U.S. patent application number 16/993333 was filed with the patent office on 2020-12-10 for polymer probes and methods.
This patent application is currently assigned to Buckman Laboratories International, Inc.. The applicant listed for this patent is Buckman Laboratories International, Inc., Universite du Quebec a Trois-Rivieres. Invention is credited to Marc Beauregard, Yannick Hebert-Ouellet, Bernard Janse, Kevin J. MacDonald, Fatma Meddeb-Mouelhi.
Application Number | 20200386736 16/993333 |
Document ID | / |
Family ID | 1000005038026 |
Filed Date | 2020-12-10 |
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United States Patent
Application |
20200386736 |
Kind Code |
A1 |
Beauregard; Marc ; et
al. |
December 10, 2020 |
Polymer Probes And Methods
Abstract
A polymer detection probe is provided that includes a binding
module that specifically binds to at least one polymer and a
reporter module that is spectroscopically detectable. The binding
module can be a carbohydrate-binding module (CBM). The reporter
module can be a fluorescent protein. A complex is provided that
includes a probe specifically bound to a pulp or paper product
including at least one surface available lignocellulosic polymer. A
pulp or paper product is provided that includes at least one
surface available lignocellulosic polymer and at least one probe
bound thereto. Methods are provided that employ a lignocellulosic
probe. A method of detecting a lignocellulosic polymer or other
type of polymer is provided. A method of determining the
effectiveness of an industrial treatment on pulp or a paper product
is also provided. A method of determining a physical property of
pulp or a paper product is further provided.
Inventors: |
Beauregard; Marc;
(Drummondville, CA) ; Meddeb-Mouelhi; Fatma;
(Trois-Rivieres, CA) ; Hebert-Ouellet; Yannick;
(Trois-Rivieres, CA) ; Janse; Bernard;
(Collierville, TN) ; MacDonald; Kevin J.; (Middle
Sackville, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Buckman Laboratories International, Inc.
Universite du Quebec a Trois-Rivieres |
Memphis
Trois-Riveres |
TN |
US
CA |
|
|
Assignee: |
Buckman Laboratories International,
Inc.
Memphis
TN
Universite du Quebec a Trois-Rivieres
Trois-Rivieres
QC
|
Family ID: |
1000005038026 |
Appl. No.: |
16/993333 |
Filed: |
August 14, 2020 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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15332588 |
Oct 24, 2016 |
10788477 |
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16993333 |
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62246231 |
Oct 26, 2015 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
G01N 2400/26 20130101;
D21H 23/76 20130101; G01N 33/343 20130101; C07K 14/001 20130101;
G01N 33/5308 20130101 |
International
Class: |
G01N 33/34 20060101
G01N033/34; G01N 33/53 20060101 G01N033/53; D21H 23/76 20060101
D21H023/76; C07K 14/00 20060101 C07K014/00 |
Claims
1-28. (canceled)
29. A method of detecting a lignocellulosic polymer, the method
comprising: contacting a lignocellulosic polymer detection probe
with a biomass material; and measuring a property associated with
the reporter module to determine the presence or absence of at
least one lignocellulosic polymer in the biomass material based on
specific binding of the probe to the at least one lignocellulosic
polymer.
30. The method of claim 29, wherein the property measured is
fluorescence.
31. The method of claim 29, further comprising calculating the
amount of the at least one lignocellulosic polymer, determining the
type of the at least one lignocellulosic polymer, or both.
32. (canceled)
33. (canceled)
34. (canceled)
35. (canceled)
36. (canceled)
37. (canceled)
38. The method of claim 31, further comprising performing at least
one treatment of the biomass material based on the amount of the at
least one lignocellulosic polymer measured, the type of
lignocellulosic polymer measured, or both.
39. The method of claim 31, wherein the amount of lignocellulosic
polymer measured correlates negatively or positively with at least
one physical property of the biomass product.
40. The method of claim 39, wherein the at least one physical
property comprises burst index, drainage rate, tear index, tensile
index, or internal bond strength, or any combination thereof.
41. The method of claim 31, further comprising dosing at least one
enzyme based on the amount of lignocellulosic polymer measured, the
type of lignocellulosic polymer measured, or both.
42. The method of claim 31, further comprising adjusting mill speed
based on the amount of lignocellulosic polymer measured, the type
of lignocellulosic polymer measured, or both.
43. The method of claim 31, further comprising adjusting total
water content of the biomass material based on the amount of
lignocellulosic polymer measured, the type of lignocellulosic
polymer measured, or both.
44. The method of claim 29, wherein the probe comprises a plurality
of probes.
45. A method of determining the effectiveness of an industrial
treatment on pulp or a paper product comprising: contacting a
lignocellulosic polymer detection probe with a pulp or a paper
product, said lignocellulosic polymer detection probe comprising a)
a binding module that specifically binds to at least one
lignocellulosic polymer and b) a reporter module that is
spectroscopically detectable and wherein the binding module is a
binding module polypeptide and the reporter module is a reporter
module polypeptide that comprises a fluorescent protein and wherein
the reporter module is not an antibody or a fragment thereof and
wherein the binding module polypeptide is not an antibody or a
fragment thereof; detecting the specific binding of the probe to
the pulp or the paper product; calculating the amount of at least
one lignocellulosic polymer on a surface of the pulp or the paper
product; and determining the effectiveness of an industrial
treatment on the pulp or paper product based on the amount of the
at least one lignocellulosic polymer detected, wherein the
fluorescent protein comprises Sirius, TagBFP, mTagBFP2, Azurite,
EBFP2, mKalama1, Sirius, Sapphire, T-Sapphire, ECFP, mAmetrine,
Cerulean, mCerulean3, SCFP3A, CyPet, mTurguoise, mTurquoise2,
monomeric Midoriishi-Cyan, Aquamarine, eCFP, TagCFP, mTFP1,
AmCyanl, EGFP, Emerald, Superfolder GFP, monomeric Azami Green,
TurboGFP, TagGFP2, mUKG, mWasabi, Clover, mNeonGreen, eGFP, AcGFP1,
ZGreen1, ZsYellow1, mBanana, EYFP, Topaz, Citrine, Venus, SYFP2,
Ypet, IanRFP-deltaS83, mPapaya1, TagYFP, mOrange, mOrange2,
monomeric Kusabira-Orange, mKOk, mKO2, mTangerine, mNectarine,
TagRFP, TagRFP-T, mApple, mRuby, mRuby2, DsRed-Express2,
DsRed-Express, tdTomato, DsRed-Monomer, DsRed-Monomer, DsRed2,
AsRed2, mStrawberry, mCherry, HcRed1, FusionRed, mRaspberry,
E2-Crimson, mPlum, HcRed-Tandem, mKate2, mNeptune, NirFP,
TagRFP657, TagRFP675, iFP1.4, iRFP(iRFP713), iRFP670, iRFP682,
iRFP702, iRFP720, iFP2.0, mIFP, mKeima Red, LSS-mKate1, LSS-mKate2,
LSSmOrange, mBeRFP, PA-GFP, PATag RFP, Dendra2, Timer, PAmCherry,
Kaede (green), Kaeda (red), KikGR1 (green), KikGR1 (red), PS-CFP2,
mEos2 (green), mEos2 (red), mEos3.2 (green), mEos3.2(red),
PSmOrange, Dropna, or any combination thereof and wherein the
binding module is a carbohydrate-binding module (CBM) comprising
CBM1, CBM2, CBM3, CBM3a CBM4, CBM5, CBM6, CBM9, CBM10, CBM11,
CBM12, CBM14, CBM15, CBM17, CBM18, CBM19, CBM20, CBM21, CBM25,
CBM27, CBM28, CBM33, CBM48, CBM49, or any combination thereof.
46. (canceled)
47. (canceled)
48. The method of claim 45, wherein the lignocellulosic polymer
detection probe is detectable at a distinct wavelength.
49. A method of determining a physical property of pulp or a paper
product comprising: contacting a lignocellulosic polymer detection
probe with a pulp or a paper product, said lignocellulosic polymer
detection probe comprising a) a binding module that specifically
binds to at least one lignocellulosic polymer and b) a reporter
module that is spectroscopically detectable and wherein the binding
module is a binding module polypeptide and the reporter module is a
reporter module polypeptide that comprises a fluorescent protein
and wherein the reporter module is not an antibody or a fragment
thereof and wherein the binding module polypeptide is not an
antibody or a fragment thereof; detecting the specific binding of
the probe to the pulp or the paper product; calculating the amount
of at least one lignocellulosic polymer on a surface of the pulp or
the paper product; and determining at least one physical property
of the pulp or paper product based on the amount of the at least
one lignocellulosic polymer detected, wherein the fluorescent
protein comprises Sirius, TagBFP, mTagBFP2, Azurite, EBFP2,
mKalama1, Sirius, Sapphire, T-Sapphire, ECFP, mAmetrine, Cerulean,
mCerulean3, SCFP3A, CyPet, mTurguoise, mTurquoise2, monomeric
Midoriishi-Cyan, Aquamarine, eCFP, TagCFP, mTFP1, AmCyanl, EGFP,
Emerald, Superfolder GFP, monomeric Azami Green, TurboGFP, TagGFP2,
mUKG, mWasabi, Clover, mNeonGreen, eGFP, AcGFP1, ZGreen1,
ZsYellow1, mBanana, EYFP, Topaz, Citrine, Venus, SYFP2, Ypet,
IanRFP-deltaS83, mPapaya1, TagYFP, mOrange, mOrange2, monomeric
Kusabira-Orange, mKOk, mKO2, mTangerine, mNectarine, TagRFP,
TagRFP-T, mApple, mRuby, mRuby2, DsRed-Express2, DsRed-Express,
tdTomato, DsRed-Monomer, DsRed-Monomer, DsRed2, AsRed2,
mStrawberry, mCherry, HcRed1, FusionRed, mRaspberry, E2-Crimson,
mPlum, HcRed-Tandem, mKate2, mNeptune, NirFP, TagRFP657, TagRFP675,
iFP1.4, iRFP(iRFP713), iRFP670, iRFP682, iRFP702, iRFP720, iFP2.0,
mIFP, mKeima Red, LSS-mKate1, LSS-mKate2, LSSmOrange, mBeRFP,
PA-GFP, PATag RFP, Dendra2, Timer, PAmCherry, Kaede (green), Kaeda
(red), KikGR1 (green), KikGR1 (red), PS-CFP2, mEos2 (green), mEos2
(red), mEos3.2 (green), mEos3.2(red), PSmOrange, Dropna, or any
combination thereof and wherein the binding module is a
carbohydrate-binding module (CBM) comprising CBM1, CBM2, CBM3,
CBM3a CBM4, CBM5, CBM6, CBM9, CBM10, CBM11, CBM12, CBM14, CBM15,
CBM17, CBM18, CBM19, CBM20, CBM21, CBM25, CBM27, CBM28, CBM33,
CBM48, CBM49, or any combination thereof.
