the recovered lignocellulosic material of the
present invention. In some embodiments, the protein content of the
recovered lignocellulosic material is higher than that of the
starting lignocellulosic material.
[0069] In some embodiments, the present invention comprises methods
of improving the performance of an animal which comprises
administering to the animal the feed additive of the present
invention.
[0070] In some embodiments, the present invention comprises methods
for improving the nutritional quality of an animal feed comprising
adding the feed additive of the present invention to an animal
feed.
[0071] In some embodiments, the present invention comprises methods
for stonewashing a fabric, comprising contacting the fabric with at
least one isolated protein of the present invention.
[0072] In some embodiments, the present invention comprises methods
for stonewashing a fabric, comprising contacting the fabric with at
least one multi-enzyme composition of the present invention.
[0073] In some embodiments, the fabric is denim.
[0074] In some embodiments, the present invention comprises methods
for enhancing the softness or feel of a fabric or depilling a
fabric, comprising contacting the fabric with at least one isolated
protein of the present invention, or a fragment thereof comprising
a cellulose binding module (CBM) of the protein.
[0075] In some embodiments, the present invention comprises methods
for enhancing the softness or feel of a fabric or depilling a
fabric, comprising contacting the fabric with at least one
multi-enzyme composition of the present invention.
[0076] In some embodiments, the present invention comprises methods
for restoring color to or brightening a fabric, comprising
contacting the fabric with at least one isolated protein of the
present invention.
[0077] In some embodiments, the present invention comprises methods
for restoring color to or brightening a fabric, comprising
contacting the fabric with at least one multi-enzyme composition of
the present invention.
[0078] In some embodiments, the present invention comprises methods
of biopolishing, defibrillating, bleaching, dyeing or desizing a
fabric, comprising contacting the fabric with at least one isolated
protein of the present invention.
[0079] In some embodiments, the present invention comprises methods
of biopolishing, defibrillating, bleaching, dyeing or desizing a
fabric, comprising contacting the fabric with at least one
multi-enzyme composition of the present invention.
[0080] In some embodiments, the present invention comprises methods
of biorefining, deinking or biobleaching paper or pulp, comprising
contacting the paper or pulp with at least one isolated protein of
the present invention.
[0081] In some embodiments, the present invention comprises methods
of biorefining, deinking or biobleaching paper or pulp, comprising
contacting the paper or pulp with at least one multi-enzyme
composition of the present invention
[0082] In some embodiments, the present invention comprises methods
for enhancing the cleaning ability of a detergent composition,
comprising adding at least one isolated protein of the present
invention to the detergent composition.
[0083] In some embodiments, the present invention comprises methods
for enhancing the cleaning ability of a detergent composition,
comprising adding at least one multi-enzyme composition of the
present invention to the detergent composition.
[0084] In some embodiments, the present invention comprises a
detergent composition, comprising at least one isolated protein of
the present invention and at least one surfactant.
[0085] In some embodiments, the present invention comprises a
detergent composition, comprising at least one multi-enzyme
composition of the present invention and at least one
surfactant.
[0086] In some embodiments, the present invention comprises methods
for inhibiting or reducing fungal growth, comprising contacting a
fungus or an area susceptible to fungal growth with an isolated
protein comprising an amino acid sequence that is at least about
95% identical to the amino acid sequence of SEQ ID NO: 188.
[0087] In some embodiments, the present invention comprises methods
for reducing or preventing insect infestation on a plant,
comprising contacting the plant with an isolated protein comprising
an amino acid sequence that is at least about 95% identical to the
amino acid sequence of SEQ ID NO: 188.
[0088] In some embodiments, the present invention comprises methods
for reducing or preventing allergic inflammation or asthma,
comprising administering an isolated protein comprising an amino
acid sequence that is at least about 95% identical to the amino
acid sequence of SEQ ID NO: 188.
[0089] In some embodiments, the present invention comprises a
lysing enzyme for the generation of protoplasts from fungi,
comprising an isolated protein comprising an amino acid sequence
that is at least about 95% identical to the amino acid sequence of
SEQ ID NO: 188.
[0090] In some embodiments, the present invention comprises an
insecticide composition, comprising an isolated protein comprising
an amino acid sequence that is at least 95% identical to the amino
acid sequence of SEQ ID NO: 188.
[0091] In some embodiments, the present invention comprises methods
for releasing cellular contents comprising contacting a cell with
at least one protein of the present invention.
[0092] In some embodiments, the cell may be a bacterium, an algal
cell, a fungal cell or a plant cell. In preferred embodiments, the
cell is an algal cell.
[0093] In some embodiments, contacting the cell with at least one
protein of the present invention degrades the cell wall.
[0094] In some embodiments, the cellular contents are selected from
the group consisting of: alcohols and oils.
[0095] In some embodiments, the present invention comprises
compositions for degrading cell walls comprising at least one
protein of the present invention.
[0096] In some embodiments, the present invention comprises methods
for improving the nutritional quality of food comprising adding to
the food at least one protein of the present invention.
[0097] In some embodiments, the present invention comprises methods
for improving the nutritional quality of food comprising
pretreating the food with at least one protein of the present
invention.
[0098] In some embodiments, the present invention comprises methods
for improving the nutritional quality of animal feed comprising
adding to the animal feed at least one protein of the present
invention.
[0099] In some embodiments, the present invention comprises methods
for improving the nutritional quality of animal feed comprising
pretreating the feed with at least one isolated protein of the
present invention.
[0100] In some embodiments, the present invention comprises a
genetically modified organism comprising at least one nucleic acid
molecule encoding a protein of the present invention, in which the
activity of one or more of the proteins is upregulated, the
activity of one or more of the proteins downregulated, or the
activity of one or more of the proteins is upregulated and the
activity of one or more of the proteins is downregulated.
BRIEF DESCRIPTION OF THE FIGURES
[0101] FIG. 1 shows HPAEC diagrams of wheat arabinoxylan (WAX)
incubated with the enzyme Pentopan (A), and WAX incubated with
Pentopan followed by Abn7 (B). A indicates arabinose, while X
indicates xylose.
[0102] FIG. 2 shows HPAEC diagrams of wheat arabinoxylan (WAX)
incubated with the enzyme Pentopan (A), WAX incubated with Pentopan
followed by Abf1 (B), WAX incubated with Pentopan followed by Abf1
and Abn7 (C), and WAX incubated with Pentopan followed by Abf1 and
AXHd.sub.3 from B. adolescentis (D). A indicates arabinose, while X
indicates xylose.
[0103] FIG. 3 shows HPAEC spectra of EW-XOS or saponified EW-XOS
before digestion (A), after digestion of EW-XOS by Agu1 (B), and
after digestion of saponified EW-XOS by Agu1 (C). The experiments
were performed at pH 6.0, 40.degree. C.
[0104] FIG. 4 shows CE electropherograms of a standard mixture (A),
saponified EW-XOS (B) and saponified EW-XOS digested with Agu1 (C).
The experiments were performed at pH 6.0, 40.degree. C. during 24
hours. The arrows indicate the peaks of XOS that changed by the
action of Agu1. X indicates xylose, G indicates glucuronic acid and
4-O-M indicates 4-O-methyl glucuronic acid.
[0105] FIG. 5 shows HPAEC spectra of wheat arabinoxylan
oligosaccharides before (A) and after digestion with the
arabinofuranosidase Abf5 (B). The experiments were performed at pH
5.0, 30.degree. C. during 20 hours. X indicates xylose, A indicates
arabinose and G indicates glucose.
[0106] FIG. 6 shows HPAEC spectra of wheat arabinoxylan before (A),
after 1 hour of digestion with the xylanase Xyl7 (B), and 24 hours
of digestion with the xylanase Xyl7 (C). The experiments were
performed at pH 5.0 and 37.degree. C. indicates xylose and
diamond-solid. indicates arabinose.
[0107] FIG. 7 shows MALDI-TOF MS mass spectra of the hydrolysis
products of acetylated EW-XOS (A) after digestion by Axe2 (B) and
Axe3 (C). The experiment was performed at pH 7.0 and 40.degree. C.
during 24 h of incubation.
[0108] FIG. 8 shows CE electropherograms of the EW-XOS (A) and
EW-XOS digested with Axe2 (B). The red dotted line shows the
results obtained when the samples were subsequently incubated with
a GH10 xylanase from Aspergillus awamori (enzyme collection
Laboratory of Food Chemistry, Wageningen University, The
Netherlands). The experiments were performed at pH 7.0, 40.degree.
C. for 5 hours. X indicates xylose.
[0109] FIG. 9 shows HPAEC spectra of xylobiose after 24 hours of
digestion with a negative control (A), and the .beta.-xylosidase
Bxl1 (B). The experiments were performed at pH 5.0 and 50.degree.
C. X indicates xylose and X.sub.2 indicates xylobiose.
DETAILED DESCRIPTION OF THE INVENTION
[0110] The present invention relates generally to proteins that
play a role in the degradation of cellulose and hemicellulose and
nucleic acids encoding the same. In particular, the present
invention relates to enzymes isolated from a filamentous fungal
strain denoted herein as C1 (Accession No. VKM F-3500-D), nucleic
acids encoding the enzymes, and methods of producing and using the
enzymes. The invention also provides compositions that include at
least one of the enzymes described herein for uses including, but
not limited to, the hydrolysis of lignocellulose. The invention
stems, in part, from the discovery of a variety of novel cellulases
and hemicellulases produced by the C1 fungus that exhibit high
activity toward cellulose and other components of biomass.
[0111] The present invention also provides methods and compositions
for the conversion of plant biomass to fermentable sugars that can
be converted to useful products. Such products may include, without
limitation, bioplastics, biopolymers and biofuels. The methods
include methods for degrading lignocellulosic material using enzyme
mixtures to liberate sugars. The compositions of the invention
include enzyme combinations that break down lignocellulose. As used
herein the terms "biomass" or "lignocellulosic material" includes
materials containing cellulose and/or hemicellulose. Generally,
these materials also contain pectin, lignin, protein, carbohydrates
(such as starch and sugar) and ash. Lignocellulose is generally
found, for example, in the stems, leaves, hulls, husks, and cobs of
plants or leaves, branches, and wood of trees. The process of
converting a complex carbohydrate (such as starch or cellulose)
into fermentable sugars is also referred to herein as
"saccharification." Fermentable sugars, as used herein, refers to
simple sugars, such as glucose, xylose, arabinose, galactose,
mannose, rhamnose, sucrose and fructose.
[0112] Biomass can include virgin biomass and/or non-virgin biomass
such as agricultural biomass, commercial organics, construction and
demolition debris, municipal solid waste, waste paper and yard
waste. Common forms of biomass include trees, shrubs and grasses,
wheat, wheat straw, sugar cane bagasse, corn, corn husks, corn
kernel including fiber from kernels, products and by-products from
milling of grains such as corn, wheat and barley (including wet
milling and dry milling) as well as municipal solid waste, waste
paper and yard waste. The biomass can also be, but is not limited
to, herbaceous material, agricultural residues, forestry residues,
municipal solid wastes, waste paper, and pulp and paper mill
residues. "Agricultural biomass" includes branches, bushes, canes,
corn and corn husks, energy crops, algae, fruits, flowers, grains,
grasses, herbaceous crops, leaves, bark, needles, logs, roots,
saplings, short rotation woody crops, shrubs, switch grasses,
trees, vegetables, fruit peels, vines, sugar beet pulp, wheat
midlings, oat hulls, peat moss, mushroom compost and hard and soft
woods (not including woods with deleterious materials). In
addition, agricultural biomass includes organic waste materials
generated from agricultural processes including farming and
forestry activities, specifically including forestry wood waste.
Agricultural biomass may be any of the aforestated singularly or in
any combination or mixture thereof.
[0113] Energy crops are fast-growing crops that are grown for the
specific purpose of producing energy, including without limitation,
biofuels, from all or part of the plant. Energy crops can include
crops that are grown (or are designed to grow) for their increased
cellulose, xylose and sugar contents. Examples of such plants
include, without limitation, switchgrass, willow and poplar. Energy
crops may also include algae, for example, designer algae that are
genetically engineered for enhanced production of hydrogen,
alcohols, and oils, which can be further processed into diesel and
jet fuels, as well as other bio-based products.
[0114] Biomass high in starch, sugar, or protein such as corn,
grains, fruits and vegetables are usually consumed as food.
Conversely, biomass high in cellulose, hemicellulose and lignin are
not readily digestible and are primarily utilized for wood and
paper products, animal feed, fuel, or are typically disposed.
Generally, the substrate is of high lignocellulose content,
including distillers' dried grains corn stover, corn cobs, rice
straw, wheat straw, hay, sugarcane bagasse, sugar cane pulp, citrus
peels and other agricultural biomass, switchgrass, forestry wastes,
poplar wood chips, pine wood chips, sawdust, yard waste, and the
like, including any combination thereof.
[0115] In one embodiment, the lignocellulosic material is
distillers' dried grains (DDG). DDG (also known as dried
distiller's grain, or distiller's spent grain) is spent, dried
grains recovered after alcohol fermentation. The lignocellulosic
material can also be distiller's dried grain with soluble material
recycled back (DDGS). While reference will be made herein to DDG
for convenience and simplicity, it should be understood that both
DDG and DDGS are contemplated as desired lignocellulosic materials.
These are largely considered to be waste products and can be
obtained after the fermentation of the starch derived from any of a
number of grains, including corn, wheat, barley, oats, rice and
rye. In one embodiment the DDG is derived from corn.
[0116] It should be noted that the distiller's grains do not
necessarily have to be dried. Although the grains normally,
currently dried, water and enzymes are added to the DDG substrate
in the present invention. If the saccharification were done on
site, the drying step could be eliminated and enzymes could be
added to the distiller's grains without drying.
[0117] Due in part to the many components that comprise biomass and
lignocellulosic materials, enzymes or a mixture of enzymes capable
of degrading xylan, lignin, protein, and carbohydrates are needed
to achieve saccharification. The present invention includes enzymes
or compositions thereof with, for example, cellobiohydrolase,
endoglucanase, xylanase, .beta.-glucosidase, and hemicellulase
activities.
[0118] The enzymes of the present invention may also be used for
stone washing cellulosic fabrics such as cotton (e.g., denim),
linen, hemp, ramie, cupro, lyocell, newcell, rayon and the like.
See, for example, U.S. Pat. No. 6,015,707. The enzymes and
compositions of the present invention are suitable for industrial
textile applications in addition to the stone washing process. For
example, cellulases are used in detergent compositions, either for
the purpose of enhancing the cleaning ability of the composition or
as a softening agent. When so used, the cellulase will degrade a
portion of the cellulosic material, e.g., cotton fabric, in the
wash, which facilitates the cleaning and/or softening of the
fabric. The endoglucanase components of fungal cellulases have also
been used for the purposes of enhancing the cleaning ability of
detergent compositions, for use as a softening agent, and for use
in improving the feel of cotton fabrics, and the like. Enzymes and
compositions of the present invention may also be used in the
treatment of paper pulp (e.g., for improving the drainage or for
de-inking of recycled paper) or for the treatment of wastewater
streams (e.g., to hydrolyze waste material containing cellulose,
hemicellulose and pectins to soluble lower molecular weight
polymers).
[0119] The enzymes of the present invention may also be used to
release the contents of a cell. In some embodiments, contacting or
mixing the cells with the enzymes of the present invention will
degrade the cell walls, resulting in cell lysis and release of the
cellular contents. Such cells can include bacteria, plant cells,
fungi, and algae. For example, the enzymes of the present invention
may be used to degrade the cell walls of algal cells in order to
release the materials contained within the algal cells. In some
embodiments, such materials may include, without limitation,
alcohols and oils. The alcohols and oils so released can be further
processed to produce diesel, jet fuels, as well as other
economically important bio-products.
[0120] The enzymes of the present invention may be used alone, or
in combination with other enzymes, chemicals or biological
materials. The enzymes of the present invention may be used for in
vitro applications in which the enzymes or mixtures thereof are
added to or mixed with the appropriate substrates to catalyze the
desired reactions. Additionally, the enzymes of the present
invention may be used for in vivo applications in which nucleic
acid molecules encoding the enzymes are introduced into cells and
are expressed therein to produce the enzymes and catalyze the
desired reactions within the cells. For example, in some
embodiments, enzymes capable of promoting cell wall degradation may
be added to algal cells suspended in solutions to degrade the algal
cell walls and release their content, whereas in some embodiments,
nucleic acid molecules encoding such enzymes may be introduced into
the algal cells to express the enzymes therein, so that these
enzymes can degrade the algal cell walls from within. Some
embodiments may combine the in vitro applications with the in vivo
applications. For example, nucleic acids encoding enzymes capable
of catalyzing cell wall degradation may be introduced into algal
cells to express the enzymes in those cells and to degrade their
cell walls, while enzymes may also added to or mixed with the cells
to further promote the cell wall degradation. In some embodiments,
the enzymes used for in vitro applications may be different from
the enzymes used for in vivo applications. For example, an enzyme
with the laminarinase activity may be mixed with the cells, while
an enzyme with the xyloglucanase activity is expressed within the
cells.
[0121] In one aspect, the present invention includes proteins
isolated from, or derived from the knowledge of enzymes from, a
fungus such as C. lucknowense or a mutant or other derivative
thereof, and more particularly, from the fungal strain denoted
herein as C1 (Accession No. VKM F-3500-D). Preferably, the proteins
of the invention possess enzymatic activity. As described in U.S.
Pat. No. 6,015,707 or U.S. Pat. No. 6,573,086, each of which is
incorporated herein by reference for all purposes, a strain called
C1 (Accession No. VKM F-3500-D), was isolated from samples of
forest alkaline soil from Sola Lake, Far East of the Russian
Federation. This strain was deposited at the All-Russian Collection
of Microorganisms of Russian Academy of Sciences (VKM), Bakhurhina
St. 8, Moscow, Russia, 113184, under the terms of the Budapest
Treaty on the International Regulation of the Deposit of
Microorganisms for the Purposes of Patent Procedure on Aug. 29,
1996, as Chrysosporium lucknowense Garg 27K, VKM-F 3500 D. Various
mutant strains of C. lucknowense C1 have been produced and these
strains have also been deposited at the All-Russian Collection of
Microorganisms of Russian Academy of Sciences (VKM), Bakhurhina St.
8, Moscow, Russia, 113184, under the terms of the Budapest Treaty
on the International Regulation of the Deposit of Microorganisms
for the Purposes of Patent Procedure on Sep. 2, 1998. For example,
Strain C1 was mutagenized by subjecting it to ultraviolet light to
generate strain UV13-6 (Accession No. VKM F-3632 D). This strain
was subsequently further mutated with
N-methyl-N'-nitro-N-nitrosoguanidine to generate strain NG7C-19
(Accession No. VKM F-3633 D). This latter strain in turn was
subjected to mutation by ultraviolet light, resulting in strain
UV18-25 (VKM F-3631 D). Strain C1 was classified as a Chrysosporium
lucknowense based on morphological and growth characteristics of
the microorganism, as discussed in detail in U.S. Pat. No.
6,015,707 and U.S. Pat. No. 6,573,086.
[0122] In certain embodiments of the present invention, a protein
of the invention comprises, consists essentially of, or consists of
an amino acid sequence selected from: SEQ ID NO: 2, SEQ ID NO: 5,
SEQ ID NO: 8, SEQ ID NO: 11, SEQ ID NO: 14, SEQ ID NO: 17, SEQ ID
NO: 20, SEQ ID NO: 23, SEQ ID NO: 26, SEQ ID NO: 29, SEQ ID NO: 32,
SEQ ID NO: 35, SEQ ID NO: 38, SEQ ID NO: 41, SEQ ID NO: 44, SEQ ID
NO: 47, SEQ ID NO: 50, SEQ ID NO: 53, SEQ ID NO: 56, SEQ ID NO: 59,
SEQ ID NO: 62, SEQ ID NO: 65, SEQ ID NO: 68, SEQ ID NO: 71, SEQ ID
NO: 74, SEQ ID NO: 77, SEQ ID NO: 80, SEQ ID NO: 83, SEQ ID NO: 86,
SEQ ID NO: 89, SEQ ID NO: 92, SEQ ID NO: 95, SEQ ID NO: 98, SEQ ID
NO: 101, SEQ ID NO: 104, SEQ ID NO: 107, SEQ ID NO: 110, SEQ ID NO:
113, SEQ ID NO: 116, SEQ ID NO: 119, SEQ ID NO: 122, SEQ ID NO:
125, SEQ ID NO: 128, SEQ ID NO: 131, SEQ ID NO: 134, SEQ ID NO:
137, SEQ ID NO: 140, SEQ ID NO: 143, SEQ ID NO: 146, SEQ ID NO:
149, SEQ ID NO: 152, SEQ ID NO: 155, SEQ ID NO: 158, SEQ ID NO:
161, SEQ ID NO: 164, SEQ ID NO: 167, SEQ ID NO: 170, SEQ ID NO:
173, SEQ ID NO: 176, SEQ ID NO: 179, SEQ ID NO: 182, SEQ ID NO:
185, SEQ ID NO: 188, SEQ ID NO: 191, SEQ ID NO: 194, SEQ ID NO:
197, SEQ ID NO: 200, SEQ ID NO: 203, SEQ ID NO: 206, SEQ ID NO:
209, SEQ ID NO: 212, SEQ ID NO: 215, SEQ ID NO: 218, SEQ ID NO:
221, SEQ ID NO: 224, SEQ ID NO: 227, SEQ ID NO: 230, or SEQ ID NO:
233. The present invention also includes homologues of any of the
above sequences, including fragments and sequences having a given
identity to any of the above sequences, wherein the homologue or
fragment has at least one biological activity of the wild-type
protein, as described herein.
[0123] In general, the proteins disclosed herein possess
carbohydrase enzymatic activity, or the ability to degrade
carbohydrate-containing materials. A review of enzymes involved in
the degradation of polysaccharides can be found in de Vries et al.,
Microbiol. Mol. Biol. Rev. 65:497-522 (2001). More specifically,
the proteins may possess cellulase activity such as endoglucanase
activity (e.g., 1,4.beta.-D-glucan-4-glucanohydrolases),
exoglucanase activity (e.g., 1,4-.beta.-D-glucan
cellobiohydrolases), and .beta.-glucosidase activity. The proteins
may possess hemicellulase activity such as endoxylanase activity,
exoxylanase activity, or .beta.-xylosidase activity. The proteins
may possess laminarinase, xyloglucanase, galactanase, glucoamylase,
pectate lyase, chitosanase, exo-.beta.-D-glucosaminidase,
cellobiose dehydrogenase, acetylxylan esterase, ligninase, amylase,
glucuronidase, ferulic acid esterase, arabinofuranosidase, pectin
methyl esterase, arabinase, lipase, glucosidase,
.beta.-hexosaminidase, rhamnogalacturonan acetylesterase,
exo-rhamnogalacturonase, rhamnogalacturonan lyase,
exo-polygalacturonase, lichenase, pectate lyase, .beta.-mannanase,
mannan endo 1,6-.alpha.-mannosidase, or glucomannanase activities.
Physical properties, biochemical characteristics and substrate
specificities of proteins of the present invention are illustrated
below.
[0124] As used herein, "carbohydrase" refers to any protein that
catalyzes the hydrolysis of carbohydrates. "Glycoside hydrolase",
"glycosyl hydrolase" or "glycosidase" refers to a protein that
catalyzes the hydrolysis of the glycosidic bonds between
carbohydrates or between a carbohydrate and a non-carbohydrate
residue. Endoglucanases, cellobiohydrolases, .beta.-glucosidases,
.alpha.-glucosidases, xylanases, .beta.-xylosidases, galactanases,
.alpha.-galactosidases, .beta.-galactosidases, .alpha.-amylases,
glucoamylases, endo-arabinases, arabinofuranosidases, mannanases,
.beta.-mannosidases, pectinases, acetyl xylan esterases, acetyl
mannan esterases, ferulic acid esterases, coumaric acid esterases,
pectin methyl esterases, and chitosanases are examples of
glycosidases.
[0125] "Cellulase" refers to a protein that catalyzes the
hydrolysis of 1,4-.beta.-D-glycosidic linkages in cellulose (such
as bacterial cellulose, cotton, filter paper, phosphoric acid
swollen cellulose, Avicel); cellulose derivatives (such as
carboxymethylcellulose and hydroxyethylcellulose); plant
lignocellulosic materials, beta-D-glucans or xyloglucans. Cellulose
is a linear beta-(1-4) glucan consisting of anhydrocellobiose
units. Endoglucanases, cellobiohydrolases, and .beta.-glucosidases
are examples of cellulases. "Endoglucanase" refers to a protein
that catalyzes the hydrolysis of cellulose to oligosaccharide
chains at random locations by means of an endoglucanase activity.
"Cellobiohydrolase" refers to a protein that catalyzes the
hydrolysis of cellulose to cellobiose via an exoglucanase activity,
sequentially releasing molecules of cellobiose from the reducing or
non-reducing ends of cellulose or cello-oligosaccharides.
".beta.-glucosidase" refers to an enzyme that catalyzes the
conversion of cellobiose and oligosaccharides to glucose.
[0126] "Hemicellulase" refers to a protein that catalyzes the
hydrolysis of hemicellulose, such as that found in lignocellulosic
materials. Hemicellulose is a complex polymer, and its composition
often varies widely from organism to organism, and from one tissue
type to another. Hemicelluloses include a variety of compounds,
such as xylans, arabinoxylans, xyloglucans, mannans, glucomannans,
and galactomannans. Hemicellulose can also contain glucan, which is
a general term for beta-linked glucose residues. In general, a main
component of hemicellulose is beta-1,4-linked xylose, a five carbon
sugar. However, this xylose is often branched as beta-1,3 linkages
or beta-1,2 linkages, and can be substituted with linkages to
arabinose, galactose, mannose, glucuronic acid, or by
esterification to acetic acid. The composition, nature of
substitution, and degree of branching of hemicellulose is very
different in dicotyledonous plants (dicots, i.e., plant whose seeds
have two cotyledons or seed leaves such as lima beans, peanuts,
almonds, peas, kidney beans) as compared to monocotyledonous plants
(monocots; i.e., plants having a single cotyledon or seed leaf such
as corn, wheat, rice, grasses, barley). In dicots, hemicellulose is
comprised mainly of xyloglucans that are 1,4-beta-linked glucose
chains with 1,6-alpha-linked xylosyl side chains. In monocots,
including most grain crops, the principal components of
hemicellulose are heteroxylans. These are primarily comprised of
1,4-beta-linked xylose backbone polymers with 1,2- or 1,3-beta
linkages to arabinose, galactose and mannose as well as xylose
modified by ester-linked acetic acids. Also present are branched
beta glucans comprised of 1,3- and 1,4-beta-linked glucosyl chains.
In monocots, cellulose, heteroxylans and beta glucans are present
in roughly equal amounts, each comprising about 15-25% of the dry
matter of cell walls. Hemicellulolytic enzymes, i.e.
hemicellulases, include both endo-acting and exo-acting enzymes,
such as xylanases, .beta.-xylosidases. galactanases,
.alpha.-galactosidases, .beta.-galactosidases, endo-arabinases,
arabinofuranosidases, mannanases, .beta.-mannosidases.
Hemicellulases also include the accessory enzymes, such as
acetylesterases, ferulic acid esterases, and coumaric acid
esterases. Among these, xylanases and acetyl xylan esterases cleave
the xylan and acetyl side chains of xylan and the remaining
xylo-oligomers are unsubstituted and can thus be hydrolysed with
.beta.-xylosidase only. In addition, several less known side
activities have been found in enzyme preparations which hydrolyze
hemicellulose. Accordingly, xylanases, acetylesterases and
.beta.-xylosidases are examples of hemicellulases.
[0127] "Xylanase" specifically refers to an enzyme that hydrolyzes
the .beta.-1,4 bond in the xylan backbone, producing short
xylooligosaccharides.
[0128] ".beta.-Mannanase" or "endo-1,4-.beta.-mannosidase" refers
to a protein that hydrolyzes mannan-based hemicelluloses (mannan,
glucomannan, galactomannan) and produces short
.beta.-1,4-mannooligosaccharides.
[0129] "Mannan endo-1,6-.alpha.-mannosidase" refers to a protein
that hydrolyzes 1,6-amannosidic linkages in unbranched
1,6-mannans.
[0130] ".beta.-Mannosidase" (.beta.-1,4-mannoside mannohydrolase;
EC 3.2.1.25) refers to a protein that catalyzes the removal of
.beta.-D-mannose residues from the nonreducing ends of
oligosaccharides.
[0131] "Galactanase", "endo-.beta.-1,6-galactanse" or
"arabinogalactan endo-1,4-.beta.-galactosidase" refers to a protein
that catalyzes the hydrolysis of endo-1,4-.beta.-D-galactosidic
linkages in arabinogalactans.
[0132] "Glucoamylase" refers to a protein that catalyzes the
hydrolysis of terminal 1,4-linked .alpha.-D-glucose residues
successively from non-reducing ends of the chains with the release
of .beta.-D-glucose.
[0133] ".beta.-hexosaminidase" or ".beta.-N-acetylglucosaminidase"
refers to a protein that catalyzes the hydrolysis of terminal
N-acetyl-D-hexosamine residues in
N-acetyl-.beta.-D-hexosaminides.
[0134] ".alpha.-L-arabinofuranosidase",
".alpha.-N-arabinofuranosidase", ".alpha.-arabinofuranosidase",
"arabinosidase" or "arabinofuranosidase" refers to a protein that
hydrolyzes arabinofuranosyl-containing hemicelluloses. Some of
these enzymes remove arabinofuranoside residues from O-2 or O-3
single substituted xylose residues, as well as from O-2 and/or O-3
double substituted xylose residues.
[0135] "Endo-arabinase" refers to a protein that catalyzes the
hydrolysis of 1,5-.alpha.-arabinofuranosidic linkages in
1,5-arabinans.
[0136] "Exo-arabinase" refers to a protein that catalyzes the
hydrolysis of 1,5-.alpha.-linkages in 1,5-arabinans or
1,5-.alpha.-L arabino-oligosaccharides, releasing mainly
arabinobiose, although a small amount of arabinotriose can also be
liberated.
[0137] ".beta.-xylosidase" refers to a protein that hydrolyzes
short 1,4-O-D-xylooligomers into xylose.
[0138] "Cellobiose dehydrogenase" refers to a protein that oxidizes
cellobiose to cellobionolactone.
[0139] "Chitosanase" refers to a protein that catalyzes the
endohydrolysis of .beta.-1,4-linkages between D-glucosamine
residues in acetylated chitosan (i.e., deacetylated chitin).
[0140] "Exo-polygalacturonase" refers to a protein that catalyzes
the conversion of polygalacturonides to galacturonic acid.
[0141] "Acetyl xylan esterase" refers to a protein that catalyzes
the removal of the acetyl groups from xylose residues. "Acetyl
mannan esterase" refers to a protein that catalyzes the removal of
the acetyl groups from mannose residues. "ferulic esterase" or
"ferulic acid esterase" refers to a protein that hydrolyzes the
ester bond between the arabinose substituent group and ferulic
acid. "Coumaric acid esterase" refers to a protein that hydrolyzes
the ester bond between the arabinose substituent group and coumaric
acid. Acetyl xylan esterases, ferulic acid esterases and pectin
methyl esterases are examples of carbohydrate esterases.
[0142] "Pectate lyase" refers to a protein that catalyzes the
cleavage of 1,4-.alpha.-D-galacturonan in oligosaccharide
substrates.
[0143] "Endo-1,3-.beta.-glucanase" or "laminarinase" refers to a
protein that catalyzes the cleavage of 1,3-linkages in
.beta.-D-glucans such as laminarin or lichenin. Laminarin is a
linear polysaccharide made up of .beta.-1,3-glucan with
.beta.-1,6-linkages.
[0144] "Lichenase" refers to a protein that catalyzes the
hydrolysis of lichenan, a linear, 1,3-1,4-.beta.-D glucan.
[0145] Rhamnogalacturonan is composed of alternating
.alpha.-1,4-rhamnose and .alpha.-1,2-linked galacturonic acid, with
side chains linked 1,4 to rhamnose. The side chains include Type I
galactan, which is .beta.-1,4-linked galactose with
.alpha.-1,3-linked arabinose substituents; Type II galactan, which
is .beta.-1,3-1,6-linked galactoses (very branched) with arabinose
substituents; and arabinan, which is .alpha.-1,5-linked arabinose
with .alpha.-1,3-linked arabinose branches. The galacturonic acid
substituents may be acetylated and/or methylated.
[0146] "Exo-rhamnogalacturonanase" refers to a protein that
catalyzes the degradation of the rhamnogalacturonan backbone of
pectin from the nonreducing end.
[0147] "Rhamnogalacturonan acetylesterase" refers to a protein that
catalyzes the removal of the acetyl groups ester-linked to the
highly branched rhamnogalacturonan (hairy) regions of pectin.
[0148] "Rhamnogalacturonan lyase" refers to a protein that
catalyzes the degradation of the rhamnogalacturonan backbone of
pectin via a .beta.-elimination mechanism (see, e.g., Pages et al.,
J. Bacteriol. 185:4727-4733 (2003)).
[0149] Glycosidases (glycoside hydrolases; GH), a large family of
enzymes that includes cellulases and hemicellulases, catalyze the
hydrolysis of glycosidic linkages, predominantly in carbohydrates.
Glycosidases such as the proteins of the present invention may be
assigned to families on the basis of sequence similarities, and
there are now over 100 different such families defined (see the
CAZy (Carbohydrate Active EnZymes database) website, maintained by
the Architecture of Fonction de Macromolecules Biologiques of the
Centre National de la Recherche Scientifique, which describes the
families of structurally-related catalytic and carbohydrate-binding
modules (or functional domains) of enzymes that degrade, modify, or
create glycosidic bonds; Coutinho, P. M. & Henrissat, B. (1999)
Carbohydrate-active enzymes: an integrated database approach. In
"Recent Advances in Carbohydrate Bioengineering", H. J. Gilbert, G.
Davies, B. Henrissat and B. Svensson eds., The Royal Society of
Chemistry, Cambridge, pp. 3-12). Because there is a direct
relationship between the amino acid sequence of a protein and its
folding similarities, such a classification reflects the structural
features of these enzymes and their substrate specificity. Such a
classification system can help to reveal the evolutionary
relationships between these enzymes and provide a convenient tool
to determine information such as an enzyme's activity and function.
Thus, enzymes assigned to a particular family based on sequence
homology with other members of the family are expected to have
similar enzymatic activities and related substrate specificities.
CAZy family classifications also exist for glycosyltransferases
(GT), polysaccharide lyases (PL), and carbohydrate esterases (CE).
Likewise, sequence homology may be used to identify particular
domains within proteins, such as cellulose binding modules (CBMs;
also known as cellulose binding domains (CBDs)). The CAZy
homologies of proteins of the present invention are disclosed
below. An enzyme assigned to a particular CAZy family may exhibit
one or more of the enzymatic activities or substrate specificities
associated with the CAZy family. In other embodiments, the enzymes
of the present invention may exhibit one or more of the enzyme
activities discussed above.
[0150] Certain proteins of the present invention may be classified
as "Family 61 glycosidases" based on homology of the polypeptides
to CAZy Family GH61. Family 61 glycosidases may exhibit
cellulolytic enhancing activity or endoglucanase activity.
Additional information on the properties of Family 61 glycosidases
may be found in U.S. Patent Application Publication Nos.
2005/0191736, 2006/0005279, 2007/0077630, and in PCT Publication
No. WO 2004/031378.
[0151] As used herein, "cellulolytic enhancing activity" refers to
a biological activity that enhances the hydrolysis of a cellulosic
material by proteins having cellulolytic activity. In other words,
saccharifying a cellulosic material with a cellulolytic protein in
the presence of a Family 61 glycosidases may increase the
degradation of cellulosic material compared to the presence of only
the cellulolytic protein. The cellulosic material can be any
material containing cellulose. The cellulolytic activity is a
biological activity that hydrolyzes a cellulosic material.
Cellulolytic enhancing activity can be determined by measuring the
increase in sugars from the hydrolysis of a cellulosic material by
cellulolytic protein.
[0152] Proteins of the present invention may also include
homologues and fragments of the proteins disclosed herein. The
protein fragments include, but are not limited to, fragments
comprising a catalytic domain (CD) and/or a cellulose-binding
domain (also known as a cellulose binding module (CBM); both are
referred to herein as CBM). The identity and location of domains
within proteins of the present invention are disclosed in detail
below. The present invention encompasses all combinations of the
disclosed domains. For example, a protein fragment may comprise a
CD of a protein but not a CBM of the protein or a CBM of a protein
but not a CD. Similarly, domains from different proteins may be
combined. Protein fragments comprising a CD, CBM or combinations
thereof for each protein disclosed herein can be readily produced
using standard techniques known in the art. In some embodiments, a
protein fragment comprises a domain of a protein that has at least
one biological activity of the full-length protein. Homologues of
proteins of the invention that have at least one biological
activity of the full-length protein are described in detail below.
As used herein, the phrase "biological activity" of a protein
refers to any function(s) exhibited or performed by the protein
that is ascribed to the naturally occurring form of the protein as
measured or observed in vitro or in vivo. In certain embodiments, a
protein fragment comprises a domain of a protein that has the
catalytic activity of the full-length enzyme. Specific biological
activities of the proteins of the invention, and structures within
the proteins that are responsible for the activities, are described
below.
[0153] Descriptions of the enzymes of the present invention are
provided below, along with activities and homologies. Although each
enzyme is expected to exhibit the activity exemplified below,
enzymes of the present invention may also exhibit any of the enzyme
activities or substrate specificities discussed throughout this
disclosure.
[0154] The enzyme CDH1 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 1 and the cDNA sequence
represented herein as SEQ ID NO: 3. The CDH1 nucleic acid sequence
encodes a 828 amino acid sequence, represented herein as SEQ ID NO:
2. The signal peptide for CDH1 is located from positions 1 to about
position 21 of SEQ ID NO: 2, with the mature protein spanning from
about position 22 to position 828 of SEQ ID NO: 2. Within CDH1 are
two domains: a catalytic domain (CD) and a cellulose-binding module
(CBM). The amino acid sequence containing the CD of CDH1 spans from
a starting point of about position 252 of SEQ ID NO: 2 to an ending
point of about position 780 of SEQ ID NO: 2. The amino acid
sequence containing the CBM of CDH1 spans from a starting point of
about position 781 of SEQ ID NO: 2 to an ending point of about
position 817 of SEQ ID NO: 2. CDH1 possesses significant homology
(about 62% from amino acids 1 to 788 of CDH1) with a cellobiose
dehydrogenase from Neosartorya fischeri NRRL 181 (Gen Bank
Accession No. EAW19340). Based on this degree of homology, CDH1 is
expected to exhibit similar cellobiose dehydrogenase enzymatic
activity. Based on homology, CDH1 also contains a putative
cellulose binding module assigned to CAZy Family CBM 1. As
evidenced below in Example 4, CDH1 contains a carbohydrate binding
module.
[0155] The enzyme FaeB1 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 4 and the cDNA sequence
represented herein as SEQ ID NO: 6. The FaeB1 nucleic acid sequence
encodes a 319 amino acid sequence, represented herein as SEQ ID NO:
5. The signal peptide for FaeB1 is located from positions 1 to
about position 22 of SEQ ID NO: 5, with the mature protein spanning
from about position 23 to position 319 of SEQ ID NO: 5. Within
FaeB1 is a catalytic domain (CD). The amino acid sequence
containing the CD of FaeB1 spans from a starting point of about
position 63 of SEQ ID NO: 5 to an ending point of about position
278 of SEQ ID NO: 5. FaeB1 possesses significant homology (about
67% from amino acids 46 to 319 of FaeB1) with a ferulic acid
esterase from Neurospora crassa (GenBank Accession No. CACO5587).
