U.S. patent application number 11/911683 was filed with the patent office on 2009-05-28 for arabinofuranosidases.
This patent application is currently assigned to Novozymes A/S. Invention is credited to Lars Hylling Christensen, Carsten Hoerslev Hansen, Christel Thea Joergensen, Christian Isak Joergensen, Lene Venke Kofod, Hanne Risbjerg Soerensen.
Application Number | 20090136476 11/911683 |
Document ID | / |
Family ID | 36579681 |
Filed Date | 2009-05-28 |
United States Patent
Application |
20090136476 |
Kind Code |
A1 |
Soerensen; Hanne Risbjerg ;
et al. |
May 28, 2009 |
ARABINOFURANOSIDASES
Abstract
The present invention relates to isolated polypeptides having
alpha-L-arabinofuranosidase activity and isolated nucleic acid
sequences encoding the polypeptides. The invention also relates to
nucleic acid constructs, vectors, and host cells comprising the
nucleic acid sequences as well as methods for producing and using
the polypeptides.
Inventors: |
Soerensen; Hanne Risbjerg;
(Holte, DK) ; Joergensen; Christel Thea; (Lyngby,
DK) ; Christensen; Lars Hylling; (Alleroed, DK)
; Joergensen; Christian Isak; (Bagsvaerd, DK) ;
Hansen; Carsten Hoerslev; (Copenhagen, DK) ; Kofod;
Lene Venke; (Uggerloese, DK) |
Correspondence
Address: |
NOVOZYMES NORTH AMERICA, INC.
500 FIFTH AVENUE, SUITE 1600
NEW YORK
NY
10110
US
|
Assignee: |
Novozymes A/S
Bagsvaerd
DK
|
Family ID: |
36579681 |
Appl. No.: |
11/911683 |
Filed: |
April 25, 2006 |
PCT Filed: |
April 25, 2006 |
PCT NO: |
PCT/DK2006/000213 |
371 Date: |
October 31, 2007 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
60676115 |
Apr 29, 2005 |
|
|
|
60735661 |
Nov 10, 2005 |
|
|
|
Current U.S.
Class: |
424/94.6 ;
435/195; 435/252.3; 435/320.1; 435/69.1; 536/23.2 |
Current CPC
Class: |
A23K 20/168 20160501;
C12N 9/2402 20130101; Y02E 50/10 20130101; A21D 8/042 20130101;
A23K 20/189 20160501; C12Y 302/01055 20130101; A23L 29/06
20160801 |
Class at
Publication: |
424/94.6 ;
435/195; 536/23.2; 435/320.1; 435/252.3; 435/69.1 |
International
Class: |
A61K 38/46 20060101
A61K038/46; C12N 9/14 20060101 C12N009/14; C07H 21/04 20060101
C07H021/04; C12N 15/63 20060101 C12N015/63; C12N 1/21 20060101
C12N001/21; C12P 21/06 20060101 C12P021/06 |
Foreign Application Data
Date |
Code |
Application Number |
Apr 26, 2005 |
DK |
PA 2005 00609 |
Nov 10, 2005 |
DK |
PA 2005 01562 |
Claims
1-18. (canceled)
19. An isolated arabinofuranosidase which is selected from the
group consisting of: a) a polypeptide having an amino acid sequence
as the mature peptide shown in SEQ ID NO: 2, or which can be
obtained there from by substitution, deletion, and/or insertion of
one or more amino acids; b) an analogue of the polypeptide of (a)
which: i) has at least 80% homology with said polypeptide, or ii)
is an allelic variant of said polypeptide, c) a polypeptide which
is encoded by a nucleic acid sequence which hybridizes under high
stringency conditions with a complementary strand of the nucleic
acid sequence of SEQ ID NO: 1 encoding the mature polypeptide or a
subsequence thereof having at least 100 nucleotides; d) a
polypeptide having an amino acid sequence as the mature peptide
shown in SEQ ID NO: 4, or which can be obtained therefrom by
substitution, deletion, and/or insertion of one or more amino
acids; e) an analogue of the polypeptide of (d) which: i) has at
least 60% homology with said polypeptide, or ii) is an allelic
variant of said polypeptide, and f) a polypeptide which is encoded
by a nucleic acid sequence which hybridizes under high stringency
conditions with a complementary strand of the nucleic acid sequence
of SEQ ID NO: 3 encoding the mature polypeptide or a subsequence
thereof having at least 100 nucleotides.
20. The arabinofuranosidase of claim 19, which is native to a
strain of Humicola.
21. The arabinofuranosidase of claim 19, which is native to a
strain of H. insolens.
22. The arabinofuranosidase of claim 19, which is native to a
strain of Meripilus.
23. The arabinofuranosidase of claim 19, which is native to a
strain of Meripilus giganteus.
24. A composition comprising the arabinofuranosidase of claim
19.
25. A process of treating an arabinoxylan-containing substrate,
comprising treating the arabinoxylan substrate with an
arabinofuranosidase of claim 19.
26. The process of claim 25, wherein the arabinoxylan-containing
substrate is selected from the group consisting of herbaceous
and/or woody energy crops, agricultural food and feed crops, animal
feed products, tubers, roots, stems, legumes, cassava peels, cocoa
pods, rice husks and/or hulls, rice bran from rice polishing, cobs,
straw, hulls and/or husks from cereal grain, pressed sugar cane
stalk, sugar beet pulp, locust bean pulp, vegetable or fruit
pomaces, cereals or whole grain agricultural crop waste, straw,
stalks, leaves, corn bran, husks, cobs, rind, shells, pods, wood
waste, bark, shavings, sawdust, wood pulp, pulping liquor, waste
paper, cardboard, construction and demolition wood waste,
industrial or municipal waste water solids or sludge, manure,
by-product from brewing and/or fermentation processes, wet
distillers grain, dried distillers grain, spent grain, vinasse and
bagasse.
27. A nucleic acid sequence comprising a nucleic acid sequence
which encodes the arabinofuranosidase of claim 19.
28. A nucleic acid construct, recombinant expression vector, or
recombinant host cell comprising the nucleic acid sequence of claim
27 operably linked to one or more control sequences capable of
directing the expression of the arabinofuranosidase in a suitable
expression host.
29. A method for producing an arabinofuranosidase comprising (a)
cultivating the host cell of claim 28 under conditions conducive to
production of the arabinofuranosidase, and (b) recovering the
arabinofuranosidase.
Description
FIELD OF THE INVENTION
[0001] The present invention relates to isolated polypeptides
having alpha-L-arabinofuranosidase activity and isolated nucleic
acid sequences encoding the polypeptides. The invention also
relates to nucleic acid constructs, vectors, and host cells
comprising the nucleic acid sequences as well as methods for
producing and using the polypeptides.
BACKGROUND OF THE INVENTION
[0002] Arabinofuranosidases are capable of hydrolyzing terminal
non-reducing alpha-L-arabinofuranoside residues in
alpha-L-arabinosides and are classified as EC 3.2.1.55.
Arabinofuranosidases have been isolated from several organisms
including filamentous fungi. However, very few
alpha-arabinofuranosidases able to liberate arabinose from
di-substituted xyloses are known. From Bifidobacterium adolescentis
an intracellular enzyme able to release arabinose from C3 of
disubstituted xylose (also internally) has been described (Van
Laere, 1997, Appl. Microbiol. Biotechnol, 47, 231-235 and Van den
Broek, 2005, Applied Microbiology and Biotechnology). From barley
an enzyme active on mono- and terminally di-sustituted xyloses has
been isolated, but it has little activity on internally
di-substituted xyloses (Ferre, 2000, Eur. J. Biochem., 267,
6633-6641). An enzyme from Trichoderma reesei is possibly active on
terminally disubstituted residues (activity seen on
3,5-di-O-alpha-Larabinofuranosyl-alpha-L-arabinofuranoside), but
has no activity towards an oligo-substrate with internally C3
substituted arabinose (Nogawa, 1999, Appl. Environ. Microbiol., 65,
3964-3968).
[0003] A comparison with full-length prior-art sequences shows that
the mature amino acid sequence of the invention has 72% homology
with an amino acid sequence from Chaetomium globosum, and the DNA
sequence of the invention shows 73% homology with that of the
corresponding Chaetomium globosum DNA sequence.
SUMMARY OF THE INVENTION
[0004] The inventors have isolated an alpha-L-arabinofuranosidase
from a strain of the filamentous fungi Humicola insolens able to
liberate arabinose from di-substituted xyloses, i.e. the
alpha-L-arabinofuranosidase is active on xylose units of wheat
arabinoxylan with arabinose attached to C2 and C3. The inventors
also isolated the gene encoding the novel
alpha-L-arabinofuranosidase. The activity towards di-substituted
xyloses is essential for total hydrolysis of arabinoxylan to
monosaccharides e.g. in production of ethanol from biomass.
[0005] Accordingly, in a first aspect the invention provides an
arabinofuranosidase which is: a) a polypeptide having an amino acid
sequence as the mature peptide shown in SEQ ID NO: 2, or which can
be obtained there from by substitution, deletion, and/or insertion
of one or more amino acids; b) an analogue of the polypeptide
defined in (a) or (b) which: i) has at least 80% homology with said
polypeptide, ii) is an allelic variant of said polypeptide, c) a
polypeptide which is encoded by a nucleic acid sequence which
hybridizes under high stringency conditions with a complementary
strand of the nucleic acid sequence of SEQ ID NO:2 encoding the
mature polypeptide or a subsequence thereof having at least 100
nucleotides.
[0006] In a second aspect the invention provides a nucleic acid
sequence comprising a nucleic acid sequence which encodes the
arabinofuranosidase the first aspect.
[0007] In a third aspect the invention provides a nucleic acid
sequence which comprises: a) the DNA sequence encoding the
arabinofuranosidase shown in SEQ ID NO:2, b) an analog DNA sequence
which i) has at least 80% homology with said DNA sequence, or ii)
hybridizes at high stringency with a complementary strand of said
DNA sequence or a subsequence thereof having at least 100
nucleotides, iii) is an allelic variant thereof, or a complementary
strand to a) or b).
[0008] In a fourth aspect the invention provides a nucleic acid
sequence which has at least 80% homology with the DNA sequence
shown in SEQ ID NO:1, or a) hybridizes at high stringency with a
complementary strand of said DNA sequence or a subsequence thereof
having at least 100 nucleotides, b) is an allelic variant thereof,
or a complementary strand to a) or b).
[0009] In a fifth aspect the invention provides a nucleic acid
construct comprising the nucleic acid sequence of the second, third
and fourth aspect operably linked to one or more control sequences
capable of directing the expression of the arabinofuranosidase in a
suitable expression host.
[0010] In a sixth aspect the invention provides a recombinant
expression vector comprising the nucleic acid construct of the
fifth aspect.
[0011] In a seventh aspect the invention provides a recombinant
host cell comprising the nucleic acid construct of the sixth
aspect.
[0012] In an eight aspect the invention provides a method for
producing an arabinofuranosidase comprising cultivating the host
cell of the seventh aspect under conditions conducive to production
of the arabinofuranosidase, and recovering the
arabinofuranosidase.
[0013] In a ninth aspect the invention provides a use of the
arabinofuranosidase of the first aspect.
DETAILED DESCRIPTION OF THE INVENTION
[0014] In a first embodiment of the present invention, the isolated
polypeptide has an amino acid sequence which has at least 80%
identity with the amino acid sequence shown as amino acids 1 to 558
of SEQ ID NO:2 (i.e., the mature polypeptide). In an interesting
embodiment of the invention the polypeptide has at least 75%, at
least 85%, at least 90%, at least 95%, at least 96%, at least 97%,
at least 98%, or at least 99% identity with the amino acid sequence
shown as amino acids 1 to 558 of SEQ ID NO:2 (hereinafter
"homologous polypeptides").