50. The method of claim 49, wherein the at least one physical
property comprises burst index, drainage rate, tear index, tensile
index, or internal bond strength, or any combination thereof.
51-64. (canceled)
65. A method of detecting a polymer, the method comprising:
contacting a polymer detection probe with a material, said polymer
detection probe comprising a) a binding module that specifically
binds to at least one polymer and b) a reporter module that is
spectroscopically detectable and wherein the binding module is a
binding module polypeptide and the reporter module is a reporter
module polypeptide that comprises a fluorescent protein and wherein
the reporter module is not an antibody or a fragment thereof and
wherein the binding module polypeptide is not an antibody or a
fragment thereof; and measuring a property associated with the
reporter module to determine the presence or absence of at least
one polymer in the material based on specific binding of the probe
to the at least one polymer, wherein the fluorescent protein
comprises Sirius, TagBFP, mTagBFP2, Azurite, EBFP2, mKalama1,
Sirius, Sapphire, T-Sapphire, ECFP, mAmetrine, Cerulean,
mCerulean3, SCFP3A, CyPet, mTurguoise, mTurquoise2, monomeric
Midoriishi-Cyan, Aquamarine, eCFP, TagCFP, mTFP1, AmCyanl, EGFP,
Emerald, Superfolder GFP, monomeric Azami Green, TurboGFP, TagGFP2,
mUKG, mWasabi, Clover, mNeonGreen, eGFP, AcGFP1, ZGreen1,
ZsYellow1, mBanana, EYFP, Topaz, Citrine, Venus, SYFP2, Ypet,
IanRFP-deltaS83, mPapaya1, TagYFP, mOrange, mOrange2, monomeric
Kusabira-Orange, mKOk, mKO2, mTangerine, mNectarine, TagRFP,
TagRFP-T, mApple, mRuby, mRuby2, DsRed-Express2, DsRed-Express,
tdTomato, DsRed-Monomer, DsRed-Monomer, DsRed2, AsRed2,
mStrawberry, mCherry, HcRed1, FusionRed, mRaspberry, E2-Crimson,
mPlum, HcRed-Tandem, mKate2, mNeptune, NirFP, TagRFP657, TagRFP675,
iFP1.4, iRFP(iRFP713), iRFP670, iRFP682, iRFP702, iRFP720, iFP2.0,
mIFP, mKeima Red, LSS-mKate1, LSS-mKate2, LSSmOrange, mBeRFP,
PA-GFP, PATag RFP, Dendra2, Timer, PAmCherry, Kaede (green), Kaeda
(red), KikGR1 (green), KikGR1 (red), PS-CFP2, mEos2 (green), mEos2
(red), mEos3.2 (green), mEos3.2(red), PSmOrange, Dropna, or any
combination thereof and wherein the binding module is a
carbohydrate-binding module (CBM) comprising CBM1, CBM2, CBM3,
CBM3a CBM4, CBM5, CBM6, CBM9, CBM10, CBM11, CBM12, CBM14, CBM15,
CBM17, CBM18, CBM19, CBM20, CBM21, CBM25, CBM27, CBM28, CBM33,
CBM48, CBM49, or any combination thereof.
66. The method of claim 65, wherein the property measured is
fluorescence.
67. The method of claim 65, further comprising calculating the
amount of the at least one polymer, determining the type of the at
least one polymer, or both.
68. The method of claim 65, wherein the material comprises a blood
sample.
69. The method of 68, further comprising determining at least one
of a blood antigen, type, group, and subgroup of the blood
sample.
70. The method of claim 65, wherein the probe comprises a plurality
of probes.
71. (canceled)
72. (canceled)
73. The method of claim 29, wherein the binding module polypeptide
is fused directly to the reporter module polypeptide.
74. The method of claim 29, wherein the binding module polypeptide
is linked to the reporter polypeptide via a linker polypeptide.
75. The method of claim 29, wherein the probe comprises an amino
acid sequence of any one of SEQ ID NOS: 2, 6, 8, 10, and 12.
76. The method of claim 29, wherein the binding module specifically
binds to cellulose, hemicellulose, lignin, xylan, mannan, or any
combination thereof.
77. The method of claim 29, wherein the lignocellulosic polymer
detection probe comprises a plurality of lignocellulosic polymer
detection probes, each lignocellulosic polymer detection probe
specifically binding to a different lignocellulosic polymer.
78. The method of claim 65, wherein the binding module specifically
binds to cellulose, hemicellulose, lignin, xylan, mannan,
glucuronoxylan, arabinoxylan, glucomannan, xyloglucan, or any
combination thereof or a linear fragment thereof, or a branched
fragment thereof, or an oligomer thereof, or a monomer and/or
macromer thereof.
79. The method of claim 65, wherein the binding module specifically
binds to a glycoprotein, carbohydrate, or both, specific to a
particular blood antigen, type, group, or subgroup.
80. The method of claim 65, wherein the binding module specifically
binds to a polyaryletherketone (PAEK), a polyether ether ketone
(PEEK), a polyethylene, a polypropylene, a polystyrene, a
polytetrfluoroethylene, a polyvinylchloride, a polyamide, a
para-aramid, a polyethylene terephthalate, a polyimide, a
polycarbonate, a polypeptide, a polynucleotide, a glycoprotein, a
protein, a phosphorylated protein, a modified protein, a lipid, a
surfactant, lecithin, or a biosurfactant, or any combination
thereof.
81. The method of claim 29, said lignocellulosic polymer detection
probe comprising a) a binding module that specifically binds to at
least one lignocellulosic polymer and b) a reporter module that is
spectroscopically detectable and wherein the binding module is a
binding module polypeptide and the reporter module is a reporter
module polypeptide that comprises a fluorescent protein and wherein
the reporter module is not an antibody or a fragment thereof and
wherein the binding module polypeptide is not an antibody or a
fragment thereof; and measuring a property associated with the
reporter module to determine the presence or absence of at least
one lignocellulosic polymer in the biomass material based on
specific binding of the probe to the at least one lignocellulosic
polymer, wherein the fluorescent protein comprises Sirius, TagBFP,
mTagBFP2, Azurite, EBFP2, mKalama1, Sirius, Sapphire, T-Sapphire,
ECFP, mAmetrine, Cerulean, mCerulean3, SCFP3A, CyPet, mTurguoise,
mTurquoise2, monomeric Midoriishi-Cyan, Aquamarine, eCFP, TagCFP,
mTFP1, AmCyanl, EGFP, Emerald, Superfolder GFP, monomeric Azami
Green, TurboGFP, TagGFP2, mUKG, mWasabi, Clover, mNeonGreen, eGFP,
AcGFP1, ZGreen1, ZsYellow1, mBanana, EYFP, Topaz, Citrine, Venus,
SYFP2, Ypet, IanRFP-deltaS83, mPapaya1, TagYFP, mOrange, mOrange2,
monomeric Kusabira-Orange, mKOk, mKO2, mTangerine, mNectarine,
TagRFP, TagRFP-T, mApple, mRuby, mRuby2, DsRed-Express2,
DsRed-Express, tdTomato, DsRed-Monomer, DsRed-Monomer, DsRed2,
AsRed2, mStrawberry, mCherry, HcRed1, FusionRed, mRaspberry,
E2-Crimson, mPlum, HcRed-Tandem, mKate2, mNeptune, NirFP,
TagRFP657, TagRFP675, iFP1.4, iRFP(iRFP713), iRFP670, iRFP682,
iRFP702, iRFP720, iFP2.0, mIFP, mKeima Red, LSS-mKate1, LSS-mKate2,
LSSmOrange, mBeRFP, PA-GFP, PATag RFP, Dendra2, Timer, PAmCherry,
Kaede (green), Kaeda (red), KikGR1 (green), KikGR1 (red), PS-CFP2,
mEos2 (green), mEos2 (red), mEos3.2 (green), mEos3.2(red),
PSmOrange, Dropna, or any combination thereof and wherein the
binding module is a carbohydrate-binding module (CBM) comprising
CBM1, CBM2, CBM3, CBM3a CBM4, CBM5, CBM6, CBM9, CBM10, CBM11,
CBM12, CBM14, CBM15, CBM17, CBM18, CBM19, CBM20, CBM21, CBM25,
CBM27, CBM28, CBM33, CBM48, CBM49, or any combination thereof.
Description
[0001] This application claims the benefit under 35 U.S.C. .sctn.
119(e) of prior U.S. Provisional Patent Application No. 62/246,231,
filed Oct. 26, 2015, which is incorporated in its entirety by
reference herein.
BACKGROUND OF THE INVENTION
[0002] The present invention relates to detection,
characterization, and quantification of specific polymers, for
example, lignocellulosic polymers such as polysaccharides, in
biomass, and further relates to detection of any polymer, such as
oligosaccharides, for instance, for a variety of uses as described
herein.
[0003] In the field of pulp and papermaking, industries rely on a
number of physical, chemical, and biological treatments to enhance
the value of their product. Treatments include, for example,
mechanical shearing (refining) of the fibers to help develop
desired paper properties. Currently, there is no practical way to
predict the outcome of such treatments without a thorough analysis
of pulp and paper properties. Such an analysis involves pilot or
industrial scale trials that are costly and time-consuming.
[0004] Current methods for polymer detection and fiber surface
characterization include, for example, X-ray photoelectron
spectroscopy (XPS), scanning electron microscopy (SEM);
time-of-flight secondary ion mass spectrometry (ToF-SIMS) and
Fourier transform infra-red (FTIR). These techniques involve
specialized equipment, specific expertise, and lengthy manipulation
and interpretation. These techniques also do not distinguish
between cellulose and hemicellulose. Other approaches have been
developed for indirect detection of polymers based on the use of
dyes, for example, acrydin orange and phenanthren. They have been
successfully used for studying plant cell morphology, but they
employ sophisticated microscopes and are not quantitative. Still
other techniques detect hemicellulose using antibodies raised
against representative molecules. However, such antibodies are
expensive and only detect a segment of polymers that resemble the
molecules used for antibody production. If the exact epitope
recognized by a particular antibody is not found or accessible,
then the polymers will not be detected. Antibody techniques are
lengthy and also involve use of secondary antibodies.
[0005] Carbohydrate binding modules (CBMs) are a group of molecules
specialized for biomass polymer detection. CBMs are proteins
optimized for specific detection of various targets, for example,
carbohydrates such as crystalline cellulose and xylan. In order to
detect binding of such CBM to biomass, one can attach a reporter
dye to it. Such techniques involve microscopy. However, none of
these methods have been successfully used for rapid
characterization of fiber surface polymers that would enable the
prediction of the impact of various treatments on pulp or
paper.