Based on this degree of homology, FaeB1 is expected to exhibit
similar ferulic acid esterase enzymatic activity.
[0156] The enzyme Rga1 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 7 and the cDNA sequence
represented herein as SEQ ID NO: 9. The Rga1 nucleic acid sequence
encodes a 263 amino acid sequence, represented herein as SEQ ID NO:
8. The signal peptide for Rga1 is located from positions 1 to about
position 19 of SEQ ID NO: 8, with the mature protein spanning from
about position 20 to position 263 of SEQ ID NO: 8. Within Rga1 is a
catalytic domain (CD). The amino acid sequence containing the CD of
Rga1 spans from a starting point of about position 30 of SEQ ID NO:
8 to an ending point of about position 258 of SEQ ID NO: 8. Based
on homology, Rga1 can be assigned to CAZy Family CE 12. Rga1 also
possesses significant homology (about 56% from amino acids 31 to
241 of Rga1) with a rhamnogalacturonan acetylesterase from
Aspergillus aculeatus (GenBank Accession No. CAA61858); see also
Kauppinen et al., J. Biol. Chem. 270:27172 (1995)). Based on this
degree of homology, Rga1 is expected to exhibit similar
rhamnogalacturonan acetylesterase enzymatic activity. As evidenced
below in Example 10, Rga1 exhibits acetyl esterase activity.
[0157] The enzyme Gln is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 10 and the cDNA sequence
represented herein as SEQ ID NO: 12. The Gln nucleic acid sequence
encodes a 482 amino acid sequence, represented herein as SEQ ID NO:
11. The signal peptide for Gln is located from positions 1 to about
position 22 of SEQ ID NO: 11, with the mature protein spanning from
about position 23 to position 482 of SEQ ID NO: 11. Within Gln is a
catalytic domain (CD). The amino acid sequence containing the CD of
Gln spans from a starting point of about position 37 of SEQ ID NO:
11 to an ending point of about position 385 of SEQ ID NO: 11. Based
on homology, Gln can be assigned to CAZy Family GH 5. Gln also
possesses significant homology (about 57% from amino acids 6 to 482
of Gln) with an endo-.beta.-1,6-galactanase from Trichoderma viride
(GenBank Accession No. BAC84995; see also Kotake et al., Biochem.
J. 377(Pt. 3):749 (2004)). Based on this degree of homology, Gln is
expected to exhibit similar endo-.beta.-1,6-galactanase enzymatic
activity.
[0158] The enzyme Abn2 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 13 and the cDNA sequence
represented herein as SEQ ID NO: 15. The Abn2 nucleic acid sequence
encodes a 378 amino acid sequence, represented herein as SEQ ID NO:
14. The signal peptide for Abn2 is located from positions 1 to
about position 17 of SEQ ID NO: 14, with the mature protein
spanning from about position 18 to position 378 of SEQ ID NO: 14.
Within Abn2 is a catalytic domain (CD). The amino acid sequence
containing the CD of Abn2 spans from a starting point of about
position 78 of SEQ ID NO: 14 to an ending point of about position
153 of SEQ ID NO: 14. Based on homology, Abn2 can be assigned to
CAZy Family GH 93. Abn2 also possesses significant homology (about
55% from amino acids 19 to 378 of Abn2) with an exo-arabinase from
Penicillium chrysogenum (GenBank Accession No. BAC76689; see also
Sakamoto et al., FEBS Lett. 560:199 (2004)). Based on this degree
of homology, Abn2 is expected to exhibit similar exo-arabinase
enzymatic activity.
[0159] The enzyme Abn3 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 16 and the cDNA sequence
represented herein as SEQ ID NO: 18. The Abn3 nucleic acid sequence
encodes a 354 amino acid sequence, represented herein as SEQ ID NO:
17. The signal peptide for Abn3 is located from positions 1 to
about position 25 of SEQ ID NO: 17, with the mature protein
spanning from about position 26 to position 354 of SEQ ID NO: 17.
Within Abn3 is a catalytic domain (CD). The amino acid sequence
containing the CD of Abn3 spans from a starting point of about
position 86 of SEQ ID NO: 17 to an ending point of about position
354 of SEQ ID NO: 17. Based on homology, Abn3 can be assigned to
CAZy Family GH 43. Abn3 also possesses significant homology (about
49% from amino acids 41 to 351 of Abn3) with a putative
arabinosidase from Aspergillus fumigatus (GenBank Accession No.
XP-749202). Based on this degree of homology, Abn3 is expected to
exhibit similar arabinosidase enzymatic activity.
[0160] The enzyme Abn4 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 19 and the cDNA sequence
represented herein as SEQ ID NO: 21. The Abn4 nucleic acid sequence
encodes a 320 amino acid sequence, represented herein as SEQ ID NO:
20. The signal peptide for Abn4 is located from positions 1 to
about position 19 of SEQ ID NO: 20, with the mature protein
spanning from about position 20 to position 320 of SEQ ID NO: 20.
Within Abn4 is a catalytic domain (CD). The amino acid sequence
containing the CD of Abn4 spans from a starting point of about
position 22 of SEQ ID NO: 20 to an ending point of about position
318 of SEQ ID NO: 20. Based on homology, Abn4 can be assigned to
CAZy Family GH 43. As shown in Example 1 below, Abn4 exhibits
.alpha.-arabinofuranosidase activity based on the ability to
hydrolyze p-nitrophenyl .alpha.-L-arabinofuranoside (PNPA). As
shown in Example 11, Abn4 is able to release more arabinose when
incubated with branched arabinan than when incubated with linear
arabinan. Abn4 also possesses significant homology (about 44% from
amino acids 18 to 320 of Abn4) with an
.alpha.-N-arabinofuranosidase from Shewanella sp. (GenBank
Accession No. YP-963351). Based on this degree of homology, Abn4 is
expected to exhibit similar .alpha.-arabinofuranosidase enzymatic
activity.
[0161] The enzyme Abn5 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 22 and the cDNA sequence
represented herein as SEQ ID NO: 24. The Abn5 nucleic acid sequence
encodes a 451 amino acid sequence, represented herein as SEQ ID NO:
23. The signal peptide for Abn5 is located from positions 1 to
about position 18 of SEQ ID NO: 23, with the mature protein
spanning from about position 19 to position 451 of SEQ ID NO: 23.
Within Abn5 is a catalytic domain (CD). The amino acid sequence
containing the CD of Abn5 spans from a starting point of about
position 19 of SEQ ID NO: 23 to an ending point of about position
312 of SEQ ID NO: 23. Based on homology, Abn5 can be assigned to
CAZy Families GH 43 and CBM 35. As shown in Examples 1 and 6 below,
Abn5 exhibits .alpha.-arabinofuranosidase activity based on the
ability to hydrolyze p-nitrophenyl .alpha.-L-arabinofuranoside
(PNPA). Abn5 also possesses significant homology (about 54% from
amino acids 1 to 449 of Abn5) with a glycosyl hydrolase family 43
protein from Neosartorya fischeri (GenBank Accession No. EAW20002).
As shown in Example 11, Abn5 was able to release arabinose when
incubated with linear arabinan.
[0162] The enzyme Abn7 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 25 and the cDNA sequence
represented herein as SEQ ID NO: 27. The Abn7 nucleic acid sequence
encodes a 558 amino acid sequence, represented herein as SEQ ID NO:
26. The signal peptide for Abn7 is located from positions 1 to
about position 23 of SEQ ID NO: 26, with the mature protein
spanning from about position 24 to position 558 of SEQ ID NO: 26.
Within Abn7 is a catalytic domain (CD). The amino acid sequence
containing the CD of Abn7 spans from a starting point of about
position 24 of SEQ ID NO: 26 to an ending point of about position
444 of SEQ ID NO: 26. Based on homology, Abn7 can be assigned to
CAZy Family GH 43. As shown in Examples 1 and 2 below, Abn7
exhibits .alpha.-arabinofuranosidase activity based on the ability
to hydrolyze p-nitrophenyl .alpha.-L-arabinofuranoside (PNPA).
Example 2 further demonstrates that Abn7 possesses the ability to
remove .alpha.-L-arabinofuranosyl residues from double substituted
xylose residues and also possesses .beta.-xylosidase activity.
[0163] Abn7 also possesses significant homology (about 66%) with an
arabinofuranosidase from Humicola insolens (GenBank Accession No.
CAL81199; see also International Publication No. WO 2006/114094)
that is active towards the arabinosyl side chain of arabinoxylan
(the arabinosyl residue at the 0-3 position of double substituted
xylose). Based on this degree of homology, Abn7 is expected to
exhibit similar arabinofuranosidase enzymatic activity.
[0164] The enzyme CL01470 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 28 and the cDNA sequence
represented herein as SEQ ID NO: 30. The CL01470 nucleic acid
sequence encodes a 303 amino acid sequence, represented herein as
SEQ ID NO: 29. The signal peptide for CL01470 is located from
positions 1 to about position 19 of SEQ ID NO: 29, with the mature
protein spanning from about position 20 to position 303 of SEQ ID
NO: 29. Within CL01470 are two domains: a catalytic domain (CD) and
a cellulose-binding module (CBM). The amino acid sequence
containing the CD of CL01470 spans from a starting point of about
position 137 of SEQ ID NO: 29 to an ending point of about position
216 of SEQ ID NO: 29. The amino acid sequence containing the CBM of
CL01470 spans from a starting point of about position 268 of SEQ ID
NO: 29 to an ending point of about position 303 of SEQ ID NO: 29.
Based on homology, CL01470 can be assigned to CAZy Families GH 61
and CBM 1. CL01470 also possesses significant homology (about 38%
from amino acids 1 to 303 of CL01470) with an endoglucanase from
Volvariella volvacea (GenBank Accession No. AAT64005; see also Ding
et al., FEMS Microbiol. Lett. 263:207 (2006)).
[0165] The enzyme CL03248 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 31 and the cDNA sequence
represented herein as SEQ ID NO: 33. The CL03248 nucleic acid
sequence encodes a 223 amino acid sequence, represented herein as
SEQ ID NO: 32. The signal peptide for CL03248 is located from
positions 1 to about position 20 of SEQ ID NO: 32, with the mature
protein spanning from about position 21 to position 223 of SEQ ID
NO: 32. Within CL03248 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL03248 spans from a starting point
of about position 137 of SEQ ID NO: 32 to an ending point of about
position 217 of SEQ ID NO: 32. Based on homology, CL03248 can be
assigned to CAZy Family GH 61. CL03248 also possesses significant
homology (about 38% from amino acids 1 to 222 of CL03248) with an
endoglucanase from Volvariella volvacea (GenBank Accession No.
AAT64005; see also Ding et al., FEMS Microbiol. Lett. 263:207
(2006)).
[0166] The enzyme CL03778 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 34 and the cDNA sequence
represented herein as SEQ ID NO: 36. The CL03778 nucleic acid
sequence encodes a 242 amino acid sequence, represented herein as
SEQ ID NO: 35. The signal peptide for CL03778 is located from
positions 1 to about position 20 of SEQ ID NO: 35, with the mature
protein spanning from about position 21 to position 242 of SEQ ID
NO: 35. Within CL03778 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL03778 spans from a starting point
of about position 21 of SEQ ID NO: 35 to an ending point of about
position 231 of SEQ ID NO: 35. Based on homology, CL03778 can be
assigned to CAZy Family GH 61. CL03778 also possesses significant
homology (about 49% from amino acids 40 to 238 of CL03778) with an
endoglucanase from Aspergillus kawachii (GenBank Accession No.
BAB62318).
[0167] The enzyme CL04725 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 37 and the cDNA sequence
represented herein as SEQ ID NO: 39. The CL04725 nucleic acid
sequence encodes a 255 amino acid sequence, represented herein as
SEQ ID NO: 38. The signal peptide for CL04725 is located from
positions 1 to about position 19 of SEQ ID NO: 38, with the mature
protein spanning from about position 20 to position 255 of SEQ ID
NO: 38. Within CL04725 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL04725 spans from a starting point
of about position 20 of SEQ ID NO: 38 to an ending point of about
position 236 of SEQ ID NO: 38. Based on homology, CL04725 can be
assigned to CAZy Family GH 61. CL04725 also possesses significant
homology (about 36% from amino acids 7 to 242 of CL04725) with a
cellulose binding protein from Agaricus bisporus (GenBank Accession
No. AAA53434; see also Armesilla et al., FEMS Microbiol. Lett.
116:293 (1994)) and significant homology (about 34% from amino
acids 5 to 242 of CL04725) with an endoglucanase from Aspergillus
terreus NIH 2642 (GenBank Accession No. EAU39094).
[0168] The enzyme CL04750 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 40 and the cDNA sequence
represented herein as SEQ ID NO: 42. The CL04750 nucleic acid
sequence encodes a 237 amino acid sequence, represented herein as
SEQ ID NO: 41. The signal peptide for CL04750 is located from
positions 1 to about position 15 of SEQ ID NO: 41, with the mature
protein spanning from about position 16 to position 237 of SEQ ID
NO: 41. Within CL04750 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL04750 spans from a starting point
of about position 16 of SEQ ID NO: 41 to an ending point of about
position 229 of SEQ ID NO: 41. Based on homology, CL04750 can be
assigned to CAZy Family GH 61. CL04750 also possesses significant
homology (about 54% from amino acids 2 to 237 of CL04750) with an
endoglucanase from Volvariella volvacea (GenBank Accession No.
AAT64005; see also Ding et al., FEMS Microbiol. Lett. 263:207
(2006)). As evidenced below in example 12, the protein CL04750 is
able to bind to chitin.
[0169] The enzyme CL04874 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 43 and the cDNA sequence
represented herein as SEQ ID NO: 45. The CL04874 nucleic acid
sequence encodes a 342 amino acid sequence, represented herein as
SEQ ID NO: 44. The signal peptide for CL04874 is located from
positions 1 to about position 19 of SEQ ID NO: 44, with the mature
protein spanning from about position 20 to position 342 of SEQ ID
NO: 44. Within CL04874 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL04874 spans from a starting point
of about position 20 of SEQ ID NO: 44 to an ending point of about
position 237 of SEQ ID NO: 44. The amino acid sequence containing
the CBM of CL04874 spans from a starting point of about position
307 of SEQ ID NO: 44 to an ending point of about position 342 of
SEQ ID NO: 44. Based on homology, CL04874 can be assigned to CAZy
Families GH 61 and CBM 1. CL04874 also possesses significant
homology (about 55% from amino acids 4 to 342 of CL04874) with an
endoglucanase from Hypocrea jecorina (GenBank Accession No.
CAA71999; see also Saloheimo et al., Eur. J. Biochem. 249:584
(1997)).
[0170] The enzyme CL05022 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 46 and the cDNA sequence
represented herein as SEQ ID NO: 48. The CL05022 nucleic acid
sequence encodes a 306 amino acid sequence, represented herein as
SEQ ID NO: 47. The signal peptide for CL05022 is located from
positions 1 to about position 15 of SEQ ID NO: 47, with the mature
protein spanning from about position 16 to position 306 of SEQ ID
NO: 47. Within CL05022 are two domains: a catalytic domain (CD) and
a cellulose-binding module (CBM). The amino acid sequence
containing the CD of CL05022 spans from a starting point of about
position 135 of SEQ ID NO: 47 to an ending point of about position
209 of SEQ ID NO: 47. The amino acid sequence containing the CBM of
CL05022 spans from a starting point of about position 245 of SEQ ID
NO: 47 to an ending point of about position 279 of SEQ ID NO: 47.
Based on homology, CL05022 can be assigned to CAZy Families GH 61
and CBM 1. CL05022 also possesses significant homology (about 48%
from amino acids 5 to 305 of CL05022) with an endoglucanase from
Volvariella volvacea (GenBank Accession No. AAT64005; see also Ding
et al., FEMS Microbiol. Lett. 263:207 (2006)). As evidenced below
in Example 12, the protein CL05022 is able to bind to chitin.
[0171] The enzyme CL05366 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 49 and the cDNA sequence
represented herein as SEQ ID NO: 51. The CL05366 nucleic acid
sequence encodes a 246 amino acid sequence, represented herein as
SEQ ID NO: 50. The signal peptide for CL05366 is located from
positions 1 to about position 19 of SEQ ID NO: 50, with the mature
protein spanning from about position 20 to position 246 of SEQ ID
NO: 50. Within CL05366 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL05366 spans from a starting point
of about position 20 of SEQ ID NO: 50 to an ending point of about
position 228 of SEQ ID NO: 50. Based on homology, CL05366 can be
assigned to CAZy Family GH 61. CL05366 also possesses significant
homology (about 48% from amino acids 3 to 246 of CL05366) with an
endoglucanase from Volvariella volvacea (GenBank Accession No.
AAT64005; see also Ding et al., FEMS Microbiol. Lett. 263:207
(2006)). As evidenced below in Example 4, the protein CL05366
contains a carbohydrate binding module.
[0172] The enzyme CL06230 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 52 and the cDNA sequence
represented herein as SEQ ID NO: 54. The CL06230 nucleic acid
sequence encodes a 323 amino acid sequence, represented herein as
SEQ ID NO: 53. The signal peptide for CL06230 is located from
positions 1 to about position 18 of SEQ ID NO: 53, with the mature
protein spanning from about position 19 to position 323 of SEQ ID
NO: 53. Within CL06230 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL06230 spans from a starting point
of about position 19 of SEQ ID NO: 53 to an ending point of about
position 233 of SEQ ID NO: 53. The amino acid sequence containing
the CBM of CL06230 spans from a starting point of about position
286 of SEQ ID NO: 53 to an ending point of about position 323 of
SEQ ID NO: 53. Based on homology, CL06230 can be assigned to CAZy
Families GH 61 and CBM 1. CL06230 also possesses significant
homology (about 40% from amino acids 1 to 321 of CL06230) with an
endoglucanase from Volvariella volvacea (GenBank Accession No.
AAT64005; see also Ding et al., FEMS Microbiol. Lett. 263:207
(2006)). As evidenced below in Example 12, the protein CL06230 is
able to bind to chitin.
[0173] The enzyme CL08101 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 55 and the cDNA sequence
represented herein as SEQ ID NO: 57. The CL08101 nucleic acid
sequence encodes a 346 amino acid sequence, represented herein as
SEQ ID NO: 56. The signal peptide for CL08101 is located from
positions 1 to about position 20 of SEQ ID NO: 56, with the mature
protein spanning from about position 21 to position 346 of SEQ ID
NO: NO:56. Within CL08101 is a catalytic domain (CD). The amino
acid sequence containing the CD of CL08101 spans from a starting
point of about position 20 of SEQ ID NO: NO:56 to an ending point
of about position 304 of SEQ ID NO: NO:56. Based on homology,
CL08101 can be assigned to CAZy Families GH 61 and CBM 1. CL08101
also possesses significant homology (about 64% from amino acids 6
to 267 of CL08101) with an endoglucanase from Aspergillus terreus
NIH 2642 (GenBank Accession No. EAU38213).
[0174] The enzyme CL09768 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 58 and the cDNA sequence
represented herein as SEQ ID NO: 60. The CL09768 nucleic acid
sequence encodes a 225 amino acid sequence, represented herein as
SEQ ID NO: 59. The signal peptide for CL09768 is located from
positions 1 to about position 17 of SEQ ID NO: 59, with the mature
protein spanning from about position 18 to position 225 of SEQ ID
NO: 59. Within CL09768 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL09768 spans from a starting point
of about position 140 of SEQ ID NO: 59 to an ending point of about
position 207 of SEQ ID NO: 59. Based on homology, CL09768 can be
assigned to CAZy Family GH 61. CL09768 also possesses significant
homology (about 42% from amino acids 60 to 225 of CL09768) with an
endoglucanase from Volvariella volvacea (GenBank Accession No.
AAT64005; see also Ding et al., FEMS Microbiol. Lett. 263:207
(2006)). As evidenced below in Example 12, the protein CL09768 is
able to bind to chitin.
[0175] The enzyme CL10391 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 61 and the cDNA sequence
represented herein as SEQ ID NO: 63. The CL10391 nucleic acid
sequence encodes a 227 amino acid sequence, represented herein as
SEQ ID NO: 62. The signal peptide for CL10391 is located from
positions 1 to about position 17 of SEQ ID NO: 62, with the mature
protein spanning from about position 18 to position 227 of SEQ ID
NO: 62. Within CL10391 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL10391 spans from a starting point
of about position 139 of SEQ ID NO: 62 to an ending point of about
position 210 of SEQ ID NO: 62. Based on homology, CL10391 can be
assigned to CAZy Family GH 61. CL10391 also possesses significant
homology (about 39% from amino acids 42 to 227 of CL10391) with an
endoglucanase from Volvariella volvacea (GenBank Accession No.
AAT64005; see also Ding et al., FEMS Microbiol. Lett. 263:207
(2006)).
[0176] The enzyme CL10518 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 64 and the cDNA sequence
represented herein as SEQ ID NO: 66. The CL10518 nucleic acid
sequence encodes a 235 amino acid sequence, represented herein as
SEQ ID NO: 65. The signal peptide for CL10518 is located from
positions 1 to about position 15 of SEQ ID NO: 65, with the mature
protein spanning from about position 16 to position 235 of SEQ ID
NO: 65. Within CL10518 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL10518 spans from a starting point
of about position 16 of SEQ ID NO: 65 to an ending point of about
position 227 of SEQ ID NO: 65. Based on homology, CL10518 can be
assigned to CAZy Family GH 61. CL10518 also possesses significant
homology (about 54% from amino acids 2 to 235 of CL10518) with an
endoglucanase from Volvariella volvacea (GenBank Accession No.
AAT64005; see also Ding et al., FEMS Microbiol. Lett. 263:207
(2006)).
[0177] The enzyme CL10824 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 67 and the cDNA sequence
represented herein as SEQ ID NO: 69. The CL10824 nucleic acid
sequence encodes a 232 amino acid sequence, represented herein as
SEQ ID NO: 68. The signal peptide for CL10824 is located from
positions 1 to about position 17 of SEQ ID NO: 68, with the mature
protein spanning from about position 18 to position 232 of SEQ ID
NO: 68. Within CL10824 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL10824 spans from a starting point
of about position 18 of SEQ ID NO: 68 to an ending point of about
position 224 of SEQ ID NO: 68. Based on homology, CL10824 can be
assigned to CAZy Family GH 61. CL10824 also possesses significant
homology (about 37% from amino acids 9 to 232 of CL10824) with an
endoglucanase from Volvariella volvacea (GenBank Accession No.
AAT64005; see also Ding et al., FEMS Microbiol. Lett. 263:207
(2006)).
[0178] The enzyme Axe4 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 70 and the cDNA sequence
represented herein as SEQ ID NO: 72. The Axe4 nucleic acid sequence
encodes a 299 amino acid sequence, represented herein as SEQ ID NO:
71. The signal peptide for Axe4 is located from positions 1 to
about position 23 of SEQ ID NO: 71, with the mature protein
spanning from about position 24 to position 299 of SEQ ID NO: 71.
Within Axe4 is a catalytic domain (CD). The amino acid sequence
containing the CD of Axe4 spans from a starting point of about
position 42 of SEQ ID NO: 71 to an ending point of about position
140 of SEQ ID NO: 71. Based on homology, Axe4 can be assigned to
CAZy Family CE 1. Axe4 also possesses significant homology (about
31% from amino acids 19 to 299 of Axe4 with an acetyl xylan
esterase from Penicllium purpurogenum (GenBank Accession No.
AAM93261; see also Gordillo et al., Mycol. Res. 110:1129 (2006)).
Based on this degree of homology, Axe4 is expected to exhibit
similar acetyl xylan esterase enzymatic activity.
[0179] The enzyme Pec11 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 73 and the cDNA sequence
represented herein as SEQ ID NO: 75. The Pec11 nucleic acid
sequence encodes a 330 amino acid sequence, represented herein as
SEQ ID NO: 74. The signal peptide for Pec11 is located from
positions 1 to about position 15 of SEQ ID NO: 74, with the mature
protein spanning from about position 16 to position 330 of SEQ ID
NO: 74. Within Pec11 is a catalytic domain (CD). The amino acid
sequence containing the CD of Pec11 spans from a starting point of
about position 30 of SEQ ID NO: 74 to an ending point of about
position 326 of SEQ ID NO: 74. Based on homology, Pec11 can be
assigned to CAZy Family PL 1. Pec11 also possesses significant
homology (about 65% from amino acids 5 to 330 of Pec11) with a
pectate lyase from Colletotrichum gloeosporioides f. sp. malvae
(GenBank Accession No. AAD43564; see also Shih et al., Gene 243:139
(2000)). Based on this degree of homology, Pec11 is expected to
exhibit similar pectate lyase enzymatic activity.
[0180] The enzyme Pec12 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 76 and the cDNA sequence
represented herein as SEQ ID NO: 78. The Pec12 nucleic acid
sequence encodes a 326 amino acid sequence, represented herein as
SEQ ID NO: 77. The signal peptide for Pec12 is located from
positions 1 to about position 18 of SEQ ID NO: 77, with the mature
protein spanning from about position 19 to position 326 of SEQ ID
NO: 77. Within Pec12 is a catalytic domain (CD). The amino acid
sequence containing the CD of Pec12 spans from a starting point of
about position 31 of SEQ ID NO: 77 to an ending point of about
position 322 of SEQ ID NO: 77. Based on homology, Pec12 can be
assigned to CAZy Family PL 1. Pec12 also possesses significant
homology (about 55% from amino acids 12 to 326 of Pec12) with a
pectate lyase from Aspergillus niger (GenBank Accession No.
CAC33162; see also Benen et al., Biochemistry 39:15563 (2000)).
Based on this degree of homology, Pec12 is expected to exhibit
similar pectate lyase enzymatic activity.
[0181] The enzyme Pec13 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 79 and the cDNA sequence
represented herein as SEQ ID NO: 81. The Pec13 nucleic acid
sequence encodes a 336 amino acid sequence, represented herein as
SEQ ID NO: 80. The signal peptide for Pec13 is located from
positions 1 to about position 18 of SEQ ID NO: 80, with the mature
protein spanning from about position 19 to position 336 of SEQ ID
NO: 80. Within Pec13 is a catalytic domain (CD). The amino acid
sequence containing the CD of Pec13 spans from a starting point of
about position 21 of SEQ ID NO: 80 to an ending point of about
position 336 of SEQ ID NO: 80. Based on homology, Pec13 can be
assigned to CAZy Family PL 1. Pec13 also possesses significant
homology (about 43% from amino acids 51 to 253 of Pec13) with a
pectate lyase from Aspergillus sp. (GenBank Accession No. 551509;
see also Ho et al., Curr. Genet. 27:142 (1995)). Based on this
degree of homology, Pec13 is expected to exhibit similar pectate
lyase enzymatic activity.
[0182] The enzyme Pec14 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 82 and the cDNA sequence
represented herein as SEQ ID NO: 84. The Pec14 nucleic acid
sequence encodes a 311 amino acid sequence, represented herein as
SEQ ID NO: 83. The signal peptide for Pec14 is located from
positions 1 to about position 20 of SEQ ID NO: 83, with the mature
protein spanning from about position 21 to position 311 of SEQ ID
NO: 83. Within Pec14 is a catalytic domain (CD). The amino acid
sequence containing the CD of Pec14 spans from a starting point of
about position 21 of SEQ ID NO: 83 to an ending point of about
position 304 of SEQ ID NO: 83. Based on homology, Pec14 can be
assigned to CAZy Family PL 1. Pec14 also possesses significant
homology (about 39% from amino acids 47 to 304 of Pec14) with a
pectate lyase from Bacillus halodurans C-125 (GenBank Accession No.
NP-241564; see also Takami et al., Nucleic Acid Res. 28:4317
(2000)). Based on this degree of homology, Pec14 is expected to
exhibit similar pectate lyase enzymatic activity.
[0183] The enzyme Pec15 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 85 and the cDNA sequence
represented herein as SEQ ID NO: 87. The Pec15 nucleic acid
sequence encodes a 250 amino acid sequence, represented herein as
SEQ ID NO: 86. The signal peptide for Pec15 is located from
positions 1 to about position 23 of SEQ ID NO: 86, with the mature
protein spanning from about position 24 to position 250 of SEQ ID
NO: 86. Within Pec15 is a catalytic domain (CD). The amino acid
sequence containing the CD of Pec15 spans from a starting point of
about position 24 of SEQ ID NO: 86 to an ending point of about
position 231 of SEQ ID NO: 86. Based on homology, Pec15 can be
assigned to CAZy Family PL 3. Pec15 also possesses significant
homology (about 71% from amino acids 20 to 250 of Pec15) with a
pectate lyase from Fusarium oxysporum f. sp. lycopersici (GenBank
Accession No. AAC64368; see also Huertas-Gonzalez et al., Curr.
Genet. 35:36 (1999)). Based on this degree of homology, Pec15 is
expected to exhibit similar pectate lyase enzymatic activity.
[0184] The enzyme Rgl1 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 88 and the cDNA sequence
represented herein as SEQ ID NO: 90. The Rgl1 nucleic acid sequence
encodes a 551 amino acid sequence, represented herein as SEQ ID NO:
89. The signal peptide for Rgl1 is located from positions 1 to
about position 23 of SEQ ID NO: 89, with the mature protein
spanning from about position 24 to position 551 of SEQ ID NO: 89.
Within Rgl1 is a catalytic domain (CD). The amino acid sequence
containing the CD of Rgl1 spans from a starting point of about
position 229 of SEQ ID NO: 89 to an ending point of about position
337 of SEQ ID NO: 89. Based on homology, Rgl1 can be assigned to
CAZy Family PL 4. Rgl1 also possesses significant homology (about
78% from amino acids 1 to 533 of Rgl1) with a rhamnogalacturonan
lyase from Neurospora crassa OR74A (GenBank Accession No.
XP-960560). Based on this degree of homology, Rgl1 is expected to
exhibit similar rhamnogalacturonan lyase enzymatic activity.
[0185] The enzyme CL10366 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 94 and the cDNA sequence
represented herein as SEQ ID NO: 96. The CL10366 nucleic acid
sequence encodes a 254 amino acid sequence, represented herein as
SEQ ID NO: 95. The signal peptide for CL10366 is located from
positions 1 to about position 23 of SEQ ID NO: 95, with the mature
protein spanning from about position 24 to position 254 of SEQ ID
NO: 95. Within CL10366 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL10366 spans from a starting point
of about position 24 of SEQ ID NO: 95 to an ending point of about
position 246 of SEQ ID NO: 95. Based on homology, CL10366 can be
assigned to CAZy Family GH 61. CL10366 also possesses significant
homology (about 39% from amino acids 8 to 252 of CL10366) with a
cellulose binding protein from Agaricus bisporus (GenBank Accession
No. AAA53434; see also Armesilla et al., FEMS Microbiol. Lett.
116:293 (1994)) and significant homology (about 30% from amino
acids 1 to 252 of CL10366) with an endoglucanase from Aspergillus
terreus NIH 2642 (GenBank Accession No. EAU39094). Based on this
degree of homology, CL10366 is expected to exhibit similar
cellulose binding activity and endoglucanase enzymatic
activity.
[0186] The enzyme CL02839 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 97 and the cDNA sequence
represented herein as SEQ ID NO: 99. The CL02839 nucleic acid
sequence encodes a 222 amino acid sequence, represented herein as
SEQ ID NO: 98. The signal peptide for CL02839 is located from
positions 1 to about position 18 of SEQ ID NO: 98, with the mature
protein spanning from about position 19 to position 222 of SEQ ID
NO: 98. Within CL02839 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL02839 spans from a starting point
of about position 19 of SEQ ID NO: 98 to an ending point of about
position 214 of SEQ ID NO: 98. Based on homology, CL02839 can be
assigned to CAZy Family GH 61. CL02839 also possesses significant
homology (about 38% from amino acids 4 to 222 of CL02839) with an
endoglucanase from Volvariella volvacea (GenBank Accession No.
AAT64005; see also Ding et al., FEMS Microbiol. Lett. 263:207
(2006)).
[0187] The enzyme CL03723 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 100 and the cDNA sequence
represented herein as SEQ ID NO: 102. The CL03723 nucleic acid
sequence encodes a 445 amino acid sequence, represented herein as
SEQ ID NO: 101. The signal peptide for CL03723 is located from
positions 1 to about position 21 of SEQ ID NO: 101, with the mature
protein spanning from about position 22 to position 445 of SEQ ID
NO: 101. Within CL03723 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL03723 spans from a starting point
of about position 129 of SEQ ID NO: 101 to an ending point of about
position 241 of SEQ ID NO: 101. Based on homology, CL03723 can be
assigned to CAZy Family GH 61. CL03723 also possesses significant
homology (about 32% from amino acids 7 to 261 of CL03723) with an
endoglucanase from Volvariella volvacea (GenBank Accession No.
AAT64005; see also Ding et al., FEMS Microbiol. Lett. 263:207
(2006)).
[0188] The enzyme CL04859 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 103 and the cDNA sequence
represented herein as SEQ ID NO: 105. The CL04859 nucleic acid
sequence encodes a 245 amino acid sequence, represented herein as
SEQ ID NO: 104. The signal peptide for CL04859 is located from
positions 1 to about position 19 of SEQ ID NO: 104, with the mature
protein spanning from about position 20 to position 245 of SEQ ID
NO: 104. Within CL04859 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL04859 spans from a starting point
of about position 133 of SEQ ID NO: 104 to an ending point of about
position 227 of SEQ ID NO: 104. Based on homology, CL04859 can be
assigned to CAZy Family GH 61. CL04859 also possesses significant
homology (about 36% from amino acids 20 to 236 of CL04859) with an
endoglucanase from Aspergillus kawachii (GenBank Accession No.
BAB62318).
[0189] The enzyme CL09767 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 106 and the cDNA sequence
represented herein as SEQ ID NO: 108. The CL09767 nucleic acid
sequence encodes a 224 amino acid sequence, represented herein as
SEQ ID NO: 107. The signal peptide for CL09767 is located from
position 1 to about position 16 of SEQ ID NO: 107, with the mature
protein spanning from about position 17 to position 224 of SEQ ID
NO: 107. Within CL09767 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL09767 spans from a starting point
of about position 18 of SEQ ID NO: 107 to an ending point of about
position 216 of SEQ ID NO: 107. Based on homology, CL09767 can be
assigned to CAZy Family GH 61. CL09767 also possesses significant
homology (about 37% from amino acids 4 to 222 of CL09767) with an
endoglucanase from Volvariella volvacea (GenBank Accession No.
AAT64005; see also Ding et al., FEMS Microbiol. Lett. 263:207
(2006)).
[0190] The enzyme Bxl4 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 109 and the cDNA sequence
represented herein as SEQ ID NO: 111. The Bxl4 nucleic acid
sequence encodes a 537 amino acid sequence, represented herein as
SEQ ID NO: 110. Within Bxl4 is a catalytic domain (CD). The amino
acid sequence containing the CD of Bxl4 spans from a starting point
of about position 4 of SEQ ID NO: 110 to an ending point of about
position 311 of SEQ ID NO: 110. Based on homology, Bxl4 can be
assigned to CAZy Family GH 43. Bxl4 also possesses significant
homology (about 60% from amino acids 4 to 525 of Bxl4) with an
.beta.-xylosidase from Rhizobium etli CFN 42 (GenBank Accession No.
ABC91230). Based on this degree of homology, Bxl4 is expected to
exhibit similar a .beta.-xylosidase enzymatic activity.
[0191] The enzyme Abn9 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 112 and the cDNA sequence
represented herein as SEQ ID NO: 114. The Abn9 nucleic acid
sequence encodes a 327 amino acid sequence, represented herein as
SEQ ID NO: 113. Within Abn9 is a catalytic domain (CD). The amino
acid sequence containing the CD of Abn9 spans from a starting point
of about position 4 of SEQ ID NO: 113 to an ending point of about
position 323 of SEQ ID NO: 113. Based on homology, Abn9 can be
assigned to CAZy Family GH 43. Abn9 also possesses significant
homology (about 71% from amino acids 3 to 321 of Abn9) with an
.beta.-xylosidase from Aspergillus terreus NIH 2642 (GenBank
Accession No. EAU38739) and significant homology (about 60% from
amino acids 3 to 326 of Abn9) with an .alpha.-N-arabinofuranosidase
from Flavobacterium johnsoniae UW101 (GenBank Accession No.
ABQ05030). Based on these degrees of homology, Abn9 is expected to
exhibit similar .beta.-xylosidase and .alpha.-N-arabinofuranosidase
enzymatic activities.
[0192] The enzyme CL02469 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 115 and the cDNA sequence
represented herein as SEQ ID NO: 117. The CL02469 nucleic acid
sequence encodes a 1106 amino acid sequence, represented herein as
SEQ ID NO: 118. The signal peptide for CL02469 is located from
positions 1 to about position 16 of SEQ ID NO: 118, with the mature
protein spanning from about position 17 to position 1106 of SEQ ID
NO: 118. Within CL02469 are two domains: a catalytic domain (CD)
and a cellulose-binding module (CBM). The amino acid sequence
containing the CD of CL02469 spans from a starting point of about
position 110 of SEQ ID NO: 118 to an ending point of about position
662 of SEQ ID NO: 118. The amino acid sequence containing the CBM
of CL02469 spans from a starting point of about position 663 of SEQ
ID NO: 118 to an ending point of about position 703 of SEQ ID NO:
118. Based on homology, CL02469 can be assigned to CAZy Family GH
3. CL02469 also possesses significant homology (about 37% from
amino acids 40 to 764 of CL02469) with an .beta.-xylosidase from
Sulfolobus solfataricus P2 (GenBank Accession No. AAK43134) and
significant homology (about 65% from amino acids 28 to 764 of
CL02469) with an (3-glucosidase Aspergillus clavatus NRRL 1
(GenBank Accession No. EAW12608). Based on these degrees of
homology, CL02469 is expected to exhibit similar .beta.-xylosidase
and .beta.-glucosidase enzymatic activities.
[0193] The enzyme CL05182 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 118 and the cDNA sequence
represented herein as SEQ ID NO: 120. The CL05182 nucleic acid
sequence encodes a 919 amino acid sequence, represented herein as
SEQ ID NO: 119. The signal peptide for CL05182 is located from
positions 1 to about position 23 of SEQ ID NO: 119, with the mature
protein spanning from about position 24 to position 919 of SEQ ID
NO: 119. Within CL05182 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL05182 spans from a starting point
of about position 45 of SEQ ID NO: 119 to an ending point of about
position 663 of SEQ ID NO: 119. Based on homology, CL05182 can be
assigned to CAZy Family GH 3. CL05182 also possesses significant
homology (about 58% from amino acids 29 to 904 of CL05182) with a
.beta.-glucosidase from Thermoascus auramtiacus (GenBank Accession
No. AAY33983; see also Hong et al., Appl. Microbiol. Biotechnol.
73:80 (2006)). Based on this degree of homology, CL05182 is
expected to exhibit similar .beta.-glucosidase enzymatic
activity.