[0015] In a preferred embodiment, the homologous polypeptides have
an amino acid sequence which differs by five amino acids, e.g. by
four amino acids, such as by three amino acids, by two amino acids,
or by one amino acid from the amino acid sequence shown as amino
acids 1 to 558 of SEQ ID NO:2.
[0016] Alignments of sequences and calculation of homology may
suitably be determined by means of computer programs known in the
art such as GAP provided in the GCG program package (Program Manual
for the Wisconsin Package, Version 8, August 1994, Genetics
Computer Group, 575 Science Drive, Madison, Wis., USA 53711)
(Needleman, S. B. and Wunsch, C. D., (1970), Journal of Molecular
Biology, 48, 443-453. The following settings for amino acid
sequence comparison are used: GAP creation penalty of 3.0 and GAP
extension penalty of 0.1. The relevant part of the amino acid
sequence for the homology determination is the mature polypeptide,
i.e. without the signal peptide.
[0017] Preferably, the polypeptides of the present invention
comprise the amino acid sequence shown as amino acids 1 to 558 of
SEQ ID NO:2, an allelic variant thereof, or a fragment thereof that
has arabinofuranosidase activity. Obviously, the polypeptide of the
invention may also consist of the amino acid sequence shown as
amino acids 1 to 558 of SEQ ID NO:2.
[0018] In an embodiment of the invention, the isolated polypeptide
is an alpha-L-arabinofuranosidase derived from a filamentous
fungus, e.g. Humicola insolens, and able to liberate arabinose from
di-substituted xyloses, e.g. the alpha-L-arabinofuranosidase is
active on xylose units of wheat arabinoxylan with arabinose
attached to C2 and C3.
[0019] An allelic variant denotes any of two or more alternative
forms of a gene occupying the same chromosomal locus. Allelic
variation arises naturally through mutation, and may result in
polymorphism within populations. Gene mutations can be silent (no
change in the encoded polypeptide) or may encode polypeptides
having altered amino acid sequences. An allelic variant of a
polypeptide is a polypeptide encoded by an allelic variant of a
gene.
[0020] In an embodiment of the invention, the isolated polypeptide
is encoded by a nucleic acid sequence which hybridizes under low
stringency conditions, preferably under medium stringency
conditions, more preferably under high stringency conditions with
(i) a complementary strand of the nucleic acid sequence shown as
nucleotides 1 to 1677 of SEQ ID NO:1, or (ii) a subsequence of (i)
of at least 100 nucleotides (J. Sambrook, E. F. Fritsch, and T.
Maniatus, 1989, Molecular Cloning, A Laboratory Manual, 2d edition,
Cold Spring Harbor, N.Y.).
[0021] The subsequence of the complementary strand of the nucleic
acid sequence shown as nucleotides 1 to 1677 of SEQ ID NO:1 may be
at least 100 nucleotides or preferably at least 200 nucleotides.
Moreover, the subsequence should encode a polypeptide fragment
which has arabinofuranosidase activity. The polypeptides may also
be allelic variants or fragments of the polypeptides that have
arabinofuranosidase activity.
[0022] The nucleic acid sequence of SEQ ID NO:1 or a subsequence
thereof, as well as the amino acid sequence of SEQ ID NO:2 or a
fragment thereof, may be used to design a nucleic acid probe to
identify and clone DNA encoding polypeptides having
arabinofuranosidase activity from strains of different genera or
species according to methods well known in the art. In particular,
such probes can be used for hybridization with the genomic or cDNA
of the genus or species of interest, following standard Southern
blotting procedures, in order to identify and isolate the
corresponding gene therein. Such probes can be considerably shorter
than the entire sequence, but should be at least 15, preferably at
least 25, and more preferably at least 35 nucleotides in length.
Longer probes can also be used. Both DNA and RNA probes can be
used. The probes are typically labeled for detecting the
corresponding gene (for example, with .sup.32P, .sup.3H, .sup.35S,
biotin, or avidin). Such probes are encompassed by the present
invention.
[0023] Thus, a genomic DNA or cDNA library prepared from such other
organisms may be screened for DNA which hybridizes with the probes
described above and which encodes a polypeptide having
arabinofuranosidase activity. Genomic or other DNA from such other
organisms may be separated by agarose or polyacrylamide get
electrophoresis, or other separation techniques known by the
skilled person. DNA from the libraries or the separated DNA may be
transferred to and immobilized on nitrocellulose or other suitable
carrier materials. In order to identify a clone or DNA which is
homologous with SEQ ID NO:1 or a subsequence thereof, the carrier
material is used in a Southern blot. For purposes of the present
invention, hybridization indicates that the nucleic acid sequence
hybridizes to a labeled nucleic acid probe corresponding to the
nucleic acid sequence shown in SEQ ID NO:1, its complementary
strand, or a subsequence thereof, under low to high stringency
conditions. Molecules to which the nucleic acid probe hybridizes
under these conditions are detected using X-ray film.
[0024] In another interesting embodiment, the nucleic acid probe is
a nucleic acid sequence which encodes the (mature) polypeptide of
SEQ ID NO:2, or a subsequence thereof. In a third interesting
embodiment, the nucleic acid probe is SEQ ID NO:1. In a fourth
interesting embodiment, the nucleic acid probe is the mature
polypeptide coding region of SEQ ID NO:1.
[0025] For long probes of at least 100 nucleotides in length, low
to high stringency conditions are defined as prehybridization and
hybridization at 42.degree. C. in 5.times.SSPE, 0.3% SDS, 200
.mu.g/ml sheared and denatured salmon sperm DNA, and either 25%
formamide for low stringency, 35% formamide for medium stringency,
or 50% formamide for high stringency, following standard Southern
blotting procedures.
[0026] For long probes of at least 100 nucleotides in length, the
carrier material is finally washed three times each for 15 minutes
using 2.times.SSC, 0.2% SDS preferably at least at 50.degree. C.
(low stringency), more preferably at least at 55.degree. C. (medium
stringency), even more preferably at least at 65.degree. C. (high
stringency).
[0027] For short probes which are about 15 nucleotides to about 70
nucleotides in length, stringency conditions are defined as
prehybridization, hybridization, and washing post-hybridization at
5.degree. C. to 10.degree. C. below the calculated T.sub.m using
the calculation according to Bolton and McCarthy (1962, Proceedings
of the National Academy of Sciences USA 48:1390) in 0.9 M NaCl,
0.09 M Tris-HCl pH 7.6, 6 mM EDTA, 0.5% NP-40, 1.times.Denhardt's
solution, 1 mM sodium pyrophosphate, 1 mM sodium monobasic
phosphate, 0.1 mM ATP, and 0.2 mg of yeast RNA per ml, following
standard Southern blotting procedures.
[0028] For short probes which are about 15 nucleotides to about 70
nucleotides in length, the carrier material is washed once in
6.times.SCC plus 0.1% SDS for 15 minutes and twice each for 15
minutes using 6.times.SSC at 5.degree. C. to 10.degree. C. below
the calculated T.sub.m.
[0029] As indicated above, the polypeptide of the invention may be
a polypeptide having an amino acid sequence of SEQ ID NO:2 or the
mature polypeptide thereof, wherein one or more amino acid(s) has
(have) been substituted by another (other) amino acid(s), wherein
one or more amino acid(s) has (have) been deleted, and/or wherein
one more amino acid(s) has (have) been inserted.
[0030] Preferably, amino acid changes are of a minor nature, that
is conservative amino acid substitutions that do not significantly
affect the folding and/or activity of the protein; small deletions,
typically of one to about 30 amino acids; small amino- or
carboxyl-terminal extensions, such as an amino-terminal methionine
residue; a small linker peptide of up to about 20-25 residues; or a
small extension that facilitates purification by changing net
charge or another function, such as a poly-histidine tract, an
antigenic epitope or a binding domain.
[0031] Examples of conservative substitutions are within the group
of basic amino acids (arginine, lysine and histidine), acidic amino
acids (glutamic acid and aspartic acid), polar amino acids
(glutamine and asparagine), hydrophobic amino acids (leucine,
isoleucine and valine), aromatic amino acids (phenylalanine,
tryptophan and tyrosine), and small amino acids (glycine, alanine,
serine, threonine and methionine). Amino acid substitutions which
do not generally alter the specific activity are known in the art
and are described, for example, by H. Neurath and R. L. Hill, 1979,
In, The Proteins, Academic Press, New York. The most commonly
occurring exchanges are Ala/Ser, Val/Ile, Asp/Glu, Thr/Ser,
Ala/Gly, Ala/Thr, Ser/Asn, Ala/Val, Ser/Gly, Tyr/Phe, Ala/Pro,
Lys/Arg, Asp/Asn, Leu/Ile, Leu/Val, Ala/Glu, and Asp/Gly as well as
these in reverse.
[0032] In general, it is preferred that the polypeptides of the
invention have at least 20% of the arabinofuranosidase activity of
the polypeptide having the amino acid sequence shown as amino acids
1 to 558 of SEQ ID NO:2. Particular preferred are polypeptides,
which have at least 30%, such as at least 40%, e.g. at least 50%,
preferably at least 60%, such as at least 70%, e.g. at least 80%,
more preferred at least 90%, or at least 95% of the
arabinofuranosidase activity of the polypeptide having the amino
acid sequence shown as amino acids 1 to 558 of SEQ ID NO:2.
[0033] A polypeptide of the present invention may be obtained from
microorganisms of any genus. For purposes of the present invention,
the term "obtained from" as used herein in connection with a given
source shall mean that the polypeptide encoded by the nucleic acid
sequence is produced by the source or by a cell in which the
nucleic acid sequence from the source has been inserted. In a
preferred embodiment, the polypeptide is secreted
extracellularly.
[0034] A polypeptide of the present invention may be a fungal
polypeptide, and more preferably a filamentous fungal polypeptide
such as an Acremonium, Aspergillus, Aureobasidium, Cryptococcus,
Filibasidium, Fusarium, Humicola, Magnaporthe, Mucor,
Myceliophthora, Neocallimastix, Neurospora, Paecilomyces,
Penicillium, Piromyces, Schizophyllum, Talaromyces, Thermoascus,
Thielavia, Tolypocladium, or Trichoderma polypeptide.
[0035] In another preferred embodiment, the polypeptide is an
Aspergillus aculeatus, Aspergillus awamori, Aspergillus foetidus,
Aspergillus japonicus, Aspergillus nidulans, Aspergillus niger,
Aspergillus oryzae, Fusarium bactridioides, Fusarium cerealis,
Fusarium crookwellense, Fusarium culmorum, Fusarium graminearum,
Fusarium graminum, Fusarium heterosporum, Fusarium negundi,
Fusarium oxysporum, Fusarium reticulatum, Fusarium roseum, Fusarium
sambucinum, Fusarium sarcochroum, Fusarium sporotrichioides,
Fusarium sulphureum, Fusarium torulosum, Fusarium trichothecioides,
Fusarium venenatum, Humicola insolens, Humicola lanuginosa, Mucor
miehei, Myceliophthora thermophila, Neurospora crassa, Penicillium
purpurogenum, Trichoderma harzianum, Trichoderma koningii,
Trichoderma longibrachiatum, Trichoderma reesei, or Trichoderma
viride polypeptide.
[0036] It will be understood that for the aforementioned species,
the invention encompasses both the perfect and imperfect states,
and other taxonomic equivalents, e.g., anamorphs, regardless of the
species name by which they are known. Those skilled in the art will
readily recognize the identity of appropriate equivalents.
[0037] Strains of these species are readily accessible to the
public in a number of culture collections, such as the American
Type Culture Collection (ATCC), Deutsche Sammlung von
Mikroorganismen und Zellkulturen GmbH (DSM), Centraalbureau Voor
Schimmelcultures (CBS), and Agricultural Research Service Patent
Culture Collection, Northern Regional Research Center (NRRL).