[0006] Accordingly, there is a need for better materials and
methods for detecting lignocellulosic polymers in biomass, and for
the detection, in general, of polymers, such as oligosaccharides,
in various applications.
SUMMARY OF THE PRESENT INVENTION
[0007] A feature of the present invention is to provide materials
and methods for detecting and measuring lignocellulosic polymers in
biomass, such as in a time and cost effective manner.
[0008] Another feature of the present invention is to provide
materials and methods for determining the effectiveness of
industrial treatments on pulp or paper before, during, and/or after
a particular treatment is applied.
[0009] A further feature of the present invention is to provide
materials and methods for determining a physical property of pulp
or a paper product indirectly based on the presence and/or content
of lignocellulosic polymers in the pulp or the paper product.
[0010] An additional feature of the present invention is to provide
materials and methods for simultaneously measuring the presence
and/or amounts of multiple, different lignocellulosic polymers in
biomass independent of separate or sequential testing
procedures.
[0011] A further feature of the present invention is to provide
materials and methods for detection of any polymer, such as one or
more oligosaccharides.
[0012] Additional features and advantages of the present invention
will be set forth in part in the description that follows, and in
part will be apparent from the description, or may be learned by
practice of the present invention. The objectives and other
advantages of the present invention will be realized and attained
by means of the elements and combinations particularly pointed out
in the description and appended claims.
[0013] To achieve these and other advantages, and in accordance
with the purposes of the present invention, as embodied and broadly
described herein, the present invention, in part, relates to a
lignocellulosic polymer detection probe including a binding module
that specifically binds at least one lignocellulosic polymer and a
reporter module that is spectroscopically detectable. Either or
both of the modules can include a polypeptide. The binding module
can be a carbohydrate-binding module (CBM). The reporter module can
be a fluorescent protein. The probe can contain a plurality of
probes with each probe specific to a particular lignocellulosic
polymer and each probe containing a unique fluorescent spectral
profile.
[0014] The present invention also relates to a complex including a
probe specifically bound to a pulp or paper product including at
least one surface available lignocellulosic polymer.
[0015] The present invention further relates to a pulp or paper
product including at least one surface available lignocellulosic
polymer and at least one probe specifically bound thereto.
[0016] The present invention also relates to method of detecting a
lignocellulosic polymer. The method can include contacting the
probe with a biomass material, and measuring a property associated
with the reporter module to determine the presence or absence of at
least one lignocellulosic polymer in the biomass material.
[0017] The present invention further relates to a method of
determining the effectiveness of an industrial treatment on pulp or
a paper product. A lignocellulosic polymer detection probe can be
contacted with a pulp or a paper product. The specific binding of
the probe to the pulp or the paper product can be detected. The
amount of at least one lignocellulosic polymer on a surface of the
pulp or the paper product can be calculated. The effectiveness or
need of an industrial treatment on the pulp or paper product can be
determined based on the amount of the at least one lignocellulosic
polymer detected.
[0018] The present invention also relates to a method of
determining a physical property of pulp or a paper product. A
lignocellulosic polymer detection probe can be contacted with a
pulp or a paper product. The specific binding of the probe to the
pulp or the paper product can be detected. The amount of at least
one lignocellulosic polymer on a surface of the pulp or the paper
product can be determined (e.g., calculated). The at least one
physical property of the pulp or paper product can be determined
based on the amount of the at least one lignocellulosic polymer
detected.
[0019] The present invention further relates to a polymer detection
probe. The probe can have, for example, one or more characteristics
or functions of the lignocellulosic polymer probes described
herein, overlapping characteristics or functions, or different
characteristics or functions. The polymer detection probe can
include, for example, a binding module that specifically binds to
at least one polymer (e.g., oligosaccharides or other saccharide
polymers) and a reporter module that is spectroscopically
detectable. A complex is provided including the probe specifically
bound to a material including at least one surface available
polymer.
[0020] The present invention also relates to a method of detecting
a polymer (e.g., oligosaccharides or other saccharide polymers). A
probe of the present invention can be contacted with a material. A
property associated with the reporter module can be measured to
determine the presence or absence of at least one polymer in the
material based on specific binding of the probe to the at least one
polymer. The detection or non-detection has a number of
applications as described herein.
[0021] The materials and methods disclosed herein enable rapid and
simultaneous detection of various lignocellulosic polymers at the
surface of fibers used in pulp and paper, for example, cellulose
and hemicellulose using fusion proteins. Signal patterns can be
correlated to various changes in pulp and paper properties. The
methods enable prediction of various treatments impact on paper
properties. Such prediction allows for rapid and accurate choice of
treatment, dosage, and/or other conditions for a given target, for
example, conditions leading to a paper with higher burst index, a
pulp with higher drainage rate, and/or the optimal xylanase
concentration for bleaching boost. The methods enable optimal use
of chemical, enzymatic, or physical treatments alike. The methods
can be used in any industry based on wood biomass.
[0022] Further, the present invention has many applications. The
effect of any relevant chemical, physical, or biological treatment
that has an impact on fiber polymer exposure or distribution or
hydrolysis on pulp and paper properties can be determined or
predicted. For instance, an enzymatic sequence for optimizing pulp
refining can be determined or predicted. Xylanase treatment for
boosting bleaching can be optimized. Degradation of hemicelluloses
when hydrolyzing biomass can be monitored. Production conditions
for purified cellulosic materials, for example, nanocellulose or
filaments, can be optimized by monitoring the presence of amorphous
cellulose versus crystalline cellulose using the methods of the
present invention.
[0023] It is to be understood that both the foregoing general
description and the following detailed description are exemplary
and explanatory only and intended to provide a further explanation
of the present invention, as claimed.
BRIEF DESCRIPTION OF DRAWINGS
[0024] FIG. 1 is a schematic depiction of an example of polymer
detection using the probes of the present invention.
[0025] FIG. 2 is a schematic diagram of an expression vector of the
pet11A-eGFP (eGFP reporter module).
[0026] FIG. 3 is a schematic diagram of an expression vector of the
pet11A-mCherry (mCherry reporter module).
[0027] FIG. 4 is a schematic diagram of an expression vector of the
pet11A-mOrange2 (mOrange2 reporter module).
[0028] FIG. 5 is a schematic diagram of an expression vector of the
pet11A-eCFP (eCFP reporter module).
[0029] FIG. 6 is a SDS-PAGE example of purified fluorescence
proteins. The arrow highlights the protein of interest.
[0030] FIG. 7 is an SDS-PAGE example of purified CBMs. The arrow
highlights the protein of interest.
[0031] FIG. 8 is an example of a graph depicting emission spectra
of reporter modules (eGFP and mCherry) and of a pulp handsheet disk
after excitation at 549 nm.
[0032] FIG. 9 is an example of emission spectra of FPs (eGFP and
mCherry) and a pulp handsheet disk using an excitation wavelength
of 488 nm.
[0033] FIG. 10 is an example of a schematic diagram of a
pET11A-eGFP-CBM3a expression vector (Probe 1).
[0034] FIG. 11 is an example of a schematic diagram of a
pET11A-mCherry-CBM4-1 expression vector (Probe 2a).
[0035] FIG. 12 is an example of a schematic diagram of a
pET11A-mCherry-CBM17 expression vector (Probe 2b).
[0036] FIG. 13 is an example of a schematic diagram of a
pET11A-mOrange2-CBM15 expression vector (Probe 3).
[0037] FIG. 14 is an example of a schematic diagram of a
pET11A-eCFP-CBM27 expression vector (Probe 4).
[0038] FIG. 15. is a SDS-PAGE example analysis of Probes 1 to 4.
From left to right: Probe 1, Probe 2a, Probe 2b (not used here has
a higher affinity to amorphous cellulose than Probe 2a), Probe 3
and Probe 4. Shown on the left side of the last four gels is a
standard size ladder allowing estimation of sizes for proteins
migrated on the same gel.
[0039] FIGS. 16A-16D are examples of graphs of excitation (dashed)
and emission (full) spectra of the FP-CBM proteins for probes 1,
2b, 3, and 4, respectively.
[0040] FIG. 17 is an example of a graph of binding saturation from
a solid state depletion assay using Probe 1.
[0041] FIG. 18 is an example of a schematic diagram describing a
probe-binding experiment on a paper disk.
[0042] FIG. 19 is an example of a graph of fluorescence intensity
(FI) of reporter module (eGFP) alone bound to untreated and
cellulase-treated pulp (after two levels of refining).
[0043] FIG. 20 is an example of a graph of fluorescence intensity
of Probe 1 bound to untreated and cellulase-treated pulp (after two
level of refining).
[0044] FIG. 21 is an example of a graph showing the impact of PFI
refining on the quantification of crystalline cellulose on the
surface of pulp 1 handsheets.
[0045] FIG. 22 is an example of a graph showing the impact of
cellulase-treatment on the quantification of crystalline cellulose
on the surface of pulp 1 handsheets.
[0046] FIG. 23 is an example of graph depicting quantification
(.mu.g/mm.sup.2) of Probe 1 bound on the surface of
xylanase-treated handsheets.
[0047] FIG. 24 is an example of a graph depicting quantification of
crystalline cellulose (.mu.g/mm.sup.2) on the surface of PFI
refined handsheet produced at two different plants.
[0048] FIGS. 25A-25D are examples of graphs depicting correlations
between crystalline cellulose quantification using Probe 1
(.mu.g/mm.sup.2) and pulp 2/paper physical properties as a function
of refining energy (PFI revolutions) including, respectively, tear
index (mN m.sup.2/g), tensile index (N m/g), internal bond strength
(J/m.sup.2), an fibers mean length (mm).
[0049] FIGS. 26A-26D are examples of graphs depicting correlations
between crystalline cellulose quantification using Probe 1
(.mu.g/mm.sup.2) and pulp 1/paper physical properties as a function
of refining energy (PFI revolutions) including, respectively, tear
index (mN m.sup.2/g), tensile index (N m/g), internal bond strength
(J/m.sup.2), an fibers mean length (mm).
[0050] FIG. 27 is an example of a graph depicting fluorescence
intensity of Probe 3 bound to xylan at the surface of five
different paper disks including, respectively, UBKPR: Unbleached
Kraft pulp (pulp 2), UBMP: unbleached mechanical pulp (pulp 5),
BMP: bleached mechanical pulp (pulp 6), UBKP: unbleached Kraft pulp
(pulp 3), and BKP: bleached Kraft pulp (pulp 4).
[0051] FIG. 28 is an example of a graph depicting fluorescence
intensity of Probe 3 bound to xylan at the surface of untreated and
xylanase treated Pulp 4 (BKP) paper.