[0194] The enzyme Bgl2 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 121 and the cDNA sequence
represented herein as SEQ ID NO: 123. The Bgl2 nucleic acid
sequence encodes a 968 amino acid sequence, represented herein as
SEQ ID NO: 122. Within Bgl2 is a catalytic domain (CD). The amino
acid sequence containing the CD of Bgl2 spans from a starting point
of about position 166 of SEQ ID NO: 122 to an ending point of about
position 773 of SEQ ID NO: 122. Based on homology, CL11589 can be
assigned to CAZy Family GH 3. Bgl2 also possesses significant
homology (about 55% from amino acids 241 to 968 of Bgl2) with a
.beta.-glucosidase from Coccidioides immitis (GenBank Accession No.
AAL09827). Based on this degree of homology, Bgl2 is expected to
exhibit similar .beta.-glucosidase enzymatic activity.
[0195] The enzyme CL08144 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 124 and the cDNA sequence
represented herein as SEQ ID NO: 126. The CL08144 nucleic acid
sequence encodes a 922 amino acid sequence, represented herein as
SEQ ID NO: 125. Within CL08144 is a catalytic domain (CD). The
amino acid sequence containing the CD of CL08144 spans from a
starting point of about position 69 of SEQ ID NO: 125 to an ending
point of about position 298 of SEQ ID NO: 125. Based on homology,
CL11589 can be assigned to CAZy Family GH 3. CL08144 also possesses
significant homology (about 70% from amino acids 4 to 798 of
CL08144) with a .beta.-N-acetylglucosaminidase from Neurospora
crassa (GenBank Accession No. CAE85548). Based on this degree of
homology, CL08144 is expected to exhibit similar
.beta.-N-acetylglucosaminidase enzymatic activity.
[0196] The enzyme CL09335 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 127 and the cDNA sequence
represented herein as SEQ ID NO: 129. The CL09335 nucleic acid
sequence encodes a 356 amino acid sequence, represented herein as
SEQ ID NO: 128. The signal peptide for CL09335 is located from
positions 1 to about position 19 of SEQ ID NO: 128, with the mature
protein spanning from about position 20 to position 356 of SEQ ID
NO: 128. Within CL09335 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL09335 spans from a starting point
of about position 27 of SEQ ID NO: 128 to an ending point of about
position 355 of SEQ ID NO: 128. Based on homology, CL09335 can be
assigned to CAZy Family GH 3. CL09335 also possesses significant
homology (about 79% from amino acids 23 to 347 of CL09335) with a
.beta.-hexosaminidase from Aspergillus nidulans FGSC A4 (GenBank
Accession No. EAA63328). Based on this degree of homology, CL09335
is expected to exhibit similar .beta.-hexosaminidase enzymatic
activity.
[0197] The enzyme CL04514 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 130 and the cDNA sequence
represented herein as SEQ ID NO: 132. The CL04514 nucleic acid
sequence encodes a 513 amino acid sequence, represented herein as
SEQ ID NO: 131. The signal peptide for CL04514 is located from
positions 1 to about position 18 of SEQ ID NO: 131, with the mature
protein spanning from about position 19 to position 513 of SEQ ID
NO: 131. Within CL04514 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL04514 spans from a starting point
of about position 228 of SEQ ID NO: 131 to an ending point of about
position 372 of SEQ ID NO: 131. Based on homology, CL04514 can be
assigned to CAZy Family GH 3. CL04514 also possesses significant
homology (about 29% from amino acids 33 to 377 of CL04514) with a
.beta.-N-acetylglucosaminidase from Aspergillus clavatus NRRL 1
(GenBank Accession No. EAW15083). Based on this degree of homology,
CL04514 is expected to exhibit similar 13-N-acetylglucosaminidase
enzymatic activity.
[0198] The enzyme CL06190 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 133 and the cDNA sequence
represented herein as SEQ ID NO: 135. The CL06190 nucleic acid
sequence encodes a 464 amino acid sequence, represented herein as
SEQ ID NO: 134. The signal peptide for CL06190 is located from
positions 1 to about position 22 of SEQ ID NO: 134, with the mature
protein spanning from about position 23 to position 464 of SEQ ID
NO: 134. Within CL06190 are two domains: a catalytic domain (CD)
and a cellulose-binding module (CBM). The amino acid sequence
containing the CD of CL06190 spans from a starting point of about
position 24 of SEQ ID NO: 134 to an ending point of about position
398 of SEQ ID NO: 134. The amino acid sequence containing the CBM
of CL06190 spans from a starting point of about position 429 of SEQ
ID NO: 134 to an ending point of about position 464 of SEQ ID NO:
134. Based on homology, CL06190 can be assigned to CAZy Families GH
7 and CBM 1. CL06190 also possesses significant homology (about 63%
from amino acids 5 to 464 of CL06190) with an endoglucanase from
Hypocrea pseudokoningii (GenBank Accession No. ABM90986). Based on
this degree of homology, CL06190 is expected to exhibit similar
endoglucanase enzymatic activity.
[0199] The enzyme CL00455 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 136 and the cDNA sequence
represented herein as SEQ ID NO: 138. The CL00455 nucleic acid
sequence encodes a 456 amino acid sequence, represented herein as
SEQ ID NO: 137. The signal peptide for CL00455 is located from
positions 1 to about position 20 of SEQ ID NO: 137, with the mature
protein spanning from about position 21 to position 456 of SEQ ID
NO: 137. Within CL00455 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL00455 spans from a starting point
of about position 21 of SEQ ID NO: 137 to an ending point of about
position 455 of SEQ ID NO: 137. Based on homology, CL00455 can be
assigned to CAZy Family GH 7. CL00455 also possesses significant
homology (about 66% from amino acids 1 to 455 of CL00455) with a
cellobiohydrolase from Irpex lacteus (GenBank Accession No.
BAD16575). Based on this degree of homology, CL00455 is expected to
exhibit similar cellobiohydrolase enzymatic activity.
[0200] The enzyme CL02823 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 139 and the cDNA sequence
represented herein as SEQ ID NO: 141. The CL02823 nucleic acid
sequence encodes a 280 amino acid sequence, represented herein as
SEQ ID NO: 140. The signal peptide for CL02823 is located from
positions 1 to about position 21 of SEQ ID NO: 140, with the mature
protein spanning from about position 22 to position 280 of SEQ ID
NO: 140. Within CL02823 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL02823 spans from a starting point
of about position 62 of SEQ ID NO: 140 to an ending point of about
position 280 of SEQ ID NO: 140. Based on homology, CL02823 can be
assigned to CAZy Family GH 16. CL02823 possesses significant
homology (about 64% from amino acids 6 to 278 of CL02823) with a
.beta.-glucosidase from Neosartorya fischeri NRRL 181 (GenBank
Accession No. XP-001258587). Based on this degree of homology,
CL02823 is expected to exhibit similar .beta.-glucosidase enzymatic
activity. .beta.-glucosidases often have broad substrate
specificity, and can hydrolyze .beta.-1,3 bonds between glucose
residues in addition to .beta.-1,4 bonds. Therefore, CL02823 is
also expected to possess the ability to bind to lichenan and
lichenase activity (the ability to hydrolyze lichenan, a linear
1,3-1,4-.beta.-D glucan). As evidenced below in Example 13, the
protein CL02823 binds to lichenan.
[0201] CL02823 also possesses significant homology (about 59% from
amino acids 19 to 271 of CL02823) with an endo-1,3-.beta.-glucanase
(laminarinase) from Neurospora crassa NRRL 181 (GenBank Accession
No. CAF06015). Based on this degree of homology, CL02823 is
expected to exhibit similar endo-1,3-.beta.-glucanase
(laminarinase) enzymatic activity. The enzyme Xyl11 is encoded by
the nucleic acid sequence represented herein as SEQ ID NO: 142 and
the cDNA sequence represented herein as SEQ ID NO: 144. The Xyl11
nucleic acid sequence encodes a 326 amino acid sequence,
represented herein as SEQ ID NO: 143. The signal peptide for Xyl11
is located from positions 1 to about position 15 of SEQ ID NO: 143,
with the mature protein spanning from about position 16 to position
326 of SEQ ID NO: 143. Within Xyl11 is a catalytic domain (CD). The
amino acid sequence containing the CD of Xyl11 spans from a
starting point of about position 23 of SEQ ID NO: 143 to an ending
point of about position 324 of SEQ ID NO: 143. Based on homology,
CL08529 can be assigned to CAZy Family GH 10. Xyl11 also possesses
significant homology (about 71% from amino acids 23 to 324 of
Xyl11) with a xylanase from Cryptovalsa sp. BCC 7197 (GenBank
Accession No. AAU89274; see also Boonyapakron et al., DNA Seq.
16:372 (2005)). Based on this degree of homology, Xyl11 is expected
to exhibit similar xylanase enzymatic activity. As evidenced below
in Example 14, the enzyme Xyl 11 exhibits endo-xylanase
activity.
[0202] The enzyme Xyl10 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 145 and the cDNA sequence
represented herein as SEQ ID NO: 147. The Xyl10 nucleic acid
sequence encodes a 222 amino acid sequence, represented herein as
SEQ ID NO: 146. The signal peptide for Xyl10 is located from
positions 1 to about position 18 of SEQ ID NO: 146, with the mature
protein spanning from about position 19 to position 222 of SEQ ID
NO: 146. Within Xyl10 is a catalytic domain (CD). The amino acid
sequence containing the CD of Xyl10 spans from a starting point of
about position 35 of SEQ ID NO: 146 to an ending point of about
position 222 of SEQ ID NO: 146. Based on homology, Xyl10 can be
assigned to CAZy Family GH 11. Xyl10 also possesses significant
homology (about 69% from amino acids 1 to 222 of Xyl10) with a
xylanase from Chaetomium thermophilum (GenBank Accession No.
CAD48751; see also Mantyla et al., Appl. Microbiol. Biotechnol.
(2007)). Based on this degree of homology, Xyl10 is expected to
exhibit similar xylanase enzymatic activity. As evidenced below in
Examples 14 and 15, the enzyme Xyl10 possesses exo-xylanase
activity.
[0203] The enzyme CL09769 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 151 and the cDNA sequence
represented herein as SEQ ID NO: 153. The CL09769 nucleic acid
sequence encodes a 578 amino acid sequence, represented herein as
SEQ ID NO: 152. The signal peptide for CL09769 is located from
positions 1 to about position 24 of SEQ ID NO: 152, with the mature
protein spanning from about position 25 to position 578 of SEQ ID
NO: 152. Within CL09769 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL09769 spans from a starting point
of about position 30 of SEQ ID NO: 152 to an ending point of about
position 574 of SEQ ID NO: 152. CL09769 possesses significant
homology (about 66% from amino acids 35 to 570 of CL09769) with a
cellobiose dehydrogenase from Humicola insolens (GenBank Accession
No. AAF69005; see also Xu et al., Enzyme Microb. Technol. 28:744
(2001)). Based on this degree of homology, CL09769 is expected to
exhibit similar cellobiose dehydrogenase enzymatic activity.
[0204] The enzyme Xyl7 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 154 and the cDNA sequence
represented herein as SEQ ID NO: 156. The Xyl7 nucleic acid
sequence encodes a 278 amino acid sequence, represented herein as
SEQ ID NO: 155. The signal peptide for Xyl7 is located from
positions 1 to about position 19 of SEQ ID NO: 155, with the mature
protein spanning from about position 20 to position 278 of SEQ ID
NO: 155. Within Xyl7 are two domains: a catalytic domain (CD) and a
cellulose-binding module (CBM). The amino acid sequence containing
the CD of Xyl7 spans from a starting point of about position 30 of
SEQ ID NO: 155 to an ending point of about position 225 of SEQ ID
NO: 155. The amino acid sequence containing the CBM of Xyl7 spans
from a starting point of about position 244 of SEQ ID NO: 155 to an
ending point of about position 278 of SEQ ID NO: 155. Based on
homology, Xyl7 can be assigned to CAZy Families GH 11 and CBM 1.
Xyl7 also possesses significant homology (about 55% from amino
acids 1 to 278 of Xyl7) with a xylanase from Phanerochaete
chrysosprium (GenBank Accession No. AAG44994). Based on this degree
of homology, Xyl7 is expected to exhibit similar xylanase enzymatic
activity. As evidenced below in Examples 14 and 15, the enzyme Xyl7
exhibits endo-xylanase activity.
[0205] The enzyme Xyl8 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 157 and the cDNA sequence
represented herein as SEQ ID NO: 159. The Xyl8 nucleic acid
sequence encodes a 230 amino acid sequence, represented herein as
SEQ ID NO: 158. The signal peptide for Xyl8 is located from
positions 1 to about position 16 of SEQ ID NO: 158, with the mature
protein spanning from about position 17 to position 230 of SEQ ID
NO: 158. Within Xyl8 is a catalytic domain (CD). The amino acid
sequence containing the CD of Xyl8 spans from a starting point of
about position 42 of SEQ ID NO: 158 to an ending point of about
position 230 of SEQ ID NO: 158. Based on homology, Xyl8 can be
assigned to CAZy Family GH 11. Xyl8 also possesses significant
homology (about 73% from amino acids 1 to 230 of Xyl8) with a
xylanase from Acrophialophora nainiana (GenBank Accession No.
ABG37635). Based on this degree of homology, Xyl8 is expected to
exhibit similar xylanase enzymatic activity. As evidenced below in
Examples 14 and 16, the enzyme Xyl8 is able to bind to xylan and
exhibits endo-xylanase activity.
[0206] The enzyme Xyl9 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 148 and the cDNA sequence
represented herein as SEQ ID NO: 150. The Xyl9 nucleic acid
sequence encodes a 223 amino acid sequence, represented herein as
SEQ ID NO: 149. The signal peptide for Xyl9 is located from
positions 1 to about position 18 of SEQ ID NO: 149, with the mature
protein spanning from about position 19 to position 223 of SEQ ID
NO: 149. Within Xyl9 is a catalytic domain (CD). The amino acid
sequence containing the CD of Xyl9 spans from a starting point of
about position 40 of SEQ ID NO: 149 to an ending point of about
position 221 of SEQ ID NO: 149. Based on homology, Xyl9 can be
assigned to CAZy Family GH 11. Xyl9 also possesses significant
homology (about 82% from amino acids 19 to 221 of Xyl9) with a
xylanase from Chaetomium gracile (GenBank Accession No. BAA08649).
Based on this degree of homology, Xyl9 is expected to exhibit
similar xylanase enzymatic activity. As evidenced below in Example
14, the enzyme Xyl9 exhibits endo-xylanase activity.
[0207] The enzyme Pgx1 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 160 and the cDNA sequence
represented herein as SEQ ID NO: 162. The Pgx1 nucleic acid
sequence encodes a 469 amino acid sequence, represented herein as
SEQ ID NO: 161. The signal peptide for Pgx1 is located from
positions 1 to about position 19 of SEQ ID NO: 161, with the mature
protein spanning from about position 20 to position 469 of SEQ ID
NO: 161. Within Pgx1 is a catalytic domain (CD). The amino acid
sequence containing the CD of Pgx1 spans from a starting point of
about position 107 of SEQ ID NO: 161 to an ending point of about
position 455 of SEQ ID NO: 161. Based on homology, Pgx1 can be
assigned to CAZy Family GH 28. Pgx1 also possesses significant
homology (about 69% from amino acids 71 to 435 of Pgx1) with an
exo-polygalacturonase from Aspergillus nidulans (GenBank Accession
No. AA061898). Based on this degree of homology, Pgx1 is expected
to exhibit similar exo-polygalacturonase enzymatic activity. As
evidenced below in Example 17, the enzyme Pgx1 exhibits
polygalacturonase activity.
[0208] The enzyme Rgx1 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 163 and the cDNA sequence
represented herein as SEQ ID NO: 165. The Rgx1 nucleic acid
sequence encodes a 423 amino acid sequence, represented herein as
SEQ ID NO: 164. The signal peptide for Rgx1 is located from
positions 1 to about position 19 of SEQ ID NO: 164, with the mature
protein spanning from about position 20 to position 423 of SEQ ID
NO: 164. Within Rgx1 is a catalytic domain (CD). The amino acid
sequence containing the CD of Rgx1 spans from a starting point of
about position 65 of SEQ ID NO: 164 to an ending point of about
position 403 of SEQ ID NO: 164. Based on homology, Rgx1 can be
assigned to CAZy Family GH 28. Rgx1 also possesses significant
homology (about 34% from amino acids 50 to 414 of Rgx1) with an
exo-rhamnogalacturonase from Aspergillus niger (GenBank Accession
No. ABD61567). Based on this degree of homology, Rgx1 is expected
to exhibit similar exo-rhamnogalacturonase enzymatic activity.
[0209] The enzyme CL07563 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 166 and the cDNA sequence
represented herein as SEQ ID NO: 168. The CL07563 nucleic acid
sequence encodes a 342 amino acid sequence, represented herein as
SEQ ID NO: 167. The signal peptide for CL07563 is located from
positions 1 to about position 18 of SEQ ID NO: 167, with the mature
protein spanning from about position 19 to position 342 of SEQ ID
NO: 167. Within CL07563 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL07563 spans from a starting point
of about position 75 of SEQ ID NO: 167 to an ending point of about
position 342 of SEQ ID NO: 167. Based on homology, CL07563 can be
assigned to CAZy Family GH 5. CL07563 also possesses significant
homology (about 58% from amino acids 1 to 342 of CL07563) with an
endoglucanase from Thermoascus aurantiacus (GenBank Accession No.
AAL88714). Based on this degree of homology, CL07563 is expected to
exhibit similar endoglucanase enzymatic activity.
[0210] The enzyme CL00103 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 169 and the cDNA sequence
represented herein as SEQ ID NO: 171. The CL00103 nucleic acid
sequence encodes a 420 amino acid sequence, represented herein as
SEQ ID NO: 170. The signal peptide for CL00103 is located from
positions 1 to about position 26 of SEQ ID NO: 170, with the mature
protein spanning from about position 27 to position 420 of SEQ ID
NO: 170. Within CL00103 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL00103 spans from a starting point
of about position 59 of SEQ ID NO: 170 to an ending point of about
position 420 of SEQ ID NO: 170. Based on homology, CL00103 can be
assigned to CAZy Family GH 5. CL00103 also possesses significant
homology (about 37% from amino acids 62 to 398 of CL00103) with a
cellulase from Stigmatella aurantiaca (GenBank Accession No.
CAD19084). Based on this degree of homology, CL00103 is expected to
exhibit similar cellulase enzymatic activity.
[0211] The enzyme CL02959 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 172 and the cDNA sequence
represented herein as SEQ ID NO: 174. The CL02959 nucleic acid
sequence encodes a 370 amino acid sequence, represented herein as
SEQ ID NO: 173. The signal peptide for CL02959 is located from
positions 1 to about position 17 of SEQ ID NO: 173, with the mature
protein spanning from about position 18 to position 370 of SEQ ID
NO: 173. Within CL02959 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL02959 spans from a starting point
of about position 31 of SEQ ID NO: 173 to an ending point of about
position 337 of SEQ ID NO: 173. Based on homology, CL02959 can be
assigned to CAZy Family GH 5. CL02959 also possesses significant
homology (about 62% from amino acids 19 to 366 of CL02959) with a
.beta.-mannanase from Hypocrea jecorina (GenBank Accession No.
AAA34208) and significant homology (about 60% from amino acids 19
to 364 of CL02959) with an endo-1,4-.beta.-mannosidase from
Aspergillus fumigatus Af293 (GenBank Accession No. XP-746824).
Based on these degrees of homology, CL02959 is expected to exhibit
similar .beta.-mannanase and endo-1,4-.beta.-mannosidase enzymatic
activity.
[0212] The enzyme Man2 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 175 and the cDNA sequence
represented herein as SEQ ID NO: 177. The Man2 nucleic acid
sequence encodes a 410 amino acid sequence, represented herein as
SEQ ID NO: 176. The signal peptide for Man2 is located from
positions 1 to about position 21 of SEQ ID NO: 176, with the mature
protein spanning from about position 22 to position 410 of SEQ ID
NO: 176. Within Man2 is a catalytic domain (CD). The amino acid
sequence containing the CD of Man2 spans from a starting point of
about position 25 of SEQ ID NO: 176 to an ending point of about
position 401 of SEQ ID NO: 176. Based on homology, Man2 can be
assigned to CAZy Family GH 5. Man2 also possesses significant
homology (about 72% from amino acids 25 to 407 of Man2) with an
endo-1,4-.beta.-mannanase from Emericella nidulans (GenBank
Accession No. ABF50878) and significant homology (about 39% from
amino acids 6 to 402 of Man2) with an endo-1,4-.beta.-mannosidase
from Aspergillus fumigatus Af293 (GenBank Accession No. XP-746824).
Based on these degrees of homology, Man2 is expected to exhibit
similar endo-1,4-.beta.-mannanase and endo-1,4-.beta.-mannosidase
enzymatic activity.
[0213] The enzyme CL06986 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 178 and the cDNA sequence
represented herein as SEQ ID NO: 180. The CL06986 nucleic acid
sequence encodes a 408 amino acid sequence, represented herein as
SEQ ID NO: 179. The signal peptide for CL06986 is located from
positions 1 to about position 21 of SEQ ID NO: 179, with the mature
protein spanning from about position 22 to position 408 of SEQ ID
NO: 179. Within CL06986 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL06986 spans from a starting point
of about position 123 of SEQ ID NO: 179 to an ending point of about
position 204 of SEQ ID NO: 179. Based on homology, CL06986 can be
assigned to CAZy Family GH 5. CL06986 also possesses significant
homology (about 72% from amino acids 25 to 405 of CL06986) with an
endo-1,4-.beta.-mannosidase from Emericella nidulans (GenBank
Accession No. ABF50878). Based on this degree of homology, CL06986
is expected to exhibit similar endo-1,4-.beta.-mannosidase
enzymatic activity. CL06986 may also possess galactanase enzymatic
activity.
[0214] The enzyme Man3 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 181 and the cDNA sequence
represented herein as SEQ ID NO: 183. The Man3 nucleic acid
sequence encodes a 503 amino acid sequence, represented herein as
SEQ ID NO: 182. The signal peptide for Man3 is located from
positions 1 to about position 21 of SEQ ID NO: 182, with the mature
protein spanning from about position 22 to position 503 of SEQ ID
NO: 182. Within Man3 are two domains: a catalytic domain (CD) and a
cellulose-binding module (CBM). The amino acid sequence containing
the CD of Man3 spans from a starting point of about position 184 of
SEQ ID NO: 182 to an ending point of about position 501 of SEQ ID
NO: 182. The amino acid sequence containing the CBM of Man3 spans
from a starting point of about position 42 of SEQ ID NO: 182 to an
ending point of about position 182 of SEQ ID NO: 182. Based on
homology, Man3 can be assigned to CAZy Families GH 26 and CBM 35.
Man3 also possesses significant homology (about 47% from amino
acids 111 to 497 of Man3) with a .beta.-mannanase from Dictyoglomus
thermophilum (GenBank Accession No. AAB82454; see also Gibbs et
al., Curr. Microbiol. 39:351 (1999)) and significant homology with
a .beta.-mannanase from Humicola insolens (GenBank Accession No.
AAQ31840) Based on this degree of homology, Man3 is expected to
exhibit similar .beta.-mannanase enzymatic activity.
[0215] The enzyme Abf4 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 184 and the cDNA sequence
represented herein as SEQ ID NO: 186. The Abf4 nucleic acid
sequence encodes a 512 amino acid sequence, represented herein as
SEQ ID NO: 185. Within Abf4 is a catalytic domain (CD). The amino
acid sequence containing the CD of Abf4 spans from a starting point
of about position 41 of SEQ ID NO: 185 to an ending point of about
position 502 of SEQ ID NO: 185. Based on homology, Abf4 can be
assigned to CAZy Family GH 51. Abf4 also possesses significant
homology (about 66% from amino acids 1 to 509 of Abf4) with an
.alpha.-arabinofuranosidase from Emericella nidulans (GenBank
Accession No. ABF50847). Based on this degree of homology, Abf4 is
expected to exhibit similar .alpha.-arabinofuranosidase enzymatic
activity.
[0216] The enzyme CL11246 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 187 and the cDNA sequence
represented herein as SEQ ID NO: 189. The CL11246 nucleic acid
sequence encodes a 316 amino acid sequence, represented herein as
SEQ ID NO: 188. The signal peptide for CL11246 is located from
positions 1 to about position 28 of SEQ ID NO: 188, with the mature
protein spanning from about position 29 to position 316 of SEQ ID
NO: 188. Within CL11246 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL11246 spans from a starting point
of about position 24 of SEQ ID NO: 188 to an ending point of about
position 282 of SEQ ID NO: 188. Based on homology, CL11246 can be
assigned to CAZy Family GH 75. CL11246 also possesses significant
homology (about 48% from amino acids 17 to 271 of CL11246) with a
chitosanase from Fusarium solani f. robiniae (GenBank Accession No.
BAC10609). Based on this degree of homology, CL11246 is expected to
exhibit similar chitosanase enzymatic activity.
[0217] The enzyme CL02619 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 190 and the cDNA sequence
represented herein as SEQ ID NO: 192. The CL02619 nucleic acid
sequence encodes a 399 amino acid sequence, represented herein as
SEQ ID NO: 191. The signal peptide for CL02619 is located from
positions 1 to about position 15 of SEQ ID NO: 191, with the mature
protein spanning from about position 16 to position 399 of SEQ ID
NO: 191. Within CL02619 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL02619 spans from a starting point
of about position 26 of SEQ ID NO: 191 to an ending point of about
position 394 of SEQ ID NO: 191. Based on homology, CL02619 can be
assigned to CAZy Family GH 76. CL02619 also possesses significant
homology (about 28% from amino acids 119 to 335 of CL02619) with a
mannan endo-1,6-.alpha.-mannosidase from Lodderomyces elongisporus
NRRL YB-4239 (GenBank Accession No. XP-001528696) and significant
homology (about 52% from amino acids 44 to 367 of CL02619) with a
glycosyl hydrolase from Metarhizium anisopliae (GenBank Accession
No. ABD49724). Based on these degrees of homology, CL02619 is
expected to exhibit similar mannan endo-1,6-.alpha.-mannosidase and
glycosyl hydrolase enzymatic activity.
[0218] The enzyme CL06776 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 193 and the cDNA sequence
represented herein as SEQ ID NO: 195. The CL06776 nucleic acid
sequence encodes a 417 amino acid sequence, represented herein as
SEQ ID NO: 194. The signal peptide for CL06776 is located from
positions 1 to about position 21 of SEQ ID NO: 194, with the mature
protein spanning from about position 22 to position 417 of SEQ ID
NO: 194. Within CL06776 is a catalytic domain (CD). The amino acid
sequence containing the CD of CL06776 spans from a starting point
of about position 59 of SEQ ID NO: 194 to an ending point of about
position 417 of SEQ ID NO: 194. Based on homology, CL06776 can be
assigned to CAZy Family GH 76. CL06776 also possesses significant
homology (about 25% from amino acids 93 to 377 of CL06776) with a
mannan endo-1,6-.alpha.-mannosidase from Lodderomyces elongisporus
NRRL YB-4239 (GenBank Accession No. EDK42968) and significant
homology (about 44% from amino acids 93 to 415 of CL06776) with a
glycosyl hydrolase from Streptomyces avermitilis MA-4680 (GenBank
Accession No. NP-821802). Based on these degrees of homology,
CL06776 is expected to exhibit similar mannan
endo-1,6-.alpha.-mannosidase and glycosyl hydrolase enzymatic
activity.
[0219] The enzyme Man5 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 196 and the cDNA sequence
represented herein as SEQ ID NO: 198. The Man5 nucleic acid
sequence encodes a 513 amino acid sequence, represented herein as
SEQ ID NO: 197. The signal peptide for Man5 is located from
positions 1 to about position 21 of SEQ ID NO: 197, with the mature
protein spanning from about position 22 to position 513 of SEQ ID
NO: 197. Within Man5 is a catalytic domain (CD). The amino acid
sequence containing the CD of Man5 spans from a starting point of
about position 23 of SEQ ID NO: 197 to an ending point of about
position 402 of SEQ ID NO: 197. Based on homology, Man5 can be
assigned to CAZy Family GH 76. Man5 also possesses significant
homology (about 52% from amino acids 51 to 453 of Man5) with a
glycosyl hydrolase from Aspergillus clavatus NRRL 1 (GenBank
Accession No. EAW08810) and significant homology (about 44% from
amino acids 6 to 453 of Man5) with a mannosidase from Saccharomyces
cerevisiae (GenBank Accession No. EDN59863. Based on these degrees
of homology, Man5 is expected to exhibit similar glycosyl hydrolase
and mannosidase enzymatic activity.
[0220] The enzyme Man4 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 199 and the cDNA sequence
represented herein as SEQ ID NO: 201. The Man4 nucleic acid
sequence encodes a 443 amino acid sequence, represented herein as
SEQ ID NO: 200. The signal peptide for Man4 is located from
positions 1 to about position 19 of SEQ ID NO: 200, with the mature
protein spanning from about position 20 to position 443 of SEQ ID
NO: 200. Within Man4 is a catalytic domain (CD). The amino acid
sequence containing the CD of Man4 spans from a starting point of
about position 20 of SEQ ID NO: 200 to an ending point of about
position 389 of SEQ ID NO: 200. Based on homology, Man4 can be
assigned to CAZy Family GH 76. Man4 also possesses significant
homology (about 52% from amino acids 19 to 443 of Man4) with a
glycosyl hydrolase from Aspergillus clavatus NRRL 1 (GenBank
Accession No. EAW08810) and significant homology (about 44% from
amino acids 23 to 443 of Man4) with a mannosidase from
Saccharomyces cerevisiae (GenBank Accession No. EDN59863. Based on
these degrees of homology, Man4 is expected to exhibit similar
glycosyl hydrolase and mannosidase enzymatic activity.
[0221] The enzyme Man6 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 202 and the cDNA sequence
represented herein as SEQ ID NO: 204. The Man6 nucleic acid
sequence encodes a 474 amino acid sequence, represented herein as
SEQ ID NO: 203. The signal peptide for Man6 is located from
positions 1 to about position 30 of SEQ ID NO: 203, with the mature
protein spanning from about position 31 to position 474 of SEQ ID
NO: 203. Within Man6 is a catalytic domain (CD). The amino acid
sequence containing the CD of Man6 spans from a starting point of
about position 32 of SEQ ID NO: 203 to an ending point of about
position 421 of SEQ ID NO: 203. Based on homology, Man6 can be
assigned to CAZy Family GH 76. Man6 also possesses significant
homology (about 42% from amino acids 39 to 470 of Man6) with a
mannosidase from Saccharomyces cerevisiae (GenBank Accession No.
EDN59863. Based on this degree of homology, Man6 is expected to
exhibit similar mannosidase enzymatic activity.
[0222] The enzyme Man7 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 91 and the cDNA sequence
represented herein as SEQ ID NO: 93. The Man7 nucleic acid sequence
encodes a 454 amino acid sequence, represented herein as SEQ ID NO:
92. The signal peptide for Man7 is located from positions 1 to
about position 19 of SEQ ID NO: 92, with the mature protein
spanning from about position 20 to position 454 of SEQ ID NO: 92.
Within Man7 is a catalytic domain (CD). The amino acid sequence
containing the CD of Man7 spans from a starting point of about
position 20 of SEQ ID NO: 92 to an ending point of about position
400 of SEQ ID NO: 92. Based on homology, Man7 can be assigned to
CAZy Family GH 76. Man7 also possesses significant homology (about
51% from amino acids 50 to 450 of Man7) with a glycosyl hydrolase
from Aspergillus clavatus NRRL 1 (GenBank Accession No. EAW08810)
and significant homology (about 44% from amino acids 27 to 450 of
Man7) with a mannosidase from Saccharomyces cerevisiae (GenBank
Accession No. EDN59863. Based on these degrees of homology, Man7 is
expected to exhibit similar glycosyl hydrolase and mannosidase
enzymatic activity.
[0223] The enzyme Xgl1 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 205 and the cDNA sequence
represented herein as SEQ ID NO: 207. The Xgl1 nucleic acid
sequence encodes a 751 amino acid sequence, represented herein as
SEQ ID NO: 206. The signal peptide for Xgl1 is located from
positions 1 to about position 22 of SEQ ID NO: 206, with the mature
protein spanning from about position 23 to position 751 of SEQ ID
NO: 206. Within Xgl1 is a catalytic domain (CD). The amino acid
sequence containing the CD of Xgl1 spans from a starting point of
about position 26 of SEQ ID NO: 206 to an ending point of about
position 708 of SEQ ID NO: 206. Based on homology Xgl1 can be
assigned to CAZy Family GH74. Xgl1 also possesses significant
homology with the following enzymes: about 62.91% homology (from
amino acids 26 to 751 of Xgl1) with the enzyme EGV endoglucanase
from a fungal source (GenBank Accession No. ABJ18610) and about
59.92% homology (from amino acids 10 to 751) of Xgl1 with the
hypothetical protein MG00582.4 from Magnaporthe grisea (GenBank
Accession No. EAA48924). As evidenced below in Example 3, Xgl1
exhibits xyloglucanase activity.
[0224] The enzyme Agu1 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 208 and the cDNA sequence
represented herein as SEQ ID NO: 210. The Agu1 nucleic acid
sequence encodes a 878 amino acid sequence, represented herein as
SEQ ID NO: 209. The signal peptide for Agu1 is located from
positions 1 to about position 17 of SEQ ID NO: 209, with the mature
protein spanning from about position 18 to position 878 of SEQ ID
NO: 209. Within Agu1 is a catalytic domain (CD). The amino acid
sequence containing the CD of Agu1 spans from a starting point of
about position 18 of SEQ ID NO: 209 to an ending point of about
position 763 of SEQ ID NO: 209. Based on homology Agu1 can be
assigned to CAZy Family GH67. Agu1 also possesses significant
homology (about 71.23% homology from amino acids 3 to 876 of Agu1)
with the hypothetical protein AN9286.2 from Aspergillus nidulans
(GenBank Accession No. EAA66353) and (about 62% from amino acids 8
to 878 of Agu1) with an .alpha.-glucuronidase from Aspergillus
fumigatus A1163 (GenBank Accession No. EDP52172). As evidenced
below in Example 5, Agu1 exhibits .alpha.-glucuronidase
activity.
[0225] The enzyme Abf3 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 211 and the cDNA sequence
represented herein as SEQ ID NO: 213. The Abf3 nucleic acid
sequence encodes a 654 amino acid sequence, represented herein as
SEQ ID NO: 212. The signal peptide for Abf3 is located from
positions 1 to about position 18 of SEQ ID NO: 212, with the mature
protein spanning from about position 19 to position 654 of SEQ ID
NO: 212. Within Abf3 is a catalytic domain (CD). The amino acid
sequence containing the CD of Abf3 spans from a starting point of
about position 53 of SEQ ID NO: 212 to an ending point of about
position 645 of SEQ ID NO: 212. Based on homology Agu1 can be
assigned to CAZy Family GH51. Abf3 also possesses significant
homology (about 53.23% from amino acids 4 to 649 of Abf3) with an
unnamed protein product from Aspergillus oryzae (GenBank Accession
No. BAE60499) and (about 53% from amino acids 4 to 653 of Abf3)
with an .alpha.-L-arabinofuranosidase from Neosartorya fischeri
(GenBank Accession No. EAW19083). As evidenced below in Examples 6
and 7, Abf3 exhibits arabinofuranosidase activity and
.beta.-glucosidase activity.
[0226] The enzyme Bxl1 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 214 and the cDNA sequence
represented herein as SEQ ID NO: 216. The Bxl1 nucleic acid
sequence encodes a 731 amino acid sequence, represented herein as
SEQ ID NO: 215. The signal peptide for Bxl1 is located from
positions 1 to about position 21 of SEQ ID NO: 215, with the mature
protein spanning from about position 22 to position 731 of SEQ ID
NO: 215. Within Bxl1 is a catalytic domain (CD). The amino acid
sequence containing the CD of Bxl1 spans from a starting point of
about position 36 of SEQ ID NO: 215 to an ending point of about
position 591 of SEQ ID NO: 215. Based on homology, Bxl1 can be
assigned to CAZy Family GH3. Bxl1 also possesses significant
homology (about 52.25% from amino acids 4 to 726 of Bxl1) with a
protein related to xylan 1,4-beta-xylosidase from Neurospora crassa
(GenBank Accession No. CAB91343.2). As evidenced below in Examples
8 and 22, Bxl1 exhibits .beta.-xylosidase activity.
[0227] The enzyme Abf5 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 217 and the cDNA sequence
represented herein as SEQ ID NO: 219. The Abf5 nucleic acid
sequence encodes a 583 amino acid sequence, represented herein as
SEQ ID NO: 218. The signal peptide for Abf5 is located from
positions 1 to about position 21 of SEQ ID NO: 218, with the mature
protein spanning from about position 22 of SEQ ID NO: 218 to
position 583 of SEQ ID NO: 218. Within Abf5 is a catalytic domain
(CD). The amino acid sequence containing the CD of Abf5 spans from
a starting point of about position 38 to an ending point of about
position 319 of SEQ ID NO: 218. Based on homology, Abf5 can be
assigned to CAZy Family GH43. Abf5 also possesses significant
homology (about 53% from amino acids 42 to 571 of Abf5) with an
enzyme from the glycosyl hydrolase family 43 from Neosartoya
fischeri NRRL 181 (GenBank Accession No. EAW17743). As evidenced
below in Examples 7 and 21, Abf5 exhibits arabinofuranosidase and
.beta.-glucosidase activity.
[0228] The enzyme Bga2 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 220 and the cDNA sequence
represented herein as SEQ ID NO: 222. The Bga2 nucleic acid
sequence encodes a 900 amino acid sequence, represented herein as
SEQ ID NO: 221. The signal peptide for Bga2 is located from
positions 1 to about position 26 of SEQ ID NO: 221, with the mature
protein spanning from about position 27 to position 900 of SEQ ID
NO: 221. Within Bga2 is a catalytic domain (CD). The amino acid
sequence containing the CD of Bga2 spans from a starting point of
about position 106 of SEQ ID NO: 221 to an ending point of about
position 703 of SEQ ID NO: 221. Bga2 also contains a GH2 sugar
binding module; the amino acid sequence containing this domain
spans from a starting point of about position 106 of SEQ ID NO: 221
to an ending point of about position 243 of SEQ ID NO: 221. Based
on homology, Bga2 can be assigned to CAZy Family GH2. Bga2 also
possesses significant homology (about 58% from amino acids 30 to
900 of Bga2) with a hypothetical protein from Aspergillus nidulans
FGSC A4 (GenBank Accession No. EAA58410) and (about 54% from amino
acids 3 to 900 of Bga2) with .beta.-galactosidase from Xanthomonas
campestris pv. campestris (GenBank Accession No. AAP86765). As
evidenced below in Examples 9 and 18, Bga2 exhibits
.beta.-galactosidase activity.
[0229] The enzyme Cip1 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 223 and the cDNA sequence
represented herein as SEQ ID NO: 225. The Cip1 nucleic acid
sequence encodes a 236 amino acid sequence, represented herein as
SEQ ID NO: 224. The signal peptide for Cip1 is located from
positions 1 to about position 18 of SEQ ID NO: 224, with the mature
protein spanning from about position 19 to position 236 of SEQ ID
NO: 224. Within Cip1 is a catalytic domain (CD). The amino acid
sequence containing the CD of Cip1 spans from a starting point of
about position 19 of SEQ ID NO: 224 to an ending point of about
position 236 of SEQ ID NO: 227. Based on homology, Cip1 can be
assigned to CAZy Family CBM1. Cip1 also possesses significant
homology (about 80% from amino acids 1 to 236 of Cip1) with a
hypothetical protein from Chaetomium globosum (GenBank Accession
No. EAQ87122) and (about 67% from amino acids 1 to 235 of Cip1)
with Cip1 from Hypocrea jecorina (GenBank Accession No. AAP57751).