[0038] In a most preferred embodiment of the invention the
polypeptide of the invention is derived from a strain within the
Ascomycota, e.g., within the genus Humicola, such as within H.
lanuginosa H. fuscoatra, H. grisea, H. lutea, H. nigrescens and in
particular within H. insolens. In a particularly preferred
embodiment of the invention the polypeptide of the invention is
derived from the H. insolens strain described in WO9117243 and
deposited Apr. 14, 1980 at the German Collection of Microorganisms
and Cell cultures (DSM, Deutsche Sammlung von Mikroorganismen und
Zellkulturen) Gottingen, Germany, under the DSM number 1800) in
accordance with the provisions of the Budapest Treaty.
[0039] Furthermore, such polypeptides may be identified and
obtained from other sources including microorganisms isolated from
nature (e.g., soil, composts, water, etc.) using the
above-mentioned probes, Techniques for isolating microorganisms
from natural habitats are well known in the art. The nucleic acid
sequence may then be derived by similarly screening a genomic or
cDNA library of another microorganism. Once a nucleic acid sequence
encoding a polypeptide has been detected with the probe(s), the
sequence may be isolated or cloned by utilizing techniques which
are known to those of ordinary skill in the art (see, e.g.,
Sambrook et al., 1989, supra).
[0040] Polypeptides encoded by nucleic acid sequences of the
present invention also include fused polypeptides or cleavable
fusion polypeptides in which another polypeptide is fused at the
N-terminus or the C-terminus of the polypeptide or fragment
thereof. A fused polypeptide is produced by fusing a nucleic acid
sequence (or a portion thereof) encoding another polypeptide to a
nucleic acid sequence (or a portion thereof) of the present
invention. Techniques for producing fusion polypeptides are known
in the art, and include ligating the coding sequences encoding the
polypeptides so that they are in frame and that expression of the
fused polypeptide is under control of the same promoter(s) and
terminator.
Nucleic Acid Sequences
[0041] The present invention also relates to isolated nucleic acid
sequences which encode a polypeptide of the present invention.
[0042] In one interesting embodiment, the nucleic acid sequence has
at least 80% identity with the nucleic acid sequence shown as
nucleotides 1 to 1677 of SEQ ID NO:1. Preferably, the nucleic acid
sequence has at least at least 85%, at least 90%, at least 95%, at
least 96%, at least 97%, at least 98%, or at least 99% identity
with the nucleic acid sequence shown as nucleotides 1 to 1677 of
SEQ ID NO:1. In another interesting embodiment of the invention the
nucleic acid sequence comprises the amino acid sequence shown as
nucleotides 1 to 1677 of SEQ ID NO:1, an allelic variant thereof,
or a fragment thereof capable of encoding a polypeptide according
to the invention. Obviously, the nucleic acid sequence may consist
of the amino acid sequence shown as nucleotides 1 to 1677 of SEQ ID
NO:1.
[0043] The present invention also encompasses nucleic acid
sequences which encode a polypeptide having the amino acid sequence
of SEQ ID NO:2 or the mature polypeptide thereof, which differ from
SEQ ID NO:1 by virtue of the degeneracy of the genetic code. The
present invention also relates to subsequences of SEQ ID NO:1 which
encode fragments of SEQ ID NO:2 that have arabinofuranosidase
activity.
[0044] A subsequence of SEQ ID NO:1 is a nucleic acid sequence
encompassed by nucleotides 1 to 1677 SEQ ID NO:1 except that one or
more nucleotides from the 5' and/or 3'end have been deleted.
[0045] The present invention also relates to isolated nucleic acid
sequences encoding a polypeptide of the present invention, which
hybridize under low stringency conditions, preferably under medium
stringency conditions, more preferably under high stringency
conditions, with (i) a complementary strand of the nucleic acid
sequence shown as nucleotides 1 to 1677 of SEQ ID NO:1, or (ii) a
subsequence of (i) of at least 100 nucleotides. The present
invention also relates to complementary strands of (i), (ii), and
(iii).
[0046] The techniques used to isolate or clone a nucleic acid
sequence encoding a polypeptide are known in the art and include
isolation from genomic DNA, preparation from cDNA, or a combination
thereof. The cloning of the nucleic acid sequences of the present
invention from such genomic DNA can be effected, e.g., by using the
well known polymerase chain reaction (PCR) or antibody screening of
expression libraries to detect cloned DNA fragments with shared
structural features. See, e.g., Innis et al. 1990, PCR: A Guide to
Methods and Application, Academic Press, New York. Other nucleic
acid amplification procedures such as ligase chain reaction (LCR),
ligated activated transcription (LAT) and nucleic acid
sequence-based amplification (NASBA) may be used. The nucleic acid
sequence may be cloned from a strain of Humicola insolens or
another or related organism and may, for example, be an allelic or
species variant of the polypeptide encoding region of the nucleic
acid sequence.
[0047] An isolated nucleic acid sequence can, for example, be
obtained by standard cloning procedures used in genetic engineering
to relocate the nucleic acid sequence from its natural location to
a different site where it will be reproduced. The cloning
procedures may involve excision and isolation of a desired nucleic
acid fragment comprising the nucleic acid sequence encoding the
polypeptide, insertion of the fragment into a vector molecule, and
incorporation of the recombinant vector into a host cell where
multiple copies or clones of the nucleic acid sequence will be
replicated. The nucleic acid sequence may be of genomic, cDNA, RNA,
semisynthetic, synthetic origin, or any combinations thereof.
[0048] For purposes of the present invention, the degree of
identity between two nucleic acid sequences is determined as
described above.
[0049] Modification of a nucleic acid sequence encoding a
polypeptide of the present invention may be necessary for the
synthesis of polypeptides substantially similar to the polypeptide.
The term "substantially similar" to the polypeptide refers to
non-naturally occurring forms of the polypeptide. These
polypeptides may differ in some engineered way from the polypeptide
isolated from its native source, e.g., variants that differ in
specific activity, thermostability, pH optimum, or the like. The
variant sequence may be constructed on the basis of the nucleic
acid sequence presented as the polypeptide encoding part of SEQ ID
NO:1, e.g., a subsequence thereof, and/or by introduction of
nucleotide substitutions which do not give rise to another amino
acid sequence of the polypeptide encoded by the nucleic acid
sequence, but which correspond to the codon usage of the host
organism intended for production of the enzyme, or by introduction
of nucleotide substitutions which may give rise to a different
amino acid sequence. For a general description of nucleotide
substitution, see, e.g., Ford et al, 1991, Protein Expression and
Purification 2: 95-107.
[0050] It will be apparent to those skilled in the art that such
substitutions can be made outside the regions critical to the
function of the molecule and still result in an active polypeptide.
Amino acid residues essential to the activity of the polypeptide
encoded by the isolated nucleic acid sequence of the invention, and
therefore preferably not subject to substitution, may be identified
according to procedures known in the art such as site-directed
mutagenesis or alanine-scanning mutagenesis (see, e.g., Cunningham
and Wells, 1989, Science 244: 1081-1085). In the latter technique,
mutations are introduced at every positively charged residue in the
molecule, and the resultant mutant molecules are tested for
arabinofuranosidase activity to identify amino acid residues that
are critical to the activity of the molecule. Sites of
substrate-enzyme interaction can also be determined by analysis of
the three-dimensional structure as determined by such techniques as
nuclear magnetic resonance analysis, crystallography or
photoaffinity labelling (see, e.g., de Vos et al. 1992, Science
255: 306-312; Smith et al. 1992, Journal of Molecular Biology 224:
899-904; Wlodaver et al., 1992, FEBS Letters 309: 59-64).
Nucleic Acid Constructs
[0051] The present invention also relates to nucleic acid
constructs comprising a nucleic acid sequence of the present
invention operably linked to one or more control sequences capable
of directing the expression of the polypeptide in a suitable host
cell.
[0052] An isolated nucleic acid sequence encoding a polypeptide of
the present invention may be manipulated in a variety of ways to
provide for expression of the polypeptide. Manipulation of the
nucleic acid sequence prior to its insertion into a vector may be
desirable or necessary depending on the expression vector. The
techniques for modifying nucleic acid sequences utilizing
recombinant DNA methods are well known in the art.
[0053] The control sequences include all components which are
necessary or advantageous for the expression of a polypeptide of
the present invention. Each control sequence may be native or
foreign to the nucleic acid sequence encoding the polypeptide. Such
control sequences include, but are not limited to, a leader,
polyadenylation sequence, propeptide sequence, promoter, signal
peptide sequence, and transcription terminator. At a minimum, the
control sequences include a promoter, and transcriptional and
translational stop signals. The control sequences may be provided
with linkers for the purpose of introducing specific restriction
sites facilitating ligation of the control sequences with the
coding region of the nucleic acid sequence encoding a
polypeptide.
[0054] The control sequence may be an appropriate promoter
sequence, a nucleic acid sequence which is recognized by a host
cell for expression of the nucleic acid sequence. The promoter
sequence contains transcriptional control sequences which mediate
the expression of the polypeptide. The promoter may be any nucleic
acid sequence which shows transcriptional activity in the host cell
of choice including mutant, truncated, and hybrid promoters, and
may be obtained from genes encoding extracellular or intracellular
polypeptides either homologous or heterologous to the host
cell.
[0055] Examples of suitable promoters for directing the
transcription of the nucleic acid constructs of the present
invention, especially in a bacterial host cell, are the promoters
obtained from the E. coli lac operon, Streptomyces coelicolor
agarase gene (dagA), Bacillus subtilis levansucrase gene (sacB),
Bacillus licheniformis alpha-amylase gene (amyL), Bacillus
stearothermophilus maltogenic amylase gene (amyM), Bacillus
amyloliquefaciens alpha-amylase gene (amyQ), Bacillus licheniformis
penicillinase gene (penP), Bacillus subtilis xylA and xylB genes,
and prokaryotic beta-lactamase gene (Villa-Kamaroff et al., 1978,
Proceedings of the National Academy of Sciences USA 75: 3727-3731),
as well as the tac promoter (DeBoer et al., 1983, Proceedings of
the National Academy of Sciences USA 80: 21-25) Further promoters
are described in "Useful proteins from recombinant bacteria" in
Scientific American, 1980, 242: 74-94; and in Sambrook et al. 1989,
supra.
[0056] Examples of suitable promoters for directing the
transcription of the nucleic acid constructs of the present
invention in a filamentous fungal host cell are promoters obtained
from the genes for Aspergillus oryzae TAKA amylase, Rhizomucor
miehei aspartic proteinase, Aspergillus niger neutral
alpha-amylase, Aspergillus niger acid stable alpha-amylase,
Aspergillus niger or Aspergillus awamori glucoamylase (glaA),
Rhizomucor miehei lipase, Aspergillus oryzae alkaline protease,
Aspergillus oryzae triose phosphate isomerase, Aspergillus nidulans
acetamidase, and Fusarium oxysporum trypsin-like protease (WO
96/00787), as well as the NA2-tpi promoter (a hybrid of the
promoters from the genes for Aspergillus niger neutral
alpha-amylase and Aspergillus oryzae triose phosphate isomerase),
and mutant, truncated, and hybrid promoters thereof.
[0057] In a yeast host, useful promoters are obtained from the
genes for Saccharomyces cerevisiae enolase (ENO-1), Saccharomyces
cerevisiae galactokinase (GAL1), Saccharomyces cerevisiae alcohol
dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP),
and Saccharomyces cerevisiae 3-phosphoglycerate kinase. Other
useful promoters for yeast host cells are described by Romanos et
al., 1992, Yeast 8: 423-488.
[0058] The control sequence may also be a suitable transcription
terminator sequence, a sequence recognized by a host cell to
terminate transcription. The terminator sequence is operably linked
to the 3' terminus of the nucleic acid sequence encoding the
polypeptide. Any terminator which is functional in the host cell of
choice may be used in the present invention.