[0052] FIG. 29 is an example of a graph depicting fluorescence
intensity of Probe 4 (eCFP-CBM27) bound to mannan at the surface of
two different paper disks--unbleached Kraft pulp (Pulp 3, UBKP) and
bleached Kraft pulp (Pulp 4, BKP).
[0053] FIG. 30 is an example of a graph depicting fluorescence
intensity of Probe 4 bound to mannan at the surface of
mannanase-treated bleached Kraft pulp (Pulp 4, BKP) paper.
DETAILED DESCRIPTION OF THE PRESENT INVENTION
[0054] The present invention in part relates to a lignocellulosic
polymer detection probe including a) a binding module that
specifically binds to at least one lignocellulosic polymer and b) a
reporter module that is spectroscopically detectable. Any suitable
binding module and reporter module can be employed. A given probe
can vary with respect to the number and/or kind of binding module
and reporter module. A probe can contain a single binding module
and a single reporter module. A probe can contain more binding
modules than reporter modules, more reporter modules than binding
modules, or an equal number of binding modules and reporter
modules. A probe can contain from one to three, one to five, one to
ten, or more binding modules and/or reporter modules. Each binding
module can specifically bind a particular lignocellulosic polymer
or a particular subset of lignocellulosic polymers.
[0055] The lignocellulosic polymer detection probe can include at
least one probe polypeptide. All or part of a probe can be
constructed from a polypeptide(s). Polypeptides are understood to
contain proteins including the standard twenty amino acids modified
in whole or part. One or more non-standard amino acids can replace
or be used in addition to one or more standard amino acids. The
polypeptides can be constructed by chemical synthesis or using
molecular biological expression systems whether in vitro or in
vivo. Any suitable expression system can be employed, for example,
prokaryotic expression systems, eukaryotic expression systems,
plasmid based expression systems, chromosomally integrated
expression systems, or any combination thereof. Modification can be
done synthetically, via post-translation modification in an
expression system, or both. Any suitable modification can be
employed, for example, phosphorylation, sulfonation, fluorination,
acetylation, addition of carbohydrate groups, addition of lipid
groups, addition of nucleic acids, addition of polynucleotides,
addition of other amino acids, addition of other polypeptides,
addition of synthetic organic molecules, addition of inorganic
groups, or any combination thereof.
[0056] The binding module can be or include a binding module
polypeptide. The reporter module can be or include a reporter
module polypeptide. The binding module and reporter module
polypeptide can be directly or indirectly connected to each other.
For example, the binding module polypeptide can be fused directly
to the reporter module polypeptide. The binding module polypeptide
can be linked to the reporter polypeptide covalently, for example,
via a linker polypeptide. The linker can be of any suitable length,
for example, at least one amino acid, from 2 to about 2,000 amino
acids (residues), from about 5 to about 1,000 amino acids, from
about 10 to about 500 amino acids, from about 25 to about 250 amino
acids, from about 50 to about 100 amino acids, or more than 2,000
amino acids. The linker can include a molecule other than or in
addition to a polypeptide, for example, a carbohydrate, a
polynucleotide, a lipid, a synthetic organic small molecule, a
non-naturally occurring polymer, a metal, or any combination
thereof. For example, the binding module and reporter module can be
cross-linked using formaldehyde, glutaraldehyde, or both. The
connection or attachment between the binding module and the
reporter module can be an ionic bonding, hydrogen bonding,
hydrophobic interactions, hydrophilic interactions,
solvent-excluding interactions, or any combination thereof. The
connection or attachment can include at least a covalent bond to
ensure that the reporter module is tethered or otherwise stably
attached to the binding module.
[0057] The probe polypeptide can be or include, for example, an
amino acid sequence of any one of SEQ ID NOS: 2, 6, 8, 10, and 12,
or a combination thereof; encoded by a nucleic acid sequence of SEQ
ID NOS: 1, 5, 7, 9, and 11, respectively. The binding module
polypeptide can be or include, for example, an amino acid sequence
of any one of SEQ ID NOS: 14, 16, 18, 20, and 22; encoded by a
nucleic acid sequence of 13, 15, 17, 19, and 21, respectively. The
reporter module polypeptide can be or include, for example, an
amino acid sequence of any one of SEQ ID NOS: 24, 26, 28, and 30;
encoded by a nucleic acid sequence of 23, 25, 27, and 29,
respectively. Histidine tag sequences can be omitted from the
sequences for the probes, binding modules, and/or reporting
modules, for example, if purification methods do not employ a
nickel column.
[0058] The probes of the present invention are advantageous as they
can function independent of, without including, or without using an
antibody or a polypeptide including an antigen-binding fragment of
an antibody. Neither the binding module polypeptide nor the
reporter module need be or include an antibody or a fragment
thereof. Either the binding module polypeptide or the reporter
module can be or include an antibody or a fragment thereof. Both
the binding module polypeptide and the reporter module can be or
include an antibody or a fragment thereof. Even if a binding module
is not an antibody or antigen-binding fragment thereof, the binding
module can still bind a target with the specificity of an antibody.
The binding of the binding module to its target lignocellulosic can
occur under conditions similar to or different from the binding of
an antibody to its antigen. Binding can be performed under any
suitable conditions that increase specific binding of a binding
module to its desired target(s), and decrease, minimize, or prevent
non-specific binding of the binding module to non-targets. Binding
can be assisted by the presence of one or more additional factors,
for example, probe concentration, ions, for example calcium ions,
ionic strength, pH, and/or temperature, and the like. Both,
neither, or just one of the binding module and reporter module can
be or include a polypeptide of any kind. Binding modules and/or
reporter modules can be or include nucleotides, carbohydrates,
lipids, synthetic organic groups, and/or inorganic groups instead
of or in addition to polypeptides. For example, polynucleotides,
polysaccharides, fatty acids, esters, sterols, and/or non-naturally
occurring polymers can be used. Binding modules and/or reporter
modules and/or other portions of a probe can contain any suitable
type or number of molecules, for example, molecules described
herein.
[0059] Any suitable reporter module or combination of reporter
modules can be used in the probes and methods of the present
invention. For example, the reporter module in whole or part can be
fluorescent. The reporter module can have any suitable fluorescent
excitation and emission spectra. The reporter module can have a
unique excitation spectrum and/or excitation peak maximum. For
example, the reporter module can have a fluorescence excitation
peak (maximum) of, for example, lower than 300 nm, from about 300
nm to about 750 nm, from about 350 nm to about 700 nm, from about
400 nm to about 650 nm, from about 350 nm to about 400 nm, from
about 400 nm to about 450 nm, from about 450 nm to about 500 nm,
from about 500 nm to about 550 nm, from about 550 nm to about 600
nm, from about 600 nm to about 650 nm, from about 650 nm to about
700 nm, greater than 700 nm or any intervening range (for example,
a 1-3 nm, 5 nm, 10 nm, or 25 nm range) or value. The reporter
module can have a unique emission spectrum (.+-.1 nm, or .+-.3 nm,
or .+-.5 nm) and/or emission peak maximum (.+-.1 nm, or .+-.3 nm,
or .+-.5 nm). For example, the reporter module can have a
fluorescence emission peak (maximum) of less than 350 nm, from
about 350 nm to about 800 nm, from about 400 nm to about 750 nm,
from about 450 nm to about 700 nm, from about 350 nm to about 400
nm, from about 400 nm to about 450 nm, from about 450 nm to about
500 nm, from about 500 nm to about 550 nm, from about 550 nm to
about 600 nm, from about 600 nm to about 650 nm, from about 650 nm
to about 700 nm, from about 700 nm to about 750 nm, greater than
750 nm, or any intervening range (for example, a 1-3 nm, 5 nm, 10
nm, or 25 nm range) or value.
[0060] The reporter module can include any number or type of
fluorescent moieties. For example, the fluorescent moiety can be or
include a polypeptide, a polynucleotide, a polysaccharide, a small
organic molecule, a metal, a coordination complex, or any
combination thereof. For example, the reporter module can be or
include a fluorescent protein or a combination of fluorescent
proteins. The fluorescent protein can be or include an ultraviolet
fluorescent protein, a blue fluorescent protein, a cyan fluorescent
protein, a green fluorescent protein, a yellow fluorescent protein,
an orange fluorescent protein, a red fluorescent protein, a far-red
fluorescent protein, a near infrared fluorescent protein, an
infrared fluorescent protein, a sapphire-type fluorescent protein,
a long Stokes shift fluorescent protein, a switchable fluorescent
protein, or any combination thereof. The fluorescent protein can be
or include, for example, Sirius, TagBFP, mTagBFP2, Azurite, EBFP2,
mKalama1, Sirius, Sapphire, T-Sapphire, ECFP, mAmetrine, Cerulean,
mCerulean3, SCFP3A, CyPet, mTurguoise, mTurquoise2, monomeric
Midoriishi-Cyan, Aquamarine, eCFP, TagCFP, mTFP1, AmCyanl, EGFP,
Emerald, Superfolder GFP, monomeric Azami Green, TurboGFP, TagGFP2,
mUKG, mWasabi, Clover, mNeonGreen, eGFP, AcGFP1, ZGreen1,
ZsYellow1, mBanana, EYFP, Topaz, Citrine, Venus, SYFP2, Ypet,
IanRFP-deltaS83, mPapaya1, TagYFP, mOrange, mOrange2, monomeric
Kusabira-Orange, mKOk, mKO2, mTangerine, mNectarine, TagRFP,
TagRFP-T, mApple, mRuby, mRuby2, DsRed-Express2, DsRed-Express,
tdTomato, DsRed-Monomer, DsRed-Monomer, DsRed2, AsRed2,
mStrawberry, mCherry, HcRed1, FusionRed, mRaspberry, E2-Crimson,
mPlum, HcRed-Tandem, mKate2, mNeptune, NirFP, TagRFP657, TagRFP675,
iFP1.4, iRFP(iRFP713), iRFP670, iRFP682, iRFP702, iRFP720, iFP2.0,
mIFP, mKeima Red, LSS-mKate1, LSS-mKate2, LSSmOrange, mBeRFP,
PA-GFP, PATag RFP, Dendra2, Timer, PAmCherry, Kaede (green), Kaeda
(red), KikGR1 (green), KikGR1 (red), PS-CFP2, mEos2 (green), mEos2
(red), mEos3.2 (green), mEos3.2(red), PSmOrange, Dropna, or any
combination thereof. Reporter modules other than fluorescent
reporter modules can be employed in addition to or in the
alternative to fluorescent reporter modules. For example,
antibodies, antibody fragments, radioisotopes, dyes, synthetic
organic molecules, phosphorescent molecules, enzymes, or the like,
or any combination thereof can be used. Reporter modules described
in Knox P. J. (2012) Methods in Enzymology, volume 510, 233-245,
which is incorporated by reference herein in its entirety, can be
used. The accessible primary amines of binding modules, for
example, CBMs, can be labelled using a reactive dye that contains a
tetrafluoropheneyl ester moiety (Invitrogen).