As evidenced below in Example 4, Cip1 binds to bacitracin Sepharose
column, indicating that it contains a carbohydrate binding
module.
[0230] The enzyme Axe3 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 226 and the cDNA sequence
represented herein as SEQ ID NO: 228. The Axe3 nucleic acid
sequence encodes a 313 amino acid sequence, represented herein as
SEQ ID NO: 227. The signal peptide for Axe3 is located from
position 1 to about position 21 of SEQ ID NO: 227, with the mature
protein spanning from about position 22 to position 313 of SEQ ID
NO: 227. Within Axe3 is a catalytic domain (CD). The amino acid
sequence containing the CD of Axe3 spans from a starting point of
about position 22 of SEQ ID NO: 227 to an ending point of about
position 255 of SEQ ID NO: 227. Based on homology, Axe3 can be
assigned to CAZy families of CE1 and CBM1. Axe3 also possesses
significant homology (about 69.85% from amino acids 41 to 312 of
Axe3) with acetyl xylan esterase from Penicillium purpurogenum
(GenBank Accession No. AAM93261.1). As evidenced below in Examples
19 and 20, Axe3 possesses acetyl xylan esterase activity.
[0231] The enzyme Axe2 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 229 and the cDNA sequence
represented herein as SEQ ID NO: 231. The Axe2 nucleic acid
sequence encodes a 228 amino acid sequence, represented herein as
SEQ ID NO: 230. The signal peptide for Axe2 is located from
positions 1 to about position 17 of SEQ ID NO: 230, with the mature
protein spanning from about position 18 to position 228 of SEQ ID
NO: 230. Within Axe2 is a catalytic domain (CD). The amino acid
sequence containing the CD of Axe2 spans from a starting point of
about position 26 of SEQ ID NO: 230 to an ending point of about
position 228 of SEQ ID NO: 230. Based on homology, Axe2 can be
assigned to CAZy families of CE5 and CBM1. Axe2 also possesses
significant homology (about 67.62% from amino acids 1 to 225 of
Axe2) with a hypothetical protein from Magnaporthe grisea (GenBank
Accession No. XP-368098) and (about 56.85% from amino acids 14 to
225 of Axe2) with acetyl xylan esterase from Neurospora crassa
(GenBank Accession No. CAD70564.1). As evidenced below in Examples
19 and 20, Axe2 possesses acetyl xylan esterase activity.
[0232] The enzyme Bxl2 is encoded by the nucleic acid sequence
represented herein as SEQ ID NO: 232 and the cDNA sequence
represented herein as SEQ ID NO: 234. The Bxl2 nucleic acid
sequence encodes a 733 amino acid sequence, represented herein as
SEQ ID NO: 233. The signal peptide for Bxl2 is located from
positions 1 to about position 17 of SEQ ID NO: 233, with the mature
protein spanning from about position 18 to position 733 of SEQ ID
NO: 233. Within Bxl2 is a catalytic domain (CD). The amino acid
sequence containing the CD of Bxl2 spans from a starting point of
about position 26 of SEQ ID NO: 233 to an ending point of about
position 602 of SEQ ID NO: 233. Based on homology, Bxl2 can be
assigned to CAZy families of CBM1 and GH3. Bxl2 also possesses
significant homology (about 54.33% from amino acids 34 to 730 of
Bxl2) with beta-glucosidase from Phanerochaete chrysosporium
(GenBank Accession No. BAB85988.1) and (about 72.22% from amino
acids 34 to 733 of Bxl2) with a hypothetical protein MGG-09353 from
Magnaporthe grisea 70-15 (GenBank Accession No. XP-364573.1). As
evidenced below in Examples 21, Bxl2 possesses .beta.-glucosidase
activity.
[0233] Physical properties of enzymes of the present invention are
illustrated in Table 1 below, including the molecular weight and
isoelectric point, as calculated from the primary amino acid
sequence using the ProtParam program (available at the ExPASy
Proteomics Server).
TABLE-US-00001 TABLE 1 Physical Properties of C1 Enzymes Enzyme SEQ
ID NO: MW (kDa) pI CDH1 2 85.2 5.44 CDH1 (observed) 2 91 4.5 FaeB1
5 31.68 6.87 Rga1 8 25.99 5.42 Rga1 (observed) 8 30 Gln 11 51.26
5.71 Abn2 14 40.05 4.89 Abn3 17 35.92 5.12 Abn4 20 33.15 4.71 Abn4
(observed) 20 35 Abn5 23 47.32 5.1 Abn7 26 59.24 4.71 Abn7
(observed) 26 70 Pecl1 74 37.86 4.83 Pecl2 77 33.72 5.67 Pecl3 80
45.10 6.19 Pecl4 83 33.33 5.68 Pecl5 86 26.21 5.21 Rgl1 89 58.75
7.26 Bxl4 110 61.23 5.83 Abn9 113 37.12 4.69 Pgx1 161 52.03 6.33
Rgx1 164 46.14 5.96 Abf4 185 57.68 5.75 Xgl1 206 76.62 4.42 Agu1
209 96.5 5.82 Agu1 (observed) 209 90 5.5 Abf3 212 69.61 5.75 Bxl1
215 76.49 5.38 Abf5 218 61.23 4.58 Bga2 221 96.29 6.35 Cip1 224
23.50 4.25 Axe3 227 31.58 6.21 Axe3 (observed) 227 31.5 5.38 Axe2
230 21.99 5.31 Axe2 (observed) 230 22.3 3.71 Bxl2 233 75.89 4.80 MW
= Molecular Weight in kiloDaltons (kDa), as calculated based on
amino acid sequence with Clone Manager 9 Professional Edition pI =
isoelectric point, as calculated based on amino acid sequence with
Clone Manager 9 Professional Edition
[0234] As used herein, reference to an isolated protein or
polypeptide in the present invention, including any of the enzymes
disclosed herein, includes full-length proteins, fusion proteins,
or any fragment or homologue of such a protein. More specifically,
an isolated protein, such as an enzyme according to the present
invention, is a protein (including a polypeptide or peptide) that
has been removed from its natural milieu (i.e., that has been
subject to human manipulation) and can include purified proteins,
partially purified proteins, recombinantly produced proteins,
synthetically produced proteins, proteins complexed with lipids,
soluble proteins, and isolated proteins associated with other
proteins, for example. As such, "isolated" does not reflect the
extent to which the protein has been purified. Preferably, an
isolated protein of the present invention is produced
recombinantly. In addition, and by way of example, a "C.
lucknowense protein" or "C. lucknowense enzyme" refers to a protein
(generally including a homologue of a naturally occurring protein)
from Chrysosporium lucknowense or to a protein that has been
otherwise produced from the knowledge of the structure (e.g.,
sequence) and perhaps the function of a naturally occurring protein
from Chrysosporium lucknowense. In other words, a C. lucknowense
protein includes any protein that has substantially similar
structure and function of a naturally occurring C. lucknowense
protein or that is a biologically active (i.e., has biological
activity) homologue of a naturally occurring protein from C.
lucknowense as described in detail herein. As such, a C.
lucknowense protein can include purified, partially purified,
recombinant, mutated/modified and synthetic proteins. According to
the present invention, the terms "modification" and "mutation" can
be used interchangeably, particularly with regard to the
modifications/mutations to the amino acid sequence of a C.
lucknowense protein (or nucleic acid sequences) described herein.
An isolated protein according to the present invention can be
isolated from its natural source, produced recombinantly or
produced synthetically.
[0235] According to the present invention, the terms "modification"
and "mutation" can be used interchangeably, particularly with
regard to the modifications/mutations to the primary amino acid
sequences of a protein or peptide (or nucleic acid sequences)
described herein. The term "modification" can also be used to
describe post-translational modifications to a protein or peptide
including, but not limited to, methylation, farnesylation,
carboxymethylation, geranyl geranylation, glycosylation,
phosphorylation, acetylation, myristoylation, prenylation,
palmitation, and/or amidation. Modifications can also include, for
example, complexing a protein or peptide with another compound.
Such modifications can be considered to be mutations, for example,
if the modification is different than the post-translational
modification that occurs in the natural, wild-type protein or
peptide.
[0236] As used herein, the term "homologue" is used to refer to a
protein or peptide which differs from a naturally occurring protein
or peptide (i.e., the "prototype" or "wild-type" protein) by minor
modifications to the naturally occurring protein or peptide, but
which maintains the basic protein and side chain structure of the
naturally occurring form. Such changes include, but are not limited
to: changes in one or a few amino acid side chains; changes one or
a few amino acids, including deletions (e.g., a truncated version
of the protein or peptide), insertions and/or substitutions;
changes in stereochemistry of one or a few atoms; and/or minor
derivatizations, including but not limited to: methylation,
glycosylation, phosphorylation, acetylation, myristoylation,
prenylation, palmitation, amidation and/or addition of
glycosylphosphatidyl inositol. A homologue can have either
enhanced, decreased, or substantially similar properties as
compared to the naturally occurring protein or peptide. A homologue
can include an agonist of a protein or an antagonist of a
protein.
[0237] Homologues can be the result of natural allelic variation or
natural mutation. A naturally occurring allelic variant of a
nucleic acid encoding a protein is a gene that occurs at
essentially the same locus (or loci) in the genome as the gene
which encodes such protein, but which, due to natural variations
caused by, for example, mutation or recombination, has a similar
but not identical sequence. Allelic variants typically encode
proteins having similar activity to that of the protein encoded by
the gene to which they are being compared. One class of allelic
variants can encode the same protein but have different nucleic
acid sequences due to the degeneracy of the genetic code. Allelic
variants can also comprise alterations in the 5' or 3' untranslated
regions of the gene (e.g., in regulatory control regions). Allelic
variants are well known to those skilled in the art.
[0238] Homologues can be produced using techniques known in the art
for the production of proteins including, but not limited to,
direct modifications to the isolated, naturally occurring protein,
direct protein synthesis, or modifications to the nucleic acid
sequence encoding the protein using, for example, classic or
recombinant DNA techniques to effect random or targeted
mutagenesis.
[0239] Modifications in protein homologues, as compared to the
wild-type protein, either agonize, antagonize, or do not
substantially change, the basic biological activity of the
homologue as compared to the naturally occurring protein.
Modifications of a protein, such as in a homologue, may result in
proteins having the same biological activity as the naturally
occurring protein, or in proteins having decreased or increased
biological activity as compared to the naturally occurring protein.
Modifications which result in a decrease in protein expression or a
decrease in the activity of the protein, can be referred to as
inactivation (complete or partial), down-regulation, or decreased
action of a protein. Similarly, modifications which result in an
increase in protein expression or an increase in the activity of
the protein, can be referred to as amplification, overproduction,
activation, enhancement, up-regulation or increased action of a
protein.
[0240] According to the present invention, an isolated protein,
including a biologically active homologue or fragment thereof, has
at least one characteristic of biological activity of a wild-type,
or naturally occurring, protein. As discussed above, in general,
the biological activity or biological action of a protein refers to
any function(s) exhibited or performed by the protein that is
ascribed to the naturally occurring form of the protein as measured
or observed in vivo (i.e., in the natural physiological environment
of the protein) or in vitro (i.e., under laboratory conditions).
The biological activity of a protein of the present invention can
include an enzyme activity (catalytic activity and/or substrate
binding activity), such as cellulase activity, hemicellulase
activity, .beta.-glucanase activity, .beta.-glucosidase activity,
.alpha.-galactosidase activity, .beta.-galactosidase activity,
xylanase activity or any other activity disclosed herein. Specific
biological activities of the proteins disclosed herein are
described in detail above and in the Examples. Methods of detecting
and measuring the biological activity of a protein of the invention
include, but are not limited to, the assays described in the
Examples section below. Such assays include, but are not limited
to, measurement of enzyme activity (e.g., catalytic activity),
measurement of substrate binding, and the like. It is noted that an
isolated protein of the present invention (including homologues) is
not required to have a biological activity such as catalytic
activity. A protein can be a truncated, mutated or inactive
protein, or lack at least one activity of the wild-type enzyme, for
example. Inactive proteins may be useful in some screening assays,
for example, or for other purposes such as antibody production.
[0241] Methods to measure protein expression levels of a protein
according to the invention include, but are not limited to: western
blotting, immunocytochemistry, flow cytometry or other
immunologic-based assays; assays based on a property of the protein
including but not limited to, ligand binding or interaction with
other protein partners. Binding assays are also well known in the
art. For example, a BIAcore machine can be used to determine the
binding constant of a complex between two proteins. The
dissociation constant for the complex can be determined by
monitoring changes in the refractive index with respect to time as
buffer is passed over the chip (O'Shannessy et al. Anal. Biochem.
212:457-468 (1993); Schuster et al., Nature 365:343-347 (1993)).
Other suitable assays for measuring the binding of one protein to
another include, for example, immunoassays such as enzyme linked
immunoabsorbent assays (ELISA) and radioimmunoassays (RIA), or
determination of binding by monitoring the change in the
spectroscopic or optical properties of the proteins through
fluorescence, UV absorption, circular dichroism, or nuclear
magnetic resonance (NMR).
[0242] Many of the enzymes and proteins of the present invention
may be desirable targets for modification and use in the processes
described herein. These proteins have been described in terms of
function and amino acid sequence (and nucleic acid sequence
encoding the same) of representative wild-type proteins. In one
embodiment of the invention, homologues of a given protein (which
can include related proteins from other organisms or modified forms
of the given protein) are encompassed for use in the invention.
Homologues of a protein encompassed by the present invention can
comprise, consist essentially of, or consist of, in one embodiment,
an amino acid sequence that is at least about 35% identical, and
more preferably at least about 40% identical, and more preferably
at least about 45% identical, and more preferably at least about
50% identical, and more preferably at least about 55% identical,
and more preferably at least about 60% identical, and more
preferably at least about 65% identical, and more preferably at
least about 70% identical, and more preferably at least about 75%
identical, and more preferably at least about 80% identical, and
more preferably at least about 85% identical, and more preferably
at least about 90% identical, and more preferably at least about
95% identical, and more preferably at least about 96% identical,
and more preferably at least about 97% identical, and more
preferably at least about 98% identical, and more preferably at
least about 99% identical, or any percent identity between 35% and
99%, in whole integers (i.e., 36%, 37%, etc.), to an amino acid
sequence disclosed herein that represents the amino acid sequence
of an enzyme or protein according to the invention (including a
biologically active domain of a full-length protein). Preferably,
the amino acid sequence of the homologue has a biological activity
of the wild-type or reference protein or of a biologically active
domain thereof (e.g., a catalytic domain).
[0243] In one embodiment, a protein of the present invention
comprises, consists essentially of, or consists of an amino acid
sequence that, alone or in combination with other characteristics
of such proteins disclosed herein, is less than 100% identical to
an amino acid sequence selected from: SEQ ID NO: 2, SEQ ID NO: 5,
SEQ ID NO: 8, SEQ ID NO: 11, SEQ ID NO: 14, SEQ ID NO: 17, SEQ ID
NO: 20, SEQ ID NO: 23, SEQ ID NO: 26, SEQ ID NO: 29, SEQ ID NO: 32,
SEQ ID NO: 35, SEQ ID NO: 38, SEQ ID NO: 41, SEQ ID NO: 44, SEQ ID
NO: 47, SEQ ID NO: 50, SEQ ID NO: 53, SEQ ID NO: 56, SEQ ID NO: 59,
SEQ ID NO: 62, SEQ ID NO: 65, SEQ ID NO: 68, SEQ ID NO: 71, SEQ ID
NO: 74, SEQ ID NO: 77, SEQ ID NO: 80, SEQ ID NO: 83, SEQ ID NO: 86,
SEQ ID NO: 89, SEQ ID NO: 92, SEQ ID NO: 95, SEQ ID NO: 98, SEQ ID
NO: 101, SEQ ID NO: 104, SEQ ID NO: 107, SEQ ID NO: 110, SEQ ID NO:
113, SEQ ID NO: 116, SEQ ID NO: 119, SEQ ID NO: 122, SEQ ID NO:
125, SEQ ID NO: 128, SEQ ID NO: 131, SEQ ID NO: 134, SEQ ID NO:
137, SEQ ID NO: 140, SEQ ID NO: 143, SEQ ID NO: 146, SEQ ID NO:
149, SEQ ID NO: 152, SEQ ID NO: 155, SEQ ID NO: 158, SEQ ID NO:
161, SEQ ID NO: 164, SEQ ID NO: 167, SEQ ID NO: 170, SEQ ID NO:
173, SEQ ID NO: 176, SEQ ID NO: 179, SEQ ID NO: 182, SEQ ID NO:
185, SEQ ID NO: 188, SEQ ID NO: 191, SEQ ID NO: 194, SEQ ID NO:
197, SEQ ID NO: 200, or SEQ ID NO: 203, SEQ ID NO: 206, SEQ ID NO:
209, SEQ ID NO: 212, SEQ ID NO: 215, SEQ ID NO: 218, SEQ ID NO:
221, SEQ ID NO: 224, SEQ ID NO: 227, SEQ ID NO: 230, or SEQ ID NO:
233 (i.e., a homologue). For example, a protein of the present
invention can be less than 100% identical, in combination with
being at least about 35% identical, to a given disclosed sequence.
In another aspect of the invention, a homologue according to the
present invention has an amino acid sequence that is less than
about 99% identical to any of such amino acid sequences, and in
another embodiment, is less than about 98% identical to any of such
amino acid sequences, and in another embodiment, is less than about
97% identical to any of such amino acid sequences, and in another
embodiment, is less than about 96% identical to any of such amino
acid sequences, and in another embodiment, is less than about 95%
identical to any of such amino acid sequences, and in another
embodiment, is less than about 94% identical to any of such amino
acid sequences, and in another embodiment, is less than about 93%
identical to any of such amino acid sequences, and in another
embodiment, is less than about 92% identical to any of such amino
acid sequences, and in another embodiment, is less than about 91%
identical to any of such amino acid sequences, and in another
embodiment, is less than about 90% identical to any of such amino
acid sequences, and so on, in increments of whole integers.
[0244] As used herein, unless otherwise specified, reference to a
percent (%) identity refers to an evaluation of homology which is
performed using: (1) a BLAST 2.0 Basic BLAST homology search using
blastp for amino acid searches and blastn for nucleic acid searches
with standard default parameters, wherein the query sequence is
filtered for low complexity regions by default (described in
Altschul, S. F., Madden, T. L., Schaaffer, A. A., Zhang, J., Zhang,
Z., Miller, W. & Lipman, D. J. (1997) "Gapped BLAST and
PSI-BLAST: a new generation of protein database search programs."
Nucleic Acids Res. 25:3389-3402, incorporated herein by reference
in its entirety); (2) a BLAST 2 alignment (using the parameters
described below); (3) PSI-BLAST with the standard default
parameters (Position-Specific Iterated BLAST; and/or (4) CAZy
homology determined using standard default parameters from the
Carbohydrate Active EnZymes database (Coutinho, P. M. &
Henrissat, B. (1999) Carbohydrate-active enzymes: an integrated
database approach. In "Recent Advances in Carbohydrate
Bioengineering", H. J. Gilbert, G. Davies, B. Henrissat and B.
Svensson eds., The Royal Society of Chemistry, Cambridge, pp.
3-12).
[0245] It is noted that due to some differences in the standard
parameters between BLAST 2.0 Basic BLAST and BLAST 2, two specific
sequences might be recognized as having significant homology using
the BLAST 2 program, whereas a search performed in BLAST 2.0 Basic
BLAST using one of the sequences as the query sequence may not
identify the second sequence in the top matches. In addition,
PSI-BLAST provides an automated, easy-to-use version of a "profile"
search, which is a sensitive way to look for sequence homologues.
The program first performs a gapped BLAST database search. The
PSI-BLAST program uses the information from any significant
alignments returned to construct a position-specific score matrix,
which replaces the query sequence for the next round of database
searching. Therefore, it is to be understood that percent identity
can be determined by using any one of these programs.
[0246] Two specific sequences can be aligned to one another using
BLAST 2 sequence as described in Tatusova and Madden, (1999),
"Blast 2 sequences--a new tool for comparing protein and nucleotide
sequences", FEMS Microbiol Lett. 174:247-250, incorporated herein
by reference in its entirety. BLAST 2 sequence alignment is
performed in blastp or blastn using the BLAST 2.0 algorithm to
perform a Gapped BLAST search (BLAST 2.0) between the two sequences
allowing for the introduction of gaps (deletions and insertions) in
the resulting alignment. For purposes of clarity herein, a BLAST 2
sequence alignment is performed using the standard default
parameters as follows.
[0247] For blastn, using 0 BLOSUM62 matrix:
[0248] Reward for match=1
[0249] Penalty for mismatch=-2
[0250] Open gap (5) and extension gap (2) penalties
[0251] gap x_dropoff (50) expect (10) word size (11) filter (on)
For blastp, using 0 BLOSUM62 matrix:
[0252] Open gap (11) and extension gap (1) penalties
[0253] gap x_dropoff (50) expect (10) word size (3) filter
(on).
[0254] A protein of the present invention can also include proteins
having an amino acid sequence comprising at least 10 contiguous
amino acid residues of any of the sequences described herein (i.e.,
10 contiguous amino acid residues having 100% identity with 10
contiguous amino acids of SEQ ID NO: 2). In other embodiments, a
homologue of a protein amino acid sequence includes amino acid
sequences comprising at least 20, or at least 30, or at least 40,
or at least 50, or at least 75, or at least 100, or at least 125,
or at least 150, or at least 175, or at least 150, or at least 200,
or at least 250, or at least 300, or at least 350 contiguous amino
acid residues of any of the amino acid sequence represented
disclosed herein. Even small fragments of proteins without
biological activity are useful in the present invention, for
example, in the preparation of antibodies against the full-length
protein or in a screening assay (e.g., a binding assay). Fragments
can also be used to construct fusion proteins, for example, where
the fusion protein comprises functional domains from two or more
different proteins (e.g., a CBM from one protein linked to a CD
from another protein). In one embodiment, a homologue has a
measurable or detectable biological activity associated with the
wild-type protein (e.g., enzymatic activity).
[0255] According to the present invention, the term "contiguous" or
"consecutive", with regard to nucleic acid or amino acid sequences
described herein, means to be connected in an unbroken sequence.
For example, for a first sequence to comprise 30 contiguous (or
consecutive) amino acids of a second sequence, means that the first
sequence includes an unbroken sequence of 30 amino acid residues
that is 100% identical to an unbroken sequence of 30 amino acid
residues in the second sequence. Similarly, for a first sequence to
have "100% identity" with a second sequence means that the first
sequence exactly matches the second sequence with no gaps between
nucleotides or amino acids.
[0256] In another embodiment, a protein of the present invention,
including a homologue, includes a protein having an amino acid
sequence that is sufficiently similar to a natural amino acid
sequence that a nucleic acid sequence encoding the homologue is
capable of hybridizing under moderate, high or very high stringency
conditions (described below) to (i.e., with) a nucleic acid
molecule encoding the natural protein (i.e., to the complement of
the nucleic acid strand encoding the natural amino acid sequence).
Preferably, a homologue of a protein of the present invention is
encoded by a nucleic acid molecule comprising a nucleic acid
sequence that hybridizes under low, moderate, or high stringency
conditions to the complement of a nucleic acid sequence that
encodes a protein comprising, consisting essentially of, or
consisting of, an amino acid sequence represented by any of: SEQ ID
NO: 2, SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 1, SEQ ID NO: 14, SEQ
ID NO: 17, SEQ ID NO: 20, SEQ ID NO: 23, SEQ ID NO: 26, SEQ ID NO:
29, SEQ ID NO: 32, SEQ ID NO: 35, SEQ ID NO: 38, SEQ ID NO: 41, SEQ
ID NO: 44, SEQ ID NO: 47, SEQ ID NO: 50, SEQ ID NO: 53, SEQ ID NO:
56, SEQ ID NO: 59, SEQ ID NO: 62, SEQ ID NO: 65, SEQ ID NO: 68, SEQ
ID NO: 71, SEQ ID NO: 74, SEQ ID NO: 77, SEQ ID NO: 80, SEQ ID NO:
83, SEQ ID NO: 86, SEQ ID NO: 89, SEQ ID NO: 92, SEQ ID NO: 95, SEQ
ID NO: 98, SEQ ID NO: 101, SEQ ID NO: 104, SEQ ID NO: 107, SEQ ID
NO: 110, SEQ ID NO: 113, SEQ ID NO: 116, SEQ ID NO: 119, SEQ ID NO:
122, SEQ ID NO: 125, SEQ ID NO: 128, SEQ ID NO: 131, SEQ ID NO:
134, SEQ ID NO: 137, SEQ ID NO: 140, SEQ ID NO: 143, SEQ ID NO:
146, SEQ ID NO: 149, SEQ ID NO: 152, SEQ ID NO: 155, SEQ ID NO:
158, SEQ ID NO: 161, SEQ ID NO: 164, SEQ ID NO: 167, SEQ ID NO:
170, SEQ ID NO: 173, SEQ ID NO: 176, SEQ ID NO: 179, SEQ ID NO:
182, SEQ ID NO: 185, SEQ ID NO: 188, SEQ ID NO: 191, SEQ ID NO:
194, SEQ ID NO: 197, SEQ ID NO: 200, or SEQ ID NO: 203, SEQ ID NO:
206, SEQ ID NO: 209, SEQ ID NO: 212, SEQ ID NO: 215, SEQ ID NO:
218, SEQ ID NO: 221, SEQ ID NO: 224, SEQ ID NO: 227, SEQ ID NO:
230, or SEQ ID NO: 233. Such hybridization conditions are described
in detail below.
[0257] A nucleic acid sequence complement of nucleic acid sequence
encoding a protein of the present invention refers to the nucleic
acid sequence of the nucleic acid strand that is complementary to
the strand which encodes the protein. It will be appreciated that a
double stranded DNA which encodes a given amino acid sequence
comprises a single strand DNA and its complementary strand having a
sequence that is a complement to the single strand DNA. As such,
nucleic acid molecules of the present invention can be either
double-stranded or single-stranded, and include those nucleic acid
molecules that form stable hybrids under stringent hybridization
conditions with a nucleic acid sequence that encodes an amino acid
sequence such as SEQ ID NO: 2, and/or with the complement of the
nucleic acid sequence that encodes an amino acid sequence such as
SEQ ID NO: 2. Methods to deduce a complementary sequence are known
to those skilled in the art. It should be noted that since nucleic
acid sequencing technologies are not entirely error-free, the
sequences presented herein, at best, represent apparent sequences
of the proteins of the present invention.
[0258] As used herein, reference to hybridization conditions refers
to standard hybridization conditions under which nucleic acid
molecules are used to identify similar nucleic acid molecules. Such
standard conditions are disclosed, for example, in Sambrook et al.,
Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Labs
Press, 1989. Sambrook et al., ibid., is incorporated by reference
herein in its entirety (see specifically, pages 9.31-9.62). In
addition, formulae to calculate the appropriate hybridization and
wash conditions to achieve hybridization permitting varying degrees
of mismatch of nucleotides are disclosed, for example, in Meinkoth
et al., 1984, Anal. Biochem. 138, 267-284; Meinkoth et al., ibid.,
is incorporated by reference herein in its entirety.
[0259] More particularly, moderate stringency hybridization and
washing conditions, as referred to herein, refer to conditions
which permit isolation of nucleic acid molecules having at least
about 70% nucleic acid sequence identity with the nucleic acid
molecule being used to probe in the hybridization reaction (i.e.,
conditions permitting about 30% or less mismatch of nucleotides).
High stringency hybridization and washing conditions, as referred
to herein, refer to conditions which permit isolation of nucleic
acid molecules having at least about 80% nucleic acid sequence
identity with the nucleic acid molecule being used to probe in the
hybridization reaction (i.e., conditions permitting about 20% or
less mismatch of nucleotides). Very high stringency hybridization
and washing conditions, as referred to herein, refer to conditions
which permit isolation of nucleic acid molecules having at least
about 90% nucleic acid sequence identity with the nucleic acid
molecule being used to probe in the hybridization reaction (i.e.,
conditions permitting about 10% or less mismatch of nucleotides).
As discussed above, one of skill in the art can use the formulae in
Meinkoth et al., ibid. to calculate the appropriate hybridization
and wash conditions to achieve these particular levels of
nucleotide mismatch. Such conditions will vary, depending on
whether DNA:RNA or DNA:DNA hybrids are being formed. Calculated
melting temperatures for DNA:DNA hybrids are 10.degree. C. less
than for DNA:RNA hybrids. In particular embodiments, stringent
hybridization conditions for DNA:DNA hybrids include hybridization
at an ionic strength of 6.times.SSC (0.9 M Na.sup.+) at a
temperature of between about 20.degree. C. and about 35.degree. C.
(lower stringency), more preferably, between about 28.degree. C.
and about 40.degree. C. (more stringent), and even more preferably,
between about 35.degree. C. and about 45.degree. C. (even more
stringent), with appropriate wash conditions. In particular
embodiments, stringent hybridization conditions for DNA:RNA hybrids
include hybridization at an ionic strength of 6.times.SSC (0.9 M
Na.sup.+) at a temperature of between about 30.degree. C. and about
45.degree. C., more preferably, between about 38.degree. C. and
about 50.degree. C., and even more preferably, between about
45.degree. C. and about 55.degree. C., with similarly stringent
wash conditions. These values are based on calculations of a
melting temperature for molecules larger than about 100
nucleotides, 0% formamide and a G+C content of about 40%.
Alternatively, T.sub.m can be calculated empirically as set forth
in Sambrook et al., supra, pages 9.31 to 9.62. In general, the wash
conditions should be as stringent as possible, and should be
appropriate for the chosen hybridization conditions. For example,
hybridization conditions can include a combination of salt and
temperature conditions that are approximately 20-25.degree. C.
below the calculated T.sub.m of a particular hybrid, and wash
conditions typically include a combination of salt and temperature
conditions that are approximately 12-20.degree. C. below the
calculated T.sub.m of the particular hybrid. One example of
hybridization conditions suitable for use with DNA:DNA hybrids
includes a 2-24 hour hybridization in 6.times.SSC (50% formamide)
at about 42.degree. C., followed by washing steps that include one
or more washes at room temperature in about 2.times.SSC, followed
by additional washes at higher temperatures and lower ionic
strength (e.g., at least one wash as about 37.degree. C. in about
0.1.times.-0.5.times.SSC, followed by at least one wash at about
68.degree. C. in about 0.1.times.-0.5.times.SSC).
[0260] The minimum size of a protein and/or homologue of the
present invention is a size sufficient to have biological activity
or, when the protein is not required to have such activity,
sufficient to be useful for another purpose associated with a
protein of the present invention, such as for the production of
antibodies that bind to a naturally occurring protein. In one
embodiment, the protein of the present invention is at least 20
amino acids in length, or at least about 25 amino acids in length,
or at least about 30 amino acids in length, or at least about 40
amino acids in length, or at least about 50 amino acids in length,
or at least about 60 amino acids in length, or at least about 70
amino acids in length, or at least about 80 amino acids in length,
or at least about 90 amino acids in length, or at least about 100
amino acids in length, or at least about 125 amino acids in length,
or at least about 150 amino acids in length, or at least about 175
amino acids in length, or at least about 200 amino acids in length,
or at least about 250 amino acids in length, and so on up to a full
length of each protein, and including any size in between in
increments of one whole integer (one amino acid). There is no
limit, other than a practical limit, on the maximum size of such a
protein in that the protein can include a portion of a protein or a
full-length protein, plus additional sequence (e.g., a fusion
protein sequence), if desired.
[0261] The present invention also includes a fusion protein that
includes a domain of a protein of the present invention (including
a homologue) attached to one or more fusion segments, which are
typically heterologous in sequence to the protein sequence (i.e.,
different than protein sequence). Suitable fusion segments for use
with the present invention include, but are not limited to,
segments that can: enhance a protein's stability; provide other
desirable biological activity; and/or assist with the purification
of the protein (e.g., by affinity chromatography). A suitable
fusion segment can be a domain of any size that has the desired
function (e.g., imparts increased stability, solubility, action or
biological activity; and/or simplifies purification of a protein).
Fusion segments can be joined to amino and/or carboxyl termini of
the domain of a protein of the present invention and can be
susceptible to cleavage in order to enable straight-forward
recovery of the protein. Fusion proteins are preferably produced by
culturing a recombinant cell transfected with a fusion nucleic acid
molecule that encodes a protein including the fusion segment
attached to either the carboxyl and/or amino terminal end of a
domain of a protein of the present invention. Accordingly, proteins
of the present invention also include expression products of gene
fusions (for example, used to overexpress soluble, active forms of
the recombinant protein), of mutagenized genes (such as genes
having codon modifications to enhance gene transcription and
translation), and of truncated genes (such as genes having membrane
binding modules removed to generate soluble forms of a membrane
protein, or genes having signal sequences removed which are poorly
tolerated in a particular recombinant host).
[0262] In one embodiment of the present invention, any of the amino
acid sequences described herein can be produced with from at least
one, and up to about 20, additional heterologous amino acids
flanking each of the C- and/or N-terminal ends of the specified
amino acid sequence. The resulting protein or polypeptide can be
referred to as "consisting essentially of" the specified amino acid
sequence. According to the present invention, the heterologous
amino acids are a sequence of amino acids that are not naturally
found (i.e., not found in nature, in vivo) flanking the specified
amino acid sequence, or that are not related to the function of the
specified amino acid sequence, or that would not be encoded by the
nucleotides that flank the naturally occurring nucleic acid
sequence encoding the specified amino acid sequence as it occurs in
the gene, if such nucleotides in the naturally occurring sequence
were translated using standard codon usage for the organism from
which the given amino acid sequence is derived.
[0263] The present invention also provides enzyme combinations that
break down lignocellulose material. Such enzyme combinations or
mixtures can include a multi-enzyme composition that contains at
least one protein of the present invention in combination with one
or more additional proteins of the present invention or one or more
enzymes or other proteins from other microorganisms, plants, or
similar organisms. Synergistic enzyme combinations and related
methods are contemplated. The invention includes methods to
identify the optimum ratios and compositions of enzymes with which
to degrade each lignocellulosic material. These methods entail
tests to identify the optimum enzyme composition and ratios for
efficient conversion of any lignocellulosic substrate to its
constituent sugars. The Examples below include assays that may be
used to identify optimum ratios and compositions of enzymes with
which to degrade lignocellulosic materials.
[0264] Any combination of the proteins disclosed herein is suitable
for use in the multi-enzyme compositions of the present invention.
Due to the complex nature of most biomass sources, which can
contain cellulose, hemicellulose, pectin, lignin, protein, and ash,
among other components, preferred enzyme combinations may contain
enzymes with a range of substrate specificities that work together
to degrade biomass into fermentable sugars in the most efficient
manner. One example of a multi-enzyme complex for lignocellulose
saccharification is a mixture of cellobiohydrolase(s), xylanase(s),
endoglucanase(s), .beta.-glucosidase(s), .beta.-xylosidase(s), and
accessory enzymes. However, it is to be understood that any of the
enzymes described specifically herein can be combined with any one
or more of the enzymes described herein or with any other available
and suitable enzymes, to produce a multi-enzyme composition. The
invention is not restricted or limited to the specific exemplary
combinations listed below.
[0265] In one embodiment, the cellobiohydrolase(s) comprise between
about 30% and about 90% or between about 40% and about 70% of the
enzymes in the composition, and more preferably, between about 55%
and 65%, and more preferably, about 60% of the enzymes in the
composition (including any percentage between 40% and 70% in 0.5%
increments (e.g., 40%, 40.5%, 41%, etc.).
[0266] In one embodiment, the xylanase(s) comprise between about
10% and about 30% of the enzymes in the composition, and more
preferably, between about 15% and about 25%, and more preferably,
about 20% of the enzymes in the composition (including any
percentage between 10% and 30% in 0.5% increments).
[0267] In one embodiment, the endoglucanase(s) comprise between
about 5% and about 15% of the enzymes in the composition, and more
preferably, between about 7% and about 13%, and more preferably,
about 10% of the enzymes in the composition (including any
percentage between 5% and 15% in 0.5% increments).
[0268] In one embodiment, the .beta.-glucosidase(s) comprise
between about 1% and about 15% of the enzymes in the composition,
and preferably between about 2% and 10%, and more preferably, about
3% of the enzymes in the composition (including any percentage
between 1% and 15% in 0.5% increments).
[0269] In one embodiment, the .beta.-xylosidase(s) comprise between
about 1% and about 3% of the enzymes in the composition, and
preferably, between about 1.5% and about 2.5%, and more preferably,
about 2% of the enzymes in the composition (including any
percentage between 1% and 3% in 0.5% increments.
[0270] In one embodiment, the accessory enzymes comprise between
about 2% and about 8% of the enzymes in the composition, and
preferably, between about 3% and about 7%, and more preferably,
about 5% of the enzymes in the composition (including any
percentage between 2% and 8% in 0.5% increments.
[0271] One particularly preferred example of a multi-enzyme complex
for lignocellulose saccharification is a mixture of about 60%
cellobiohydrolase(s), about 20% xylanase(s), about 10%
endoglucanase(s), about 3% .beta.-glucosidase(s), about 2%
.beta.-xylosidase(s) and about 5% accessory enzyme(s).
[0272] Enzymes and multi-enzyme compositions of the present
invention may also be used to break down arabinoxylan or
arabinoxylan-containing substrates. Arabinoxylan is a
polysaccharide composed of xylose and arabinose, wherein
.alpha.-L-arabinofuranose residues are attached as branch-points to
a .beta.-(1,4)-linked xylose polymeric backbone. The xylose
residues may be mono-substituted at the C2 or C3 position, or
di-substituted at both positions. Ferulic acid or coumaric acid may
also be ester-linked to the C5 position of arabinosyl residues.
Further details on the hydrolysis of arabinoxylan can be found in
International Publication No. WO 2006/114095, the contents of which
are incorporated herein by reference.
[0273] The substitutions on the xylan backbone can inhibit the
enzymatic activity of xylanases, and the complete hydrolysis of
arabinoxylan typically requires the action of several different
enzymes. One example of a multi-enzyme complex for arabinoxylan
hydrolysis is a mixture of endoxylanase(s), .beta.-xylosidase(s),
and arabinofuranosidase(s), including those with specificity
towards single and double substituted xylose residues. In some
embodiments, the multi-enzyme complex may further comprise one or
more carbohydrate esterases, such as acetyl xylan esterases,
ferulic acid esterases, coumaric acid esterases or pectin methyl
esterases. Any combination of two or more of the above-mentioned
enzymes is suitable for use in the multi-enzyme complexes. However,
it is to be understood that the invention is not restricted or
limited to the specific exemplary combinations listed herein.
[0274] In one embodiment, the endoxylanase(s) comprise at least
about 5%, at least about 10%, at least about 15%, at least about
20%, at least about 25%, at least about 30%, at least about 40%, at
least about 50%, at least about 70% of the enzymes in the
composition (including any percentage between 5% and 70% in 0.5%
increments (e.g., 5.0%, 5.5%, 6.0%, etc.). Endoxylanase(s), either
alone or as part of a multi-enzyme complex, may be used in amounts
of 0.001 to 2.0 g/kg, 0.005 to 1.0 g/kg, or 0.05 to 0.2 g/kg of
substrate.