[0059] Preferred terminators for filamentous fungal host cells are
obtained from the genes for Aspergillus oryzae TAKA amylase,
Aspergillus niger glucoamylase, Aspergillus nidulans anthranilate
synthase, Aspergillus niger alpha-glucosidase, and Fusarium
oxysporum trypsin-like protease.
[0060] Preferred terminators for yeast host cells are obtained from
the genes for Saccharomyces cerevisiae enolase, Saccharomyces
cerevisiae cytochrome C (CYC1), and Saccharomyces cerevisiae
glyceraldehyde-3-phosphate dehydrogenase. Other useful terminators
for yeast host cells are described by Romanos et al., 1992,
supra.
[0061] The control sequence may also be a suitable leader sequence,
a nontranslated region of an mRNA which is important for
translation by the host cell. The leader sequence is operably
linked to the 5' terminus of the nucleic acid sequence encoding the
polypeptide. Any leader sequence that is functional in the host
cell of choice may be used in the present invention.
[0062] Preferred leaders for filamentous fungal host cells are
obtained from the genes for Aspergillus oryzae TAKA amylase and
Aspergillus nidulans triose phosphate isomerase.
[0063] Suitable leaders for yeast host cells are obtained from the
genes for Saccharomyces cerevisiae enolase (ENO-1), Saccharomyces
cerevisiae 3-phosphoglycerate kinase, Saccharomyces cerevisiae
alpha-factor, and Saccharomyces cerevisiae alcohol
dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase
(ADH2/GAP).
[0064] The control sequence may also be a polyadenylation sequence,
a sequence operably linked to the 3' terminus of the nucleic acid
sequence and which, when transcribed, is recognized by the host
cell as a signal to add polyadenosine residues to transcribed mRNA.
Any polyadenylation sequence which is functional in the host cell
of choice may be used in the present invention.
[0065] Preferred polyadenylation sequences for filamentous fungal
host cells are obtained from the genes for Aspergillus oryzae TAKA
amylase, Aspergillus niger glucoamylase, Aspergillus nidulans
anthranilate synthase, Fusarium oxysporum trypsin-like protease,
and Aspergillus niger alpha-glucosidase.
[0066] Useful polyadenylation sequences for yeast host cells are
described by Guo and Sherman, 1995, Molecular Cellular Biology 15:
5983-5990.
[0067] The control sequence may also be a signal peptide coding
region that codes for an amino acid sequence linked to the amino
terminus of a polypeptide and directs the encoded polypeptide into
the cell's secretory pathway. The 5' end of the coding sequence of
the nucleic acid sequence may inherently contain a signal peptide
coding region naturally linked in translation reading frame with
the segment of the coding region which encodes the secreted
polypeptide. Alternatively, the 5' end of the coding sequence may
contain a signal peptide coding region which is foreign to the
coding sequence. The foreign signal peptide coding region may be
required where the coding sequence does not naturally contain a
signal peptide coding region. Alternatively, the foreign signal
peptide coding region may simply replace the natural signal peptide
coding region in order to enhance secretion of the polypeptide.
However, any signal peptide coding region which directs the
expressed polypeptide into the secretory pathway of a host cell of
choice may be used in the present invention.
[0068] Effective signal peptide coding regions for bacterial host
cells are the signal peptide coding regions obtained from the genes
for Bacillus NCIB 11837 maltogenic amylase, Bacillus
stearothermophilus alpha-amylase, Bacillus licheniformis
subtilisin, Bacillus licheniformis beta-lactamase, Bacillus
stearothermophilus neutral proteases (nprT, nprS, nprM), and
Bacillus subtilis prsA. Further signal peptides are described by
Simonen and Palva, 1993, Microbiological Reviews 57: 109-137.
[0069] Effective signal peptide coding regions for filamentous
fungal host cells are the signal peptide coding regions obtained
from the genes for Aspergillus oryzae TAKA amylase, Aspergillus
niger neutral amylase, Aspergillus niger glucoamylase, Rhizomucor
miehei aspartic proteinase, Humicola insolens cellulase, and
Humicola lanuginosa lipase.
[0070] Useful signal peptides for yeast host cells are obtained
from the genes for Saccharomyces cerevisiae alpha-factor and
Saccharomyces cerevisiae invertase. Other useful signal peptide
coding regions are described by Romanos et al., 1992, supra.
[0071] The control sequence may also be a propeptide coding region
that codes for an amino acid sequence positioned at the amino
terminus of a polypeptide. The resultant polypeptide is known as a
proenzyme or propolypeptide (or a zymogen in some cases). A
propolypeptide is generally inactive and can be converted to a
mature active polypeptide by catalytic or autocatalytic cleavage of
the propeptide from the propolypeptide. The propeptide coding
region may be obtained from the genes for Bacillus subtilis
alkaline protease (aprE), Bacillus subtilis neutral protease
(nprT), Saccharomyces cerevisiae alpha-factor, Rhizomucor miehei
aspartic proteinase, and Myceliophthora thermophila laccase (WO
95/33836).
[0072] Where both signal peptide and propeptide regions are present
at the amino terminus of a polypeptide, the propeptide region is
positioned next to the amino terminus of a polypeptide and the
signal peptide region is positioned next to the amino terminus of
the propeptide region.
[0073] It may also be desirable to add regulatory sequences which
allow the regulation of the expression of the polypeptide relative
to the growth of the host cell. Examples of regulatory systems are
those which cause the expression of the gene to be turned on or off
in response to a chemical or physical stimulus, including the
presence of a regulatory compound. Regulatory systems in
prokaryotic systems include the lac, tac, and tip operator systems.
In yeast, the ADH2 system or GAL1 system may be used. In
filamentous fungi, the TAKA alpha-amylase promoter, Aspergillus
niger glucoamylase promoter, and Aspergillus oryzae glucoamylase
promoter may be used as regulatory sequences. Other examples of
regulatory sequences are those which allow for gene amplification.
In eukaryotic systems, these include the dihydrofolate reductase
gene which is amplified in the presence of methotrexate, and the
metallothionein genes which are amplified with heavy metals. In
these cases, the nucleic acid sequence encoding the polypeptide
would be operably linked with the regulatory sequence.
Expression Vectors
[0074] The present invention also relates to recombinant expression
vectors comprising a nucleic acid sequence of the present
invention, a promoter, and transcriptional and translational stop
signals. The various nucleic acid and control sequences described
above may be joined together to produce a recombinant expression
vector which may include one or more convenient restriction sites
to allow for insertion or substitution of the nucleic acid sequence
encoding the polypeptide at such sites. Alternatively, the nucleic
acid sequence of the present invention may be expressed by
inserting the nucleic acid sequence or a nucleic acid construct
comprising the sequence into an appropriate vector for expression.
In creating the expression vector, the coding sequence is located
in the vector so that the coding sequence is operably linked with
the appropriate control sequences for expression.
[0075] The recombinant expression vector may be any vector (e.g., a
plasmid or virus) which can be conveniently subjected to
recombinant DNA procedures and can bring about the expression of
the nucleic acid sequence. The choice of the vector will typically
depend on the compatibility of the vector with the host cell into
which the vector is to be introduced. The vectors may be linear or
closed circular plasmids.
[0076] The vector may be an autonomously replicating vector, i.e.,
a vector which exists as an extrachromosomal entity, the
replication of which is independent of chromosomal replication,
e.g., a plasmid, an extrachromosomal element, a minichromosome, or
an artificial chromosome. The vector may contain any means for
assuring self-replication. Alternatively, the vector may be one
which, when introduced into the host cell, is integrated into the
genome and replicated together with the chromosome(s) into which it
has been integrated. Furthermore, a single vector or plasmid or two
or more vectors or plasmids which together contain the total DNA to
be introduced into the genome of the host cell, or a transposon may
be used.
[0077] The vectors of the present invention preferably contain one
or more selectable markers which permit easy selection of
transformed cells. A selectable marker is a gene the product of
which provides for biocide or viral resistance, resistance to heavy
metals, prototrophy to auxotrophs, and the like. Examples of
bacterial selectable markers are the dal genes from Bacillus
subtilis or Bacillus licheniformis, or markers which confer
antibiotic resistance such as ampicillin, kanamycin,
chloramphenicol or tetracycline resistance. Suitable markers for
yeast host cells are ADE2, HIS3, LEU2, LYS2, MET3, TRP1, and URA3.
Selectable markers for use in a filamentous fungal host cell
include, but are not limited to, amdS (acetamidase), argB
(ornithine carbamoyltransferase), bar (phosphinothricin
acetyltransferase), hygB (hygromycin phosphotransferase), niaD
(nitrate reductase), pyrG (orotidine-5'-phosphate decarboxylase),
sC (sulfate adenyltransferase), trpC (anthranilate synthase), as
well as equivalents thereof. Preferred for use in an Aspergillus
cell are the amdS and pyrG genes of Aspergillus nidulans or
Aspergillus oryzae and the bar gene of Streptomyces
hygroscopicus.
[0078] The vectors of the present invention preferably contain an
element(s) that permits stable integration of the vector into the
host cell's genome or autonomous replication of the vector in the
cell independent of the genome.
[0079] For integration into the host cell genome, the vector may
rely on the nucleic acid sequence encoding the polypeptide or any
other element of the vector for stable integration of the vector
into the genome by homologous or nonhomologous recombination.
Alternatively, the vector may contain additional nucleic acid
sequences for directing integration by homologous recombination
into the genome of the host cell. The additional nucleic acid
sequences enable the vector to be integrated into the host cell
genome at a precise location(s) in the chromosome(s). To increase
the likelihood of integration at a precise location, the
integrational elements should preferably contain a sufficient
number of nucleic acids, such as 100 to 1,500 base pairs,
preferably 400 to 1,500 base pairs, and most preferably 800 to
1,500 base pairs, which are highly homologous with the
corresponding target sequence to enhance the probability of
homologous recombination. The integrational elements may be any
sequence that is homologous with the target sequence in the genome
of the host cell.
[0080] Furthermore, the integrational elements may be non-encoding
or encoding nucleic acid sequences. On the other hand, the vector
may be integrated into the genome of the host cell by
non-homologous recombination.
[0081] For autonomous replication, the vector may further comprise
an origin of replication enabling the vector to replicate
autonomously in the host cell in question. Examples of bacterial
origins of replication are the origins of replication of plasmids
pBR322, pUC19, pACYC177, and pACYC184 permitting replication in E.
coli, and pUB110, pE194, pTA1060, and pAM.beta.1 permitting
replication in Bacillus. Examples of origins of replication for use
in a yeast host cell are the 2 micron origin of replication, ARS1,
ARS4, the combination of ARS1 and CEN3, and the combination of ARS4
and CEN6. The origin of replication may be one having a mutation
which makes its functioning temperature-sensitive in the host cell
(see, e.g., Ehrlich, 1978, Proceedings of the National Academy of
Sciences USA 75: 1433).
[0082] More than one copy of a nucleic acid sequence of the present
invention may be inserted into the host cell to increase production
of the gene product. An increase in the copy number of the nucleic
acid sequence can be obtained by integrating at least one
additional copy of the sequence into the host cell genome or by
including an amplifiable selectable marker gene with the nucleic
acid sequence where cells containing amplified copies of the
selectable marker gene, and thereby additional copies of the
nucleic acid sequence, can be selected for by cultivating the cells
in the presence of the appropriate selectable agent.
[0083] The procedures used to ligate the elements described above
to construct the recombinant expression vectors of the present
invention are well known to one skilled in the art (see, e.g.,
Sambrook et al., 1989, supra).
Host Cells
[0084] The present invention also relates to recombinant host
cells, comprising a nucleic acid sequence of the invention, which
are advantageously used in the recombinant production of the
polypeptides.