[0061] Any suitable binding module or combination of binding
modules can be used in the probes and methods of the present
invention. For example, the binding module can be or include a
carbohydrate-binding module (CBM) including CBM1, CBM2, CBM3,
CBM3a, CBM4, CBM5, CBM6, CBM7, CBM8, CBM9, CBM10, CBM11, CBM12,
CBM13, CBM14, CBM15, CBM16, CBM17, CBM18, CBM19, CBM20, CBM21,
CBM22, CBM23, CBM24, CBM25, CBM26, CBM27, CBM28, CBM29, CBM30,
CBM31, CBM32, CBM33, CBM34, CBM35, CBM36, CBM37, CBM38, CBM39,
CBM40, CBM41, CBM42, CBM43, CBM44, CBM45, CBM46, CBM47, CBM48,
CBM49, CBM50, CBM51, CBM52, CBM53, CBM54, CBM55, CBM56, CBM57,
CBM58, CBM59, CBM60, CBM61, CBM62, CBM63, CBM64, CBM65, CBM66,
CBM67, CBM68, CBM69, CBM70, CBM71, or a family member thereof, or
any combination thereof. Binding specificities can be or include
those of particular CBM families or specific CBM family members,
for example, CBM1 (cellulose), CBM2 (cellulose), CBM3 (crystalline
cellulose), CBM4 (amorphous cellulose), CBM5 (chitin), CBM6
(cello-oligosaccharides, laminarins, xylooligosaccharides,
beta1,4,-beta1,3-mixed linked glucans), CBM8 (cellulose), CBM9
(crystalline cellulose), CBM10 (cellulose), CBM11 (cellulose),
CBM12 (chitin), CBM13 (cellulose, xylans, mannose), CBM14 (chitin),
CBM15 (xylans and xylooligosaccharides), CBM16 (cellulose and
glucomannans), CBM17 (amorphous cellulose), CBM18 (chitin), CBM19
(chitin), CBM20 (starch), CBM21 (glycogen), CBM22 (mixed
.beta.-1,3/.beta.-1,4-glucans), CBM23 (mannans), CBM24
(.alpha.-1,3-glucan), CBM25 (alpha-glucooligosaccharides and
granular starch), CBM 26 (starch), CBM27
(beta-1,4-mannooligosaccharides, carob galactomannan, and konjac
glucomannans, mannans), CBM28 (amorphous cellulose,
cellooligosaccharides, and .beta.-(1,3)(1,4)-glucans), CBM29
(mannans and glucomannans), CBM30 (cellulose), CBM31
(.beta.-1,3-xylans), CBM32 (galactose, lactose, polygalacturonic
acid, and .beta.-D-galactosyl-1,4-.beta.-D-N-acetylglucosamine),
CBM33 (chitin), CBM34 (granular starch), CBM35 (xylans, mannans,
and .beta.-galactans), CBM36 (xylans and xylooligosaccharides),
CBM37 (xylans, chitin, microcrystalline cellulose, and
phosphoric-acid swollen cellulose), CBM38 (inulin), CBM39
(.beta.-1,3-glucan, lipopolysaccharide, and lipoteichoic acid)
CBM48 (glycogen), CBM40 (sialic acid), CBM 41 (.alpha.-glucans,
amylose, amylopectin, and pullulans), CBM42 (arabinofuranose and
arabinoxylans), CBM43 (.beta.-1,3-glucans), CBM44 (cellulose and
xyloglucans), CBM45 (starch), CBM46 (cellulose), CBM47 (fucose),
CBM48 (glycogens), CBM49 (crystalline cellulose), CBM50 (chitin and
chitopentaose), CBM51 (galactose and AB blood group antigens),
CBM52 (.beta.-1,3-glucans), CBM53 (starch), CBM54 (xylans), CBM55
(chitin), CBM56 (.beta.-1,3-glucans), CBM58 (maltoheptaose), CBM59
(mannans, xylans, and cellulose), CBM60 (xylans), CBM61
(.beta.-1,4-galactans), CBM62 (galactose, xyloglucans,
arabinogalactans, and galactomannans), CBM63 (cellulose), CBM64
(cellulose), CBM65 (xyloglucans), CBM66 (fructans), CBM67
(L-rhamnose), CBM68 (maltotriose and maltotetraose), CBM69
(starch), CBM70 (hyaluronan), CBM71 (lactose and
.beta.-D-galactosyl-1,4-.beta.-D-N-acetylglucosamine), or any
combination thereof. Any suitable carbohydrate binding module can
be employed, for example, as described in Boraston et al., Biochem
J., 382: 769-781 (2004), Shoseyov et al., Microbiology and
Molecular Biology Reviews, 70(2): 283-295 (2006) or Christiansen et
al., FEBS Journal, 276:5006-5029 (2009). CBMs or other binding
modules can be synthetically or genetically evolved or otherwise
generated to bind to any desired target whether carbohydrates,
other types of polymers, or non-polymer compounds. Techniques such
as phage display, for example, can be used. For example, CBMs can
be produced that bind to polymers, for example, a
polyaryletherketone (PAEK), a polyether ether ketone (PEEK), a
polyethylene, a polypropylene, a polystyrene, a
polytetrfluoroethylene, a polyvinylchloride, a polyamide, a
para-aramid, a polyethylene terephthalate, a polyimide, a
polycarbonate, a polypeptide, a polynucleotide, a glycoprotein, a
protein, a phosphorylated protein, a modified protein, a lipid, a
surfactant, lecithin, or a biosurfactant, or any combination
thereof. The CBMs can be replaced by antibodies and the detection
method can be tailored for antibodies. See, for example, Knox P. J.
(2012) Methods in Enzymology, volume 510, 233-245, which is
incorporated by reference herein in its entirety.
[0062] A binding module can bind specifically to any desired
polymer (e.g., lignocellulosic polymer or combination thereof, or
any oligosaccharide). For example, the binding module can
specifically bind to cellulose, hemicellulose, lignin, xylan,
mannan, glucuronoxylan, arabinoxylan, glucomannan, xyloglucan, or
any combination thereof or a linear fragment thereof, or a branched
fragment thereof, or an oligomer thereof (for example, an
oligosaccharide), or a monomer and/or macromer thereof, for
example, glucose, D-glucose, mannose, xylose, galactose, rhamnose,
arabinose, monolignol, p-coumaryl alcohol, coniferyl alcohol,
sinapyl alcohol, p-hydroxyphenyl phenylpropanoid, guaiacyl
phenylpropanoid, syringyl phenylpropanoid, or a combination
thereof. The binding module can bind to an amorphous or crystalline
lignocellulosic polymer. The binding module can recognize both an
amorphous and crystalline form of a particular lignocellulosic
polymer or be specific to one or the other. For example, the
binding module can specifically bind to crystallized cellulose (and
not to amorphous cellulose). A binding module can specifically bind
to amorphous cellulose (and not to crystallized cellulose).
[0063] The lignocellulosic polymer detection probe can include a
plurality of lignocellulosic polymer detection probes, each
lignocellulosic polymer detection probe binding solely or
essentially solely to a different lignocellulosic polymer. The
plurality of probes can include any number or kind of probes. For
example, a plurality can include at least two probes, at least
three probes, at least four probes, at least five probes, at least
ten probes, from two probes to twenty probes, from two probes to
ten probes, or from two probes to four probes. A plurality of
probes can be provided as a pre-formulated composition or combined
from separate stock solutions of individual probes. The
concentration, for example, weight percentage, of each probe in a
composition can be the same or differ between types of probes based
on the total weight of the composition. For example, the weight
ratio of probes in a composition including four different types of
probes could be 1:1:1:1, or some other ratio. The relative amounts,
ratio, and/or concentration of probes can be adjusted based on the
lignocellulosic polymer profile of a particular biomass.
[0064] A probe composition can include various other components,
for example, one or more stabilizers, one or more preservatives,
one or more emulsifiers, one or more thickeners, one or more
diluents, or any combination thereof.
[0065] Each lignocellulosic polymer detection probe can include a
different reporter module. For example, each reporter module can
have a different (or unique) fluorescence signature. Any
combination of fluorescent reporter modules can be used, for
example, one or more of eGFP, mCherry, mOrange2, and eCFP. Any
combination of binding modules can be used, for example, one or
more of CBM3a, CBM4-1, CBM15, and CBM27. A plurality of probes can
be provided such that each binding module is paired with a unique
reporter module and vice versa. For example, the lignocellulosic
polymer detection probe can include eGFP-CBM3a, mCherry-CBM4-1,
mOrange2-CBM15, eCFP-CBM27, or any combination thereof.
[0066] The lignocellulosic or any polymer detection probe of the
present invention can be detectable at a distinct wavelength
(.+-.0.5 nm, .+-.1 nm, 3 nm, .+-.5 nm). Thus, a combination of
different probes can be used and measured simultaneously, instead
of using different probes separately or sequentially.
[0067] The present invention also relates to a complex including
any probe or combination thereof bound to a pulp or paper product
including at least one surface available lignocellulosic polymer.
The present invention also relates to a pulp or paper product
including at least one surface available lignocellulosic polymer
and at least one probe bound thereto. The pulp can be any grade of
pulp and a pulp at any stage of production of a paper or other
biomass product. The pulp can include furnish. The pulp can include
white water. The pulp can be or include product waste, for example,
paper sludge. The pulp can be chemical pulp, mechanical pulp,
thermomechanical pulp or chemi (thermo) mechanical pulp or a Kraft
pulp. The pulp can be pulp from hardwood, softwood, or both types,
or can include textile fibers, agricultural plant pulp, or the
like. The pulp can be beached, pre-bleached, or unbleached. The
pulp can be refined or unrefined. The paper product can be an
intermediate paper product, a sample paper product useful for
testing, or a finished paper product. Paper products can be, for
example, printable or inkable paper sheets, sheets for cardboard
construction, tissue paper, hygiene and personal care sheet or
liner materials, or the like.
[0068] The present invention also is directed to various methods
that employ lignocellulosic or any polymer detection probes. The
methods can use any number or types of probes, for example a single
probe or a plurality of probes. The present invention relates to a
method of detecting a lignocellulosic polymer or any polymer. A
probe can be contacted with a biomass material. This can be
accomplished by introducing, adding, mixing, or otherwise combining
the probe with the biomass material (e.g., pulp or paper product).
Contacting can include and/or result in binding of the probe if its
specific target lignocellulosic polymer or any polymer is present.