[0275] In one embodiment, the .beta.-xylosidase(s) comprise at
least about 5%, at least about 10%, at least about 15%, at least
about 20%, at least about 25%, at least about 30%, at least about
40%, at least about 50%, at least about 70% of the enzymes in the
composition (including any percentage between 5% and 70% in 0.5%
increments (e.g., 5.0%, 5.5%, 6.0%, etc.). .beta.-xylosidase(s),
either alone or as part of a multi-enzyme complex, may be used in
amounts of 0.001 to 2.0 g/kg, 0.005 to 1.0 g/kg, or 0.05 to 0.2
g/kg of substrate.
[0276] In one embodiment, the arabinofuranosidase(s) comprise at
least about 5%, at least about 10%, at least about 15%, at least
about 20%, at least about 25%, at least about 30%, at least about
40%, at least about 50%, at least about 70% of the enzymes in the
composition (including any percentage between 5% and 70% in 0.5%
increments (e.g., 5.0%, 5.5%, 6.0%, etc.). The total percentage of
arabinofuranosidase(s) present in the composition may include
arabinofuranosidase(s) with specificity towards single substituted
xylose residues, arabinofuranosidase(s) with specificity towards
double substituted xylose residues, or any combination thereof.
Arabinofuranosidase(s), either alone or as part of a multi-enzyme
complex, may be used in amounts of 0.001 to 2.0 g/kg, 0.005 to 1.0
g/kg, or 0.05 to 0.2 g/kg of substrate.
[0277] One or more components of a multi-enzyme composition (other
than proteins of the present invention) can be obtained from or
derived from a microbial, plant, or other source or combination
thereof, and will contain enzymes capable of degrading
lignocellulosic material. Examples of enzymes included in the
multi-enzyme compositions of the invention include cellulases,
hemicellulases (such as xylanases, including endoxylanases,
exoxylanases, and .beta.-xylosidases; mannanases, including
endomannanases, exomannanases, and .beta.-mannosidases),
ligninases, amylases, glucuronidases, proteases, esterases
(including ferulic acid esterase), lipases, glucosidases (such as
.beta.-glucosidase), and xyloglucanases.
[0278] While the multi-enzyme composition may contain many types of
enzymes, mixtures comprising enzymes that increase or enhance sugar
release from biomass are preferred, including hemicellulases. In
one embodiment, the hemicellulase is selected from a xylanase, an
arabinofuranosidase, an acetyl xylan esterase, a glucuronidase, an
endo-galactanase, a mannanase, an endo-arabinase, an exo-arabinase,
an exo-galactanase, a ferulic acid esterase, a galactomannanase, a
xylogluconase, or mixtures of any of these. In particular, the
enzymes can include glucoamylase, .beta.-xylosidase and/or
.beta.-glucosidase. Also preferred are mixtures comprising enzymes
that are capable of degrading cell walls and releasing cellular
contents.
[0279] The enzymes of the multi-enzyme composition can be provided
by a variety of sources. In one embodiment, the enzymes can be
produced by growing organisms such as bacteria, algae, fungi, and
plants which produce the enzymes naturally or by virtue of being
genetically modified to express the enzyme or enzymes. In another
embodiment, at least one enzyme of the multi-enzyme composition is
a commercially available enzyme.
[0280] In some embodiments, the multi-enzyme compositions comprise
an accessory enzyme. An accessory enzyme is any additional enzyme
capable of hydrolyzing lignocellulose or enhancing or promoting the
hydrolysis of lignocellulose, wherein the accessory enzyme is
typically provided in addition to a core enzyme or core set of
enzymes. An accessory enzyme can have the same or similar function
or a different function as an enzyme or enzymes in the core set of
enzymes. These enzymes have been described elsewhere herein, and
can generally include cellulases, xylanases, ligninases, amylases,
lipidases, or glucuronidases, for example. Accessory enzymes can
include enzymes that when contacted with biomass in a reaction,
allow for an increase in the activity of enzymes (e.g.,
hemicellulases) in the multi-enzyme composition. An accessory
enzyme or enzyme mix may be composed of enzymes from (1) commercial
suppliers; (2) cloned genes expressing enzymes; (3) complex broth
(such as that resulting from growth of a microbial strain in media,
wherein the strains secrete proteins and enzymes into the media);
(4) cell lysates of strains grown as in (3); and, (5) plant
material expressing enzymes capable of degrading lignocellulose. In
some embodiments, the accessory enzyme is a glucoamylase, a
pectinase, or a ligninase.
[0281] As used herein, a ligninase is an enzyme that can hydrolyze
or break down the structure of lignin polymers, including lignin
peroxidases, manganese peroxidases, laccases, and other enzymes
described in the art known to depolymerize or otherwise break
lignin polymers. Also included are enzymes capable of hydrolyzing
bonds formed between hemicellulosic sugars (notably arabinose) and
lignin.
[0282] The multi-enzyme compositions, in some embodiments, comprise
a biomass comprising microorganisms or a crude fermentation product
of microorganisms. A crude fermentation product refers to the
fermentation broth which has been separated from the microorganism
biomass (by filtration, for example). In general, the
microorganisms are grown in fermenters, optionally centrifuged or
filtered to remove biomass, and optionally concentrated,
formulated, and dried to produce an enzyme(s) or a multi-enzyme
composition that is a crude fermentation product. In other
embodiments, enzyme(s) or multi-enzyme compositions produced by the
microorganism (including a genetically modified microorganism as
described below) are subjected to one or more purification steps,
such as ammonium sulfate precipitation, chromatography, and/or
ultrafiltration, which result in a partially purified or purified
enzyme(s). If the microorganism has been genetically modified to
express the enzyme(s), the enzyme(s) will include recombinant
enzymes. If the genetically modified microorganism also naturally
expresses the enzyme(s) or other enzymes useful for lignocellulosic
saccharification, the enzyme(s) may include both naturally
occurring and recombinant enzymes.
[0283] Another embodiment of the present invention relates to a
composition comprising at least about 500 ng, and preferably at
least about 1 .mu.g, and more preferably at least about 5 .mu.g,
and more preferably at least about 10 .mu.g, and more preferably at
least about 25 .mu.g, and more preferably at least about 50 .mu.g,
and more preferably at least about 75 .mu.g, and more preferably at
least about 100 .mu.g, and more preferably at least about 250 kg,
and more preferably at least about 500 kg, and more preferably at
least about 750 kg, and more preferably at least about 1 mg, and
more preferably at least about 5 mg, of an isolated protein
comprising any of the proteins or homologues or fragments thereof
discussed herein. Such a composition of the present invention may
include any carrier with which the protein is associated by virtue
of the protein preparation method, a protein purification method,
or a preparation of the protein for use in any method according to
the present invention. For example, such a carrier can include any
suitable buffer, extract, or medium that is suitable for combining
with the protein of the present invention so that the protein can
be used in any method described herein according to the present
invention.
[0284] In one embodiment of the invention, one or more enzymes of
the invention is bound to a solid support, i.e., an immobilized
enzyme. As used herein, an immobilized enzyme includes immobilized
isolated enzymes, immobilized microbial cells which contain one or
more enzymes of the invention, other stabilized intact cells that
produce one or more enzymes of the invention, and stabilized
cell/membrane homogenates. Stabilized intact cells and stabilized
cell/membrane homogenates include cells and homogenates from
naturally occurring microorganisms expressing the enzymes of the
invention and preferably, from genetically modified microorganisms
as disclosed elsewhere herein. Thus, although methods for
immobilizing enzymes are discussed below, it will be appreciated
that such methods are equally applicable to immobilizing microbial
cells and in such an embodiment, the cells can be lysed, if
desired.
[0285] A variety of methods for immobilizing an enzyme are
disclosed in Industrial Enzymology 2nd Ed., Godfrey, T. and West,
S. Eds., Stockton Press, New York, N.Y., 1996, pp. 267-272;
Immobilized Enzymes, Chibata, I. Ed., Halsted Press, New York,
N.Y., 1978; Enzymes and Immobilized Cells in Biotechnology, Laskin,
A. Ed., Benjamin/Cummings Publishing Co., Inc., Menlo Park, Calif.,
1985; and Applied Biochemistry and Bioengineering, Vol. 4, Chibata,
I. and Wingard, Jr., L. Eds, Academic Press, New York, N.Y., 1983,
which are incorporated herein in their entirety.
[0286] Briefly, a solid support refers to any solid organic,
biopolymer or inorganic supports that can form a bond with an
enzyme without significantly effecting the activity of the enzyme.
Exemplary organic solid supports include polymers such as
polystyrene, nylon, phenol-formaldehyde resins, acrylic copolymers
(e.g., polyacrylamide), stabilized intact whole cells, and
stabilized crude whole cell/membrane homogenates. Exemplary
biopolymer supports include cellulose, polydextrans (e.g.,
Sephadex.RTM.), agarose, collagen and chitin. Exemplary inorganic
supports include glass beads (porous and nonporous), stainless
steel, metal oxides (e.g., porous ceramics such as ZrO.sub.2,
TiO.sub.2, Al.sub.2O.sub.3, and NiO) and sand. In one embodiment,
the solid support is selected from the group consisting of
stabilized intact cells and/or crude cell homogenates (e.g.,
produced from the microbial host cells expressing recombinant
enzymes, alone or in combination with natural enzymes). Preparation
of such supports requires a minimum of handling and cost.
Additionally, such supports provide excellent stability of the
enzyme.
[0287] Stabilized intact cells and/or cell/membrane homogenates can
be produced, for example, by using bifunctional crosslinkers (e.g.,
glutaraldehyde) to stabilize cells and cell homogenates. In both
the intact cells and the cell membranes, the cell wall and
membranes act as immobilizing supports. In such a system, integral
membrane proteins are in the "best" lipid membrane environment.
Whether starting with intact cells or homogenates, in this system
the cells are either no longer "alive" or "metabolizing", or
alternatively, are "resting" (i.e., the cells maintain metabolic
potential and active enzyme, but under the culture conditions are
not growing); in either case, the immobilized cells or membranes
serve as biocatalysts.
[0288] An enzyme of the invention can be bound to a solid support
by a variety of methods including adsorption, cross-linking
(including covalent bonding), and entrapment. Adsorption can be
through van del Waal's forces, hydrogen bonding, ionic bonding, or
hydrophobic binding. Exemplary solid supports for adsorption
immobilization include polymeric adsorbents and ion-exchange
resins. Solid supports in a bead form are particularly well-suited.
The particle size of an adsorption solid support can be selected
such that the immobilized enzyme is retained in the reactor by a
mesh filter while the substrate is allowed to flow through the
reactor at a desired rate. With porous particulate supports it is
possible to control the adsorption process to allow enzymes or
cells to be embedded within the cavity of the particle, thus
providing protection without an unacceptable loss of activity.
[0289] Cross-linking of an enzyme to a solid support involves
forming a chemical bond between a solid support and the enzyme. It
will be appreciated that although cross-linking generally involves
linking the enzyme to a solid support using an intermediary
compound, it is also possible to achieve a covalent bonding between
the enzyme and the solid support directly without the use of an
intermediary compound. Cross-linking commonly uses a bifunctional
or multifunctional reagent to activate and attach a carboxyl group,
amino group, sulfur group, hydroxy group or other functional group
of the enzyme to the solid support. The term "activate" refers to a
chemical transformation of a functional group which allows a
formation of a bond at the functional group. Exemplary amino group
activating reagents include water-soluble carbodiimides,
glutaraldehyde, cyanogen bromide, N-hydroxysuccinimide esters,
triazines, cyanuric chloride, and carbonyl diimidazole. Exemplary
carboxyl group activating reagents include water-soluble
carbodiimides, and N-ethyl-5-phenylisoxazolium-3-sulfonate.
Exemplary tyrosyl group activating reagents include diazonium
compounds. And exemplary sulfhydryl group activating reagents
include dithiobis-5,5'-(2-nitrobenzoic acid), and
glutathione-2-pyridyl disulfide. Systems for covalently linking an
enzyme directly to a solid support include Eupergit.RTM., a
polymethacrylate bead support available from Rohm Pharma
(Darmstadt, Germany), kieselguhl (Macro sorbs), available from
Sterling Organics, kaolinite available from English China Clay as
"Biofix" supports, silica gels which can be activated by
silanization, available from W.R. Grace, and high-density alumina,
available from UOP (Des Plains, Ill.).
[0290] Entrapment can also be used to immobilize an enzyme.
Entrapment of an enzyme involves formation of, inter alia, gels
(using organic or biological polymers), vesicles (including
microencapsulation), semipermeable membranes or other matrices.
Exemplary materials used for entrapment of an enzyme include
collagen, gelatin, agar, cellulose triacetate, alginate,
polyacrylamide, polystyrene, polyurethane, epoxy resins,
carrageenan, and egg albumin. Some of the polymers, in particular
cellulose triacetate, can be used to entrap the enzyme as they are
spun into a fiber. Other materials such as polyacrylamide gels can
be polymerized in solution to entrap the enzyme. Still other
materials such as polyglycol oligomers that are functionalized with
polymerizable vinyl end groups can entrap enzymes by forming a
cross-linked polymer with UV light illumination in the presence of
a photosensitizer.
[0291] Further embodiments of the present invention include nucleic
acid molecules that encode a protein of the present invention, as
well as homologues or fragments of such nucleic acid molecules. A
nucleic acid molecule of the present invention includes a nucleic
acid molecule comprising, consisting essentially of, or consisting
of, a nucleic acid sequence encoding any of the isolated proteins
disclosed herein, including a fragment or a homologue of such
proteins, described above. Nucleic acid molecules can include a
nucleic acid sequence that encodes a fragment of a protein that
does not have biological activity, and can also include portions of
a gene or polynucleotide encoding the protein that are not part of
the coding region for the protein (e.g., introns or regulatory
regions of a gene encoding the protein). Nucleic acid molecules can
include a nucleic acid sequence that is useful as a probe or primer
(oligonucleotide sequences).
[0292] In one embodiment, a nucleic molecule of the present
invention includes a nucleic acid molecule comprising, consisting
essentially of, or consisting of, a nucleic acid sequence
represented by SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO:
6, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID
NO: 13, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 19,
SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID
NO: 27, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 33,
SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID
NO: 40, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 45, SEQ ID NO: 46,
SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID
NO: 54, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 60,
SEQ ID NO: 61, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID
NO: 67, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 72, SEQ ID NO: 73,
SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID
NO: 81, SEQ ID NO: 82, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 87,
SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID
NO: 94, SEQ ID NO: 96, SEQ ID NO: 97, SEQ ID NO: 99, SEQ ID NO:
100, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 105, SEQ ID NO:
106, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 111, SEQ ID NO:
112, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO:
118, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 123, SEQ ID NO:
124, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 129, SEQ ID NO:
130, SEQ ID NO: 132, SEQ ID NO: 133, SEQ ID NO: 135, SEQ ID NO:
136, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 141, SEQ ID NO:
142, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 147, SEQ ID NO:
148, SEQ ID NO: 150, SEQ ID NO: 151, SEQ ID NO: 153, SEQ ID NO:
154, SEQ ID NO: 156, SEQ ID NO: 157, SEQ ID NO: 159, SEQ ID NO:
160, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 165, SEQ ID NO:
166, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 171, SEQ ID NO:
172, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 177, SEQ ID NO:
178, SEQ ID NO: 180, SEQ ID NO: 181, SEQ ID NO: 183, SEQ ID NO:
184, SEQ ID NO: 186, SEQ ID NO: 187, SEQ ID NO: 189, SEQ ID NO:
190, SEQ ID NO: 192, SEQ ID NO: 193, SEQ ID NO: 195, SEQ ID NO:
196, SEQ ID NO: 198, SEQ ID NO: 199, SEQ ID NO: 201, SEQ ID NO:
202, SEQ ID NO: 204, SEQ ID NO: 205, SEQ ID NO: 207, SEQ ID NO:
208, SEQ ID NO: 210, SEQ ID NO: 211, SEQ ID NO: 213, SEQ ID NO:
214, SEQ ID NO: 216, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO:
220, SEQ ID NO: 222, SEQ ID NO: 223, SEQ ID NO: 225, SEQ ID NO:
226, SEQ ID NO: 228, SEQ ID NO: 229, SEQ ID NO: 231, SEQ ID NO:
232, or SEQ ID NO: 234 or fragments or homologues thereof.
Preferably, the nucleic acid sequence encodes a protein (including
fragments and homologues thereof) useful in the invention, or
encompasses useful oligonucleotides or complementary nucleic acid
sequences.
[0293] In one embodiment, a nucleic molecule of the present
invention includes a nucleic acid molecule comprising, consisting
essentially of, or consisting of, a nucleic acid sequence encoding
an amino acid sequence represented by SEQ ID NO: 2, SEQ ID NO: 5,
SEQ ID NO: 8, SEQ ID NO: 11, SEQ ID NO: 14, SEQ ID NO: 17, SEQ ID
NO: 20, SEQ ID NO: 23, SEQ ID NO: 26, SEQ ID NO: 29, SEQ ID NO: 32,
SEQ ID NO: 35, SEQ ID NO: 38, SEQ ID NO: 41, SEQ ID NO: 44, SEQ ID
NO: 47, SEQ ID NO: 50, SEQ ID NO: 53, SEQ ID NO: 56, SEQ ID NO: 59,
SEQ ID NO: 62, SEQ ID NO: 65, SEQ ID NO: 68, SEQ ID NO: 71, SEQ ID
NO: 74, SEQ ID NO: 77, SEQ ID NO: 80, SEQ ID NO: 83, SEQ ID NO: 86,
SEQ ID NO: 89, SEQ ID NO: 92, SEQ ID NO: 95, SEQ ID NO: 98, SEQ ID
NO: 101, SEQ ID NO: 104, SEQ ID NO: 107, SEQ ID NO: 110, SEQ ID NO:
113, SEQ ID NO: 116, SEQ ID NO: 119, SEQ ID NO: 122, SEQ ID NO:
125, SEQ ID NO: 128, SEQ ID NO: 131, SEQ ID NO: 134, SEQ ID NO:
137, SEQ ID NO: 140, SEQ ID NO: 143, SEQ ID NO: 146, SEQ ID NO:
149, SEQ ID NO: 152, SEQ ID NO: 155, SEQ ID NO: 158, SEQ ID NO:
161, SEQ ID NO: 164, SEQ ID NO: 167, SEQ ID NO: 170, SEQ ID NO:
173, SEQ ID NO: 176, SEQ ID NO: 179, SEQ ID NO: 182, SEQ ID NO:
185, SEQ ID NO: 188, SEQ ID NO: 191, SEQ ID NO: 194, SEQ ID NO:
197, SEQ ID NO: 200, SEQ ID NO: 203, SEQ ID NO: 206, SEQ ID NO:
209, SEQ ID NO: 212, SEQ ID NO: 215, SEQ ID NO: 218, SEQ ID NO:
221, SEQ ID NO: 224, SEQ ID NO: 227, SEQ ID NO: 230, or SEQ ID NO:
233 or fragments or homologues thereof. Preferably, the nucleic
acid sequence encodes a protein (including fragments and homologues
thereof) useful in the invention, or encompasses useful
oligonucleotides or complementary nucleic acid sequences.
[0294] In one embodiment, such nucleic acid molecules include
isolated nucleic acid molecules that hybridize under moderate
stringency conditions, and more preferably under high stringency
conditions, and even more preferably under very high stringency
conditions, as described above, with the complement of a nucleic
acid sequence encoding a protein of the present invention (i.e.,
including naturally occurring allelic variants encoding a protein
of the present invention). Preferably, an isolated nucleic acid
molecule encoding a protein of the present invention comprises a
nucleic acid sequence that hybridizes under moderate, high, or very
high stringency conditions to the complement of a nucleic acid
sequence that encodes a protein comprising an amino acid sequence
represented by SEQ ID NO: 2, SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO:
11, SEQ ID NO: 14, SEQ ID NO: 17, SEQ ID NO: 20, SEQ ID NO: 23, SEQ
ID NO: 26, SEQ ID NO: 29, SEQ ID NO: 32, SEQ ID NO: 35, SEQ ID NO:
38, SEQ ID NO: 41, SEQ ID NO: 44, SEQ ID NO: 47, SEQ ID NO: 50, SEQ
ID NO: 53, SEQ ID NO: 56, SEQ ID NO: 59, SEQ ID NO: 62, SEQ ID NO:
65, SEQ ID NO: 68, SEQ ID NO: 71, SEQ ID NO: 74, SEQ ID NO: 77, SEQ
ID NO: 80, SEQ ID NO: 83, SEQ ID NO: 86, SEQ ID NO: 89, SEQ ID NO:
92, SEQ ID NO: 95, SEQ ID NO: 98, SEQ ID NO: 101, SEQ ID NO: 104,
SEQ ID NO: 107, SEQ ID NO: 110, SEQ ID NO: 113, SEQ ID NO: 116, SEQ
ID NO: 119, SEQ ID NO: 122, SEQ ID NO: 125, SEQ ID NO: 128, SEQ ID
NO: 131, SEQ ID NO: 134, SEQ ID NO: 137, SEQ ID NO: 140, SEQ ID NO:
143, SEQ ID NO: 146, SEQ ID NO: 149, SEQ ID NO: 152, SEQ ID NO:
155, SEQ ID NO: 158, SEQ ID NO: 161, SEQ ID NO: 164, SEQ ID NO:
167, SEQ ID NO: 170, SEQ ID NO: 173, SEQ ID NO: 176, SEQ ID NO:
179, SEQ ID NO: 182, SEQ ID NO: 185, SEQ ID NO: 188, SEQ ID NO:
191, SEQ ID NO: 194, SEQ ID NO: 197, SEQ ID NO: 200, or SEQ ID NO:
203, SEQ ID NO: 206, SEQ ID NO: 209, SEQ ID NO: 212, SEQ ID NO:
215, SEQ ID NO: 218, SEQ ID NO: 221, SEQ ID NO: 224, SEQ ID NO:
227, SEQ ID NO: 230, or SEQ ID NO: 233.
[0295] In accordance with the present invention, an isolated
nucleic acid molecule is a nucleic acid molecule (polynucleotide)
that has been removed from its natural milieu (i.e., that has been
subject to human manipulation) and can include DNA, RNA, or
derivatives of either DNA or RNA, including cDNA. As such,
"isolated" does not reflect the extent to which the nucleic acid
molecule has been purified. Although the phrase "nucleic acid
molecule" primarily refers to the physical nucleic acid molecule,
and the phrase "nucleic acid sequence" primarily refers to the
sequence of nucleotides on the nucleic acid molecule, the two
phrases can be used interchangeably, especially with respect to a
nucleic acid molecule, or a nucleic acid sequence, being capable of
encoding a protein. An isolated nucleic acid molecule of the
present invention can be isolated from its natural source or
produced using recombinant DNA technology (e.g., polymerase chain
reaction (PCR) amplification, cloning) or chemical synthesis.
Isolated nucleic acid molecules can include, for example, genes,
natural allelic variants of genes, coding regions or portions
thereof, and coding and/or regulatory regions modified by
nucleotide insertions, deletions, substitutions, and/or inversions
in a manner such that the modifications do not substantially
interfere with the nucleic acid molecule's ability to encode a
protein of the present invention or to form stable hybrids under
stringent conditions with natural gene isolates. An isolated
nucleic acid molecule can include degeneracies. As used herein,
nucleotide degeneracy refers to the phenomenon that one amino acid
can be encoded by different nucleotide codons. Thus, the nucleic
acid sequence of a nucleic acid molecule that encodes a protein of
the present invention can vary due to degeneracies. It is noted
that a nucleic acid molecule of the present invention is not
required to encode a protein having protein activity. A nucleic
acid molecule can encode a truncated, mutated or inactive protein,
for example. In addition, nucleic acid molecules of the invention
are useful as probes and primers for the identification, isolation
and/or purification of other nucleic acid molecules. If the nucleic
acid molecule is an oligonucleotide, such as a probe or primer, the
oligonucleotide preferably ranges from about 5 to about 50 or about
500 nucleotides, more preferably from about 10 to about 40
nucleotides, and most preferably from about 15 to about 40
nucleotides in length.
[0296] According to the present invention, reference to a gene
includes all nucleic acid sequences related to a natural (i.e.
wild-type) gene, such as regulatory regions that control production
of the protein encoded by that gene (such as, but not limited to,
transcription, translation or post-translation control regions) as
well as the coding region itself. In another embodiment, a gene can
be a naturally occurring allelic variant that includes a similar
but not identical sequence to the nucleic acid sequence encoding a
given protein. Allelic variants have been previously described
above. The phrases "nucleic acid molecule" and "gene" can be used
interchangeably when the nucleic acid molecule comprises a gene as
described above.
[0297] Preferably, an isolated nucleic acid molecule of the present
invention is produced using recombinant DNA technology (e.g.,
polymerase chain reaction (PCR) amplification, cloning, etc.) or
chemical synthesis. Isolated nucleic acid molecules include any
nucleic acid molecules and homologues thereof that are part of a
gene described herein and/or that encode a protein described
herein, including, but not limited to, natural allelic variants and
modified nucleic acid molecules (homologues) in which nucleotides
have been inserted, deleted, substituted, and/or inverted in such a
manner that such modifications provide the desired effect on
protein biological activity or on the activity of the nucleic acid
molecule. Allelic variants and protein homologues (e.g., proteins
encoded by nucleic acid homologues) have been discussed in detail
above.
[0298] A nucleic acid molecule homologue (i.e., encoding a
homologue of a protein of the present invention) can be produced
using a number of methods known to those skilled in the art (see,
for example, Sambrook et al.). For example, nucleic acid molecules
can be modified using a variety of techniques including, but not
limited to, by classic mutagenesis and recombinant DNA techniques
(e.g., site-directed mutagenesis, chemical treatment, restriction
enzyme cleavage, ligation of nucleic acid fragments and/or PCR
amplification), or synthesis of oligonucleotide mixtures and
ligation of mixture groups to "build" a mixture of nucleic acid
molecules and combinations thereof. Another method for modifying a
recombinant nucleic acid molecule encoding a protein is gene
shuffling (i.e., molecular breeding) (See, for example, U.S. Pat.
No. 5,605,793 to Stemmer; Minshull and Stemmer; 1999, Curr. Opin.
Chem. Biol. 3:284-290; Stemmer, 1994, P.N.A.S. USA 91:10747-10751,
all of which are incorporated herein by reference in their
entirety). This technique can be used to efficiently introduce
multiple simultaneous changes in the protein. Nucleic acid molecule
homologues can be selected by hybridization with a gene or
polynucleotide, or by screening for the function of a protein
encoded by a nucleic acid molecule (i.e., biological activity).
[0299] The minimum size of a nucleic acid molecule of the present
invention is a size sufficient to encode a protein (including a
fragment or homologue of a full-length protein) having biological
activity, sufficient to encode a protein comprising at least one
epitope which binds to an antibody, or sufficient to form a probe
or oligonucleotide primer that is capable of forming a stable
hybrid with the complementary sequence of a nucleic acid molecule
encoding a natural protein (e.g., under moderate, high, or high
stringency conditions). As such, the size of the nucleic acid
molecule encoding such a protein can be dependent on nucleic acid
composition and percent homology or identity between the nucleic
acid molecule and complementary sequence as well as upon
hybridization conditions per se (e.g., temperature, salt
concentration, and formamide concentration). The minimal size of a
nucleic acid molecule that is used as an oligonucleotide primer or
as a probe is typically at least about 12 to about 15 nucleotides
in length if the nucleic acid molecules are GC-rich and at least
about 15 to about 18 bases in length if they are AT-rich. There is
no limit, other than a practical limit, on the maximal size of a
nucleic acid molecule of the present invention, in that the nucleic
acid molecule can include a portion of a protein encoding sequence,
a nucleic acid sequence encoding a full-length protein (including a
gene), including any length fragment between about 20 nucleotides
and the number of nucleotides that make up the full length cDNA
encoding a protein, in whole integers (e.g., 20, 21, 22, 23, 24, 25
. . . nucleotides), or multiple genes, or portions thereof.
[0300] The phrase "consisting essentially of", when used with
reference to a nucleic acid sequence herein, refers to a nucleic
acid sequence encoding a specified amino acid sequence that can be
flanked by from at least one, and up to as many as about 60,
additional heterologous nucleotides at each of the 5' and/or the 3'
end of the nucleic acid sequence encoding the specified amino acid
sequence. The heterologous nucleotides are not naturally found
(i.e., not found in nature, in vivo) flanking the nucleic acid
sequence encoding the specified amino acid sequence as it occurs in
the natural gene or do not encode a protein that imparts any
additional function to the protein or changes the function of the
protein having the specified amino acid sequence.
[0301] In one embodiment, the polynucleotide probes or primers of
the invention are conjugated to detectable markers. Detectable
labels suitable for use in the present invention include any
composition detectable by spectroscopic, photochemical,
biochemical, immunochemical, electrical, optical or chemical means.
Useful labels in the present invention include biotin for staining
with labeled streptavidin conjugate, magnetic beads (e.g.,
Dynabeads.TM.), fluorescent dyes (e.g., fluorescein, Texas red,
rhodamine, green fluorescent protein, and the like), radiolabels
(e.g., .sup.3H, .sup.125I, .sup.35S, .sup.14C, or .sup.32P),
enzymes (e.g., horse radish peroxidase, alkaline phosphatase and
others commonly used in an ELISA), and colorimetric labels such as
colloidal gold or colored glass or plastic (e.g., polystyrene,
polypropylene, latex, etc.) beads. Preferably, the polynucleotide
probes are immobilized on a substrate such as: artificial
membranes, organic supports, biopolymer supports and inorganic
supports.
[0302] One embodiment of the present invention relates to a
recombinant nucleic acid molecule which comprises the isolated
nucleic acid molecule described above which is operatively linked
to at least one expression control sequence. More particularly,
according to the present invention, a recombinant nucleic acid
molecule typically comprises a recombinant vector and any one or
more of the isolated nucleic acid molecules as described herein.
According to the present invention, a recombinant vector is an
engineered (i.e., artificially produced) nucleic acid molecule that
is used as a tool for manipulating a nucleic acid sequence of
choice and/or for introducing such a nucleic acid sequence into a
host cell. The recombinant vector is therefore suitable for use in
cloning, sequencing, and/or otherwise manipulating the nucleic acid
sequence of choice, such as by expressing and/or delivering the
nucleic acid sequence of choice into a host cell to form a
recombinant cell. Such a vector typically contains heterologous
nucleic acid sequences, that is, nucleic acid sequences that are
not naturally found adjacent to nucleic acid sequence to be cloned
or delivered, although the vector can also contain regulatory
nucleic acid sequences (e.g., promoters, untranslated regions)
which are naturally found adjacent to nucleic acid sequences of the
present invention or which are useful for expression of the nucleic
acid molecules of the present invention (discussed in detail
below). The vector can be either RNA or DNA, either prokaryotic or
eukaryotic, and typically is a plasmid. The vector can be
maintained as an extrachromosomal element (e.g., a plasmid) or it
can be integrated into the chromosome of a recombinant host cell,
although it is preferred if the vector remain separate from the
genome for most applications of the invention. The entire vector
can remain in place within a host cell, or under certain
conditions, the plasmid DNA can be deleted, leaving behind the
nucleic acid molecule of the present invention. An integrated
nucleic acid molecule can be under chromosomal promoter control,
under native or plasmid promoter control, or under a combination of
several promoter controls. Single or multiple copies of the nucleic
acid molecule can be integrated into the chromosome. A recombinant
vector of the present invention can contain at least one selectable
marker.
[0303] In one embodiment, a recombinant vector used in a
recombinant nucleic acid molecule of the present invention is an
expression vector. As used herein, the phrase "expression vector"
is used to refer to a vector that is suitable for production of an
encoded product (e.g., a protein of interest, such as an enzyme of
the present invention). In this embodiment, a nucleic acid sequence
encoding the product to be produced (e.g., the protein or homologue
thereof) is inserted into the recombinant vector to produce a
recombinant nucleic acid molecule. The nucleic acid sequence
encoding the protein to be produced is inserted into the vector in
a manner that operatively links the nucleic acid sequence to
regulatory sequences in the vector which enable the transcription
and translation of the nucleic acid sequence within the recombinant
host cell.
[0304] Typically, a recombinant nucleic acid molecule includes at
least one nucleic acid molecule of the present invention
operatively linked to one or more expression control sequences
(e.g., transcription control sequences or translation control
sequences). As used herein, the phrase "recombinant molecule" or
"recombinant nucleic acid molecule" primarily refers to a nucleic
acid molecule or nucleic acid sequence operatively linked to a
transcription control sequence, but can be used interchangeably
with the phrase "nucleic acid molecule", when such nucleic acid
molecule is a recombinant molecule as discussed herein. According
to the present invention, the phrase "operatively linked" refers to
linking a nucleic acid molecule to an expression control sequence
in a manner such that the molecule is able to be expressed when
transfected (i.e., transformed, transduced, transfected, conjugated
or conduced) into a host cell. Transcription control sequences are
sequences which control the initiation, elongation, or termination
of transcription. Particularly important transcription control
sequences are those which control transcription initiation, such as
promoter, enhancer, operator and repressor sequences. Suitable
transcription control sequences include any transcription control
sequence that can function in a host cell or organism into which
the recombinant nucleic acid molecule is to be introduced.
[0305] Recombinant nucleic acid molecules of the present invention
can also contain additional regulatory sequences, such as
translation regulatory sequences, origins of replication, and other
regulatory sequences that are compatible with the recombinant cell.
In one embodiment, a recombinant molecule of the present invention,
including those which are integrated into the host cell chromosome,
also contains secretory signals (i.e., signal segment nucleic acid
sequences) to enable an expressed protein to be secreted from the
cell that produces the protein. Suitable signal segments include a
signal segment that is naturally associated with the protein to be
expressed or any heterologous signal segment capable of directing
the secretion of the protein according to the present invention. In
another embodiment, a recombinant molecule of the present invention
comprises a leader sequence to enable an expressed protein to be
delivered to and inserted into the membrane of a host cell.
Suitable leader sequences include a leader sequence that is
naturally associated with the protein, or any heterologous leader
sequence capable of directing the delivery and insertion of the
protein to the membrane of a cell.
[0306] According to the present invention, the term "transfection"
is generally used to refer to any method by which an exogenous
nucleic acid molecule (i.e., a recombinant nucleic acid molecule)
can be inserted into a cell. The term "transformation" can be used
interchangeably with the term "transfection" when such term is used
to refer to the introduction of nucleic acid molecules into
microbial cells or plants and describes an inherited change due to
the acquisition of exogenous nucleic acids by the microorganism
that is essentially synonymous with the term "transfection."
Transfection techniques include, but are not limited to,
transformation, particle bombardment, electroporation,
microinjection, lipofection, adsorption, infection and protoplast
fusion.
[0307] One or more recombinant molecules of the present invention
can be used to produce an encoded product (e.g., a protein) of the
present invention. In one embodiment, an encoded product is
produced by expressing a nucleic acid molecule as described herein
under conditions effective to produce the protein. A preferred
method to produce an encoded protein is by transfecting a host cell
with one or more recombinant molecules to form a recombinant cell.
Suitable host cells to transfect include, but are not limited to,
any bacterial, fungal (e.g., filamentous fungi or yeast or
mushrooms), algal, plant, insect, or animal cell that can be
transfected. Host cells can be either untransfected cells or cells
that are already transfected with at least one other recombinant
nucleic acid molecule.
[0308] Suitable cells (e.g., a host cell or production organism)
may include any microorganism (e.g., a bacterium, a protist, an
alga, a fungus, or other microbe), and is preferably a bacterium, a
yeast or a filamentous fungus. Suitable bacterial genera include,
but are not limited to, Escherichia, Bacillus, Lactobacillus,
Pseudomonas and Streptomyces. Suitable bacterial species include,
but are not limited to, Escherichia coli, Bacillus subtilis,
Bacillus licheniformis, Lactobacillus brevis, Pseudomonas
aeruginosa and Streptomyces lividans. Suitable genera of yeast
include, but are not limited to, Saccharomyces,
Schizosaccharomyces, Candida, Hansenula, Pichia, Kluyveromyces, and
Phaffia. Suitable yeast species include, but are not limited to,
Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida
albicans, Hansenula polymorpha, Pichia pastoris, P. canadensis,
Kluyveromyces marxianus and Phaffia rhodozyma.
[0309] Suitable fungal genera include, but are not limited to,
Chrysosporium, Thielavia, Neurospora, Aureobasidium, Filibasidium,
Piromyces, Corynascus, Cryplococcus, Acremonium, Tolypocladium,
Scytalidium, Schizophyllum, Sporotrichum, Penicillium, Gibberella,
Myceliophthora, Mucor, Aspergillus, Fusarium, Humicola, and
Trichoderma, and anamorphs and teleomorphs thereof. Suitable fungal
species include, but are not limited to, Aspergillus niger,
Aspergillus nidulans, Aspergillus japonicus, Absidia coerulea,
Rhizopus oryzae, Chrysosporium lucknowense, Neurospora crassa,
Neurospora intermedia, Trichoderma reesei, Penicillium canescens,
Penicillium solitum, Penicillium funiculosum, and Talaromyces
flavus. In one embodiment, the host cell is a fungal cell of the
species Chrysosporium lucknowense. In one embodiment, the host cell
is a fungal cell of Strain C1 (VKM F-3500-D) or a mutant strain
derived therefrom (e.g., UV13-6 (Accession No. VKM F-3632 D);
NG7C-19 (Accession No. VKM F-3633 D); or UV18-25 (VKM F-3631D)).
Host cells can be either untransfected cells or cells that are
already transfected with at least one other recombinant nucleic
acid molecule. Additional embodiments of the present invention
include any of the genetically modified cells described herein.
[0310] In one embodiment, one or more protein(s) expressed by an
isolated nucleic acid molecule of the present invention are
produced by culturing a cell that expresses the protein (i.e., a
recombinant cell or recombinant host cell) under conditions
effective to produce the protein. In some instances, the protein
may be recovered, and in others, the cell may be harvested in
whole, either of which can be used in a composition.
[0311] Microorganisms used in the present invention (including
recombinant host cells or genetically modified microorganisms) are
cultured in an appropriate fermentation medium. An appropriate, or
effective, fermentation medium refers to any medium in which a cell
of the present invention, including a genetically modified
microorganism (described below), when cultured, is capable of
expressing enzymes useful in the present invention and/or of
catalyzing the production of sugars from lignocellulosic biomass.
Such a medium is typically an aqueous medium comprising assimilable
carbon, nitrogen and phosphate sources. Such a medium can also
include appropriate salts, minerals, metals and other nutrients.