[0085] A vector comprising a nucleic acid sequence of the present
invention is introduced into a host cell so that the vector is
maintained as a chromosomal integrant or as a self-replicating
extra-chromosomal vector as described earlier. The choice of a host
cell will to a large extent depend upon the gene encoding the
polypeptide and its source.
[0086] The host cell may be a unicellular microorganism, e.g., a
prokaryote, or a non-unicellular microorganism, e.g., a
eukaryote.
[0087] Useful unicellular cells are bacterial cells such as gram
positive bacteria including, but not limited to, a Bacillus cell,
e.g., Bacillus alkalophilus, Bacillus amyloliquefaciens, Bacillus
brevis, Bacillus circulans, Bacillus clausii, Bacillus coagulans,
Bacillus lautus, Bacillus lentus, Bacillus licheniformis, Bacillus
megaterium, Bacillus stearothermophilus, Bacillus subtilis, and
Bacillus thuringiensis; or a Streptomyces cell, e.g., Streptomyces
lividans or Streptomyces murinus, or gram negative bacteria such as
E. coli and Pseudomonas sp. In a preferred embodiment, the
bacterial host cell is a Bacillus lentus, Bacillus licheniformis,
Bacillus stearothermophilus, or Bacillus subtilis cell. In another
preferred embodiment, the Bacillus cell is an alkalophilic
Bacillus.
[0088] The introduction of a vector into a bacterial host cell may,
for instance, be effected by protoplast transformation (see, e.g.,
Chang and Cohen, 1979, Molecular General Genetics 168: 111-115),
using competent cells (see, e.g., Young and Spizizin, 1961, Journal
of Bacteriology 81: 823-829, or Dubnau and Davidoff-Abelson, 1971,
Journal of Molecular Biology 56: 209-221), electroporation (see,
e.g., Shigekawa and Dower, 1988, Biotechniques 6: 742-751), or
conjugation (see, e.g., Koehler and Thorne, 1987, Journal of
Bacteriology 169: 5771-5278).
[0089] The host cell may be a eukaryote, such as a mammalian,
insect, plant, or fungal cell. In a preferred embodiment, the host
cell is a fungal cell. "Fungi" as used herein includes the phyla
Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota (as
defined by Hawksworth et al., In, Ainsworth and Bisby's Dictionary
of The Fungi, 8th edition, 1995, CAB International, University
Press, Cambridge, UK) as well as the Oomycota (as cited in
Hawksworth et al., 1995, supra, page 171) and all mitosporic fungi
(Hawksworth et al. 1995, supra).
[0090] In a more preferred embodiment, the fungal host cell is a
yeast cell. "Yeast" as used herein includes ascosporogenous yeast
(Endomycetales), basidiosporogenous yeast, and yeast belonging to
the Fungi Imperfecti (Blastomycetes). Since the classification of
yeast may change in the future, for the purposes of this invention,
yeast shall be defined as described in Biology and Activities of
Yeast (Skinner, F. A., Passmore, S. M., and Davenport, R. R., eds,
Soc. App. Bacteriol. Symposium Series No. 9, 1980).
[0091] In an even more preferred embodiment, the yeast host cell is
a Candida, Hansenula, Kluyveromyces, Pichia, Saccharomyces,
Schizosaccharomyces, or Yarrowia cell.
[0092] In a most preferred embodiment, the yeast host cell is a
Saccharomyces carlsbergensis, Saccharomyces cerevisiae,
Saccharomyces diastaticus, Saccharomyces douglasii, Saccharomyces
kluyveri, Saccharomyces norbensis or Saccharomyces oviformis cell.
In another most preferred embodiment, the yeast host cell is a
Kluyveromyces lactis cell. In another most preferred embodiment,
the yeast host cell is a Yarrowia lipolytica cell.
[0093] In another more preferred embodiment, the fungal host cell
is a filamentous fungal cell. "Filamentous fungi" include all
filamentous forms of the subdivision Eumycota and Oomycota (as
defined by Hawksworth et al., 1995, supra). The filamentous fungi
are characterized by a mycelial wall composed of chitin, cellulose,
glucan, chitosan, mannan, and other complex polysaccharides.
Vegetative growth is by hyphal elongation and carbon catabolism is
obligately aerobic. In contrast, vegetative growth by yeasts such
as Saccharomyces cerevisiae is by budding of a unicellular thallus
and carbon catabolism may be fermentative.
[0094] In an even more preferred embodiment, the filamentous fungal
host cell is a cell of a species of, but not limited to,
Acremonium, Aspergillus, Fusarium, Humicola, Mucor, Myceliophthora,
Neurospora, Penicillium, Thielavia, Tolypocladium, or
Trichoderma.
[0095] In a most preferred embodiment, the filamentous fungal host
cell is an Aspergillus awamori, Aspergillus foetidus, Aspergillus
japonicus, Aspergillus nidulans, Aspergillus niger or Aspergillus
oryzae cell. In another most preferred embodiment, the filamentous
fungal host cell is a Fusarium bactridioides, Fusarium cerealis,
Fusarium crookwellense, Fusarium culmorum, Fusarium graminearum,
Fusarium graminum, Fusarium heterosporum, Fusarium negundi,
Fusarium oxysporum, Fusarium reticulatum, Fusarium roseum, Fusarium
sambucinum, Fusarium sarcochroum, Fusarium sporotrichioides,
Fusarium sulphureum, Fusarium torulosum, Fusarium trichothecioides,
or Fusarium venenatum cell. In an even most preferred embodiment,
the filamentous fungal parent cell is a Fusarium venenatum
(Nirenberg sp. nov.) cell. In another most preferred embodiment,
the filamentous fungal host cell is a Humicola insolens, Humicola
lanuginosa, Mucor miehei, Myceliophthora thermophila, Neurospora
crassa, Penicillium purpurogenum, Thielavia terrestris, Trichoderma
harzianum, Trichoderma koningii, Trichoderma longibrachiatum,
Trichoderma reesei, or Trichoderma viride cell.
[0096] Fungal cells may be transformed by a process involving
protoplast formation, transformation of the protoplasts, and
regeneration of the cell wall in a manner known per se. Suitable
procedures for transformation of Aspergillus host cells are
described in EP 238 023 and Yelton et al., 1984, Proceedings of the
National Academy of Sciences USA 81: 1470-1474. Suitable methods
for transforming Fusarium species are described by Malardier et
al., 1989, Gene 78: 147-156 and WO 96/00787. Yeast may be
transformed using the procedures described by Becker and Guarente,
In Abelson, J. N. and Simon, M. I., editors, Guide to Yeast
Genetics and Molecular Biology, Methods in Enzymology, Volume 194,
pp 182-187, Academic Press, Inc., New York; Ito et al., 1983,
Journal of Bacteriology 153: 163; and Hinnen et al., 1978,
Proceedings of the National Academy of Sciences USA 75: 1920.
Methods of Production
[0097] The present invention also relates to methods for producing
a polypeptide of the present invention, the method comprising (a)
cultivating a strain from the genus Humicola. to produce a
supernatant comprising the polypeptide; and (b) recovering the
polypeptide. Preferably, the strain is of the species Humicola
insolens.
[0098] The present invention also relates to a method for producing
a polypeptide of the invention, the method comprising (a)
cultivating a recombinant host cell as described above under
conditions conducive to the production of the polypeptide, and (b)
recovering the polypeptide from the cells and/or the culture
medium.
[0099] In the production methods of the present invention, the
cells are cultivated in a nutrient medium suitable for production
of the polypeptide using methods known in the art For example, the
cell may be cultivated by shake flask cultivation, small-scale or
large-scale fermentation (including continuous, batch, fed-batch,
or solid state fermentations) in laboratory or industrial
fermentors performed in a suitable medium and under conditions
allowing the polypeptide to be expressed and/or isolated. The
cultivation takes place in a suitable nutrient medium comprising
carbon and nitrogen sources and inorganic salts, using procedures
known in the art. Suitable media are available from commercial
suppliers or may be prepared according to published compositions
(e.g., in catalogues of the American Type Culture Collection). If
the polypeptide is secreted into the nutrient medium, the
polypeptide can be recovered directly from the medium. If the
polypeptide is not secreted, it can be recovered from cell
lysates.
[0100] The polypeptides may be detected using methods known in the
art that are specific for the polypeptides. These detection methods
may include use of specific antibodies, formation of an enzyme
product, or disappearance of an enzyme substrate. For example, an
enzyme assay may be used to determine the activity of the
polypeptide as described herein.
[0101] The resulting polypeptide may be recovered by methods known
in the art. For example, the polypeptide may be recovered from the
nutrient medium by conventional procedures including, but not
limited to, centrifugation, filtration, extraction, spray-drying,
evaporation, or precipitation.
[0102] The polypeptides of the present invention may be purified by
a variety of procedures known in the art including, but not limited
to, chromatography (e.g., ion exchange, affinity, hydrophobic,
chromatofocusing, and size exclusion), electrophoretic procedures
(e.g., preparative isoelectric focusing), differential solubility
(e.g., ammonium sulfate precipitation), SDS-PAGE, or extraction
(see, e.g., Protein Purification, J.-C. Janson and Lars Ryden,
editors, VCH Publishers, New York, 1989).
Expression of the Enzymes in Plants
[0103] A DNA sequence encoding a polypeptide of interest, such as
an arabinofuranosidase of the present invention, may be transformed
and expressed in transgenic plants as described below.
[0104] The transgenic plant can be dicotyledonous or
monocotyledonous, for short a dicot or a monocot. Examples of
monocot plants are grasses, such as meadow grass (blue grass, Poa),
forage grass such as Festuca, Lolium, temperate grass, such as
Agrostis, and cereals, e.g. wheat, oats, rye, barley, rice, sorghum
and maize (corn).
[0105] Examples of dicot plants are tobacco, legumes, such as
lupins, potato, sugar beet, pea, bean and soybean, and cruciferous
plants (family Brassicaceae), such as cauliflower, oil seed rape
and the closely related model organism Arabidopsis thaliana.
[0106] Examples of plant parts are stem, callus, leaves, root,
fruits, seeds, and tubers as well as the individual tissues
comprising these parts, e.g. epidermis, mesophyll, parenchyme,
vascular tissues, meristems. In the present context, also specific
plant cell compartments, such as chloroplast, apoplast,
mitochondria, vacuole, peroxisomes and cytoplasm are considered to
be a plant part. Furthermore, any plant cell, whatever the tissue
origin, is considered to be a plant part. Likewise, plant parts
such as specific tissues and cells isolated to facilitate the
utilisation of the invention are also considered plant parts e.g.
embryos, endosperms, aleurone and seeds coats.
[0107] Also included within the scope of the invention are the
progeny of such plants, plant parts and plant cells.
[0108] The transgenic plant or plant cell expressing the
polypeptide of interest may be constructed in accordance with
methods known in the art. In short the plant or plant cell is
constructed by incorporating one or more expression constructs
encoding the polypeptide of interest into the plant host genome and
propagating the resulting modified plant or plant cell into a
transgenic plant or plant cell.
[0109] Conveniently, the expression construct is a DNA construct
which comprises a gene encoding the polypeptide of interest in
operable association with appropriate regulatory sequences required
for expression of the gene in the plant or plant part of choice.
Furthermore, the expression construct may comprise a selectable
marker useful for identifying host cells into which the expression
construct has been integrated and DNA sequences necessary for
introduction of the construct into the plant in question (the
latter depends on the DNA introduction method to be used).
[0110] The choice of regulatory sequences, such as promoter and
terminator sequences and optionally signal or transit sequences is
determined, e.g. on the basis of when, where and how the enzyme is
desired to be expressed. For instance, the expression of the gene
encoding the enzyme of the invention may be constitutive or
inducible, or may be developmental, stage or tissue specific, and
the gene product may be targeted to a specific cell compartment,
tissue or plant part such as seeds or leaves. Regulatory sequences
are, e.g. described by Tague et al, Plant, Phys., 86, 506,
1988.