A property associated with the reporter module can be measured to
determine the presence or absence of at least one lignocellulosic
polymer in the biomass material. For example, the property measured
can be or include fluorescence. The method can also include
calculating the amount of the at least one lignocellulosic polymer,
determining the type of the at least one lignocellulosic polymer,
or both.
[0069] The biomass material measured can be or include any suitable
biomass material. The biomass material can be a raw material, a
partially processed material, or a finished product. The biomass
material can be or include a wood biomass material. The wood
biomass material can be or include pulp, furnish, white water,
paper, a paper product, paper sludge, or any combination thereof.
The method can include forming at least one handsheet from the wood
biomass product, wherein the measuring is performed on the
handsheet.
[0070] The measuring can be performed before treatment, during
treatment, and/or after treatment, or any combination thereof of
the biomass material. The treatment can include, for example, an
enzymatic treatment, bleaching, amorphogenesis, milling, or PFI
refining, or any combination thereof. The treatment can be or
include, for example, enzymatic treatment with at least one enzyme
including a cellulase, a xylanase, a mannase, a lignase, or any
combination thereof. The method can be or include performing at
least one treatment of the biomass material based on the amount of
the at least one lignocellulosic polymer measured, the type of
lignocellulosic polymer measured, or both. The amount of
lignocellulosic polymer measured can correlate negatively or
positively with at least one physical property of the biomass
product. The at least one physical property can include, for
example, burst index, drainage rate, tear index, tensile index,
internal bond strength, or any combination thereof. The at least
one physical property can include, for example, density, elastic
modulus, shear modulus, Young's modulus, Poisson's ratio, yielding
stress, ultimate stress, fiber length, elongation, or the like.
[0071] The amount of lignocellulosic polymer measured, the type of
lignocellulosic polymer measured or both can be used to determine
the amount or type of treatment to be applied to the biomass
material. For example, the method can include dosing at least one
enzyme based on the amount of lignocellulosic polymer measured, the
type of lignocellulosic polymer measured or both. For example, if
the amount of crystalline cellulose is relatively low, a greater
amount of cellulase can be added. If the amount of lignin is high,
for example, the amount of bleach can be increased. A high amount
of xylan measured can be addressed, for example, by increasing the
amount of xylanase added to the pulp. For pre-bleaching, for
example, a measurement of high mannan content can be addressed by
increasing the amount of mannase added to the pulp. The method can
include adjusting mill speed based on the amount of lignocellulosic
polymer measured, the type of lignocellulosic polymer measured or
both. For example, if the amount of crystalline cellulose is
relatively low, the intensity of refining (e.g., mill speed, in
number of rpms) can be increased. The method can include adjusting
total water content of the biomass material based on the amount of
lignocellulosic polymer measured, the type of lignocellulosic
polymer measured or both. For example, water can be added to the
pulp if the amount of crystalline cellulose is relatively high and
the amount of amorphous cellulose is relatively low. Thus, the
method can be used to adjust the concentration of pulp or one or
more components thereof.
[0072] The present invention further relates to a method of
determining the effectiveness of an industrial treatment on pulp or
a paper product. A lignocellulosic polymer detection probe can be
contacted with or attached to a pulp or a paper product. The
specific binding of the probe to the pulp or the paper product can
be detected. The amount of at least one lignocellulosic polymer on
a surface of the pulp or the paper product can be determined (e.g.,
calculated). The effectiveness of an industrial treatment on the
pulp or paper product can be determined based on the amount of the
at least one lignocellulosic polymer detected. The effectiveness of
any suitable industrial treatment can be determined. The industrial
treatment can be or include, for example, an enzymatic treatment, a
chemical treatment, a physical treatment, or any combination
thereof. The method can be performed before the industrial
treatment, during the industrial treatment, after the industrial
treatment, or any combination thereof. The polymer detection probe
can be detectable at a distinct wavelength as part of the method.
The method can be performed on paper waste, for example, paper
sludge, and the industrial treatment can include a treatment for
paper waste.
[0073] The present invention also relates to a method of
determining a physical property of pulp or a paper product. A
lignocellulosic polymer detection probe can be contacted with pulp
or a paper product. The specific binding of the probe to the pulp
or the paper product can be detected. The amount of at least one
lignocellulosic polymer on a surface of the pulp or the paper
product can be calculated. The at least one physical property of
the pulp or paper product can be determined based on the amount of
the at least one lignocellulosic polymer detected. The at least one
physical property can be or include, for example, burst index,
drainage rate, tear index, tensile index, or internal bond
strength, or any combination thereof. The at least one physical
property can be or include, for example, density, elastic modulus,
shear modulus, Young's modulus, Poisson's ratio, yielding stress,
ultimate stress, fiber length, or elongation, or the like.
[0074] The probes and methods of the present invention are
applicable in applications other than pulp and paper processing.
For example, the probes and methods can be used for environmental
compliance and/or monitoring. The probes and methods can be used,
for example, in the food industry to track the types and/or amounts
of carbohydrates present during various stages of food production,
and subsequently to detect food spoliation or other conditions or
properties. The probes and methods can be used to track the
presence and/or amounts of microbes or other cell types in any
material. The probes and methods can be used to detect cell markers
such as glycoproteins, for example, those characteristic of blood
groups, cancers, or pathogens. The probes and methods can be used
in medical contexts, for example, histology. The probes and methods
of the present invention are applicable to any relevant sector of
industrial production, food production/testing, agricultural
applications, plastics, medicine, diagnostics, microbiology,
biomass/biofuel, and/or petroleum production/testing, and the
like.
[0075] A polymer detection probe, in general, is provided by the
present invention. The probe can have, for example, one or more
characteristics or functions of the lignocellulosic polymer probes
described herein, overlapping characteristics or functions, or
different characteristics or functions. The polymer detection probe
can include, for example, a) a binding module that specifically
binds to at least one polymer and b) a reporter module that is
spectroscopically detectable. The polymer detection probe can be or
include, for example, a probe polypeptide. The reporter module can
be, for example, fluorescent. The reporter module can be or include
a fluorescent protein. The binding module can be a
carbohydrate-binding module (CBM). The binding module can
specifically bind to, for example, cellulose, hemicellulose,
lignin, xylan, mannan, glucuronoxylan, arabinoxylan, glucomannan,
xyloglucan, or any combination thereof or a linear fragment
thereof, or a branched fragment thereof, or an oligomer thereof, or
a monomer and/or macromer thereof, for example, glucose, D-glucose,
mannose, xylose, galactose, rhamnose, arabinose, monolignol,
p-coumaryl alcohol, coniferyl alcohol, sinapyl alcohol,
p-hydroxyphenyl phenylpropanoid, guaiacyl phenylpropanoid, or
syringyl phenylpropanoid, or a combination thereof. The binding
module can specifically bind to, for example, a glycoprotein,
carbohydrate, or both, specific to a particular blood antigen,
type, group, or subgroup.
[0076] The binding module can specifically bind to any particular
polymer (e.g., oligosaccharide or other saccharide polymer or other
polymer). The polymer can be naturally occurring or synthetic. The
binding module can specifically bind to, for example, a
polyaryletherketone (PAEK), a polyether ether ketone (PEEK), a
polyethylene, a polypropylene, a polystyrene, a
polytetrfluoroethylene, a polyvinylchloride, a polyamide, a
para-aramid, a polyethylene terephthalate, a polyimide, a
polycarbonate, a polypeptide, a polynucleotide, a glycoprotein, a
protein, a phosphorylated protein, a modified protein, a lipid,
lecithin, a surfactant, or a biosurfactant, or any combination
thereof or a material including or containing one or more of these
polymers. The polymer detection probe can include a plurality of
polymer detection probes, each polymer detection probe specifically
binding to a different polymer. Each polymer detection probe can
include a different reporter module. Each reporter module can have
a different fluorescence signature. The polymer detection probe can
be detectable at a distinct wavelength (.+-.0.2 nm, .+-.0.5 nm,
.+-.1 nm, .+-.3 nm, .+-.5 nm). A complex is provided including the
probe specifically bound to a material including at least one
surface available polymer. The manner in which the lignocellulosic
polymer probe is designed and used (as described herein) can
equally apply in general to the broader polymer probes of the
present invention for any polymer and for the detection of that
polymer that specifically binds to the probe.
[0077] A method of detecting a polymer (such as the classes and
specific ones described earlier) is provided. A probe of the
present invention can be contacted with a material. A property
associated with the reporter module can be measured to determine
the presence or absence of at least one polymer in the material
based on specific binding of the probe to the at least one polymer.
The property measured can be, for example, fluorescence. The method
can include calculating the amount of the at least one polymer,
determining the type of the at least one polymer, or both. The
material can be or include a biological sample, for example, a
cancer biopsy, cells, a tissue sample, a microbiological sample, or
a blood sample. The presence or absence of a cancer and/or an
identity of cancer type can be determined, for example, by using a
binding module specific to a cancer cell surface marker, such as a
glycoprotein. The presence or absence of a beneficial or pathogenic
microorganism and/or an identify of a microorganism such as a virus
or bacterium can be determined, for example, by using a binding
module specific to a microorganism cell surface marker, such as a
cell wall polysaccharide or a cell surface glycoprotein. At least
one of a blood antigen, type, group, or subgroup of the blood
sample can be determined. For example, types A, B, AB, and O can be
distinguished in the ABO blood group system. An Rh antigen, such as
the D antigen, can be detected in the Rh blood group system to
determine whether a blood sample is Rh positive or negative. A
plurality of probes, for example, different kinds of probes, can be
used in the method. Thus, the ABO group and Rh factor identities of
a blood sample, for example, can be determined simultaneously.
[0078] The present invention will be further clarified by the
following examples, which are intended to be exemplary of the
present invention.
EXAMPLES
[0079] The following examples demonstrate the utility of the
present invention and its surprising advantages over existing
techniques. Predictive methods, based on the use of CBMs fused to
various fluorescent proteins, were created. Using molecular biology
techniques and constructs, four different fusion proteins were
created. Each of these "probes" is constructed of a specific
binding module (the CBM moiety) and a reporter module (the
fluorescent protein). Each probe emits fluorescence at a distinct
wavelength, allowing for unambiguous detection of the polymer
specifically bound by the binding module. FIG. 1 is a schematic
diagram of polymer detection using a probe.
[0080] After production and characterization of the probes, they
are demonstrated as specifically binding to relevant polymers, and
change binding in response to change in surface availability of
such polymers. Accordingly, these probes demonstrate that the
present invention enables the detection of changes, and that the
signal generate by the probes can be correlated with pulp and paper
properties measured independently, with industry-standard methods.
The method can be used to predict the impact of any industrial
treatment on properties that depend on exposure of polymers. As
demonstrated by these examples, the present invention can also be
used for monitoring surface polymers at any stage for any process
involving lignocellulosic biomass.