Microorganisms and other cells of the present invention can be
cultured in conventional fermentation bioreactors. The
microorganisms can be cultured by any fermentation process which
includes, but is not limited to, batch, fed-batch, cell recycle,
and continuous fermentation. The fermentation of microorganisms
such as fungi may be carried out in any appropriate reactor, using
methods known to those skilled in the art. For example, the
fermentation may be carried out for a period of 1 to 14 days, or
more preferably between about 3 and 10 days. The temperature of the
medium is typically maintained between about 25 and 50.degree. C.,
and more preferably between 28 and 40.degree. C. The pH of the
fermentation medium is regulated to a pH suitable for growth and
protein production of the particular organism. The fermenter can be
aerated in order to supply the oxygen necessary for fermentation
and to avoid the excessive accumulation of carbon dioxide produced
by fermentation. In addition, the aeration helps to control the
temperature and the moisture of the culture medium. In general the
fungal strains are grown in fermenters, optionally centrifuged or
filtered to remove biomass, and optionally concentrated,
formulated, and dried to produce an enzyme(s) or a multi-enzyme
composition that is a crude fermentation product. Particularly
suitable conditions for culturing filamentous fungi are described,
for example, in U.S. Pat. No. 6,015,707 and U.S. Pat. No.
6,573,086, supra.
[0312] Depending on the vector and host system used for production,
resultant proteins of the present invention may either remain
within the recombinant cell; be secreted into the culture medium;
be secreted into a space between two cellular membranes; or be
retained on the outer surface of a cell membrane. The phrase
"recovering the protein" refers to collecting the whole culture
medium containing the protein and need not imply additional steps
of separation or purification. Proteins produced according to the
present invention can be purified using a variety of standard
protein purification techniques, such as, but not limited to,
affinity chromatography, ion exchange chromatography, filtration,
electrophoresis, hydrophobic interaction chromatography, gel
filtration chromatography, reverse phase chromatography,
concanavalin A chromatography, chromatofocusing and differential
solubilization.
[0313] Proteins of the present invention are preferably retrieved,
obtained, and/or used in "substantially pure" form. As used herein,
"substantially pure" refers to a purity that allows for the
effective use of the protein in any method according to the present
invention. For a protein to be useful in any of the methods
described herein or in any method utilizing enzymes of the types
described herein according to the present invention, it is
substantially free of contaminants, other proteins and/or chemicals
that might interfere or that would interfere with its use in a
method disclosed by the present invention (e.g., that might
interfere with enzyme activity), or that at least would be
undesirable for inclusion with a protein of the present invention
(including homologues) when it is used in a method disclosed by the
present invention (described in detail below). Preferably, a
"substantially pure" protein, as referenced herein, is a protein
that can be produced by any method (i.e., by direct purification
from a natural source, recombinantly, or synthetically), and that
has been purified from other protein components such that the
protein comprises at least about 80% weight/weight of the total
protein in a given composition (e.g., the protein of interest is
about 80% of the protein in a solution/composition/buffer), and
more preferably, at least about 85%, and more preferably at least
about 90%, and more preferably at least about 91%, and more
preferably at least about 92%, and more preferably at least about
93%, and more preferably at least about 94%, and more preferably at
least about 95%, and more preferably at least about 96%, and more
preferably at least about 97%, and more preferably at least about
98%, and more preferably at least about 99%, weight/weight of the
total protein in a given composition.
[0314] It will be appreciated by one skilled in the art that use of
recombinant DNA technologies can improve control of expression of
transfected nucleic acid molecules by manipulating, for example,
the number of copies of the nucleic acid molecules within the host
cell, the efficiency with which those nucleic acid molecules are
transcribed, the efficiency with which the resultant transcripts
are translated, and the efficiency of post-translational
modifications. Additionally, the promoter sequence might be
genetically engineered to improve the level of expression as
compared to the native promoter. Recombinant techniques useful for
controlling the expression of nucleic acid molecules include, but
are not limited to, integration of the nucleic acid molecules into
one or more host cell chromosomes, addition of vector stability
sequences to plasmids, substitutions or modifications of
transcription control signals (e.g., promoters, operators,
enhancers), substitutions or modifications of translational control
signals (e.g., ribosome binding sites), modification of nucleic
acid molecules to correspond to the codon usage of the host cell,
and deletion of sequences that destabilize transcripts.
[0315] Another aspect of the present invention relates to a
genetically modified microorganism that has been transfected with
one or more nucleic acid molecules of the present invention. As
used herein, a genetically modified microorganism can include a
genetically modified bacterium, alga, yeast, filamentous fungus, or
other microbe. Such a genetically modified microorganism has a
genome which is modified (i.e., mutated or changed) from its normal
(i.e., wild-type or naturally occurring) form such that the desired
result is achieved (i.e., increased or modified activity and/or
production of at least one enzyme or a multi-enzyme composition for
the conversion of lignocellulosic material to fermentable sugars).
Genetic modification of a microorganism can be accomplished using
classical strain development and/or molecular genetic techniques.
Such techniques known in the art and are generally disclosed for
microorganisms, for example, in Sambrook et al., 1989, Molecular
Cloning: A Laboratory Manual, Cold Spring Harbor Labs Press or
Molecular Cloning: A Laboratory Manual, third edition (Sambrook and
Russell, 2001), jointly referred to herein as "Sambrook"). The
references of Sambrook, ibid., are incorporated by reference herein
in its entirety. A genetically modified microorganism can include a
microorganism in which nucleic acid molecules have been inserted,
deleted or modified (i.e., mutated; e.g., by insertion, deletion,
substitution, and/or inversion of nucleotides), in such a manner
that such modifications provide the desired effect within the
microorganism.
[0316] In one embodiment, a genetically modified microorganism can
endogenously contain and express an enzyme or a multi-enzyme
composition for the conversion of lignocellulosic material to
fermentable sugars, and the genetic modification can be a genetic
modification of one or more of such endogenous enzymes, whereby the
modification has some effect on the ability of the microorganism to
convert lignocellulosic material to fermentable sugars (e.g.,
increased expression of the protein by introduction of promoters or
other expression control sequences, or modification of the coding
region by homologous recombination to increase the activity of the
encoded protein).
[0317] In another embodiment, a genetically modified microorganism
can endogenously contain and express an enzyme for the conversion
of lignocellulosic material to fermentable sugars, and the genetic
modification can be an introduction of at least one exogenous
nucleic acid sequence (e.g., a recombinant nucleic acid molecule),
wherein the exogenous nucleic acid sequence encodes at least one
additional enzyme useful for the conversion of lignocellulosic
material to fermentable sugars and/or a protein that improves the
efficiency of the enzyme for the conversion of lignocellulosic
material to fermentable sugars. In this aspect of the invention,
the microorganism can also have at least one modification to a gene
or genes comprising its endogenous enzyme(s) for the conversion of
lignocellulosic material to fermentable sugars.
[0318] In yet another embodiment, the genetically modified
microorganism does not necessarily endogenously (naturally) contain
an enzyme for the conversion of lignocellulosic material to
fermentable sugars, but is genetically modified to introduce at
least one recombinant nucleic acid molecule encoding at least one
enzyme or a multiplicity of enzymes for the conversion of
lignocellulosic material to fermentable sugars. Such a
microorganism can be used in a method of the invention, or as a
production microorganism for crude fermentation products, partially
purified recombinant enzymes, and/or purified recombinant enzymes,
any of which can then be used in a method of the present
invention.
[0319] Once the proteins (enzymes) are expressed in a host cell, a
cell extract that contains the activity to test can be generated.
For example, a lysate from the host cell is produced, and the
supernatant containing the activity is harvested and/or the
activity can be isolated from the lysate. In the case of cells that
secrete enzymes into the culture medium, the culture medium
containing them can be harvested, and/or the activity can be
purified from the culture medium. The extracts/activities prepared
in this way can be tested using assays known in the art.
Accordingly, methods to identify multi-enzyme compositions capable
of degrading lignocellulosic biomass are provided.
[0320] Artificial substrates, or complex mixtures of polymeric
carbohydrates and lignin, or actual lignocellulose can be used in
such tests. One assay that may be used to measure the release of
sugars and oligosaccharides from these complex substrates is the
dinitrosalicylic acid assay (DNS). In this assay, the
lignocellulosic material such as DDG is incubated with enzymes(s)
for various times and reducing sugars are measured.
[0321] The present invention is not limited to microorganisms and
also contemplates genetically modified organisms such as algae,
fungi and plants transformed with one or more nucleic acid
molecules of the invention. The plants may be used for production
of the enzymes, and/or as the lignocellulosic material used as a
substrate in the methods of the invention. Methods to generate
recombinant plants are known in the art. For instance, numerous
methods for plant transformation have been developed, including
biological and physical transformation protocols. See, for example,
Miki et al., "Procedures for Introducing Foreign DNA into Plants"
in Methods in Plant Molecular Biology and Biotechnology, Glick, B.
R. and Thompson, J. E. Eds. (CRC Press, Inc., Boca Raton, 1993) pp.
67-88. In addition, vectors and in vitro culture methods for plant
cell or tissue transformation and regeneration of plants are
available. See, for example, Gruber et al., "Vectors for Plant
Transformation" in Methods in Plant Molecular Biology and
Biotechnology, Glick, B. R. and Thompson, J. E. Eds. (CRC Press,
Inc., Boca Raton, 1993) pp. 89-119.
[0322] The most widely utilized method for introducing an
expression vector into plants is based on the natural
transformation system of Agrobacterium. See, for example, Horsch et
al., Science 227:1229 (1985). A. tumefaciens and A. rhizogenes are
plant pathogenic soil bacteria which genetically transform plant
cells. The Ti and Ri plasmids of A. tumefaciens and A. rhizogenes,
respectively, carry genes responsible for genetic transformation of
the plant. See, for example, Kado, C. I., Crit. Rev. Plant. Sci.
10:1 (1991). Descriptions of Agrobacterium vector systems and
methods for Agrobacterium-mediated gene transfer are provided by
numerous references, including Gruber et al., supra, Miki et al.,
supra, Moloney et al., Plant Cell Reports 8:238 (1989), and U.S.
Pat. Nos. 4,940,838 and 5,464,763.
[0323] Another generally applicable method of plant transformation
is microprojectile-mediated transformation wherein DNA is carried
on the surface of microprojectiles. The expression vector is
introduced into plant tissues with a biolistic device that
accelerates the microprojectiles to speeds sufficient to penetrate
plant cell walls and membranes. Sanford et al., Part. Sci. Technol.
5:27 (1987), Sanford, J. C., Trends Biotech. 6:299 (1988), Sanford,
J. C., Physiol. Plant 79:206 (1990), Klein et al., Biotechnology
10:268 (1992).
[0324] Another method for physical delivery of DNA to plants is
sonication of target cells. Zhang et al., Bio/Technology 9:996
(1991). Alternatively, liposome or spheroplast fusion have been
used to introduce expression vectors into plants. Deshayes et al.,
EMBO J., 4:2731 (1985), Christou et al., Proc Natl. Acad. Sci. USA
84:3962 (1987). Direct uptake of DNA into protoplasts using
CaCl.sub.2 precipitation, polyvinyl alcohol or poly-L-ornithine
have also been reported. Hain et al., Mol. Gen. Genet. 199:161
(1985) and Draper et al., Plant Cell Physiol. 23:451 (1982).
Electroporation of protoplasts and whole cells and tissues have
also been described. Donn et al., In Abstracts of VII.sup.th
International Congress on Plant Cell and Tissue Culture IAPTC,
A2-38, p. 53 (1990); D'Halluin et al., Plant Cell 4:1495-1505
(1992) and Spencer et al., Plant Mol. Biol. 24:51-61 (1994).
[0325] Some embodiments of the present invention include
genetically modified organisms comprising at least one nucleic acid
molecule encoding at least one enzyme of the present invention, in
which the activity of the enzyme is downregulated. The
downregulation may be achieved, for example, by introduction of
inhibitors (chemical or biological) of the enzyme activity, by
manipulating the efficiency with which those nucleic acid molecules
are transcribed, the efficiency with which the resultant
transcripts are translated, and the efficiency of
post-translational modifications, or by "knocking out" the
endogenous copy of the gene. A "knock out" of a gene refers to a
molecular biological technique by which the gene in the organism is
made inoperative, so that the expression of the gene is
substantially reduced or eliminated. Alternatively, in some
embodiments the activity of the enzyme may be upregulated. The
present invention also contemplates downregulating activity of one
or more enzymes while simultaneously upregulating activity of one
or more enzymes to achieve the desired outcome.
[0326] Another embodiment of the present invention relates to an
isolated binding agent capable of selectively binding to a protein
of the present invention. Suitable binding agents may be selected
from an antibody, an antigen binding fragment, or a binding
partner. The binding agent selectively binds to an amino acid
sequence selected from SEQ ID NO: 2, SEQ ID NO: 5, SEQ ID NO: 8,
SEQ ID NO: 11, SEQ ID NO: 14, SEQ ID NO: 17, SEQ ID NO: 20, SEQ ID
NO: 23, SEQ ID NO: 26, SEQ ID NO: 29, SEQ ID NO: 32, SEQ ID NO: 35,
SEQ ID NO: 38, SEQ ID NO: 41, SEQ ID NO: 44, SEQ ID NO: 47, SEQ ID
NO: 50, SEQ ID NO: 53, SEQ ID NO: 56, SEQ ID NO: 59, SEQ ID NO: 62,
SEQ ID NO: 65, SEQ ID NO: 68, SEQ ID NO: 71, SEQ ID NO: 74, SEQ ID
NO: 77, SEQ ID NO: 80, SEQ ID NO: 83, SEQ ID NO: 86, SEQ ID NO: 89,
SEQ ID NO: 92, SEQ ID NO: 95, SEQ ID NO: 98, SEQ ID NO: 101, SEQ ID
NO: 104, SEQ ID NO: 107, SEQ ID NO: 110, SEQ ID NO: 113, SEQ ID NO:
116, SEQ ID NO: 119, SEQ ID NO: 122, SEQ ID NO: 125, SEQ ID NO:
128, SEQ ID NO: 131, SEQ ID NO: 134, SEQ ID NO: 137, SEQ ID NO:
140, SEQ ID NO: 143, SEQ ID NO: 146, SEQ ID NO: 149, SEQ ID NO:
152, SEQ ID NO: 155, SEQ ID NO: 158, SEQ ID NO: 161, SEQ ID NO:
164, SEQ ID NO: 167, SEQ ID NO: 170, SEQ ID NO: 173, SEQ ID NO:
176, SEQ ID NO: 179, SEQ ID NO: 182, SEQ ID NO: 185, SEQ ID NO:
188, SEQ ID NO: 191, SEQ ID NO: 194, SEQ ID NO: 197, SEQ ID NO:
200, or SEQ ID NO: 203, SEQ ID NO: 206, SEQ ID NO: 209, SEQ ID NO:
212, SEQ ID NO: 215, SEQ ID NO: 218, SEQ ID NO: 221, SEQ ID NO:
224, SEQ ID NO: 227, SEQ ID NO: 230, or SEQ ID NO: 233 including to
any fragment of any of the above sequences comprising at least one
antibody binding epitope.
[0327] According to the present invention, the phrase "selectively
binds to" refers to the ability of an antibody, antigen binding
fragment or binding partner of the present invention to
preferentially bind to specified proteins. More specifically, the
phrase "selectively binds" refers to the specific binding of one
protein to another (e.g., an antibody, fragment thereof, or binding
partner to an antigen), wherein the level of binding, as measured
by any standard assay (e.g., an immunoassay), is statistically
significantly higher than the background control for the assay. For
example, when performing an immunoassay, controls typically include
a reaction well/tube that contain antibody or antigen binding
fragment alone (i.e., in the absence of antigen), wherein an amount
of reactivity (e.g., non-specific binding to the well) by the
antibody or antigen binding fragment thereof in the absence of the
antigen is considered to be background. Binding can be measured
using a variety of methods standard in the art including enzyme
immunoassays (e.g., ELISA), immunoblot assays, etc.).
[0328] Antibodies are characterized in that they comprise
immunoglobulin domains and as such, they are members of the
immunoglobulin superfamily of proteins. An antibody of the
invention includes polyclonal and monoclonal antibodies, divalent
and monovalent antibodies, bi- or multi-specific antibodies, serum
containing such antibodies, antibodies that have been purified to
varying degrees, and any functional equivalents of whole
antibodies. Isolated antibodies of the present invention can
include serum containing such antibodies, or antibodies that have
been purified to varying degrees. Whole antibodies of the present
invention can be polyclonal or monoclonal. Alternatively,
functional equivalents of whole antibodies, such as antigen binding
fragments in which one or more antibody domains are truncated or
absent (e.g., Fv, Fab, Fab', or F(ab).sub.2 fragments), as well as
genetically-engineered antibodies or antigen binding fragments
thereof, including single chain antibodies or antibodies that can
bind to more than one epitope (e.g., bi-specific antibodies), or
antibodies that can bind to one or more different antigens (e.g.,
bi- or multi-specific antibodies), may also be employed in the
invention. Methods for the generation and production of antibodies
are well known in the art.
[0329] Monoclonal antibodies may be produced according to the
methodology of Kohler and Milstein (Nature 256:495-497, 1975).
Non-antibody polypeptides, sometimes referred to as binding
partners, are designed to bind specifically to a protein of the
invention. Examples of the design of such polypeptides, which
possess a prescribed ligand specificity are given in Beste et al.
(Proc. Natl. Acad. Sci. 96:1898-1903, 1999), incorporated herein by
reference in its entirety. In one embodiment, a binding agent of
the invention is immobilized on a substrate such as: artificial
membranes, organic supports, biopolymer supports and inorganic
supports such as for use in a screening assay.
[0330] Proteins of the present invention, at least one protein of
the present invention, compositions comprising such protein(s) of
the present invention, and multi-enzyme compositions (examples of
which are described above) may be used in any method where it is
desirable to hydrolyze glycosidic linkages in lignocellulosic
material, or any other method wherein enzymes of the same or
similar function are useful.
[0331] In one embodiment, the present invention includes the use of
at least one protein of the present invention, compositions
comprising at least one protein of the present invention, or
multi-enzyme compositions in methods for hydrolyzing lignocellulose
and the generation of fermentable sugars therefrom. In one
embodiment, the method comprises contacting the lignocellulosic
material with an effective amount of one or more proteins of the
present invention, composition comprising at least one protein of
the present invention, or a multi-enzyme composition, whereby at
least one fermentable sugar is produced (liberated). The
lignocellulosic material may be partially or completely degraded to
fermentable sugars. Economical levels of degradation at
commercially viable costs are contemplated.
[0332] Typically, the amount of enzyme or enzyme composition
contacted with the lignocellulose will depend upon the amount of
glucan present in the lignocellulose. In some embodiments, the
amount of enzyme or enzyme composition contacted with the
lignocellulose may be from about 0.1 to about 200 mg enzyme or
enzyme composition per gram of glucan; in other embodiments, from
about 3 to about 20 mg enzyme or enzyme composition per gram of
glucan. The invention encompasses the use of any suitable or
sufficient amount of enzyme or enzyme composition between about 0.1
mg and about 200 mg enzyme per gram glucan, in increments of 0.05
mg (i.e., 0.1 mg, 0.15 mg, 0.2 mg . . . 199.9 mg, 199.95 mg, 200
mg).
[0333] In a further embodiment, the invention provides a method for
degrading DDG, preferably, but not limited to, DDG derived from
corn, to sugars. The method comprises contacting the DDG with a
protein of the present invention, a composition comprising at least
one protein of the present invention, or a multi-enzyme
composition. In certain embodiments, at least 10% of fermentable
sugars are liberated. In other embodiment, the at least 15% of the
sugars are liberated, or at least 20% of the sugars are liberated,
or at least 23% of the sugars are liberated, or at least 24% of the
sugars are liberated, or at least 25% of the sugars are liberated,
or at least 26% of the sugars are liberated, or at least 27% of the
sugars are liberated, or at least 28% of the sugars are
liberated.
[0334] In another embodiment, the invention provides a method for
producing fermentable sugars comprising cultivating a genetically
modified microorganism of the present invention in a nutrient
medium comprising a lignocellulosic material, whereby fermentable
sugars are produced.
[0335] Also provided are methods that comprise further contacting
the lignocellulosic material with at least one accessory enzyme.
Accessory enzymes have been described elsewhere herein. The
accessory enzyme or enzymes may be added at the same time, prior
to, or following the addition of a protein of the present
invention, a composition comprising at least one protein of the
present invention, or a multi-enzyme composition, or can be
expressed (endogenously or overexpressed) in a genetically modified
microorganism used in a method of the invention. When added
simultaneously, the protein of the present invention, a composition
comprising at least one protein of the present invention, or a
multi-enzyme composition will be compatible with the accessory
enzymes selected. When the enzymes are added following the
treatment with the protein of the present invention, a composition
comprising at least one protein of the present invention, or a
multi-enzyme composition, the conditions (such as temperature and
pH) may be altered to those optimal for the accessory enzyme
before, during, or after addition of the accessory enzyme. Multiple
rounds enzyme addition are also encompassed. The accessory enzyme
may also be present in the lignocellulosic material itself as a
result of genetically modifying the plant. The nutrient medium used
in a fermentation can also comprise one or more accessory
enzymes.
[0336] In some embodiments, the method comprises a pretreatment
process. In general, a pretreatment process will result in
components of the lignocellulose being more accessible for
downstream applications or so that it is more digestible by enzymes
following treatment in the absence of hydrolysis. The pretreatment
can be a chemical, physical or biological pretreatment. The
lignocellulose may have been previously treated to release some or
all of the sugars, as in the case of DDG. Physical treatments, such
as grinding, boiling, freezing, milling, vacuum infiltration, and
the like may also be used with the methods of the invention. In one
embodiment, the heat treatment comprises heating the
lignocellulosic material to 121.degree. C. for 15 minutes. A
physical treatment such as milling can allow a higher concentration
of lignocellulose to be used in the methods of the invention. A
higher concentration refers to about 20%, up to about 25%, up to
about 30%, up to about 35%, up to about 40%, up to about 45%, or up
to about 50% lignocellulose. The lignocellulose may also be
contacted with a metal ion, ultraviolet light, ozone, and the like.
Additional pretreatment processes are known to those skilled in the
art, and can include, for example, organosolv treatment, steam
explosion treatment, lime impregnation with steam explosion
treatment, hydrogen peroxide treatment, hydrogen peroxide/ozone
(peroxone) treatment, acid treatment, dilute acid treatment, and
base treatment, including ammonia fiber explosion (AFEX)
technology. Details on pretreatment technologies and processes can
be found in Wyman et al., Bioresource Tech. 96:1959 (2005); Wyman
et al., Bioresource Tech. 96:2026 (2005); Hsu, "Pretreatment of
biomass" In Handbook on Bioethanol: Production and Utilization,
Wyman, Taylor and Francis Eds., p. 179-212 (1996); and Mosier et
al., Bioresource Tech. 96:673 (2005).
[0337] In an additional embodiment, the method comprises
detoxifying the lignocellulosic material. Detoxification may be
desirable in the event that inhibitors are present in the
lignocellulosic material. Such inhibitors can be generated by a
pretreatment process, deriving from sugar degradation or are direct
released from the lignocellulose polymer. Detoxifying can include
the reduction of their formation by adjusting sugar extraction
conditions; the use of inhibitor-tolerant or inhibitor-degrading
strains of microorganisms. Detoxifying can also be accomplished by
the addition of ion exchange resins, active charcoal, enzymatic
detoxification using, e.g., laccase, and the like. In some
embodiments, the proteins, compositions or products of the present
invention further comprises detoxifying agents.
[0338] In some embodiments, the methods may be performed one or
more times in whole or in part. That is, one may perform one or
more pretreatments, followed by one or more reactions with a
protein of the present invention, composition or product of the
present invention and/or accessory enzyme. The enzymes may be added
in a single dose, or may be added in a series of small doses.
Further, the entire process may be repeated one or more times as
necessary. Therefore, one or more additional treatments with heat
and enzymes are contemplated.
[0339] The methods described above result in the production of
fermentable sugars. During, or subsequent to the methods described,
the fermentable sugars may be recovered. In the case of a
cultivation of microorganisms, the sugars can be recovered through
a continuous, batch or fed-batch method. The sugars recovered can
be concentrated or purified. Recovery may occur by any method known
in the art, including, but not limited to, washing, gravity flow,
pressure, chromatography, extraction, crystallization (e.g.,
evaporative crystallization), membrane separation, reverse osmosis,
distillation, and filtration. The sugars can be subjected further
processing; e.g., they can also be sterilized, for example, by
filtration.
[0340] In a related embodiment, the invention provides means for
improving quality of lignocellulosic material, including DDG for
animal nutrition. In one embodiment, the treated lignocellulosic
material (e.g., a lignocellulosic material which has been
saccharified) is recovered (e.g., has the soluble sugars removed).
The recovered material can be used as an animal feed additive. It
is believed that the recovered material will have beneficial
properties for animal nutrition, possibly due to a higher protein
content. In some embodiments, the amount of enzyme or enzyme
composition contacted with the lignocellulosic material may be from
about 0.0001% to about 1.0% of the weight of the lignocellulosic
material; in other embodiments, from about 0.005% to about 0.1% of
the weight of the lignocellulosic material. The invention includes
the use of any amount of enzyme or enzyme composition between about
0.0001% and about 1.0%, in increments of 0.0001 (i.e., 0.0001,
0.0002, 0.0003 . . . etc.).
[0341] In an additional embodiment, the invention provides a method
for producing an organic substance, comprising saccharifying a
lignocellulosic material with an effective amount of a protein of
the present invention or a composition comprising at least one
protein of the present invention, fermenting the saccharified
lignocellulosic material obtained with one or more fermenting
microorganisms, and recovering the organic substance from the
fermentation. Sugars released from biomass can be converted to
useful fermentation products including but not limited to amino
acids, vitamins, pharmaceuticals, animal feed supplements,
specialty chemicals, chemical feedstocks, plastics, solvents,
fuels, or other organic polymers, lactic acid, and ethanol,
including fuel ethanol. Specific products that may be produced by
the methods of the invention include, but not limited to, biofuels
(including ethanol); lactic acid; plastics; specialty chemicals;
organic acids, including citric acid, succinic acid and maleic
acid; solvents; animal feed supplements; pharmaceuticals; vitamins;
amino acids, such as lysine, methionine, tryptophan, threonine, and
aspartic acid; industrial enzymes, such as proteases, cellulases,
amylases, glucanases, lactases, lipases, lyases, oxidoreductases,
and transferases; and chemical feedstocks. The methods of the
invention are also useful to generate feedstocks for fermentation
by fermenting microorganisms. In one embodiment, the method further
comprises the addition of at least one fermenting organism. As used
herein, "fermenting organism" refers to an organism capable of
fermentation, such as bacteria and fungi, including yeast. Such
feedstocks have additional nutritive value above the nutritive
value provided by the liberated sugars.
[0342] In some embodiments, the present invention provides methods
for improving the nutritional quality of food (or animal feed)
comprising adding to the food (or the animal feed) at least one
protein of the present invention. In some embodiments, the present
invention provides methods for improving the nutritional quality of
the food (or animal feed) comprising pretreating the food (or the
animal feed) with at least one isolated protein of the present
invention. For instance, use of the enzymes xylanases and
arabinofuranosidases in bread making has been known to improve the
nutritional quality of the dough by degrading the arabinoxylans in
the dough. Improving the nutritional quality can mean making the
food (or the animal feed) more digestible and/or less allergenic,
and encompasses changes in the caloric value, taste and/or texture
of the food. In some embodiments, the proteins of the present
invention may be used as part of nutritional supplements. In some
embodiments, the proteins of the present invention may be used as
part of digestive aids, and may help in providing relief from
digestive disorders such as acid reflux and celiac disease.
[0343] Proteins of the present invention and compositions
comprising at least one protein of the present invention are also
useful in a variety of other applications involving the hydrolysis
of glycosidic linkages in lignocellulosic material, such as stone
washing, color brightening, depilling and fabric softening, as well
as other applications well known in the art. Proteins of the
present invention and compositions comprising at least one protein
of the present invention are also readily amenable to use as
additives in detergent and other media used for such applications.
These and other methods of use will readily suggest themselves to
those of skill in the art based on the invention described
herein.
[0344] In one embodiment of this invention, proteins and
compositions of the present invention can be used in stone washing
procedures for fabrics or other textiles. In some embodiments, the
proteins and compositions can be used in stone washing procedures
for denim jeans. By way of example, the method for stone washing
the fabric comprises contacting the fabric with a protein or
composition of the present invention. In an additional embodiment,
the protein or composition of the present invention is included in
a detergent composition, as described below. A preferred pH range
of stone wash applications is between about 5.5 to 7.5, most
preferably at about pH 6 to about 7. One of skill in the art will
know how to regulate the amount or concentration of the protein or
composition produced by this invention based on such factors as the
activity of the enzyme and the wash conditions, including but not
limited to temperature and pH. Examples of these uses can be found
in U.S. Patent Application Publication No. 2003/0157595, the
contents of which are hereby incorporated by reference.
[0345] In yet another embodiment of this invention, the cellulase
compositions of this invention can be used to reduce or eliminate
the harshness associated with a fabric or textile by contacting the
fabric or textile with a protein or composition of the present
invention. In some embodiments, the fabric or textile may be made
from cellulose or cotton. By way of example, a preferred range for
reducing or eliminating the harshness associated with a fabric or
textile is between about pH 8 to about 12, or between about pH 10
to about 11.
[0346] The proteins or compositions of the subject invention can be
used in detergent compositions. In one embodiment, the detergent
composition may comprise at least one protein or composition of the
present invention and one or more surfactants. The detergent
compositions may also include any additional detergent ingredient
known in the art. Detergent ingredients contemplated for use with
the detergent compositions of the subject invention include, but
are not limited to, detergents, buffers, surfactants, bleaching
agents, softeners, solvents, solid forming agents, abrasives,
alkalis, inorganic electrolytes, cellulase activators,
antioxidants, builders, silicates, preservatives, and stabilizers.
The detergent compositions of this invention preferably employ a
surface active agent, i.e., surfactant, including anionic,
non-ionic, and ampholytic surfactants well known for their use in
detergent compositions. In addition to the at least one protein or
composition of the present invention and the surface active agent,
the detergent compositions of this invention can additionally
contain one or more of the following components: the enzymes
amylases, cellulases, proteinase, lipases, oxido-reductases,
peroxidases and other enzymes; cationic surfactants and long-chain
fatty acids; builders; antiredeposition agents; bleaching agents;
bluing agents and fluorescent dyes; caking inhibitors; masking
agents for factors inhibiting the cellulase activity; cellulase
activators; antioxidants; and solubilizers. In addition, perfumes,
preservatives, dyes, and the like can be used, if desired, with the
detergent compositions of this invention. Examples of detergent
compositions employing cellulases are exemplified in U.S. Pat. Nos.
4,435,307; 4,443,355; 4,661,289; 4,479,881; 5,120,463, each of
which is incorporated herein by reference in its entirety for all
purposes.
[0347] When a detergent base used in the present invention is in
the form of a powder, it may be one which is prepared by any known
preparation method including a spray-drying method and/or a
granulation method. The granulation method are the most preferred
because of the non-dusting nature of granules compared to spray dry
products. The detergent base obtained by the spray-drying method is
hollow granules which are obtained by spraying an aqueous slurry of
heat-resistant ingredients, such as surface active agents and
builders, into a hot space. The granules have a size of from about
50 to about 2000 micrometers. After the spray-drying, perfumes,
enzymes, bleaching agents, and/or inorganic alkaline builders may
be added. With a highly dense, granular detergent base obtained by
such as the spray-drying-granulation method, various ingredients
may also be added after the preparation of the base. When the
detergent base is a liquid, it may be either a homogenous solution
or an inhomogeneous solution.
[0348] Other textile applications in which proteins and
compositions of the present invention may be used include, but are
not limited to, garment dyeing applications such as enzymatic
mercerizing of viscose, biopolishing applications, enzymatic
surface polishing; biowash (washing or washing down treatment of
textile materials), enzymatic microfibrillation, enzymatic
"cottonization" of linen, ramie and hemp; and treatment of Lyocel
or Newcell (i.e., "TENCEL" from Courtauld's), Cupro and other
cellulosic fibers or garments, dye removal from dyed cellulosic
substrates such as dyed cotton (Leisola & Linko--(1976)
Analytical Biochemistry, v. 70, p. 592. Determination Of The
Solubilizing Activity Of A Cellulase Complex With Dyed Substrates;
Blum & Stahl--Enzymic Degradation Of Cellulose Fibers; Reports
of the Shizuoka Prefectural Hamamatsu Textile Industrial Research
Institute No. 24 (1985)), as a bleaching agent to make new indigo
dyed denim look old (Fujikawa--Japanese Patent Application Kokai
No. 50-132269), to enhance the bleaching action of bleaching agents
(Suzuki--Great Britain Patent No. 2 094 826), and in a process for
compositions for enzymatic desizing and bleaching of textiles
(Windbichtler et al., U.S. Pat. No. 2,974,001. Another example of
enzymatic desizing using cellulases is provided in Bhatawadekar
(May 1983) Journal of the Textile Association, pages 83-86.
[0349] The amount of enzyme or enzyme composition contacted with a
textile may vary with the particular application. Typically, for
biofinishing and denim washing applications, from about 0.02 wt. %
to about 5 wt. % of an enzyme or enzyme composition may be
contacted with the textile. In some embodiments, from about 0.5 wt.
% to about 2 wt. % of an enzyme or enzyme composition may be
contacted with the textile. For bio scouring, from about 0.1 to
about 10, or from about 0.1 to about 1.0 grams of an enzyme or
enzyme composition per kilogram of textile may be used, including
any amount between about 0.1 grams and about 10 grams, in
increments of 0.1 grams.
[0350] In other embodiments, the proteins or compositions of the
present invention can be used in the saccharification of
lignocellulose biomass from agriculture, forest products, municipal
solid waste, and other sources, for biobleaching of wood pulp, and
for de-inking of recycled print paper all by methods known to one
skilled in the art.
[0351] The amount of enzyme or enzyme composition used for pulp and
paper modification (e.g., biobleaching of wood pulp, de-inking of
paper, or biorefining of pulp for paper making) typically varies
depending upon the stock that is used, the pH and temperature of
the system, and the retention time. In certain embodiments, the
amount of enzyme or enzyme composition contacted with the paper or
pulp may be from about 0.01 to about 50 U; from about 0.1 to about
15 U; or from about 0.1 to about 5 U of enzyme or enzyme
composition per dry gram of fiber, including any amount between
about 0.01 and about 50 U, in 0.01 U increments. In other
embodiments, the amount of enzyme or enzyme composition contacted
with the paper or pulp may be from about 1 to about 2000 grams or
from about 100 to about 500 grams enzyme or enzyme composition per
dry ton of pulp, including any amount between about 1 and about
2000 grams, in 1 gram increments.
[0352] Proteins or compositions of the present invention can added
to wastewater to reduce the amount of solids such as sludge or to
increase total biochemical oxygen demand (BOD) and chemical oxygen
demand (COD) removal. For example, proteins or compositions of the
present invention can be used to transform particulate COD to
soluble COD in wastewater produced from grain/fruit/cellulose
industrial processes or to increase the BOD/COD ratio by increasing
waste biodegradability (soluble lower molecular weight polymers in
cellulosic/hemicellulosic wastes are typically more readily
biodegradable than non-soluble material). In biological wastewater
treatment systems, proteins or compositions of the present
invention can also be used to increase waste digestion by aerobic
and/or anaerobic bacteria.
[0353] Chitosanases of the present invention (e.g., SEQ ID NO: 188)
can hydrolyze the .beta.-1,4-linkages between D-glucosamine
residues in acetylated chitosan (i.e., deacetylated chitin) and
thus may be used to degrade chitin- or chitosan-containing
materials. Examples of chitin-containing materials include fungal
cell walls, insect exoskeletons, the eggs of parasitic worms, and
crustacean shells.
[0354] Chitosanases may be used to inhibit or reduce fungal growth,
including the treatment of fungal infections such as those caused
by nail fungi. For example, chitosanases of the present invention
may be applied to any fungus or area susceptible to fungal growth.
Chitosanases may also be used to coat or treat seeds and flower
bulbs to prevent the growth of fungi. Further, chitosanases may be
added to fungal cultures to lower culture viscosity by increasing
cell wall degradation. Chitosanases may also by used as lysing
enzymes for the generation of protoplasts from fungi (see, e.g.,
Yano et al., Biosci Biotechnol Biochem. 70:1754 (2006).
[0355] Chitosanases or compositions containing chitosanases may be
used as a biological control agent such as an insecticide (see,
e.g., Kramer et al., Insect Biochem Mol. Biol. 27:887 (1997).
Chitin-degrading enzymes such as chitinases and chitosanases have
been shown to be effective for controlling white-fly larvae in
laboratory tests. Thus, chitosanases may be applied to crops,
plants and the like to control insect infestations.
[0356] Chitin has also been suggested to play a role in inducing
allergic inflammation and asthma (see Reese et al., Nature 447:92
(2007)). Accordingly, chitosanases of the present invention may be
administered to a subject to reduce allergic inflammatory responses
induced by chitin or to reduce the symptoms of asthma.
[0357] Exemplary methods according to the invention are presented
below. Examples of the methods described above may also be found in
the following references, all of which are incorporated herein in
their entireties: Trichoderma & Gliocladium, Volume 2, Enzymes,
biological control and commercial applications, Editors: Gary E.
Harman, Christian P. Kubicek, Taylor & Francis Ltd. 1998, 393
(in particular, chapters 14, 15 and 16); Helmut Uhlig, Industrial
enzymes and their applications, Translated and updated by Elfriede
M. Linsmaier-Bednar, John Wiley & Sons, Inc 1998, p. 454 (in
particular, chapters 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.9, 5.10,
5.11, and 5.13). For saccharification applications: Hahn-Hagerdal,
B., Galbe, M., Gorwa-Grauslund, M. F. Liden, Zacchi, G.
Bio-ethanol--the fuel of tomorrow from the residues of today,
Trends in Biotechnology, 2006, 24 (12), 549-556; Mielenz, J. R.
Ethanol production from biomass: technology and commercialization
status, Current Opinion in Microbiology, 2001, 4, 324-329; Himmel,
M. E., Ruth, M. F., Wyman, C. E., Cellulase for commodity products
from cellulosic biomass, Current Opinion in Biotechnology, 1999,
10, 358-364; Sheehan, J., Himmel, M. Enzymes, energy, and the
environment: a strategic perspective on the U.S. Department of
Energy's Research and Development Activities for Bioethanol,
Biotechnology Progress. 1999, 15, 817-827. For textile processing
applications: Galante, Y. M., Formantici, C., Enzyme applications
in detergency and in manufacturing industries, Current Organic
Chemistry, 2003, 7, 1399-1422. For pulp and paper applications:
Bajpai, P., Bajpai, P. K Deinking with enzymes: a review. TAPPI
Journal, 1998, 81(12), 111-117; Viikari, L., Pere, J., Suurnakki,
A., Oksanen, T., Buchert, J. Use of cellulases in pulp and paper
applications. In: "Carbohydrates from Trichoderma reesei and other
microorganisms. Structure, Biochemistry, Genetics and
Applications." Editors: Mark Claessens, Wim Nerinckx, and Kathleen
Piens, The Royal Society of Chemistry 1998, 245-254. For food and
beverage applications: Roller, S., Dea, I. C. M. Biotechnology in
the production and modification of biopolymers for foods, Critical
Reviews in Biotechnology, 1992, 12(3), 261-277.
[0358] Each publication or reference cited herein is incorporated
herein by reference in its entirety for all purposes.
[0359] The following examples are provided for the purpose of
illustration and are not intended to limit the scope of the present
invention.
EXAMPLES
[0360] The foregoing discussion may be better understood in
connection with the following representative examples that are
presented for purposes of illustrating the principle methods and
compositions of the invention, and not by way of limitation.