[0111] For constitutive expression the 35S-CaMV, the maize
ubiquitin 1 and the rice actin 1 promoter may be used (Franck et
al. 1980. Cell 21: 285-294, Christensen A H, Sharrock R A and Quail
1992, Maize polyubiquitin genes: structure, thermal perturbation of
expression and transcript splicing, and promoter activity following
transfer to protoplasts by electroporation. Plant Mo. Biol. 18,
675-689.; Zhang W, McElroy D. and Wu R 1991, Analysis of rice Act1
5' region activity in transgenic rice plants. Plant Cell 3,
1155-1165). Organ-specific promoters may, e.g. be a promoter from
storage sink tissues such as seeds, potato tubers, and fruits
(Edwards & Coruzzi, 1990. Annu. Rev. Genet. 24: 275-303), or
from metabolic sink tissues such as meristems (Ito et al., 1994.
Plant Mol. Biol. 24: 863-878), a seed specific promoter such as the
glutelin, prolamin, globulin or albumin promoter from rice (Wu et
al., Plant and Cell Physiology Vol. 39, No. 8 pp. 885-889 (1998)),
a Vicia faba promoter from the legumin B4 and the unknown seed
protein gene from Vicia faba described by Conrad U. et al, Journal
of Plant Physiology Vol. 152, No. 6 pp. 708-711 (1998), a promoter
from a seed oil body protein (Chen et al., Plant and cell
physiology vol. 39, No. 9 pp. 935-941 (1998), the storage protein
napA promoter from Brassica napus, or any other seed specific
promoter known in the art, e.g. as described in WO 91/14772.
Furthermore, the promoter may be a leaf specific promoter such as
the rbcs promoter from rice or tomato (Kyozuka et al., Plant
Physiology Vol. 102, No. 3 pp. 991-1000 (1993), the chlorella virus
adenine methyltransferase gene promoter (Mitra, A. and Higgins, D
W, Plant Molecular Biology Vol. 26, No. 1 pp. 85-93 (1994), or the
aldP gene promoter from rice (Kagaya et al., Molecular and General
Genetics Vol. 248, No. 6 pp. 668-674 (1995), or a wound inducible
promoter such as the potato pin2 promoter (Xu et al, Plant
Molecular Biology Vol. 22, No. 4 pp. 573-588 (1993). Likewise, the
promoter may inducible by abiotic treatments such as temperature,
drought or alterations in salinity or induced by exogenously
applied substances that activate the promoter e.g. ethanol,
oestrogens, plant hormones like ethylene, abscisic add and
gibberellic acid and heavy metals.
[0112] A promoter enhancer element may be used to achieve higher
expression of the enzyme in the plant. For instance, the promoter
enhancer element may be an intron which is placed between the
promoter and the nucleotide sequence encoding the enzyme. For
instance, Xu et al. op cit disclose the use of the first intron of
the rice actin 1 gene to enhance expression.
[0113] The selectable marker gene and any other parts of the
expression construct may be chosen from those available in the
art.
[0114] The DNA construct is incorporated into the plant genome
according to conventional techniques known in the art, including
Agrobacterium-mediated transformation, virus-mediated
transformation, micro injection, particle bombardment, biolistic
transformation, and electroporation (Gasser et al, Science, 244,
1293; Potrykus, Bio/Techn. 8, 535, 1990; Shimamoto et al, Nature,
338, 274, 1989).
[0115] Presently, Agrobacterium tumefaciens mediated gene transfer
is the method of choice for generating transgenic dicots (for
review Hooykas & Schilperoort, 1992. Plant Mol. Biol. 19:
15-38), and can also be used for transforming monocots, although
other transformation methods often are used for these plants.
Presently, the method of choice for generating transgenic monocots
supplementing the Agrobacterium approach is particle bombardment
(microscopic gold or tungsten particles coated with the
transforming DNA) of embryonic calli or developing embryos
(Christou, 1992. Plant J. 2: 275-281; Shimamoto, 1994. Curr. Opin.
Biotechnol. 5: 158-162; Vasil et al., 1992. Bio/Technology 10:
667-674). An alternative method for transformation of monocots is
based on protoplast transformation as described by Omirulleh S, et
al., Plant Molecular biology Vol. 21, No. 3 pp. 415-428 (1993).
[0116] Following transformation, the transformants having
incorporated the expression construct are selected and regenerated
into whole plants according to methods well-known in the art. Often
the transformation procedure is designed for the selective
elimination of selection genes either during regeneration or in the
following generations by using e.g. co-transformation with two
separate T-DNA constructs or site specific excision of the
selection gene by a specific recombinase.
Use of Arabinofuranosidases
[0117] The present invention also relates to use of the polypeptide
of the invention, i.e. the arabinofuranosidase, in various
industrial application, e.g. in biomass conversion, such as in
production of fuel ethanol from cellulose containing biomass, in
production of fuel and/or potable ethanol from starch, in mashing
for beer production, or in a dough for bread making.
[0118] The present invention also relates to compositions
comprising the polypeptide of the invention, i.e. the
arabinofuranosidase, as well as to uses of such compositions.
Assay for Activity Towards Internally Substituted Xylan
[0119] Wheat arabinoxylan may be treated with Meripilus giganteus
alpha-arabinofuranosidase to remove arabinose from xylose only
substituted at C3 to produce an arabinoxylan substrate with
arabinose present on xylose branched at both C2 and C3 with
alpha-L-arabinofuranosidase. Using this substrate, an enzyme
capable of releasing arabinose from disubstituted xyloses can be
identified.
[0120] Alpha-arabinofuranosidase activity in fractions obtained
during purification may be measured by mixing 25 .mu.l enzyme
containing fraction with 25 .mu.l buffer (0.5 M MOPS, 0.01% Tween
20, pH 7.0) and 25 .mu.l substrate solution (5 mg/ml arabinoxylan
with arabinose present on xylose branched at both C2 and C3
prepared as above) in the well of a microtiter plate. The plate is
incubated at 35.degree. C. for 2 hours with shaking. Liberated
arabinose is then analysed using a modified version of the
Boehringer Mannheim kit Cat. No. 176 303 (developed for analysing
lactose/D-galactose but also able to detect L-arabinose in the
absence of D-galactose). 10 .mu.l sample containing the liberated
arabinose is transferred to another microtiter plate well and mixed
with 10 .mu.l of bottle 1 (citrate buffer, pH 6.6, NAD, magnesium
sulphate, stabilizers), 50 .mu.l of bottle 3 (potassium diphosphate
buffer, pH 8.6, stabilizers), 2.5 .mu.l bottle 4 (galactose
dehydrogenase suspension, 40 U) and 100 .mu.l Milli Q water. After
30 min shaking at room temperature absorbance is read at 340 nm.
Sequence CWU 1
1
411677DNAHumicola insolensCDS(1)..(1677)sig_peptide(1)..(54) 1atg
cta ggc ttg aag gtc ttg tgt ctc tcc gcc gtc gtg ggg acg gcg 48Met
Leu Gly Leu Lys Val Leu Cys Leu Ser Ala Val Val Gly Thr Ala1 5 10
15gtc tct gtg ccg cac gcg ggc aat ctt ccc cgt cag gcc agc act ttc
96Val Ser Val Pro His Ala Gly Asn Leu Pro Arg Gln Ala Ser Thr Phe20
25 30acc aac ccc gtg ctt tgg gaa gat cac cca gat ctc gaa gtg ttc
cgc 144Thr Asn Pro Val Leu Trp Glu Asp His Pro Asp Leu Glu Val Phe
Arg35 40 45gtc ggc tca gta ttc tac tac tcc tcg tcc acc ttc gcc tac
tcc ccc 192Val Gly Ser Val Phe Tyr Tyr Ser Ser Ser Thr Phe Ala Tyr
Ser Pro50 55 60ggc gcg ccc gtc ctc aag tcc tac gac ctc gtc cac tgg
acg ccc gtc 240Gly Ala Pro Val Leu Lys Ser Tyr Asp Leu Val His Trp
Thr Pro Val65 70 75 80acc cat tcc gtg ccg cgt ctc aac ttc ggc tcc
aac tac gac ctc ccc 288Thr His Ser Val Pro Arg Leu Asn Phe Gly Ser
Asn Tyr Asp Leu Pro85 90 95agc ggc acc ccg ggc gcc tac gtc aag ggc
atc tgg gcc tca acc ctc 336Ser Gly Thr Pro Gly Ala Tyr Val Lys Gly
Ile Trp Ala Ser Thr Leu100 105 110cgc tac cgc cgc tcc aat gac cgc
ttc tac tgg tac ggc tgc gtc gaa 384Arg Tyr Arg Arg Ser Asn Asp Arg