[0081] Table 1 lists CBMs, binding targets, and associated
fluorophores. The emission wavelengths are separated by several
nanometers, enabling detection of individual probes even when mixed
with other probes (spectral deconvolution).
TABLE-US-00001 TABLE 1 Fluorescent protein tag Probe # CBM Target
(Ex/Em) 1 CBM3a Crystalline cellulose eGFP (488/507) 2a CBM4-1
Amorphous cellulose mCherry (587/610) 2b CBM17 Amorphous cellulose
mCherry (587/610) 3 CBM15 Xylan mOrange2 (549/565) 4 CBM27 Mannan
eCFP (434/477)
[0082] Probe 1 detects, for example, crystalline cellulose
(CBM3a-eGFP) and fluoresces at 507 nm. Probe 2a detects, for
example, amorphous cellulose (CBM4-1-mCherry) and emits
fluorescence at 610 nm. Probe 2b (CBM17-mCherry) also detects
amorphous cellulose, but with a higher affinity compared to Probe
2a. CBM15 fused to mOrange2 detects xylan (Probe 3) and is visible
at 565 nm. Probe 4 includes CBM27 fused to eCFP and emits light at
477 nm. The probes emission maxima are separated, and can be
detectable even when probes are mixed with others described
here.
Example 1
[0083] This example demonstrates the production of reporter modules
(fluorescent proteins) in accordance with the present invention.
Four reporter modules (eCFP, eGFP, mCherry and mOrange2) were
cloned in pET11 vector and expressed in prokaryotic systems. FIGS.
2-5 show the genetic maps of the respective reporter modules
(fluorescent proteins) cloned into the pET11 vector. Nucleic acid
and amino acid sequences for the reporter modules are shown in SEQ
ID NOS: 23-30, respectively. These vector constructs are used for
labeling binding modules from cloned genes with the reporter
modules. Single fluorescent proteins (reporter modules) are used to
measure the background (non-specific) binding to the pulp
polymers.
[0084] Proteins were purified using the following methodology. E.
coli BL21(DE3) GOLD pLysS cells (ThermoFisher Scientific) bearing
the selected expression plasmid (reporter module, binding module or
complete Probe) were grown at 37.degree. C. in Luria-Bertani broth
containing 100 .mu.g/ml of ampicillin. Induction of recombinant
protein expression was performed by the addition of 500 .mu.M IPTG
(ThermoFisher Scientific) to mid-log-phase cells (O.D. 600 nm of
0.6-0.8) and the subsequent incubation for 18 hours at 25.degree.
C. Cells were afterward harvested and kept at -80.degree. C. Thawed
cell pellets were resuspended in 50 mM NaPO.sub.4 pH 8 containing
300 mM NaCl, 2 mM imidazole, and 1 mM PMSF, and then lysed using
six cycles of 60 seconds of sonication (Branson Ultrasonics
Corporation) at 200 W. Clarification of the lysate was achieved by
centrifugation at 10,000 g for 30 minutes at 4.degree. C.
[0085] The protein of interest was then purified by affinity
chromatography over a HisPrep FF 16/10 column (GE Healthcare Life
Sciences) equilibrated in 50 mM NaPO.sub.4 pH 8.0 buffer containing
300 mM NaCl and 10 mM imidazole. Following a ten column volumes
buffer washes, the desired protein was eluted following a ten
column volumes gradient of imidazole (10 to 100 mM) in 50 mM
NaPO.sub.4 pH 8.0 buffer containing 300 mM NaCl. A final
purification step was performed over a SUPERDEX 200 HR 16/50 column
(GE Healthcare Life Sciences) in 50 mM Tris-HCl pH 7.5 buffer
containing 300 mM NaCl to insure its homogenous purify. The
purified probe was then dialyzed in a 20 Tris-HCl pH 7.5 buffer
containing 20 mM NaCl and 5 mM CaCl.sub.2 at 4.degree. C. and
concentrated using a 10k MACROSEP Advance centrifugal device (Pall
Corporation). Concentrated protein solutions were stored at
-80.degree. C. using flash freezing. Protein purity was verified by
SDS-PAGE. The amount of protein was quantified by the Bradford
method.
[0086] The reporter modules were successfully produced and purified
by affinity chromatography (FIG. 6). The yield of the production
was around 25 mg of protein/L of culture. FIG. 6 is a SDS-PAGE of
purified fluorescence proteins; the arrow highlights the protein of
interest. Table 2 shows the properties of the purified reporter
modules (here, fluorescent proteins).
TABLE-US-00002 TABLE 2 Protein Amino Acids (#) Mol. Wt. (Da) pI
eGFP 247 27878.1 5.99 mCherry 244 27658.8 6.06 mOrange2 244 27756.1
6.72 eCFP 247 27842.0 5.99
Example 2
[0087] This example demonstrates production of binding modules
(CBMs) in accordance with the present invention. Five CBM genes
(CBM 3a, 4-1, 15, 17, and 27) were cloned in pET11 vector and
expressed in prokaryotic systems. The CBMs were produced and
purified by affinity chromatography (FIG. 7). The yield of the
production of the CBM was around 10 mg of protein/L of culture.
FIG. 7 is a SDS-PAGE of purified CBMs; the arrow highlights the
protein of interest. Table 3 displays the properties of the
purified binding modules (here, CBMs).
TABLE-US-00003 TABLE 3 Protein Amino Acids (#) Mol. Wt. (Da) pI
CBM3a 206 22375.1 7.58 CBM4-1 161 16528.7 3.88 CBM17 221 23926.9
5.46 CBM15 171 17949.4 4.31 CBM27 185 21242.6 5.57
Example 3
[0088] This example demonstrates the fluorescence emission by
reporter modules in accordance with the present invention. Emission
spectra of pulp and reporter modules (eGFP, mCherry and mOrange2)
were measured. The spectra were acquired at 23.degree. C. and the
proteins were diluted in a 20 mM Tris-HCl pH 7.5 buffer containing
20 mM NaCl and 5 mM CaCl.sub.2. The spectra in FIGS. 8 and 9 show
that depending on the excitation wavelength (488 nm vs 549 nm), the
change in fluorescence intensity (FI) (eGFP vs mCherry) can be
measured independent of pulp auto-fluorescence or other probes.
FIG. 8 shows the emission spectra of reporter modules (eGFP and
mCherry) and of a pulp handsheet disk after excitation at 549 nm.
With this excitation wavelength, mCherry fluorescence dominates
over the other substrates signal. FIG. 9 shows emission spectra of
FPs (eGFP and mCherry) and a pulp handsheet disk using an
excitation wavelength of 488 nm. At this excitation wavelength, the
pulp and mCherry fluorescence is much weaker than eGFP.
Example 4
[0089] This example demonstrates the production of complete probes
(binding module-reporter module). The genes that were used for
production of reporter modules and binding modules were fused to
generate the probes. FIGS. 10-14 show the pET11 vectors and the
genetic map covering the fusion sequence. The resulting molecules
(probes) include a reporter module at the N-terminus, followed by
the binding module. FIG. 10 shows the vector and map for
pET11A-eGFP-CBM3a expression vector (Probe 1). FIG. 11 shows the
vector and map for pET11A-mCherry-CBM4-1 expression vector (Probe
2a). FIG. 12 shows the vector and map for pET11A-mCherry-CBM17
expression vector (Probe 2b). FIG. 13 shows the vector and map for
pET11A-mOrange2-CBM15 expression vector (Probe 3). FIG. 14 shows
the vector and map for pET11A-eCFP-CBM27 expression vector (Probe
4). The nucleotide and amino acid sequences for Probe 1 are
included in the sequence listing as SEQ ID NOS: 1 and 2
respectively. The nucleotide and amino acid sequences for the
linker (joining eGFP and CBM3a) in Probe 1 are included in the
sequence listing as SEQ ID NOS: 3 and 4 respectively. The
nucleotide and amino acid sequences for Probe 2a are included in
the sequence listing as SEQ ID NOS: 5 and 6 respectively. The
nucleotide and amino acid sequences for Probe 2b are included in
the sequence listing as SEQ ID NOS: 7 and 8 respectively. The
nucleotide and amino acid sequences for Probe 3 are included in the
sequence listing as SEQ ID NOS: 9 and 10 respectively. The
nucleotide and amino acid sequences for Probe 4 are included in the
sequence listing as SEQ ID NOS: 11 and 12 respectively. The new
molecules (Probes) start with an N-terminal reporter module
(fluorescent protein) followed by the appropriate binding module
(CBM). The sequence linking the reporter to the binding module is
composed of a glycine, except for Probe 1, wherein the linking
sequence is SEQ ID NO: 3 encoded by SEQ ID NO: 4 (including a
thrombin cleavage site).
[0090] The vectors encoding the probes were transformed in E. coli
BL21-Gold (DE3) pLysS competent cells. Transformed cells were
selected on LB-agar with ampicillin (100 .mu.g/mL). E. coli cells
harboring probe vectors were cultured in Luria-Bertani (LB) broth
containing ampicillin (100 .mu.g/mL) at 27.degree. C. to mid
exponential phase (A600 nm=0.5). Recombinant protein expression was
induced by the addition of 0.5 mM IPTG and further incubated for 16
hours at 27.degree. C. (agitation 200 rpm). Induced cells were
centrifuged at 4.degree. C. for 30 min at 4000 g and the pellet
were store at -80.degree. C. Cells were suspended in 50 mM sodium
phosphate buffer (pH 8.0) and disrupted by sonication. Cells debris
was removed by centrifugation at 15,000 rpm for 15 min. The
6.times.His tagged protein was purified under native conditions
using Ni-NTA nickel affinity resin (Qiagen) according to
manufacturer specification at pH 8 using imidazole for elution. A
second passage was utilized to increase the purity of the protein
preparation. In order to remove salts and imidazole, purified
probes were dialyzed in a buffer containing 20 mM Tris-HCl pH 7.5,
20 mM NaCl and 5 mM CaCl.sub.2) for 24 hours at 4.degree. C.
Protein concentration was determined using a Bradford protein
assay.
[0091] FIG. 15 shows a SDS PAGE analysis of each probe. The arrows
indicate the position of the probe fused proteins. The size of each
probe corresponds to the size expected on the basis of its amino
acid residue content. Shown on the left side of the last four gels
is a standard size ladder allowing estimation of sizes for proteins
migrated on the same gel. Table 4 shows the properties of the
purified Probes (reporter module-binding module).
TABLE-US-00004 TABLE 4 Protein Amino Acids (#) Mol. Wt. (Da) pI
eGFP-CBM3a 415 46260.9 5.91 mCherry-CBM4-1 397 43158.4 4.67
mCherry-CBM17 457 50556.6 5.49 mOrange2-CBM15 407 44676.4 5.10
eCFP-CBM27 424 48055.5 5.59
Example 5
[0092] This example demonstrates spectroscopic characterization of
probes after production in accordance with the present invention.