Various other examples will be apparent to the person skilled in
the art after reading the present disclosure without departing from
the spirit and scope of the invention. It is intended that all such
other examples be included within the scope of the appended
claims.
Example 1
[0361] The following example illustrates the assay used to measure
the .alpha.-arabinofuranosidase enzymatic activity.
[0362] This assay measured the release of p-nitrophenol by the
action of .alpha.-arabinofuranosidase on p-nitrophenyl
.alpha.-L-arabinofuranoside (PNPA). One .alpha.-arabinofuranosidase
unit of activity is the amount of enzyme that liberates 1 micromole
of p-nitrophenol in one minute at 37.degree. C. and pH 5.0.
[0363] Acetate buffer (0.1 M, pH 5.0) was prepared as follows: 8.2
g of anhydrous sodium acetate or 13.6 g of sodium acetate*3H.sub.2O
was dissolved in distilled water so that the final volume of the
solution was 1000 ml (Solution A). In a separate flask, 6.0 g (5.72
ml) of glacial acetic acid was mixed with distilled water to make
the total volume of 1000 ml (Solution B). The final 0.1 M acetate
buffer, pH 5.0, was prepared by mixing Solution A with Solution B
until the pH of the resulting solution was equal to 5.0.
[0364] PNPA (Fluka, Switzerland, cat. #73616) was used as the assay
substrate. 8.25 mg of PNPA was dissolved in 5 mL of distilled water
and 5 mL 0.1 M acetate buffer using a magnetic stirrer to obtain a
1 mM stock solution. The solution was stable for 2 days with
storage at 4.degree. C.
[0365] The stop reagent (0.25 M sodium carbonate solution) was
prepared as follows: 26.5 g of anhydrous sodium carbonate was
dissolved in 800 ml of distilled water, and the solution volume was
adjusted to 1000 ml. This reagent was used to terminate the
enzymatic reaction.
[0366] For the enzyme sample, 0.10 mL of 1 mM PNPA stock solution
was mixed with 0.01 mL of the enzyme sample and incubated at
37.degree. C. for 90 minutes. After 90 minutes of incubation, 0.1
mL of 0.25 M sodium carbonate solution was added and the absorbance
at 405 nm (A.sub.405) was then measured in microtiter plates as
A.sub.S.
[0367] For the substrate blank, 0.10 mL of 1 mM PNPA stock solution
was mixed with 0.01 mL of 0.05 M acetate buffer, pH 5.0. 0.1 mL of
0.25 M sodium carbonate solution was then added and the absorbance
at 405 nm (A.sub.405) was measured in microtiter plates as
A.sub.SB.
[0368] Activity was calculated as follows:
Activity (IU/ml)=(.DELTA.A.sub.405*DF*21*1.33)/(13.700*90)
[0369] where .DELTA.A.sub.405=A.sub.S-A.sub.SB, DF is the enzyme
dilution factor, 21 is the dilution of 10 .mu.l enzyme solution in
210 .mu.l reaction volume, 1.33 is the conversion factor of
microtiter plates to cuvettes, 13.700 is the extinction coefficient
13700 M.sup.-1 cm.sup.-1 of p-nitrophenol released corrected for
mol/L to .mu.mol/mL, and 90 minutes is the reaction time.
[0370] Using the above assay, the .alpha.-arabinofuranosidase
activity of Abn4 was found to be 0.005 IU/mL
(.DELTA.A.sub.405=0.200, DF=1) and the .alpha.-arabinofuranosidase
activity Abn5 was found to be 0.008 IU/ml (.DELTA.A.sub.405=0.370,
DF=1). Both enzymes were produced by microtiterplate cultures.
[0371] The assay above was also performed with a 2 mM PNPA stock
solution (16.5 mg of PNPA dissolved in 5 mL of distilled water and
5 mL 0.1 M acetate buffer) and a 30 minute reaction time (making
the necessary substitution of 30 minutes reaction time in the
activity calculation equation above). Using this assay, the
.alpha.-arabinofuranosidase activity of Abn7 was found to be 0.028
IU/mL (.DELTA.A.sub.405=0.410, DF=1). The enzyme was produced by
microtiterplate cultures.
Example 2
[0372] The following example illustrates the assay used to measure
the ability of enzymes of the present invention to remove the
.alpha.-L-arabinofuranosyl residues from double substituted xylose
residues.
[0373] For the complete degradation of arabinoxylans to arabinose
and xylose, several enzyme activities are needed, including
endo-xylanases and arabinofuranosidases. The arabinoxylan molecule
from wheat is highly substituted with arabinosyl residues. These
can be substituted either to the C.sub.2 or the C.sub.3 position of
the xylosyl residue (single substitution), or both to the C.sub.2
and C.sub.3 position of the xylose (double substitution). An
arabinofuranosidase from Bifidobacterium adolescentis (AXHd.sub.3)
has previously been isolated which was able to liberate the
arabinosyl residue substituted to the C.sub.3 position of a double
substituted xylose (Van Laere et al. 1997, Van den Broek et al.
2005). Most of the known arabinofuranosidases are only active
towards single arabinosyl substituted xyloses.
[0374] Single and double substituted oligosaccharides were prepared
by incubating wheat arabinoxylan (WAX; 10 mg/mL; Megazyme, Bray,
Ireland) in 50 mM acetate buffer pH 5 with 0.3 mg Pentopan Mono
(monocomponent endo-1,4-.beta.-xylanase, an enzyme from Thermomyces
lanuginosus produced in Aspergillus oryzae; Sigma, St. Louis, USA)
for 16 hours at 30.degree. C. The reaction was stopped by heating
the samples at 100.degree. C. for 10 minutes. The samples were
centrifuged for 5 minutes at 3100.times.g. The supernatant was used
for further experiments. Degradation of the arabinoxylan was
followed by analysis of the formed reducing sugars and High
Performance Anion Exchange Chromatography (HPAEC).
[0375] Double substituted arabinoxylan oligosaccharides were
prepared by incubation of 800 .mu.l of the supernatant described
above with 0.18 mg of the arabinofuranosidase Abf1 (Abf1 is
arabinofuranosidase from C. lucknowense with activity towards
single arabinose substituted xylose residues and is disclosed in
U.S. application Ser. No. 11/833,133, filed Aug. 2, 2007, the
contents of which are incorporated herein by reference) in 50 mM
acetate buffer pH 5 for 20 hours at 30.degree. C. The reaction was
stopped by heating the samples at 100.degree. C. for 10 minutes.
The samples were centrifuged for 5 minutes at 10,000.times.g, and
the supernatant was used for further experiments. Degradation of
the arabinoxylan was followed by analysis of the formed reducing
sugars and HPAEC.
[0376] The activity towards
p-nitrophenyl-.alpha.-L-arabinofuranoside (pNP-ara) or
p-nitrophenyl-.beta.-D-xylopyranoside (pNP-xyl) was measured at
37.degree. C. after 10 minutes of incubation. The reaction mixture
(110 .mu.l) consisted of 1.5 mg/ml pNP-ara or pNP-xyl solution, 50
.mu.g Abn7 (total protein) in 50 mM sodium acetate buffer pH 5.0.
The reaction was stopped by adding 100 .mu.t of 01.25 M NaCO.sub.3
pH 8.5. The color formation was then measured at 405 nm. One unit
of activity was defined as 1 .mu.mol of arabinose liberated per min
under the specified conditions. The molar extinction coefficient
under these assay conditions was 13,700 I/M*cm.
[0377] Abn7 (25 .mu.g total protein) was incubated with single and
double substituted arabinoxylan oligosaccharides (100 .mu.L
supernatant of Pentopan Mono treated WAX) in 50 mM acetate buffer
at 30.degree. C. during 20 hours. The reaction was stopped by
heating the samples at 100.degree. C. for 10 minutes. The samples
were centrifuged for 5 minutes at 10,000.times.g. Degradation of
the arabinoxylan was followed by analysis of the formed reducing
sugars and HPAEC.
[0378] Abn7 (25 .mu.g total protein) or AXHd.sub.3 from B.
adolescentis (10 .mu.l, 0.02 U; Megazyme, Bray, Ireland) was
incubated with double substituted arabinoxylan oligosaccharides
(125 .mu.l supernatant of Pentopan Mono and Abf1 treated WAX) in 50
mM acetate buffer at 35.degree. C. during 24 hours. The reaction
was stopped by heating the samples at 100.degree. C. for 10
minutes. The samples were centrifuged for 5 minutes at
10,000.times.g. Degradation of the arabinoxylan was followed by
analysis of the formed reducing sugars and HPAEC.
[0379] The amount of reducing sugars was measured with help of the
DNS (3,5-dinitrosalicylic acid) assay. 0.5 mL of DNS reagent
(3,5-dinitrosalicylic acid and sodium potassium tartrate dissolved
in dilute sodium hydroxide) is added to the sample (50 .mu.l),
containing 0-5 mg/ml reducing sugar. The reaction mixture was
heated at 100.degree. C. for 5 minutes and rapidly cooled in ice to
room temperature. The absorbance at 570 nm was measured. Glucose
was used as a standard.
[0380] The analysis of the samples via HPAEC was performed using a
Dionex HPLC system equipped with a Dionex CarboPac PA-1 (2 mm
ID.times.250 mm) column in combination with a CarboPac PA guard
column (1 mm ID.times.25 mm) and a Dionex EDet1 PAD-detector
(Dionex Co., Sunnyvale). A flow rate of 0.3 mil/min was used with
the following gradient of sodium acetate in 0.1 M NaOH: 0-5
minutes, 0-100 mM; 5-45 minutes, 100-400 mM. Each elution was
followed by a washing step of 5 minutes 1 M sodium acetate in 0.1 M
NaOH and an equilibration step of 15 minutes 0.1 M NaOH. Peaks were
identified according to Kormelink et al., 1993 and Gruppen et al.,
1992.
[0381] Using the assays described above, the enzyme Abn7 was found
to have arabinofuranosidase activity of about 1.21 U/ml in
end-of-fermentation samples when pNP-ara is used as a
substrate.
[0382] Single and double substituted arabinoxylan oligosaccharides
were prepared by xylanase treatment as described above. After
overnight incubation, the amount of reducing sugars increased from
0 to 4.3 mM (glucose was used as the standard). The addition of an
extra amount of enzyme did not increase this number, indicating
that the reaction was at an end point. Assuming that the average
degree of polymerization was 3, 1.8 mg of oligosaccharides were
formed, which corresponds to 30% of WAX degradation. The HPAEC
diagram of the resulting oligosaccharide solution is shown in FIG.
1, line A. Oligosaccharides were identified according to Kormelink
et al., 1993 and Gruppen et al., 1992. In addition to
non-substituted oligosaccharides (xylobiose (X.sub.2), xylotriose
(X.sub.3), xylotetraose (X.sub.4)), single (X.sub.3A, X.sub.2A) and
double substituted (X.sub.4A.sub.2, X.sub.3A.sub.2)
oligosaccharides were also present after xylanase treatment.
[0383] The activity of Abn7 towards this mixture of arabinoxylan
oligosaccharides was then determined using the assays described
above. The HPAEC diagram of this reaction is shown in FIG. 1, line
B. While the double substituted oligosaccharides (X.sub.4A.sub.2
and X.sub.3A.sub.2) disappear after Abn7 treatment, arabinose and
newly formed single substituted oligosaccharides (A and X.sub.3A)
were also found. The lower peak area of the oligosaccharide
X.sub.2A in the Abn7-treated sample might indicated that the enzyme
is also able to degrade single substituted arabinoxylan
oligosaccharides.
[0384] To generate samples with only double substituted
oligosaccharides present, the single substituted oligosaccharides
were removed from the xylanase-treated WAX mixture by the enzyme
Abf1 as described above. The HPAEC diagrams of the xylanase treated
WAX mixture (line A) and the Abf1- and xylanase-treated WAX mixture
(line B) are shown in FIG. 2. This was done to confirm which peaks
correspond to the single and double substituted
oligosaccharides.
[0385] Samples containing only double substituted oligosaccharides
were treated with Abn7 or AXHd.sub.3 from B. adolescentis as a
reference enzyme as described above. FIG. 2 shows the results of
the Abn7-treated (line C) and the AXHd.sub.3-treated samples (Line
D). As shown in FIG. 2, the doubly substituted arabinoxylan
oligosaccharides (X.sub.4A.sub.2 and X.sub.3A.sub.2) were degraded
by both Abn7 and AXHd.sub.3 treatment, forming arabinose and
mono-substituted oligosaccharides (A, X.sub.2A, X.sub.3A and
X.sub.4A). The degradation pattern Abn7 and AXHd.sub.3 were
similar, except that Abn7 was observed to form more X.sub.2A,
whereas AXHd.sub.3 formed more X.sub.3A and/or X.sub.4A (see arrows
with stars). X.sub.3 was also found to be degraded by Abn7 (slanted
arrow). The increase in xylose (X; seen in X/G peak) suggested that
Abn7 also possesses .beta.-xylosidase activity. Combining all the
data, it was concluded that Abn7 demonstrates the ability to remove
arabinose residues from double substituted xylose residues and also
possesses .beta.-xylosidase activity.
[0386] Despite the similar enzymatic activities, Abn7 was found to
have only 29% amino acid identity with AXHd.sub.3 from B.
adolescentis.
Example 3
[0387] The following examples illustrates the assay used to measure
Xyloglucanase activity. Such activity was demonstrated by using
xyloglucan as substrate and a reducing sugars assay (PAHBAH) as
detection method. The values were compared to a standard, which was
prepared using a commercial cellulase preparation from Aspergillus
niger.
Reagents
[0388] The cellulase standard solution was prepared, which
contained 2 units of cellulase per ml of 0.2 M HAc/NaOH, pH 5.
Subsequently, a standard series of 0 to 2 U/ml was prepared (12
samples).
[0389] Reagent A: 10 g of p-Hydroxy benzoic acid hydrazide (PAHBAH)
was suspended in 60 mL water. 10 mL of concentrated hydrochloric
acid was added and the volume was adjusted to 200 ml. Reagent B:
24.9 g of trisodium citrate was dissolved in 500 ml of water. To
this solution 2.2 g of calcium chloride and 40 g sodium hydroxide
were added. The volume was adjusted to 2 L with water. Both
reagents were stored at room temperature. Working Reagent: 10 ml of
Reagent A was added to 90 ml of Reagent B. This solution was
prepared freshly every day, and was stored on ice between uses.
[0390] Using the above reagents, the assay was performed as
detailed below
Enzyme Sample
[0391] The assay was conducted in micro titer plate format. Each
well contained 50 .mu.l of xyloglucan substrate (0.25% (w/v)
tamarind xyloglucan in water), 30 .mu.l of 0.2 M HAc/NaOH pH 5, 20
.mu.l xyloglucanase sample or cellulase standard sample. These were
incubated at 37.degree. C. for 2 hours. After incubation 25 .mu.l
of each well were mixed with 125 .mu.l working reagent. These
solutions were heated at 95.degree. C. for 5 minutes. After cooling
down, the samples were analyzed by measuring the absorbance at 410
nm (A.sub.410) as A.sub.S (enzyme sample). The standard curve was
determined and from that the Xgl1 activities were determined.
Substrate Blank
[0392] 50 .mu.L of xyloglucan substrate (0.25% (w/v) tamarind
xyloglucan in water) was mixed with 50 .mu.L 0.2 M sodium acetate
buffer pH 5.0 and incubated at 37.degree. C. for 2 hours. To 25
.mu.L of this reaction mixture, 125 .mu.L of working solution was
added. The samples were heated for 5 minutes at 95.degree. C. After
cooling down, the samples were analyzed by measuring the absorbance
at 410 nm (A.sub.410) as A.sub.SB (substrate blank sample).
Calculation of Activity
[0393] Activity was calculated as follows: xyloglucanase activity
was determined by reference to a standard curve of the cellulase
standard solution.
Activity(IU/ml)=.DELTA.A.sub.410/SC*DF
[0394] where .DELTA.A.sub.410=A.sub.S (enzyme sample)-A.sub.SB
(substrate blank), SC is the slope of the standard curve and DF is
the enzyme dilution factor.
Results
[0395] Xgl1 showed an activity exceeding the 2 U/ml value of the
highest standard sample (absorbance at 410 nm>1.9), whereas the
negative control exhibited an absorbance at 410 nm of only
0.25.
Example 4
[0396] The following example illustrates the assay used to measure
the ability of the enzymes of the present invention to bind to
bacitracin-Sepharose. Since Sepharose consists of cross-linked
agarose molecules, which are composed of alternating galactose
residues linked by .beta.-1,3 and .beta.-1,4 linkages, binding to
agarose indicates the presence of a carbohydrate binding module
(CBM) in the enzyme. Bacitracin is a polypeptide to which only
proteases are expected to bind.
Reagents
[0397] 4 g of CNBr-activated Sepharose 4B was washed on a glass
filter G3 with 800 mL 1 mM HCl, followed by 20 mL 0.1M NaHCO.sub.3
pH8.3+0.5 M NaCl (solution A). The gel was added to a 50 mL tube.
300 mg bacitracin was dissolved in 10 mL solution A and was added
to the Sepharose gel. The bacitracin-Sepharose gel was incubated
overnight at 4.degree. C. under constant stirring. The gel was
washed on a glass filter G3 with 30 mL solution A and 30 mL 0.1M
NaAc/HAc pH4.0+0.5M NaCl (solution B). This washing step was
repeated twice. Subsequently, the gel was washed with 30 mL
solution A. The gel was transferred to a 50 mL tube and 20 mL 0.1M
Tris/HCl pH8.0 (Solution C) was added. The tube was incubated for
2.5 hours at room temperature under constant stirring. The gel was
washed with 70 ml of solution A and subsequently with 50 ml of
solution C. The gel was stored at 4.degree. C. in solution C.
[0398] The bacitracin-Sepharose gel can be regenerated by washing
it with alternating 100 ml 0.1M Tris/HCl pH 8.5 containing 0.5M
NaCl, or 100 ml sodium acetate buffer pH 4.5 containing 0.5M
NaCl.
Isolation of Enzyme Sample with Bacitracin-Sepharose
[0399] The fermentation broth containing the target enzyme was
dialyzed overnight against 25 mM sodium acetate buffer, pH 4.0 at
4.degree. C. and subsequently filtered through a 0.45 m filter. A
plastic column (6.8.times.150 mm) was filled with 2 ml of the
bacitracin-Sepharose and subsequently equilibrated with 10 ml of 25
mM sodium acetate buffer pH4.0. The dialyzed fermentation broth was
loaded to the column and the column was washed with 25 mM sodium
acetate buffer pH4.0. The bound proteins were eluted with 10 mL
0.1M Tris/HCl pH 8.0 and analyzed by MS/MS to confirm their
identity.
Results
[0400] The enzymes CL01467, CL02507, CL05366, and CDH1 were bound
to the bacitracin-Sepharose column, indicating that these enzymes
contain a carbohydrate binding module.
Example 5
[0401] The following example illustrates the assay used to measure
the .alpha.-glucuronidase activity towards arabinoxylan
oligosaccharides from Eucalyptus wood. This assay measured the
release of glucuronic acid by the action of the
.alpha.-glucuronidase on the arabinoxylan oligosaccharides.
Reagents
[0402] Sodium acetate buffer (0.01 M, pH 5.0) was prepared as
follows. 0.82 g of anhydrous sodium acetate or 1.36 g of sodium
acetate*3H.sub.2O was dissolved in distilled water to a final
volume of 1000 mL (Solution A). In a separate flask, 0.6 g (0.572
mL) of glacial acetic acid was mixed with distilled water to make
the total volume of 1000 mL (Solution B). The final 0.01 M sodium
acetate buffer, pH 5.0, was prepared by mixing Solution A with
Solution B until the pH of the resulting solution was equal to
5.0.
[0403] Acetylated, 4-O-MeGlcA substituted xylo-oligosaccharides
with 2-4 xylose residues or 4-10 xylose residues from Eucalyptus
wood (EW-XOS) were prepared using the method described in Kabel et
al., 2002. 1 mg of xylo-oligosaccharides was dissolved in 1 mL
distilled water using magnetic stirrer. 4-O-MeGlcA was purified by
using the method described in Kabel et al. 2002. Aldo-biuronic acid
(X.sub.1G), aldo-triuronic acid (X.sub.2G), and aldo-tetrauronic
acid (X.sub.3G) were obtained from Megazyme.
[0404] To remove the acetyl groups in the XOS, either for reference
or for substrates, 1 mg of substrate was dissolved in 120 .mu.L
Millipore water and 120 .mu.L 0.1 M NaOH. After overnight
incubation at 4.degree. C., the pH of the samples was checked. A pH
above 9.0 indicated that the saponification reaction was complete.
120 .mu.L of 0.1 M acetic acid and 40 .mu.L of 0.2 M Sodium
acetate, pH 5.0 were added. After following these steps, the
substrate concentration was 2.5 mg/mL in 50 mM sodium acetate
buffer, pH 5.0.
Enzyme Sample
[0405] 1.0 mL of xylo-oligosaccharides stock solution was mixed
with 0.68 kg of the enzyme sample and incubated at 35.degree. C.
for 24 hours. The reaction was stopped by heating the samples for
10 minutes at 100.degree. C. The release of 4-O-methyl glucuronic
acid and formation of new (arabino)xylan oligosaccharides were
analyzed by High Performance Anion Exchange Chromatography and
Capillary Electrophoresis.
Substrate Blank
[0406] 1.0 mL of arabinoxylan oligosaccharides stock solution was
mixed with 0.68 kg of distilled water and incubated at 35.degree.
C. for 24 hours. The reaction was stopped by heating the samples
for 10 minutes at 100.degree. C. The release of glucuronic acid and
formation of new arabinoxylan oligosaccharides were analyzed by
High Performance Anion Exchange Chromatography and Capillary
Electrophoresis.
High Performance Anion Exchange Chromatography
[0407] The analysis was performed using a Dionex HPLC system
equipped with a Dionex CarboPac PA-1 (2 mm ID.times.250 mm) column
in combination with a CarboPac PA guard column (1 mm ID.times.25
mm) and a Dionex EDet1 PAD-detector (Dionex Co., Sunnyvale). A flow
rate of 0.3 mL/min was used with the following gradient of sodium
acetate in 0.1 M NaOH: 0-50 min, 0-500 mM. Each elution was
followed by a washing step of 5 min using 1 M sodium acetate in 0.1
M NaOH and an equilibration step of 15 min using 0.1 M NaOH.
Capillary Electrophoresis-Laser Induced Fluorescence Detector
(CE-LIF)
[0408] Samples containing about 0.4 mg of EW-XOS were substituted
with 5 nmol of maltose as an internal standard. The samples were
dried using centrifugal vacuum evaporator (Speedvac). 5 mg of APTS
labeling dye (Beckman Coulter) was dissolved in 484 of 15% acetic
acid (Beckman Coulter). The dried samples were mixed with 2 .mu.L
of the labeling dye solution and 2 .mu.L of 1 M Sodium
Cyanoborohydride (THF, Sigma-Aldrich). The samples were incubated
overnight in the dark to allow the labeling reaction to be
completed. After overnight incubation, the labeled samples were
diluted 100 times with Millipore water before analysis by
CE-LIF.
[0409] CE-LIF was performed using ProteomeLab PA800 Protein
Characterization System (Beckman Coulter), controlled by 32 Karat
Software. The capillary column used was polyvinyl alcohol coated
capillary (N--CHO capillary, Beckman Coulter), with 50 .mu.m ID,
50.2 cm length, 40 cm to detector window. 25 mM sodium acetate
buffer pH 4.75 containing 0.4% polyethyleneoxide (Carbohydrate
separation buffer, Beckman Coulter) was used as running buffer. The
sample (about 3.5 nL) was injected to the capillary by a pressure
of 0.5 psi for 3 seconds. The separation was done for 20 minutes at
30 kV separating voltage, with reversed polarity. During analysis,
the samples were stored at 10.degree. C. The labeled XOS were
detected using LIF detector at 488 nm excitation and 520 nm
emission wavelengths.
Determination of pH and Temperature Optimum
[0410] The pH optimum of Agu1 was determined by analyzing its
activity at pH 4, 5, 6, and 7. The substrate was dissolved in
McIlvain's buffer at the pH of analysis. The incubation was done at
35.degree. C. The temperature optimum of the enzyme was determined
by analyzing its activity at 35.degree. C., 40.degree. C.,
50.degree. C., 55.degree. C., 60.degree. C., 65.degree. C., and
70.degree. C. The substrate was dissolved in McIlvain's buffer at
the pH optimum obtained from the previous experiment.
Results
[0411] The optimal pH of Agu1 was found to be 6 and the optimal
temperature was found to be 50.degree. C. Agu1 was found to release
4-O-methyl glucuronic acid from Eucalyptus wood
xylo-oligosaccharides, since unsubstituted xylo-oligosaccharides
were formed after digestion with Agu1 (as indicated in FIG. 3B).
Release of 4-O-methyl glucuronic acid was observed. See FIG. 4C.
Due to the action of Agu1, X.sub.2 was degraded. The standard
mixture was composed of separate oligosaccharides, (mostly
purchased from Megazyme). The X.sub.2G was known to have the
glucuronic acid (G) at the non-reducing end of the molecule.
Degradation of this substrate indicated that the Agu1 was able to
hydrolyze the 4-O-methyl glucuronic acid which is located at the
non-reducing end of xylo-oligosaccharides, as indicated in FIG. 4.
It was also found that the activity of Agu1 was hindered by the
presence of acetyl esters in the oligosaccharides, since
saponification of the substrate increased the release of
unsubstituted xylo-oligosaccharides (FIG. 3C).
Example 6
[0412] The following example illustrates the assay used to measure
arabinofuranosidase activity. This assay measured the release of
p-nitrophenol by the action of .alpha.-arabinofuranosidase on
p-nitrophenyl .alpha.-L-arabinofuranoside (PNPA). One
.alpha.-arabinofuranosidase unit of activity is the amount of
enzyme that liberates 1 micromole of p-nitrophenol in one minute at
37.degree. C. and pH 5.0.
Reagents
[0413] Sodium acetate buffer (0.1 M, pH 5.0) was prepared as
follows. 8.2 g of anhydrous sodium acetate or 13.6 g of sodium
acetate*3H.sub.2O was dissolved in distilled water to a final
volume of 1000 mL (Solution A). In a separate flask, 6.0 g (5.72
mL) of glacial acetic acid was mixed with distilled water to make
the total volume of 1000 mL (Solution B). The final 0.1 M sodium
acetate buffer, pH 5.0, was prepared by mixing Solution A with
Solution B until the pH of the resulting solution was 5.0.
[0414] PNPA from Fluka (Switzerland, cat. #73616) was used as the
assay substrate. 16.5 mg of PNPA was dissolved in 5 mL of distilled
water and 5 mL 0.1 M sodium acetate buffer using magnetic stirrer
to obtain 2 mM stock solution. The solution was stable for 2 days
on storage at 4.degree. C.
[0415] The stop reagent (0.25 M sodium carbonate solution) was
prepared as follows. 26.5 g of anhydrous sodium carbonate was
dissolved in 800 mL of distilled water, and the solution volume was
adjusted to 1000 mL. This reagent was used to terminate the
enzymatic reaction.
[0416] Using the above reagents, the assay was performed as
detailed below.
Enzyme Sample
[0417] 0.10 mL of 2 mM PNPA stock solution was mixed with 0.01 mL
of the enzyme sample and incubated at 37.degree. C. for 30 minutes.
After exactly 30 minutes of incubation, 0.1 mL of 0.25 M sodium
carbonate solution was added and then the absorbance at 405 nm
(A.sub.405) was measured in microtiter plates as A.sub.S (enzyme
sample).
Substrate Blank
[0418] 0.10 mL of 2 mM PNPA stock solution was mixed with 0.01 mL
of 0.05 M sodium acetate buffer, pH 5.0. 0.1 mL of 0.25 M sodium
carbonate solution was added and the absorbance at 405 nm
(A.sub.405) was measured in microtiter plates as A.sub.SB
(substrate blank).
Calculation of Activity
[0419] Activity was calculated as follows:
Activity (IU/ml)=(.DELTA.A.sub.405*DF*21*1.33)/(13.700*30)
[0420] where .DELTA.A.sub.405=A.sub.S (enzyme sample)-A.sub.SB
(substrate blank), DF is the enzyme dilution factor, 21 is the
dilution of 10 .mu.l enzyme solution in 210 .mu.l reaction volume,
1.33 is the conversion factor of microtiter plates to cuvettes,
13.700 is the extinction coefficient 13700 M.sup.-1 CM.sup.-1 of
p-nitrophenol released corrected for mol/L to .mu.mol/mL, and 30
minutes is the reaction time.
[0421] Results
[0422] The .DELTA.A.sub.405 of Abf3 was found to be >3.0 with a
DF of 1 for enzyme produced in microtiter plate cultures. The
enzyme solution was not diluted to obtain an A.sub.405 between 0.05
and 1.0 units of optical density, which may affect activity
calculation. From these results it was concluded that the enzyme is
active towards p-nitrophenyl .alpha.-L-arabinofuranoside.
[0423] The .DELTA.A.sub.405 of Abn5 was found to be 0.12 IU/mL
(.DELTA.A.sub.405=1.15, DF=1, 20 minutes incubation) of enzyme
produced in 1.5 L fermentations.
Example 7
[0424] The following example illustrates the assay used to measure
arabinofuranosidase activity. This assay measured the release of
arabinose by the action of the .alpha.-arabinofuranosidase on wheat
arabinoxylan oligosaccharides (WAX).
Reagents
[0425] Sodium acetate buffer (0.05 M, pH 5.0) was prepared as
follows. 4.1 g of anhydrous sodium acetate or 6.8 g of sodium
acetate*3H.sub.2O was dissolved in distilled water to a final
volume of 1000 mL (Solution A). In a separate flask, 3.0 g (2.86
mL) of glacial acetic acid was mixed with distilled water to make
the total volume of 1000 mL (Solution B). The final 0.05 M sodium
acetate buffer, pH 5.0, was prepared by mixing Solution A with
Solution B until the pH of the resulting solution was equal to
5.0.
[0426] Wheat arabinoxylan oligosaccharides were prepared by
degradation of Wheat arabinoxylan (Megazyme, Bray Ireland, Cat. #
P-WAXYI) by endo-xylanase I from A. niger (enzyme collection
Laboratory of Food Chemistry, Wageningen University, The
Netherlands) or with Pentopan Mono (Sigma, St. Louis, USA). 50 mg
of WAX was dissolved in 10 mL 0.05 M sodium acetate buffer pH 5.0
using magnetic stirrer. 1.0 mL of WAX stock solution was mixed with
0.0075 mg of the endo-xylanase I from A. niger or 0.015 mg of the
Pentopan Mono and incubated at 35.degree. C. for 24 hours. The
reaction was stopped by heating the samples for 10 minutes at
100.degree. C. The residual material was removed by centrifugation
(15 minutes at 14000 rpm), the supernatant was used as reagents.
The assay was performed as detailed below.
[0427] Cellodextrins were purchased from Toronto Research
Chemicals.
Enzyme Sample
[0428] 1004 of substrate stock solution was mixed with 0.004 mg
(total protein) of enzyme sample and the reaction mixture was
adjusted to 200 .mu.L with 0.05 M sodium acetate buffer, pH 5.0.
This mixture was incubated at 37.degree. C. for 24 hours. The
reaction was stopped by heating the samples for 10 minutes at
100.degree. C. The release of arabinose and formation of new
arabinoxylan oligosaccharides (from WAX) or the release of glucose
and formation of new gluco-oligosaccharides (cellodextrins) were
analyzed by High Performance Anion Exchange Chromatography.
Substrate Blank
[0429] 100 .mu.L of substrate stock solution was mixed with 100
.mu.L 0.05 M sodium acetate buffer pH 5.0 and incubated at
37.degree. C. for 24 hours. The reaction was stopped by heating the
samples for 10 minutes at 100.degree. C. The release of arabinose
and formation of new arabinoxylan oligosaccharides (from WAX) or
the release of glucose and formation of new gluco-oligosaccharides
(cellodextrins) were analyzed by High Performance Anion Exchange
Chromatography.
High Performance Anion Exchange Chromatography
[0430] The analysis was performed using a Dionex HPLC system
equipped with a Dionex CarboPac PA-1 (2 mm ID.times.250 mm) column
in combination with a CarboPac PA guard column (1 mm ID.times.25
mm) and a Dionex EDet1 PAD-detector (Dionex Co., Sunnyvale). A flow
rate of 0.3 mL/min was used with the following gradient of sodium
acetate in 0.1 M NaOH: 0-50 min, 0-500 mM. Each elution was
followed by a washing step of 5 min 1,000 mM with sodium acetate in
0.1 M NaOH and an equilibration step of 15 min with 0.1 M NaOH.
Determination of pH Optimum
[0431] The pH optimum was determined by analyzing activity at pH 3,
4, 5, 6, 7, and 8. The substrate was dissolved in McIlvain's buffer
at the pH of analysis. The incubation was done at 35.degree. C.
Results
[0432] The pH optimum of Abf3 was found to be pH 5. At pH 3 and 4
the enzyme is still very active. From pH 6 onwards, the activity
decreased. At pH 8 only 20% of the activity remained. Abf3 was
found to release arabinose from wheat arabinoxylan
oligosaccharides. The enzyme was able to remove arabinose residues,
which were monosubstituted to the xylose backbone. Arabinose
residues linked to both O.sub.2 and O.sub.3 position of the xylose
residue were released. Abf3 was also found to release glucose and
cellobiose from cellodextrins with a degree of polymerization of
>=4. It had no activity towards cellotriose, suggesting the
enzyme possesses .beta.-glucosidase activity besides
.alpha.-arabinofuranosidase activity
[0433] Abf5 was found to release arabinose when incubated with
wheat arabinoxylan oligosaccharides (FIG. 5B). The enzyme was only
able to remove arabinose residues, which were mono substituted to
the xylose backbone, and not the doubly substituted arabinoxylan
oligosaccharides. The arabinose residues on the mono substituted
oligosaccharides where all linked to O.sub.3 position of the xylose
residue.
Example 8
[0434] The following example illustrates the assay used to measure
.beta.-xylosidase activity. This assay measured the release of
p-nitrophenol by the action of .beta.-xylosidase on p-nitrophenyl
.beta.-D-xylopyranoside (PNPX). One .beta.-xylosidase unit of
activity is the amount of enzyme that liberates 1 micromole of
p-nitrophenol in one minute.
Reagents
[0435] Sodium acetate buffer (0.1 M, pH 5.0) was prepared as
follows. 8.2 g of anhydrous sodium acetate or 13.6 g of sodium
acetate*3H.sub.2O was dissolved in distilled water to a final
volume of 1000 mL (Solution A). In a separate flask, 6.0 g (5.72
mL) of glacial acetic acid was mixed with distilled water to make
the total volume of 1000 mL (Solution B). The final 0.1 M sodium
acetate buffer, pH 5.0, was prepared by mixing Solution A with
Solution B until the pH of the resulting solution was equal to
5.0.
[0436] PNPX from Extrasynthese (France, cat. #4244) was used as the
assay substrate. 16.5 mg of PNPX was dissolved in 5 mL of distilled
water and 5 mL 0.1 M sodium acetate buffer using magnetic stirrer
to obtain 2 mM stock solution. The solution was stable for 2 days
on storage at 4.degree. C.
[0437] The stop reagent (0.25 M sodium carbonate solution) was
prepared as follows. 26.5 g of anhydrous sodium carbonate was
dissolved in 800 mL of distilled water, and the solution volume was
adjusted to 1000 mL. This reagent was used to terminate the
enzymatic reaction.
[0438] Using the above reagents, the assay was performed as
detailed below.
Enzyme Sample
[0439] 0.10 mL of 2 mM PNPX stock solution was mixed with 0.01 mL
of the enzyme sample and incubated at 50.degree. C. for 20 minutes.
After exactly 30 minutes of incubation, 0.1 mL of 0.25 M sodium
carbonate solution was added and then the absorbance at 405 nm (05)
was measured in microtiter plates as A.sub.S (enzyme sample).
Substrate Blank
[0440] 0.10 mL of 2 mM PNPX stock solution was mixed with 0.01 mL
of 0.05 M sodium acetate buffer, pH 5.0. 0.1 mL of 0.25 M sodium
carbonate solution was added and the absorbance at 405 nm
(A.sub.405) was measured in microtiter plates as A.sub.SB
(substrate blank).
Calculation of Activity
[0441] Activity was calculated as follows:
Activity (IU/ml)=(.DELTA.A.sub.405*DF*21*1.33)/(13.700*20)
[0442] where .DELTA.A.sub.405=A.sub.S (enzyme sample)-A.sub.SB
(substrate blank), DF is the enzyme dilution factor, 21 is the
dilution of 10 .mu.l enzyme solution in 210 .mu.l reaction volume,
1.33 is the conversion factor of microtiter plates to cuvettes,
13.700 is the extinction coefficient 13700 M.sup.-1 CM.sup.-1 of
p-nitrophenol released corrected for mol/L to .mu.mol/mL, and 20
minutes is the reaction time.
Results
[0443] .beta.-xylosidase activity of Bxl1 was found to be 0.94
IU/mL (.DELTA.A.sub.405=0.92, DF=10) of enzyme produced in 1.5 L
fermentations.
Example 9
[0444] The following example illustrates the assay used to measure
.beta.-galactosidase activity. This assay measures the action of
.beta.-galactosidase on 5-Bromo-4-chloro-3-indolyl
.beta.-D-galactoside (X-Gal) to yield galactose and
5-bromo-4-chloro-3-hydroxyindole. 5-bromo-4-chloro-3-hydroxyindole
was oxidized into 5,5'-dibromo-4,4'-dichloro-indigo, which is an
insoluble blue product.
Reagents
[0445] Sodium acetate buffer (0.05 M, pH 5.0) was prepared as
follows. 4.1 g of anhydrous sodium acetate or 6.8 g of sodium
acetate*3H.sub.2O was dissolved in distilled water to a final
volume of 1000 mL (Solution A). In a separate flask, 3.0 g (2.86
mL) of glacial acetic acid was mixed with distilled water to total
volume of 1000 mL (Solution B). The final 0.05 M sodium acetate
buffer, pH 5.0, was prepared by mixing Solution A with Solution B
until the pH of the resulting solution was 5.0.
[0446] X-Gal from Fermentas (St. Leon Rot, Germany) was used as the
assay substrate. 1.0 mg of X-Gal was dissolved in 10 mL 0.05 M
sodium acetate buffer using magnetic stirrer.
[0447] Using the above reagents, the assay was performed as
detailed below.
Enzyme Sample
[0448] 0.10 mL of 0.1 mg/mL X-Gal stock solution was mixed with
0.01 mL of the enzyme sample and incubated at 37.degree. C. for 3
hours. After 3 hours of incubation, the absorbance at 590 nm
(A.sub.590) was measured in microtiter plates as A.sub.5 (enzyme
sample).
Substrate Blank
[0449] 0.10 mL of 0.1 mg/mL X-Gal stock solution was mixed with
0.01 mL of 0.05 M sodium acetate buffer, pH 5.0 and incubated at
37.degree. C. for 3 hours. After 3 hours of incubation, the
absorbance at 590 nm (A.sub.590) was measured in microtiter plates
as A.sub.SB (substrate blank).
Calculation of Activity
[0450] Activity was calculated as follows
Activity(IU/ml)=.DELTA.A.sub.590*DF
[0451] where .DELTA.A590=A.sub.5 (enzyme sample)-A.sub.SB
(substrate blank) and DF is the enzyme dilution factor.