Phe Tyr Trp Tyr Gly Cys Val Glu115 120 125ggg aga acc tac ctc tgg
acc agc ccg ggc ggt aac gcg ctc gcc aac 432Gly Arg Thr Tyr Leu Trp
Thr Ser Pro Gly Gly Asn Ala Leu Ala Asn130 135 140aac ggc gag gtg
ccc ccc tcg gca tgg aac tgg cag cac acc gcc acc 480Asn Gly Glu Val
Pro Pro Ser Ala Trp Asn Trp Gln His Thr Ala Thr145 150 155 160atc
gac aac tgc tac tac gac gcc ggc ctg ctc atc gac gac gac gac 528Ile
Asp Asn Cys Tyr Tyr Asp Ala Gly Leu Leu Ile Asp Asp Asp Asp165 170
175acc atg tac atc gcg tac ggc aac ccg acc atc aac gtc gcg cag ctc
576Thr Met Tyr Ile Ala Tyr Gly Asn Pro Thr Ile Asn Val Ala Gln
Leu180 185 190tcc ccc gac ggc acc cgc cag gtg cgc gtg cag cag cgc
gtc tac gcg 624Ser Pro Asp Gly Thr Arg Gln Val Arg Val Gln Gln Arg
Val Tyr Ala195 200 205cac ccg cag ggc cag acg gtc gag ggc gcg cgc
atg tac aag atc cgc 672His Pro Gln Gly Gln Thr Val Glu Gly Ala Arg
Met Tyr Lys Ile Arg210 215 220ggc aac tac tac atc ctg gtg acc cgc
ccc gcc gac gca gag tac gtg 720Gly Asn Tyr Tyr Ile Leu Val Thr Arg
Pro Ala Asp Ala Glu Tyr Val225 230 235 240ctg cgg tcg acg acg ggg
tcg ccg ttc ggc ccg tac gag gcg cgc acg 768Leu Arg Ser Thr Thr Gly
Ser Pro Phe Gly Pro Tyr Glu Ala Arg Thr245 250 255ctg gtg tcg cgg
atc cag ggc ccg ctg gcc aac gcc ggg ttc gcg cac 816Leu Val Ser Arg
Ile Gln Gly Pro Leu Ala Asn Ala Gly Phe Ala His260 265 270cag ggc
ggc atc gtc gac gcg ccg gat ggg acg tgg cac tac gtc gcg 864Gln Gly
Gly Ile Val Asp Ala Pro Asp Gly Thr Trp His Tyr Val Ala275 280
285ttc atg gat gcg tat ccc ggc gga cgc atc ccc gtg gtg gcg ccg ctg
912Phe Met Asp Ala Tyr Pro Gly Gly Arg Ile Pro Val Val Ala Pro
Leu290 295 300cgg tgg acg gcg gat ggg tgg ccc gag gtg gtc acg gat
tcg caa ggg 960Arg Trp Thr Ala Asp Gly Trp Pro Glu Val Val Thr Asp
Ser Gln Gly305 310 315 320agg tgg ggg acg agc tat ccc att cca gtt
cgc gga gca aag aac gcg 1008Arg Trp Gly Thr Ser Tyr Pro Ile Pro Val
Arg Gly Ala Lys Asn Ala325 330 335acg gag ggg ctg gcg agc acg gat
ctg gac gag ttc cgc ggg acg agg 1056Thr Glu Gly Leu Ala Ser Thr Asp
Leu Asp Glu Phe Arg Gly Thr Arg340 345 350ttc agc gag cat tgg gag
tgg aat cat aac ccg gac acg agc aag ttt 1104Phe Ser Glu His Trp Glu
Trp Asn His Asn Pro Asp Thr Ser Lys Phe355 360 365acg ttg ctg ggc
ggt aac gag ggc ggg ctc atc ctc cgg aca gcg acc 1152Thr Leu Leu Gly
Gly Asn Glu Gly Gly Leu Ile Leu Arg Thr Ala Thr370 375 380gtg acg
ggg gat ttg ttt gcc gca agg aat acg ctc acg agg agg atc 1200Val Thr
Gly Asp Leu Phe Ala Ala Arg Asn Thr Leu Thr Arg Arg Ile385 390 395
400gcg gga ccc aag gcc agt gga atc ttc cgg ctg gat gtg cgc ggg atg
1248Ala Gly Pro Lys Ala Ser Gly Ile Phe Arg Leu Asp Val Arg Gly
Met405 410 415cgc gac ggt gac cgg gcc ggc gcc gtg ctg ttc cgg gat
cgt gcg gcg 1296Arg Asp Gly Asp Arg Ala Gly Ala Val Leu Phe Arg Asp
Arg Ala Ala420 425 430tac atc ggg gtg tgg aag cag ggc aac gag gcg
cgg att gtc atg gtg 1344Tyr Ile Gly Val Trp Lys Gln Gly Asn Glu Ala
Arg Ile Val Met Val435 440 445gac gac ctg cgg ttg aac gag gat ggt
tgg agg acg gcg tcc acc ggc 1392Asp Asp Leu Arg Leu Asn Glu Asp Gly
Trp Arg Thr Ala Ser Thr Gly450 455 460aga gtg gcc gcc aac ggt ccg
gtg atc gac acg aac gct cag cag gat 1440Arg Val Ala Ala Asn Gly Pro
Val Ile Asp Thr Asn Ala Gln Gln Asp465 470 475 480atc tgg ctg cga
att gat gcg gac atc aca ccg gcg ttt ggg acg aac 1488Ile Trp Leu Arg
Ile Asp Ala Asp Ile Thr Pro Ala Phe Gly Thr Asn485 490 495acg gag
cgc acg acg acg ttc tac tac agt att gat ggt ggg agg acg 1536Thr Glu
Arg Thr Thr Thr Phe Tyr Tyr Ser Ile Asp Gly Gly Arg Thr500 505
510tat acc agg ctg ggc cct gcc ttt gcg atg acc aat tct tgg aga tac
1584Tyr Thr Arg Leu Gly Pro Ala Phe Ala Met Thr Asn Ser Trp Arg
Tyr515 520 525ttc acc gga tac cgg ttt gga gtg ttc aac ttt tcg acc
aag agt ctt 1632Phe Thr Gly Tyr Arg Phe Gly Val Phe Asn Phe Ser Thr
Lys Ser Leu530 535 540gga ggt gag gtg aag gtt aag ggg ttc aag atg
aac atg atc tag 1677Gly Gly Glu Val Lys Val Lys Gly Phe Lys Met Asn
Met Ile545 550 5552558PRTHumicola insolens 2Met Leu Gly Leu Lys Val
Leu Cys Leu Ser Ala Val Val Gly Thr Ala1 5 10 15Val Ser Val Pro His
Ala Gly Asn Leu Pro Arg Gln Ala Ser Thr Phe20 25 30Thr Asn Pro Val
Leu Trp Glu Asp His Pro Asp Leu Glu Val Phe Arg35 40 45Val Gly Ser
Val Phe Tyr Tyr Ser Ser Ser Thr Phe Ala Tyr Ser Pro50 55 60Gly Ala
Pro Val Leu Lys Ser Tyr Asp Leu Val His Trp Thr Pro Val65 70 75
80Thr His Ser Val Pro Arg Leu Asn Phe Gly Ser Asn Tyr Asp Leu Pro85
90 95Ser Gly Thr Pro Gly Ala Tyr Val Lys Gly Ile Trp Ala Ser Thr
Leu100 105 110Arg Tyr Arg Arg Ser Asn Asp Arg Phe Tyr Trp Tyr Gly
Cys Val Glu115 120 125Gly Arg Thr Tyr Leu Trp Thr Ser Pro Gly Gly
Asn Ala Leu Ala Asn130 135 140Asn Gly Glu Val Pro Pro Ser Ala Trp
Asn Trp Gln His Thr Ala Thr145 150 155 160Ile Asp Asn Cys Tyr Tyr
Asp Ala Gly Leu Leu Ile Asp Asp Asp Asp165 170 175Thr Met Tyr Ile
Ala Tyr Gly Asn Pro Thr Ile Asn Val Ala Gln Leu180 185 190Ser Pro
Asp Gly Thr Arg Gln Val Arg Val Gln Gln Arg Val Tyr Ala195 200
205His Pro Gln Gly Gln Thr Val Glu Gly Ala Arg Met Tyr Lys Ile
Arg210 215 220Gly Asn Tyr Tyr Ile Leu Val Thr Arg Pro Ala Asp Ala
Glu Tyr Val225 230 235 240Leu Arg Ser Thr Thr Gly Ser Pro Phe Gly
Pro Tyr Glu Ala Arg Thr245 250 255Leu Val Ser Arg Ile Gln Gly Pro
Leu Ala Asn Ala Gly Phe Ala His260 265 270Gln Gly Gly Ile Val Asp
Ala Pro Asp Gly Thr Trp His Tyr Val Ala275 280 285Phe Met Asp Ala
Tyr Pro Gly Gly Arg Ile Pro Val Val Ala Pro Leu290 295 300Arg Trp
Thr Ala Asp Gly Trp Pro Glu Val Val Thr Asp Ser Gln Gly305 310 315
320Arg Trp Gly Thr Ser Tyr Pro Ile Pro Val Arg Gly Ala Lys Asn
Ala325 330 335Thr Glu Gly Leu Ala Ser Thr Asp Leu Asp Glu Phe Arg
Gly Thr Arg340 345 350Phe Ser Glu His Trp Glu Trp Asn His Asn Pro
Asp Thr Ser Lys Phe355 360 365Thr Leu Leu Gly Gly Asn Glu Gly Gly
Leu Ile Leu Arg Thr Ala Thr370 375 380Val Thr Gly Asp Leu Phe Ala
Ala Arg Asn Thr Leu Thr Arg Arg Ile385 390 395 400Ala Gly Pro Lys
Ala Ser Gly Ile Phe Arg Leu Asp Val Arg Gly Met405 410 415Arg Asp
Gly Asp Arg Ala Gly Ala Val Leu Phe Arg Asp Arg Ala Ala420 425
430Tyr Ile Gly Val Trp Lys Gln Gly Asn Glu Ala Arg Ile Val Met
Val435 440 445Asp Asp Leu Arg Leu Asn Glu Asp Gly Trp Arg Thr Ala
Ser Thr Gly450 455 460Arg Val Ala Ala Asn Gly Pro Val Ile Asp Thr
Asn Ala Gln Gln Asp465 470 475 480Ile Trp Leu Arg Ile Asp Ala Asp
Ile Thr Pro Ala Phe Gly Thr Asn485 490 495Thr Glu Arg Thr Thr Thr
Phe Tyr Tyr Ser Ile Asp Gly Gly Arg Thr500 505 510Tyr Thr Arg Leu
Gly Pro Ala Phe Ala Met Thr Asn Ser Trp Arg Tyr515 520 525Phe Thr
Gly Tyr Arg Phe Gly Val Phe Asn Phe Ser Thr Lys Ser Leu530 535
540Gly Gly Glu Val Lys Val Lys Gly Phe Lys Met Asn Met Ile545 550
55532200DNAMiripilus giganteusCDS(46)..(1974)sig_peptide(46)..(94)
3actagtaacg gccgccagtg tgctggaaag ggctcgctcg acacg atg aag ctg ctt
57Met Lys Leu Leu1ttc ttg ctc ggg gcc ttc gtt gcg caa tgt ctc gcg
gtc aca gtg acc 105Phe Leu Leu Gly Ala Phe Val Ala Gln Cys Leu Ala
Val Thr Val Thr5 10 15 20gtt aac aag aac cct agt cac acg gta ccg
tcc acg ctc tat ggc ctg 153Val Asn Lys Asn Pro Ser His Thr Val Pro
Ser Thr Leu Tyr Gly Leu25 30 35atg ttt gag gac atc aac cat agc ggt
gat ggc ggc ctg tac gcg gag 201Met Phe Glu Asp Ile Asn His Ser Gly
Asp Gly Gly Leu Tyr Ala Glu40 45 50ttg ttg caa aac agg gct ttc caa
cag gtt acc ccg aac acg gcc gct 249Leu Leu Gln Asn Arg Ala Phe Gln
Gln Val Thr Pro Asn Thr Ala Ala55 60 65gca ctc gct gca tgg cat ccc
atc agc aat gcg aag ctg gcc gta ata 297Ala Leu Ala Ala Trp His Pro
Ile Ser Asn Ala Lys Leu Ala Val Ile70 75 80caa gac cca tct cct gtc
tcc aat gca ttg ccg aat tcc ctt caa ttc 345Gln Asp Pro Ser Pro Val
Ser Asn Ala Leu Pro Asn Ser Leu Gln Phe85 90 95 100tcc gtg ccc agt
gga tcg agc ggc agg gtc ggc ttt acc aac gag ggt 393Ser Val Pro Ser
Gly Ser Ser Gly Arg Val Gly Phe Thr Asn Glu Gly105 110 115ttc tgg
gga atc aaa gtc gat tcc act tgg acg tac aaa gcc tcg ctc 441Phe Trp
Gly Ile Lys Val Asp Ser Thr Trp Thr Tyr Lys Ala Ser Leu120 125
130ttc ttc cgc ttc ccc aca tcg tcg tcc ttc tcg gga gcg ctc acc gtt
489Phe Phe Arg Phe Pro Thr Ser Ser Ser Phe Ser Gly Ala Leu Thr
Val135 140 145ggg ctg cag acg aac gcc ggg aga gtg ctg gca cag aac
tcc acg cag 537Gly Leu Gln Thr Asn Ala Gly Arg Val Leu Ala Gln Asn
Ser Thr Gln150 155 160atc cgc ggg acg acc acg aag tgg acg cag atc
aac ctg gag ctc cac 585Ile Arg Gly Thr Thr Thr Lys Trp Thr Gln Ile
Asn Leu Glu Leu His165 170 175 180cct acc gcc tct gcc ccc gac gtc
agc aac agc ttc ttt gtc acg att 633Pro Thr Ala Ser Ala Pro Asp Val
Ser Asn Ser Phe Phe Val Thr Ile185 190 195gac ggg gcc gct ggc gcc
ggt cag acg atc aac ttc gcc atg ttc tcg 681Asp Gly Ala Ala Gly Ala
Gly Gln Thr Ile Asn Phe Ala Met Phe Ser200 205 210ctc ttc cct ccc
acg ttc aag aac agg ccg aat ggg ctg cgc gct gac 729Leu Phe Pro Pro
Thr Phe Lys Asn Arg Pro Asn Gly Leu Arg Ala Asp215 220 225atc gcc
gag act ctg gcc gag atg ggc ccg tcc ttt ttc cgc ttc cca 777Ile Ala
Glu Thr Leu Ala Glu Met Gly Pro Ser Phe Phe Arg Phe Pro230 235
240ggt ggg aac aac ctg gag ggc caa acg acg gcg acg agg tgg cag tgg
825Gly Gly Asn Asn Leu Glu Gly Gln Thr Thr Ala Thr Arg Trp Gln
Trp245 250 255 260aat gct acc gtc ggc tcg ctg ctg gac cgc ccc ggc
cgg gtg ggc gac 873Asn Ala Thr Val Gly Ser Leu Leu Asp Arg Pro Gly
Arg Val Gly Asp265 270 275tgg gga tac gtg aac acg gac ggt cta ggt
ctt ctg gag tat ctc cag 921Trp Gly Tyr Val Asn Thr Asp Gly Leu Gly
Leu Leu Glu Tyr Leu Gln280 285 290ttc ttc gaa gat acg ggc atg gag
ccg atc atg gcg gtc tgg gca ggc 969Phe Phe Glu Asp Thr Gly Met Glu
Pro Ile Met Ala Val Trp Ala Gly295 300 305tat tct ctc ggc ggc aca
agc ctt gct gag aac cag ctc gca ccg tac 1017Tyr Ser Leu Gly Gly Thr
Ser Leu Ala Glu Asn Gln Leu Ala Pro Tyr310 315 320ata cag caa gcg
ata gat cag att aac ttt gtc atc ggg gac cct gca 1065Ile Gln Gln Ala
Ile Asp Gln Ile Asn Phe Val Ile Gly Asp Pro Ala325 330 335 340aag
agt gca cct gcg gcg ctc cgt gct tcc ctg ggc cac cca gag ccc 1113Lys
Ser Ala Pro Ala Ala Leu Arg Ala Ser Leu Gly His Pro Glu Pro345 350
355ttc acg ctc cgc ttc gtg gaa gtg gga aac gag gac ttc ttc gcg gcg
1161Phe Thr Leu Arg Phe Val Glu Val Gly Asn Glu Asp Phe Phe Ala
Ala360 365 370ggc tcg tac cca tac cgc tgg cac gac ttc gtt acc gca
ctt cag gcg 1209Gly Ser Tyr Pro Tyr Arg Trp His Asp Phe Val Thr Ala
Leu Gln Ala375 380 385caa ttc ccc cag atc aga ttc atc gcg acc acc
aac gcc tgg aac ccg 1257Gln Phe Pro Gln Ile Arg Phe Ile Ala Thr Thr
Asn Ala Trp Asn Pro390 395 400gtt ctg tcc ccc gtc ccg cag tcg tat
gat gta cac gtc tat cag aca 1305Val Leu Ser Pro Val Pro Gln Ser Tyr
Asp Val His Val Tyr Gln Thr405 410 415 420ccg acc tgg ttc tac caa
aat gct ttc tac tac gac ggc ttc cag cgc 1353Pro Thr Trp Phe Tyr Gln
Asn Ala Phe Tyr Tyr Asp Gly Phe Gln Arg425 430 435aac ggc acc aca
tac ttt gag ggg gag tac gcc gcc atc tcc acc aac 1401Asn Gly Thr Thr
Tyr Phe Glu Gly Glu Tyr Ala Ala Ile Ser Thr Asn440 445 450gcg aac
gat ttg ttc ggt act gtt gcc gac ggt cgc ttg gcg ttc cct 1449Ala Asn
Asp Leu Phe Gly Thr Val Ala Asp Gly Arg Leu Ala Phe Pro455 460
465aca gtg caa agt gct acc ggg gag gcc gca ttc atg acc ggc ttg gag
1497Thr Val Gln Ser Ala Thr Gly Glu Ala Ala Phe Met Thr Gly Leu
Glu470 475 480cgc aac agc gac atc gtc ttc gcc gcg tcc tac gca cct
ctg ctg cag 1545Arg Asn Ser Asp Ile Val Phe Ala Ala Ser Tyr Ala Pro
Leu Leu Gln485 490 495 500cac gtc aac tcc act caa tgg acc ccc gac
ctg gtt tcc tac gac gcc 1593His Val Asn Ser Thr Gln Trp Thr Pro Asp
Leu Val Ser Tyr Asp Ala505 510 515ggc tcc gtt att aag tcg acg agc
ttc ttc gcc cag aag ctg ttc gcc 1641Gly Ser Val Ile Lys Ser Thr Ser
Phe Phe Ala Gln Lys Leu Phe Ala520 525 530ttg aac aag ggc gac caa
tac ctc ccg agc acg ctc ccg acc aac ggt 1689Leu Asn Lys Gly Asp Gln
Tyr Leu Pro Ser Thr Leu Pro Thr Asn Gly535 540 545ggc acg ctg cac
tgg agc atc act cgg gcc tct agc tcc ggc aag acg 1737Gly Thr Leu His
Trp Ser Ile Thr Arg Ala Ser Ser Ser Gly Lys Thr550 555 560ttc atc
aag atc gcg aac gcc ggc agc tca gcg cag agc ctc acc ttc 1785Phe Ile
Lys Ile Ala Asn Ala Gly Ser Ser Ala Gln Ser Leu Thr Phe565 570 575
580cag ctg acc cag ttc aac tcg gtc tcc agc acc gga acg ctc cag gtc
1833Gln Leu Thr Gln Phe Asn Ser Val Ser Ser Thr Gly Thr Leu Gln
Val585 590 595ctc acc gga ccg gag acc gcc agc aac acg cct gag gcg
ccg cag gcc 1881Leu Thr Gly Pro Glu Thr Ala Ser Asn Thr Pro Glu Ala
Pro Gln Ala600 605 610atc gtt ccc aag acg agc acg atc ggc acc ggc
aag act ttc acg tac 1929Ile Val Pro Lys Thr Ser Thr Ile Gly Thr Gly
Lys Thr Phe Thr Tyr615 620 625aac gct ccc gca ttc agc gtc agt gtc
atc acc gtc acc acg aac 1974Asn Ala Pro Ala Phe Ser Val Ser Val Ile
Thr Val Thr Thr Asn630 635 640tgaacgaaga agcacaacgc agcacgagga
ccagaggacg gcgcggatgc gagactgccg 2034agataccatt gccgcgaagg
ggtgcagtgg tgccgtaact cgcaaggggg aacgggatcg 2094tccgaatcgg
atgggtgtgg attaggttgc gtcttcactg tttactaggc ggtgtatgcg
2154agcgtagcta gtgcggtcct attgtaattt tgtgaggtct atctcc
22004643PRTMiripilus giganteus 4Met Lys Leu Leu Phe Leu Leu Gly Ala
Phe Val Ala Gln Cys Leu Ala1 5 10 15Val Thr Val Thr Val Asn Lys Asn
Pro Ser His Thr Val Pro Ser Thr20 25 30Leu Tyr
Gly Leu Met Phe Glu Asp Ile Asn His Ser Gly Asp Gly Gly35 40 45Leu
Tyr Ala Glu Leu Leu Gln Asn Arg Ala Phe Gln Gln Val Thr Pro50 55
60Asn Thr Ala Ala Ala Leu Ala Ala Trp His Pro Ile Ser Asn Ala Lys65
70 75 80Leu Ala Val Ile Gln Asp Pro Ser Pro Val Ser Asn Ala Leu Pro
Asn85 90 95Ser Leu Gln Phe Ser Val Pro Ser Gly Ser Ser Gly Arg Val
Gly Phe100 105 110Thr Asn Glu Gly Phe Trp Gly Ile Lys Val Asp Ser
Thr Trp Thr Tyr115 120 125Lys Ala Ser Leu Phe Phe Arg Phe Pro Thr
Ser Ser Ser Phe Ser Gly130 135 140Ala Leu Thr Val Gly Leu Gln Thr
Asn Ala Gly Arg Val Leu Ala Gln145 150 155 160Asn Ser Thr Gln Ile
Arg Gly Thr Thr Thr Lys Trp Thr Gln Ile Asn165 170 175Leu Glu Leu
His Pro Thr Ala Ser Ala Pro Asp Val Ser Asn Ser Phe180 185 190Phe
Val Thr Ile Asp Gly Ala Ala Gly Ala Gly Gln Thr Ile Asn Phe195 200
205Ala Met Phe Ser Leu Phe Pro Pro Thr Phe Lys Asn Arg Pro Asn
Gly210 215 220Leu Arg Ala Asp Ile Ala Glu Thr Leu Ala Glu Met Gly
Pro Ser Phe225 230 235 240Phe Arg Phe Pro Gly Gly Asn Asn Leu Glu
Gly Gln Thr Thr Ala Thr245 250 255Arg Trp Gln Trp Asn Ala Thr Val
Gly Ser Leu Leu Asp Arg Pro Gly260 265 270Arg Val Gly Asp Trp Gly
Tyr Val Asn Thr Asp Gly Leu Gly Leu Leu275 280 285Glu Tyr Leu Gln
Phe Phe Glu Asp Thr Gly Met Glu Pro Ile Met Ala290 295 300Val Trp
Ala Gly Tyr Ser Leu Gly Gly Thr Ser Leu Ala Glu Asn Gln305 310 315
320Leu Ala Pro Tyr Ile Gln Gln Ala Ile Asp Gln Ile Asn Phe Val
Ile325 330 335Gly Asp Pro Ala Lys Ser Ala Pro Ala Ala Leu Arg Ala
Ser Leu Gly340 345 350His Pro Glu Pro Phe Thr Leu Arg Phe Val Glu
Val Gly Asn Glu Asp355 360 365Phe Phe Ala Ala Gly Ser Tyr Pro Tyr
Arg Trp His Asp Phe Val Thr370 375 380Ala Leu Gln Ala Gln Phe Pro
Gln Ile Arg Phe Ile Ala Thr Thr Asn385 390 395 400Ala Trp Asn Pro
Val Leu Ser Pro Val Pro Gln Ser Tyr Asp Val His405 410 415Val Tyr
Gln Thr Pro Thr Trp Phe Tyr Gln Asn Ala Phe Tyr Tyr Asp420 425
430Gly Phe Gln Arg Asn Gly Thr Thr Tyr Phe Glu Gly Glu Tyr Ala
Ala435 440 445Ile Ser Thr Asn Ala Asn Asp Leu Phe Gly Thr Val Ala
Asp Gly Arg450 455 460Leu Ala Phe Pro Thr Val Gln Ser Ala Thr Gly
Glu Ala Ala Phe Met465 470 475 480Thr Gly Leu Glu Arg Asn Ser Asp
Ile Val Phe Ala Ala Ser Tyr Ala485 490 495Pro Leu Leu Gln His Val
Asn Ser Thr Gln Trp Thr Pro Asp Leu Val500 505 510Ser Tyr Asp Ala
Gly Ser Val Ile Lys Ser Thr Ser Phe Phe Ala Gln515 520 525Lys Leu
Phe Ala Leu Asn Lys Gly Asp Gln Tyr Leu Pro Ser Thr Leu530 535
540Pro Thr Asn Gly Gly Thr Leu His Trp Ser Ile Thr Arg Ala Ser
Ser545 550 555 560Ser Gly Lys Thr Phe Ile Lys Ile Ala Asn Ala Gly
Ser Ser Ala Gln565 570 575Ser Leu Thr Phe Gln Leu Thr Gln Phe Asn
Ser Val Ser Ser Thr Gly580 585 590Thr Leu Gln Val Leu Thr Gly Pro
Glu Thr Ala Ser Asn Thr Pro Glu595 600 605Ala Pro Gln Ala Ile Val
Pro Lys Thr Ser Thr Ile Gly Thr Gly Lys610 615 620Thr Phe Thr Tyr
Asn Ala Pro Ala Phe Ser Val Ser Val Ile Thr Val625 630 635 640Thr
Thr Asn
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