Results
[0452] The .DELTA.A.sub.590 of Bga2 was found to be 0.15 with a DF
of 1 for enzyme produced in microtiter plate cultures. Bga2 was
found to possess .beta.-galactosidase activity, since it was active
towards X-Gal.
Example 10
[0453] The following example illustrates the assay used to measure
acetyl esterase activity. This assay measured the release of
p-nitrophenol by the action of acetyl esterase on p-nitrophenyl
acetate (PNPAc). One acetyl esterase unit of activity is the amount
of enzyme that liberates 1 micromole of p-nitrophenol in one minute
at 37.degree. C. and pH 5.
Reagents
[0454] Sodium acetate buffer (0.05 M, pH 5.0) was prepared as
follows. 4.1 g of anhydrous sodium acetate or 6.8 g of sodium
acetate*3H.sub.2O was dissolved in distilled water to a final
volume of 1000 mL (Solution A). In a separate flask, 3.0 g (2.86
mL) of glacial acetic acid was mixed with distilled water to make
the total volume of 1000 mL (Solution B). The final 0.05 M sodium
acetate buffer, pH 5.0, was prepared by mixing Solution A with
Solution B until the pH of the resulting solution was 5.0.
[0455] PNPAc from Fluka (Switzerland, cat. #46021) was used as the
assay substrate. 3.6 mg of PNPAc was dissolved in 10 mL of 0.05 M
sodium acetate buffer using magnetic stirrer to obtain 2 mM stock
solution. The solution was stable for 2 days on storage at
4.degree. C.
[0456] The stop reagent (0.25 M Tris-HCl, pH 8.8) was prepared as
follows. 30.29 g of Tris was dissolved in 900 mL of distilled water
(Solution A). The final 0.25 M Tris-HCl pH 8.5 was prepared by
mixing solution A with 37% HCl until the pH of the resulting
solution reached 8.8. The solution volume was adjusted to 1000 mL.
This reagent was used to terminate the enzymatic reaction.
[0457] Using the above reagents, the assay was performed as
detailed below.
Enzyme Sample
[0458] 0.10 mL of 2 mM PNPAc stock solution was mixed with 0.01 mL
of the enzyme sample and incubated at 37.degree. C. for 10 minutes.
After exactly 10 minutes of incubation, 0.1 mL of 0.25 M Tris-HCl
solution was added and the absorbance at 405 nm (A.sub.405) was
measured in microtiter plates as A.sub.S (enzyme sample).
Substrate Blank
[0459] 0.10 mL of 2 mM PNPAc stock solution was mixed with 0.01 mL
of 0.05 M sodium acetate buffer, pH 5.0. 0.1 mL of 0.25 M Tris-HCl
solution was added and the absorbance at 405 nm (A.sub.405) was
measured microtiter plates as A.sub.SB (substrate blank).
Calculation of Activity
[0460] Activity was calculated as follows:
Activity (IU/ml)=(.DELTA.A.sub.405*DF*21*1.33)/(13.700*10)
[0461] where .DELTA.A.sub.405=A.sub.S (enzyme sample)-A.sub.SB
(substrate blank), DF is the enzyme dilution factor, 21 is the
dilution of 10 .mu.t enzyme solution in 210 .mu.t reaction volume,
1.33 is the conversion factor of microtiter plates to cuvettes,
13.700 is the extinction coefficient 13700 M.sup.-1 CM.sup.-1 of
p-nitrophenol released corrected for mol/L to .mu.mol/mL, and 10
minutes is the reaction time.
Results
[0462] The acetyl esterase activity of Rga1 was found to be 1.71
IU/mL (.DELTA.A.sub.405=0.84, DF=10) of enzyme produced in 1.5 L
fermentations.
Example 11
[0463] The following example illustrates the assay used to measure
arabinofuranosidase activity. This assay measured the release of
arabinose by the action of the .alpha.-arabinofuranosidase on
branched arabinan.
Reagents
[0464] Sodium acetate buffer (0.05 M, pH 5.0) was prepared as
follows. 4.1 g of anhydrous sodium acetate or 6.8 g of sodium
acetate*3H.sub.2O was dissolved in distilled water to a final
volume of 1000 mL (Solution A). In a separate flask, 3.0 g (2.86
mL) of glacial acetic acid was mixed with distilled water to make
the total volume of 1000 mL (Solution B). The final 0.05 M sodium
acetate buffer, pH 5.0, was prepared by mixing Solution A with
Solution B until the pH of the resulting solution was equal to
5.0.
[0465] Linear and branched arabinan was purchased from British
Sugar.
[0466] The assay was performed as detailed below.
Enzyme Sample
[0467] The enzyme sample (40-55 .mu.g total protein) was incubated
with 5 mg/mL of linear or branched arabinan in 50 mM sodium acetate
buffer at 40.degree. C. during 24 hours. The reaction was stopped
by heating the samples at 100.degree. C. for 10 minutes. The
samples were centrifuged for 5 minutes at 10,000.times.g.
Degradation of the arabinan was followed by HPAEC analysis.
Substrate Blank
[0468] 10 .mu.L 50 mM sodium acetate buffer pH 5.0 was incubated
with 5 mg/mL linear or branched arabinan in 50 mM sodium acetate
buffer at 40.degree. C. during 24 hours. The reaction was stopped
by heating the samples at 100.degree. C. for 10 minutes. The
samples were centrifuged for 5 minutes at 10,000.times.g.
Degradation of the arabinan was followed by HPAEC analysis.
High Performance Anion Exchange Chromatography
[0469] The analysis of the samples was performed using a Dionex
HPLC system equipped with a Dionex CarboPac PA-1 (2 mm ID.times.250
mm) column in combination with a CarboPac PA guard column (1 mm
ID.times.25 mm) and a Dionex EDet1 PAD-detector (Dionex Co.,
Sunnyvale). A flow rate of 0.3 mL/min was used with the following
gradient of sodium acetate in 0.1 M NaOH: 0-40 min, 0-400 mM. Each
elution was followed by a washing step of 5 min 1,000 mM sodium
acetate in 0.1 M NaOH and an equilibration step of 15 min 0.1 M
NaOH.
Results
[0470] Abn4 was found to release arabinose when incubated with both
linear and branched arabinan. The amount of arabinose released from
branched arabinan was about 5 times higher compared to linear
arabinan. The enzyme was more active towards branched arabinan than
towards linear arabinan and was also active towards
pNP-.alpha.-L-arabinofuranoside (see example 1).
[0471] Abn5 was also found to release arabinose when incubated with
linear arabinan. No arabinose was released when incubated with
branched arabinan. The enzyme was active towards linear arabinan
but not towards branched arabinan.
Example 12
[0472] This enzyme illustrates the assay used to determine the
ability of a protein to bind chitin.
Assay
[0473] 30 ml fermentation broth was overnight mixed with 5 g chitin
in a 50 mL tube at 4.degree. C. Subsequently a plastic column
(6.8.times.150 mm) was filled with the mixture and it was washed
with water overnight at 4.degree. C. The method was repeated with
the unbound material and fresh chitin. The unbound material was
analyzed by SDS-gel electrophoresis. The bound proteins, including
the matrix were heated for 10 minutes at 95.degree. C. in sample
buffer and separated by SDS-gel electrophoresis. Specific bands
from this gel were analyzed by MS/MS.
Results
[0474] The protein CL04750, CL05022, CL06230, and CL09768 were
found to bind to chitin.
Example 13
[0475] This example illustrates the assay used to determine the
ability of a protein to bind lichenan (which is a
.beta.(1,3)-.beta.(1,4)-linked glucan).
Assay
[0476] 30 ml fermentation broth was overnight mixed with 5 g
lichenan in a 50 mL tube at 4.degree. C. Subsequently a plastic
column (6.8.times.150 mm) was filled with the mixture and it was
washed with water overnight at 4.degree. C. The method was repeated
with the unbound material and fresh lichenan. The unbound material
was analyzed by SDS-gel electrophoresis. The bound proteins,
including the matrix were heated for 10 minutes at 95.degree. C. in
sample buffer and separated by SDS-gel electrophoresis. Specific
bands from this gel were analyzed by MS/MS.
Results
[0477] The protein CL02823 was found to bind to lichenan.
Example 14
[0478] This example illustrates the assay used to measure the
endo-xylanase activity towards AZO-wheat arabinoxylan. This
substrate is insoluble in buffered solutions, but rapidly hydrates
to form gel particles which are readily and rapidly hydrolysed by
specific endo-xylanases releasing soluble dye-labeled
fragments.
Reagents
[0479] Sodium acetate buffer (0.2 M, pH 5.0) was prepared as
follows. 16.4 g of anhydrous sodium acetate or 27.2 g of sodium
acetate*3H.sub.2O was dissolved in distilled water to a final
volume of 1000 mL (Solution A). In a separate flask, 12.0 g (11.44
mL) of glacial acetic acid was mixed with distilled water to make
the total volume of 1000 mL (Solution B). The final 0.2 M sodium
acetate buffer, pH 5.0, was prepared by mixing Solution A with
Solution B until the pH of the resulting solution was equal to
5.0.
[0480] AZO-wheat arabinoxylan (AZO-WAX) from Megazyme (Bray,
Ireland, Cat. # I-AWAXP) was used as the assay substrate. 1 g of
AZO-WAX was suspended in 3 mL ethanol and adjusted to 100 mL with
0.2 M sodium acetate buffer pH 5.0 using magnetic stirrer.
[0481] 96% Ethanol was used to terminate the enzymatic
reaction.
[0482] Using the above reagents, the assay was performed as
detailed below.
Enzyme Sample
[0483] 0.2 mL of 10 mg/ml AZO-WAX stock solution was preheated at
40.degree. C. for 10 minutes. This preheated stock solution was
mixed with 0.2 mL of the enzyme sample (preheated at 40.degree. C.
for 10 min) and incubated at 40.degree. C. for 10 minutes. After
exactly 10 minutes of incubation, 1.0 mL of 96% ethanol was added
and then the absorbance at 590 nm (A.sub.590) was measured as
A.sub.S (enzyme sample).
Substrate Blank
[0484] 0.2 mL of 10 mg/ml AZO-WAX stock solution was preheated at
40.degree. C. for 10 minutes. This preheated stock solution was
mixed with 200 .mu.l of 0.2 M sodium acetate buffer pH 5.0
(preheated at 40.degree. C. for 10 min) and incubated at 40.degree.
C. for 10 minutes. After exactly 10 minutes of incubation, 1.0 mL
of 96% ethanol was added and then the absorbance at 590 nm
(A.sub.590) was measured as A.sub.SB (substrate blank).
Calculation of Activity
[0485] Activity was calculated as follows: endo-xylanase activity
was determined by reference to a standard curve, produced from an
endo-xylanase with known activity towards AZO-WAX.
Activity(IU/ml)=.DELTA.A.sub.590/SC*DF
[0486] where .DELTA.A.sub.590=A.sub.S (enzyme sample)-A.sub.SB
(substrate blank), SC is the slope of the standard curve and DF is
the enzyme dilution factor.
Results
[0487] The activity of Xyl7 produced in 1.5 L fermentations was
found to be 304 IU/mL (.DELTA.A.sub.590=0.03645, DF=1000 and
SC=0.12). The enzyme was found to possess endo-xylanase
activity.
[0488] The activity of Xyl8 produced in 1.5 L fermentations was
found to be 426 IU/mL (.DELTA.A.sub.590=0.2694, DF=500 and
SC=0.316). The enzyme was found to possess endo-xylanase
activity.
[0489] The activity of Xyl9 produced in 1.5 L fermentations was
found to be 955 IU/mL (.DELTA.A.sub.590=0.211, DF=1000 and
SC=0.221). The enzyme was found to possess endo-xylanase
activity.
[0490] The activity of Xyl10 produced in 1.5 L fermentations was
found to be 6 IU/mL (.DELTA.A.sub.590=0.00165, DF=500 and SC=0.13).
The endo-xylanase activity was very low compared to the other
xylanases, concluding that this enzyme does not possess
endo-xylanase activity.
[0491] The activity of Xyl11 produced in 1.5 L fermentations was
found to be 627 IU/mL (.DELTA.A.sub.590=0.6295, DF=295 and
SC=0.296). The enzyme was found to possess endo-xylanase
activity.
Example 15
[0492] This example illustrates the assay used to measure xylanase
activity. This assay measured the release of xylose and
xylo-oligosaccharides by the action of xylanases on wheat
arabinoxylan oligosaccharides (WAX).
Reagents
[0493] Sodium acetate buffer (0.05 M, pH 5.0) was prepared as
follows. 4.1 g of anhydrous sodium acetate or 6.8 g of sodium
acetate*3H.sub.2O was dissolved in distilled water to a final
volume of 1000 mL (Solution A). In a separate flask, 3.0 g (2.86
mL) of glacial acetic acid was mixed with distilled water to make
the total volume of 1000 mL (Solution B). The final 0.05 M sodium
acetate buffer, pH 5.0, was prepared by mixing Solution A with
Solution B until the pH of the resulting solution was 5.0.
[0494] Wheat arabinoxylan was purchased from Megazyme (Bray
Ireland, Cat. # P-WAXYI).
[0495] The assay was performed as detailed below.
Enzyme Sample
[0496] 5.0 mg/mL of substrate was mixed with 0.05 mg (total
protein) of the enzyme sample at 37.degree. C. for 1 hour and 24
hours. The reaction was stopped by heating the samples for 10
minutes at 100.degree. C. The release of xylose and arabinoxylan
oligosaccharides were analyzed by High Performance Anion Exchange
Chromatography.
Substrate Blank
[0497] 5.0 mg/mL of substrate was mixed with 10 .mu.l of 0.05 M
sodium acetate buffer pH 5.0 at 37.degree. C. for 1 hour and 24
hours. The reaction was stopped by heating the samples for 10
minutes at 100.degree. C. The release of xylose and arabinoxylan
oligosaccharides were analyzed by High Performance Anion Exchange
Chromatography.
High Performance Anion Exchange Chromatography
[0498] The analysis was performed using a Dionex HPLC system
equipped with a Dionex CarboPac PA-1 (2 mm ID.times.250 mm) column
in combination with a CarboPac PA guard column (1 mm ID.times.25
mm) and a Dionex EDet1 PAD-detector (Dionex Co., Sunnyvale). A flow
rate of 0.3 mL/min was used with the following gradient of sodium
acetate in 0.1 M NaOH: 0-50 min, 0-500 mM. Each elution was
followed by a washing step of 5 min 1,000 mM sodium acetate in 0.1
M NaOH and an equilibration step of 15 min 0.1 M NaOH.
Results
[0499] Xyl7 was found to release different types of arabinoxylan
oligosaccharides and xylose after 1 hour of incubation, as
indicated in FIG. 6B. The chromatogram showed the same pattern as a
known family GH11 enzyme from Aspergillus niger (enzyme collection
Laboratory of Food Chemistry, Wageningen University, The
Netherlands). After 24 hours of incubation, the amount of xylose
and xylobiose had increased. The types of different
oligosaccharides formed did not change during the incubation time
(FIG. 6C). These results indicated that the enzyme possesses
endo-xylanase activity which is similar to family GH11 enzymes.
[0500] Xyl10 was found to release mainly xylose and a small amount
of xylobiose after 1 hour of incubation. After 24 hours of
incubation the amount of both xylose and xylobiose had increased,
while no other oligosaccharides were formed. Combining these
results with the low activity towards AZO-WAX (see example 14), it
was concluded that this xylanase possesses exo-xylanase
activity.
Example 16
[0501] This example illustrates the assay used to determine the
ability of a protein to bind xylan.
Assay
[0502] 30 ml fermentation broth was overnight mixed with 5 g xylan
in a 50 mL tube at 4.degree. C. Subsequently a plastic column
(6.8.times.150 mm) was filled with the mixture and it was washed
with water overnight at 4.degree. C. The method was repeated with
the unbound material and fresh xylan. The unbound material was
analyzed by SDS-gel electrophoresis. The bound proteins, including
the matrix, were heated for 10 minutes at 95.degree. C. in sample
buffer and separated by SDS-gel electrophoresis. Specific bands
from this gel were analyzed by MS/MS.
Results
[0503] The protein Xyl8 was found to bind to xylan, indicating the
presence of a carbohydrate binding module.
Example 17
[0504] The following example illustrates the assay used to measure
polygalacturonase activity. This assay measured the amount of
reducing sugars released from polygalacturonic acid (PGA) by the
action of a polygalacturonase. One unit of activity was defined as
1 .mu.mole of reducing sugars liberated per minute under the
specified reaction conditions.
Reagents
[0505] Sodium acetate buffer (0.2 M, pH 5.0) was prepared as
follows. 16.4 g of anhydrous sodium acetate or 27.2 g of sodium
acetate*3H.sub.2O was dissolved in distilled water to a final
volume of 1000 mL (Solution A). In a separate flask, 12.0 g (11.44
mL) of glacial acetic acid was mixed with distilled water to make
the total volume of 1000 mL (Solution B). The final 0.2 M sodium
acetate buffer, pH 5.0, was prepared by mixing Solution A with
Solution B until the pH of the resulting solution was equal to
5.0.
[0506] Polygalacturonic acid (PGA) was purchased from Sigma (St.
Louis, USA).
[0507] Reagent A: 10 g of p-Hydroxy benzoic acid hydrazide (PAHBAH)
was suspended in 60 mL water. 10 mL of concentrated hydrochloric
acid was added and the volume is adjusted to 200 ml. Reagent B:
24.9 g of trisodium citrate was dissolved in 500 ml of water. 2.2 g
of calcium chloride and 40 g sodium hydroxide were added. The
volume was adjusted to 2 L with water. Both reagents were stored at
room temperature. Working Reagent: 10 ml of Reagent A was added to
90 ml of Reagent B. This solution was prepared freshly every day,
and was stored on ice between uses.
[0508] Using the above reagents, the assay was performed as
detailed below.
Enzyme Sample
[0509] 50 .mu.L of PGA (10.0 mg/mL in 0.2 M sodium acetate buffer
pH 5.0) was mixed with 30 .mu.L0.2 M sodium acetate buffer pH 5.0
and 20 .mu.L of the enzyme sample and incubated at 40.degree. C.
for 75 minutes. To 25 .mu.L of this reaction mixture, 125 .mu.L of
working solution was added. The samples were heated for 5 minutes
at 99.degree. C. After cooling down, the samples were analyzed by
measuring the absorbance at 410 nm (A.sub.410) as A.sub.S (enzyme
sample).
Substrate Blank
[0510] 50 .mu.L of PGA (10.0 mg/mL in 0.2 M sodium acetate buffer
pH 5.0) was mixed with 50 .mu.L 0.2 M sodium acetate buffer pH 5.0
and incubated at 40.degree. C. for 75 minutes. To 25 .mu.L of this
reaction mixture, 125 .mu.L of working solution was added. The
samples were heated for 5 minutes at 99.degree. C. After cooling
down, the samples were analyzed by measuring the absorbance at 410
nm (A.sub.410) as A.sub.SB (substrate blank sample).
Calculation of Activity
[0511] Activity was calculated as follows:
Activity(IU/ml)=.DELTA.A.sub.410/SC*DF
[0512] where .DELTA.A.sub.410=A.sub.S (enzyme sample)-A.sub.SB
(substrate blank), SC is the slope of the standard curve and DF is
the enzyme dilution factor.
Results
[0513] The .DELTA.A.sub.410 of Pgx1 was 1.47 with a DF of 400 for
enzyme produced in 1.5 L fermentation. Thus, Pgx1 was found to be
active towards polygalacturonic acid, indicating that it is a
polygalacturonase.
Example 18
[0514] The following example illustrates the assay used to measure
.beta.-galactosidase activity. This assay measured the release of
p-nitrophenol by the action of .beta.-galactosidase on
p-nitrophenyl-.beta.-D-galactopyranoside (PNPGa). One
.beta.-galactosidase unit of activity is the amount of enzyme that
liberates 1 micromole of p-nitrophenol in one minute.
Reagents
[0515] McIlvain buffer (pH 4.0) was prepared as follows. 21.01 g of
citric acid monohydrate (C.sub.6H.sub.8O.sub.7*H.sub.2O) was
dissolved in Millipore water so that the final volume of the
solution to be 1000 mL (Solution A). In a separate flask, 53.62 g
of Na.sub.2HPO.sub.4*7H.sub.2O was dissolved in Millipore water to
make the total volume of 1000 mL (Solution B). The final McIlvain
buffer, pH 4.0, was prepared by mixing 614.5 mL Solution A with
385.5 mL Solution B. The pH of the resulting solution was equal to
7.0
[0516] PNPGa from Fluka (Switzerland, cat. #46021) was used as the
assay substrate. 2.7 mg of PNPGa was dissolved in 10 mL of McIlvain
buffer using magnetic stirrer to obtain 1.5 mM stock solution. The
solution was stable for 2 days on storage at 4.degree. C.
[0517] The stop reagent (0.25 M sodium carbonate solution) was
prepared as follows. 26.5 g of anhydrous sodium carbonate was
dissolved in 800 mL of distilled water, and the solution volume was
adjusted to 1000 mL. This reagent was used to terminate the
enzymatic reaction.
[0518] Using the above reagents, the assay was performed as
detailed below.
Enzyme Sample
[0519] 0.25 mL of 1.5 mM PNPGa stock solution was mixed with 0.05
mL of the enzyme sample and 0.2 mL buffer and incubated at
37.degree. C. for 10 minutes. After exactly 10 minutes of
incubation, 0.5 mL of 1 M Na.sub.2CO.sub.3 solution was added and
then the absorbance at 410 nm (A.sub.410) was measured in
microtiter plates as A.sub.S (enzyme sample).
Substrate Blank
[0520] 0.25 mL of 1.5 mM PNPGa stock solution was mixed with 0.25
mL of buffer and incubated at 37.degree. C. for 10 minutes. After
exactly 10 minutes of incubation, 0.5 mL of 1 M Na.sub.2CO.sub.3
solution was added and then the absorbance at 410 nm (A.sub.410)
was measured in microtiter plates as A.sub.SB (substrate blank
sample).
Calculation of Activity
[0521] Activity was calculated as follows:
Activity (IU/ml)=(.DELTA.A.sub.410*DF*20*1.33)/(13.700*10)
[0522] where .DELTA.A.sub.410=A.sub.S (enzyme sample)-A.sub.SB
(substrate blank), DF is the enzyme dilution factor, 20 is the
dilution of 50 .mu.l enzyme solution in 1000 .mu.l reaction volume,
1.33 is the conversion factor of microtiter plates to cuvettes,
13.700 is the extinction coefficient 13700 M.sup.-1 CM.sup.-1 of
p-nitrophenol released corrected for mol/L to .mu.mol/mL, and 10
minutes is the reaction time.
Determination of pH and Temperature Optimum
[0523] The pH optimum of Bga2 was determined by analyzing its
activity towards PNPGa at pH 3, 4, 5, 6, 7, and 8. The substrate
was dissolved in McIlvain's buffer at the pH of analysis. The
incubation was done at 37.degree. C. The temperature optimum of the
enzyme was determined by analyzing its activity towards PNPGa at
30.degree. C., 40.degree. C., 50.degree. C., 60.degree. C.,
70.degree. C., and 80.degree. C. The substrate was dissolved in
McIlvain's buffer at the pH optimum obtained from previous
experiment.
Results
[0524] The .beta.-galactosidase activity of Bga2 was found to be
449 IU/mg of purified protein. The optimum temperature was found to
be 60.degree. C. and the optimum pH was 5-6.
Example 19
[0525] This example illustrates the assay used to measure the
optimal pH and optimal temperature of acetyl xylan esterases. This
assay measured the release of acetate by the action of acetyl xylan
esterase on acetylated xylooligosaccharides from Eucalyptus
wood.
Reagents
[0526] Acetylated, 4-O-MeGlcA substituted xylo-oligosaccharides
with 2-10 xylose residues from Eucalyptus globulus wood (EW-XOS),
Eucalyptus globulus wood alcohol insoluble solids (AIS) and
Eucalyptus globulus xylan polymer were obtained from Kabel et al.
2002.
[0527] Using the above reagents, the assay was performed as
detailed below.
Enzyme Sample
[0528] 5 mL of substrate solution, containing 1 mg EW-XOS in
Millipore water was mixed with 0.5% (w/w) enzyme/substrate ratio
and incubated at the desired temperature and pH. The pH of the
substrate was adjusted to the desired pH with 1 mM NaOH. The same
NaOH solution was used to adjust the pH by pH STAT (719S and 702SM
Titrino, Metrohm) to keep it constant during reaction. The amount
of NaOH solution added was recorded automatically every 10 seconds.
The added volume of NaOH solution was proportional to the release
of acetate by the acetyl xylan esterase.
Calculation of Activity
[0529] The amount of acetate released was plotted in time. The
slope of this curve at the initial stage of the reaction represents
the initial activity of the enzyme.
Determination of pH and Temperature Optimum
[0530] The pH optimum was determined by analyzing the enzyme
activity towards EW-XOS at pH 4.0, 4.5, 5.0, 5.5, 6.0, 6.5, 7.0 and
7.5 using the above described method. The incubation was done at
35.degree. C. The temperature optimum of the enzyme was determined
by analyzing its activity towards EW-XOS at 35.degree. C.,
40.degree. C., 45.degree. C., 50.degree. C., and 60.degree. C.,
using the above described method. The incubation was done at the pH
optimum obtained from previous experiment.
Results
[0531] The optimum temperature for the enzyme Axe2 was found to be
40.degree. C. and the pH optimum was found to be 7.0. The optimum
temperature for the enzyme Axe3 was found to be 40.degree. C. and
the pH optimum was found to be 7.0. Both, the specific activity of
Axe2 and Axe3 were higher towards oligosaccharides then towards
polysaccharides. However, the specific activity of Axe3 towards
oligosaccharides was lower than the one of Axe2. At the end of the
saccharification period the same amount of acetic acid was released
for both enzymes. These results showed that the Axe2 releases the
acetic acid faster than Axe3, but the total amount of acetic acid
released was equal for both enzymes.
Example 20
[0532] This example illustrates the assay used to measure acetyl
xylan esterase activity towards arabinoxylan oligosaccharides from
Eucalyptus wood. This assay measured the release of acetate by the
action of the acetyl xylan esterases on the arabinoxylan
oligosaccharides.
Reagents
[0533] Phosphate buffer (0.05 M, pH 7.0) was prepared as follows.
13.8 g of NaH.sub.2PO.sub.4*H.sub.2O was dissolved in 1 L of
Millipore water. 26.8 g Na.sub.2HPO.sub.4*7H.sub.2O was dissolved
in Millipore water. 195 mL of the NaH.sub.2PO.sub.4 solution was
mixed with 305 mL of the Na.sub.2HPO.sub.4 solution and adjusted to
1000 mL with Millipore water. The pH of the resulting solution was
equal to 7.0.
[0534] Acetylated, 4-O-MeGlcA substituted xylo-oligosaccharides
with 2-10 xylose residues from Eucalyptus globulus wood (EW-XOS),
Eucalyptus globulus wood AIS and Eucalyptus globulus xylan polymer
were obtained using the method described in Kabel et al. 2002.
Enzyme Sample
[0535] 5 mL of substrate solution, containing 1 mg EW-XOS in
Millipore water was mixed with 0.5% (w/w) enzyme/substrate ratio
and incubated at 40.degree. C. and pH 7 for 24 hours. The reaction
was stopped by heating the samples for 10 minutes at 100.degree. C.
The release of acetic acid and formation of new (arabino)xylan
oligosaccharides were analyzed by Matrix-Assisted Laser
Desorption/Ionisation Time-Of-Flight Mass Spectrometry and
Capillary Electrophoresis.
Substrate Blank
[0536] 5 mL of substrate solution, containing 1 mg EW-XOS in
Millipore water was mixed with buffer to the same volume as the
enzyme sample and incubated at 40.degree. C. and pH 7 for 24 hours.
The reaction is stopped by heating the samples for 10 minutes at
100.degree. C. The release of acetic acid and formation of new
(arabino)xylan oligosaccharides were analyzed by Matrix-Assisted
Laser Desorption/Ionisation Time-Of-Flight Mass Spectrometry and
Capillary Electrophoresis.
Matrix-Assisted Laser Desorption/Ionisation Time-Of-Flight Mass
Spectrometry (MALDI-TOF MS)
[0537] For MALDI-TOF MS an Ultraflex workstation (Bruker Daltronics
GmbH, Germany) was used with a nitrogen laser at 337 nm. The mass
spectrometer was calibrated with a mixture of malto-dextrins (mass
range 365-2309). The samples were mixed with a matrix solution (1
.mu.L each). The matrix solution was prepared by dissolving 10 mg
of 2,5-dihydroxybenzoic acid in a 1 mL mixture of Millipore water
in order to prepare a saturated solution. After thorough mixing,
the solution was centrifuged to remove undissolved material. 1
.mu.L of the prepared sample and 1 .mu.L of matrix solution was put
on a gold plate and dried with warm air.
Capillary Electrophoresis-Laser Induced Fluorescence Detector
(CE-LIF)
[0538] Samples containing about 0.4 mg of EW-XOS were substituted
with 5 nmol of maltose as an internal standard. The samples were
dried using centrifugal vacuum evaporator (Speedvac). 5 mg of APTS
labeling dye (Beckman Coulter) was dissolved in 484 of 15% acetic
acid (Beckman Coulter). The dried samples were mixed with 2 .mu.L
of the labeling dye solution and 2 .mu.L of 1 M Sodium
Cyanoborohydride (THF, Sigma-Aldrich). The samples were incubated
overnight in the dark to allow the labeling reaction to be
completed. After overnight incubation, the labeled samples were
diluted 100 times with Millipore water before analysis by
CE-LIF.
[0539] CE-LIF was performed using ProteomeLab PA800 Protein
Characterization System (Beckman Coulter), controlled by 32 Karat
Software. The capillary column used was polyvinyl alcohol coated
capillary (N--CHO capillary, Beckman Coulter), having 50 .mu.m ID,
50.2 cm length and 40 cm to detector window. 25 mM sodium acetate
buffer pH 4.75 containing 0.4% polyethyleneoxide (Carbohydrate
separation buffer, Beckman Coulter) was used as running buffer. The
sample (ca. 3.5 nL) was injected to the capillary by a pressure of
0.5 psi for 3 seconds. The separation was done for 20 minutes at 30
kV separating voltage, with reversed polarity. During analysis, the
samples were stored at 10.degree. C. The labeled EW-XOS were
detected using LIF detector at 488 nm excitation and 520 nm
emission wavelengths.
Results
[0540] The acetyl xylan esterases Axe2 and Axe3 were found to
release almost all acetyl groups from wheat arabinoxylan
oligosaccharides after 24 hours, except for one ester linkage per
oligomer (as indicated in FIG. 7). It was predicted that the
remaining acetyl group was located at a terminal xylose residue. To
determine the location of the remaining acetyl group, Capillary
Electrophoresis (CE) was performed. With help of CE acetylated
EW-XOS can be separated based on the mass and the position of
acetyl group. In order to determine the location of the remaining
acetyl group, the APTS-labeled Axe hydrolysis product was
subsequently digested with a known GH10 endoxylanase from
Aspergillus awamori (enzyme collection Laboratory of Food
Chemistry, Wageningen University, The Netherlands). Since the
xylanase will cleave xylobiose from the reducing end, the amount of
acetylated xylobiose will increase if the remaining acetyl ester
was near or on the xylose residue at the reducing end. On the
contrary, if the acetyl ester was on or near the xylose residue at
the non-reducing end, only the non-acetylated xylobiose will
increase (only the APTS labeled reducing ends are visible with
CE-LIF). The electropherogram of samples after 5 h digestion by
Axe2 (as indicated in FIG. 8B) as well as by Axe3 (data not shown),
showed that after digestion by xylanasel, there was an increase in
the non-acetylated xylobiose and but increase in the acetylated
xylobiose peaks, which shows that the resistant acetyl ester was
found to be located near the non-reducing end of the
oligosaccharide. This results indicate that the esterases are able
to cleave all acetyl ester linkages as long as they are not close
to the non-reducing end.
Example 21
[0541] This example illustrates the assay used to measure
.beta.-glucosidase activity. This assay measured the release of
p-nitrophenol by the action of .beta.-glucosidase on p-nitrophenyl
.beta.-D-glucopyranoside (PNPG). One .beta.-glucosidase unit of
activity is the amount of enzyme that liberates 1 micromole of
p-nitrophenol in one minute.
Reagents
[0542] Sodium acetate buffer (0.2 M, pH 5.0) was prepared as
follows. 16.4 g of anhydrous sodium acetate or 27.2 g of sodium
acetate*3H.sub.2O was dissolved in distilled water to a final
volume of 1000 mL (Solution A). In a separate flask, 12 g (11.44
mL) of glacial acetic acid was mixed with distilled water to make
the total volume of 1000 mL (Solution B). The final 0.1 M sodium
acetate buffer, pH 5.0, was prepared by mixing Solution A with
Solution B until the pH of the resulting solution was equal to
5.0.
[0543] PNPG from Sigma (St. Louis, USA) was used as the assay
substrate. 20 mg of PNPG was dissolved in 5 mL of sodium acetate
buffer using magnetic stirrer. The solution was stable for 2 days
on storage at 4.degree. C.
[0544] The stop reagent (0.25 M Tris-HCl, pH 8.8) was prepared as
follows. 30.29 g of Tris was dissolved in 900 mL of distilled water
(Solution A). The final 0.25 M Tris-HCl pH 8.5 was prepared by
mixing solution A with 37% HCl until the pH of the resulting
solution was equal to 8.8. The solution volume was adjusted to 1000
mL. This reagent was used to terminate the enzymatic reaction.
[0545] Using the above reagents, the assay was performed as
detailed below.
Enzyme Sample
[0546] 0.025 mL of PNPG stock solution was mixed with 1 .mu.L of
the enzyme sample, 0.075 mL buffer and 0.099 mL Millipore water and
incubated at 37.degree. C. for 4 minutes. Every minute during 4
minutes a 0.04 mL sample was taken and added to 0.06 mL stop
reagent. The absorbance at 410 nm (A.sub.410) was measured in
microtiter plates as A.sub.S (enzyme sample).
Substrate Blank
[0547] 0.025 mL of PNPG stock solution was mixed with 0.075 mL
buffer and 0.1 mL Millipore water and incubated at 37.degree. C.
for 4 minutes. Every minute during 4 minutes a 0.04 mL sample was
taken and added to 0.06 mL stop reagent. The absorbance at 410 nm
(A.sub.410) was measured in microtiter plates as A.sub.SB
(substrate blank sample).
Calculation of Activity
[0548] The A.sub.410 values were plotted against time in minutes
(X-axis). The slope of the graph was calculated (dA). Enzyme
activity was calculated by using the following formula:
Specific
activity=(dA*V.sub.a*d)/(.epsilon.*|*[protein]*V.sub.p)
[0549] dA=slope in A/min
[0550] V.sub.a=reaction volume in l (0.0002 l)
[0551] d=dilution factor of assay mix after adding stop reagent
(2.5)
[0552] .epsilon.=extinction coefficient (0.0137
.mu.W.sup.-cm.sup.-1)
[0553] l=length of cell (0.3 cm)
[0554] [protein]=protein stock concentration in mg/ml
[0555] V.sub.p=volume of protein stock added to assay (0.001
ml)
Results
[0556] The .beta.-glucosidase activity of Bxl2 was found to be
322.6 IU/mL of enzyme produced in 1.5 L fermentations. The
.beta.-glucosidase activity of Abf5 was found to be 36.6 IU/mL of
enzyme produced in 1.5 L fermentations.
Example 22
[0557] This example illustrates the assay used to measure
.beta.-xylosidase activity. This assay measured the release of
xylose by the action of .beta.-xylosidase on xylobiose.
Reagents
[0558] Sodium acetate buffer (0.05 M, pH 5.0) was prepared as
follows. 4.1 g of anhydrous sodium acetate or 6.8 g of sodium
acetate*3H.sub.2O was dissolved in distilled water to a final
volume of 1000 mL (Solution A). In a separate flask, 3.0 g (2.86
mL) of glacial acetic acid was mixed with distilled water to make
the total volume of 1000 mL (Solution B). The final 0.05 M sodium
acetate buffer, pH 5.0, was prepared by mixing Solution A with
Solution B until the pH of the resulting solution was equal to
5.0.
[0559] Xylobiose was purchased from Megazyme (Bray Ireland, Cat. #
P-WAXYI). 25 mg was dissolved in 5 mL sodium acetate buffer pH
5.0.
[0560] The assay was performed as detailed below.
Enzyme Sample
[0561] 0.1 mL of 5.0 mg/mL substrate solution was mixed with 0.02
mL of the enzyme sample at 50.degree. C. and pH 5.0 for 24 hours.
The reaction was stopped by heating the samples for 10 minutes at
100.degree. C. The release of xylose and arabinoxylan
oligosaccharides were analyzed by High Performance Anion Exchange
Chromatography.
Substrate Blank
[0562] 0.1 mL of 5.0 mg/mL substrate solution was mixed with 0.02
mL of the buffer at 50.degree. C. and pH 5.0 for 24 hours. The
reaction was stopped by heating the samples for 10 minutes at
100.degree. C. The release of xylose and arabinoxylan
oligosaccharides were analyzed by High Performance Anion Exchange
Chromatography.
High Performance Anion Exchange Chromatography
[0563] The analysis was performed using a Dionex HPLC system
equipped with a Dionex CarboPac PA-1 (2 mm ID.times.250 mm) column
in combination with a CarboPac PA guard column (1 mm ID.times.25
mm) and a Dionex EDet1 PAD-detector (Dionex Co., Sunnyvale). A flow
rate of 0.25 mL/min was used with the following gradient of sodium
acetate in 0.1 M NaOH: 0-15 min, 0-150 mM. Each elution was
followed by a washing step of 5 min using 1 M sodium acetate in 0.1
M NaOH and an equilibration step of 15 min using 0.1 M NaOH.
Results
[0564] Bxl1 (CL06028, SEQ ID NO: 51) was found to release xylose
from xylobiose, as indicated in FIG. 9. After 24 hours of
incubation the xylobiose was completely degraded into xylose. This
result indicated that Bxl1 possesses .beta.-xylosidase
activity.
[0565] While various embodiments of the present invention have been
described in detail, it is apparent that modifications and
adaptations of those embodiments will occur to those skilled in the
art. It is to be expressly understood, however, that such
modifications and adaptations are within the scope of the present
invention, as set forth in the following exemplary claims.
REFERENCES
[0566] Gruppen H, Hoffmann R A, Kormelink F J M, Voragen A G J,
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Sequence CWU 0 SQTB SEQUENCE LISTING The patent application
contains a lengthy "Sequence Listing" section. A copy of the
"Sequence Listing" is available in electronic form from the USPTO
web site
(http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20140329292A1).
An electronic copy of the "Sequence Listing" will also be available
from the USPTO upon request and payment of the fee set forth in 37
CFR 1.19(b)(3).
0 SQTB SEQUENCE LISTING The patent application contains a lengthy
"Sequence Listing" section. A copy of the "Sequence Listing" is
available in electronic form from the USPTO web site
(http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20140329292A1).
An electronic copy of the "Sequence Listing" will also be available
from the USPTO upon request and payment of the fee set forth in 37
CFR 1.19(b)(3).
* * * * *
References