In order to verify that the fusion of the reporter modules to the
binding modules did not prevent native folding, a spectroscopic
analysis was carried out. The spectra were acquired at 23.degree.
C. and the proteins were diluted in a 20 mM Tris-HCl pH 7.5 buffer
containing 20 mM NaCl and 5 mM CaCl.sub.2. The absorption and
emission spectra recorded for Probe 1, Probe 2b, Probe 3 and Probe
4 are shown in FIGS. 16A-16D. They are comparable with spectra
reported in the literature and strongly suggest that the reporter
modules are not affected by the presence of the binding modules. In
FIGS. 16A-D, excitation spectra are shown as dashed lines and
emission spectra as full lines for the FP-CBM proteins. These
results strongly indicate that the reporter modules (fluorescent
proteins) are properly folded after their recovery from bacteria
and that the close proximity of the binding module has no
appreciable impact on its reporting capacity.
Example 6
[0093] This example demonstrates binding of the probes to model
compounds in accordance with the present invention. A solid state
depletion assay was performed involving Probe 1 and AVICEL or
WHATMAN paper as the substrate. AVICEL is a commercial substrate
made of crystalline cellulose available from FMC Corporation.
WHATMAN paper is an amorphous cellulose filter paper available from
GE Healthcare Life Sciences. FIG. 17 shows the results of a solid
state depletion assay in which binding saturation of Probe 1 to
AVICEL is apparent.
[0094] Affinity (K.sub.a) of Probe 1 for AVICEL was measured using
a modified version of a solid state depletion assay in order to
ascertain that the fusion of the reporter module (eGFP) with the
binding module (CBM3a) did not negatively affect the folding and
thus the affinity of CBM3a for AVICEL. FIG. 17 shows that Probe 1
has an affinity constant (K.sub.a) of 8 .mu.M for AVICEL, a value
similar to that reported for the commercial construct for
crystalline cellulose (7.7 This result confirms that the binding
module (CBM3a) of Probe 1 is well folded and that it binds to
crystalline cellulose with a high affinity regardless of the close
proximity of the reporter module (eGFP).
[0095] Binding isotherms of eGFP-CBM3a to AVICEL (filled circle)
and WHATMAN paper (open circle) after a 1 hour incubation at
23.degree. C. of the various cellulose support with eGFP-CBM3a (100
.mu.g/well) in a 20 mM Tris-HCl pH 7.5 buffer containing 20 mM NaCl
and 5 mM CaCl.sub.2). The affinity constant (K.sub.a) was
calculated from nonlinear regression of
[P.sub.bound]=N.sub.oK.sub.a[P.sub.free]/(1+K.sub.a[P.sub.free]).
In this example, K.sub.a is equal to 8 .mu.M for AVICEL and 0.083
for WHATMAN paper.
Example 7
[0096] Example 7 sets forth parameters for a typical probe binding
experiment used in the following examples. Materials and solutions
included filtered buffer (20 mM Tris-CL pH 7.5+20 mM NaCl+5 mM
CaCl.sub.2); agitation at room temperature for 1 hour), 6% milk
(fresh) in buffer (dissolve 1.2 g of milk into 20 ml of buffer;
Centrifuge 2 min, 100 g, RT), 3% milk (fresh) in buffer, TWEEN
0.05% in buffer, pulp-derived handsheet (paper disk: 3 mm diameter)
glued onto the bottom of black microplate shining face down.
Fluorescence acquisition included endpoint and area scanning
3.times.3 500 .mu.m; excitation wavelength (reporter
module-dependent) (9 mm)/emission wavelength (reporter
module-dependent) (9 mm); gain 50; 75 and 100; and top (4.5 mm)
detection. The reaction volume was 200 .mu.l. The fluorescent
(fusion) probe (or fiber polymer) treatment method FPTM protocol
was consistent with that described in Knox P. J. (2012) Methods in
Enzymology, volume 510, 233-245, which is incorporated by reference
herein in its entirety. A similar procedure is described in Ding et
al. (2006) BioTechniques 41, 435-443, which is incorporated by
reference herein in its entirety.
[0097] The fluorescence of the untreated paper disks was measured.
The handsheet was incubated in 200 .mu.l of milk 3%, one hour at
room temperature with a slow agitation. Wash 3 (200 .mu.l).times.5
min was performed with buffer at room temperature with agitation.
The fluorescence of the blocked paper disks was measured. 200 .mu.l
of probe/milk 3% was added and incubated at room temperature for
one hour with a slow agitation. The supernatant was removed and
total fluorescence was measured. Wash 3 (200 .mu.l).times.5 min
with buffer was performed at room temperature with agitation. The
residual fluorescence was measured. Wash 3 (200 .mu.l).times.5 min
was performed with TWEEN 0.05% at room temperature with agitation.
Residual fluorescence was measured. Black 96 wells microplate
(Costar, cat #3631) were employed. A SYNERGY Mx program was run
(BioTek Instruments, Inc., Winooski, Vt.).
[0098] FIG. 18 is a schematic diagram describing the probe binding
experiments on a paper disk. The various pulps used in the
following examples are described in Table 5 (NA: Not available;
"*"=Pulp chemical composition (wt %) measured at CRML). Pulps used
were from North American paper plants.
TABLE-US-00005 TABLE 5 Chemical Composition and Available
Characteristics of Different Pulps. Pulp 1 Pulp 2 Pulp 3 Pulp 4
Pulp 5 Pulp 6 Pulp origin Plant 1 Plant 2 Plant 3 Plant 3 Plant 3
Plant 3 Pulp High yield Kraft Kraft Kraft Mechanical Mechanical
Kraft Unrefined Unrefined Unrefined Unrefined Unrefined Unrefined
Unbleached Unbleached Unbleached bleached Unbleached bleached
Furnish: Furnish: Furnish: Furnish: Furnish: Furnish: softwood
softwood softwood softwood softwood softwood (resinous) (resinous)
(resinous) (resinous) (resinous) (resinous) Pulp 5.16 4.39 2.81
4.37 3.77 4.17 Consistency (wt %) Pulp 9 7.15 9.28 7.11 4.48 4.72
Initial pH Kappa 27-29 20-25 NA NA NA NA number Cellulose* 83.91
89.49 86.7 89.7 46 46.6 Hemicellulose* 9.54 7.29 16 16.9 21.7 22.2
Lignin* 6.7 3.2 4.4 1.9 29 29
Example 8
[0099] This example demonstrates the comparison of fluorescence
from a commercial "binding-reporter" probe with the fluorescence
from a reporter module alone at the surface of paper in accordance
with the present invention. The specific detection of crystalline
cellulose on the surface of small disks of pulp 1 (.about.0.5 mg)
was achieved by binding commercial eGFP-CBM3a (NZYTech company).
The non-specific signal provided by the binding of the reporter
module on the small disks was measured after incubation with the
reporter module alone. The assay was performed into 96 wells
microplate. Excess of Probe 1 (or reporter module GFP) was removed
by washing using Tween 20 (0.05%).
[0100] The fluorescence from the reporter module (alone or as
component of the Probe) was measured at a wavelength of 511 nm
(excitation wavelength 488 nm) using a SYNERGY Mx microplate reader
(BioTek Instruments, Inc.). The fluorescence intensities are
presented here as a function of refining intensity and cellulase
treatments. FIG. 19 shows fluorescence intensity of reporter module
(eGFP) alone bound to untreated and cellulase-treated pulp (after
two levels of refining). The non-specific fluorescent signal
obtained with the reporter module alone was very low compared to
Probe 1.
[0101] FIG. 20 depicts fluorescence intensity of Probe 1 bound to
untreated and cellulases treated pulp (after two level of
refining). FIG. 20 shows the detection of crystalline cellulose at
the surface of cellulase-treated handsheet using Probe 1. Cellulase
enzyme treatments of the old pulp increased the fluorescent signal
compared to untreated pulp at all levels of refining, which
indicates that the cellulase treatments of the pulp uncovered
additional crystalline cellulose regions. Accordingly, using Probe
1 of the present invention, the impact of cellulase treatments on
pulp can be detected without using any pulp and paper classical
tests.
Example 9
[0102] This example demonstrates the detection of changes in
surface crystalline cellulose after refining and cellulase
treatments in accordance with the present invention. The method is
based on the fluorescence intensity associated to the recognition
of crystalline cellulose by the CBM3a-eGFP (Probe 1) on the surface
of handsheets. Using a standardized Probe 1 fluorescence curve, the
measured fluorescence intensity can be converted into a quantity
(.mu.g) that is then divided by the surface (mm.sup.2) of the
handsheets. The results (.mu.g/mm.sup.2) enable the quantification
of the crystalline cellulose on the surface of the handsheets.
[0103] Quantification of crystalline cellulose on the surface of
pulp 1 handsheets was performed on small disks of -0.5 mg. The
handsheets at basis weight 60 g/m.sup.2 were produced from
previously treated (cellulases at 0.05%, 1 h, 50.degree. C., pH 7)
and untreated pulp 1. The specific detection of crystalline
cellulose on the surface of pulp 1 handsheets was achieved with
Probe 1 (250 .mu.g/ml, 1 h, room temperature, pH 7.4) in a 24 wells
microplate (Gourlay et al., 2012). After three washing steps, the
green residual fluorescence was measured at 511 nm (excitation
wavelength: 488 nm) using a Synergy Mx microplate reader (Bioteck).
The fluorescence intensities were averaged and presented as
percentages, as a function of PFI revolutions (FIG. 21) or
cellulase treatments (FIG. 22).
[0104] FIG. 21 depicts the impact of PFI refining on the
quantification of crystalline cellulose on the surface of pulp 1
handsheets. The unrefined fluorescence intensity and corresponding
CSF value were set as reference points (100%). FIG. 21 shows that
the residual fluorescence, which should indicate the amount of
Probe 1-tagged crystalline cellulose at the surface of pulp 1
handsheets, increased from 2.7% to 28.6% as the PFI revolutions
increased from 1500 to 6000. This decrease is not linear and was
correlated with the decrease in CSF (from 87.9 ml to 71.1 ml),
which is an indicator of the degree of hydration of pulp.
Accordingly, the amorphogenesis process (water swelling of the
pulp), which is associated to PFI refining, is evidently
responsible for the recorded decrystallization or loss of
crystalline cellulose at the surface of pulp 1 handsheets.
[0105] FIG. 22 depicts the impact of cellulase treatment on the
quantification of crystalline cellulose on the surface of pulp 1
handsheets. The untreated fluorescence intensities at 0, 3000, and
4500 revolutions were set as the reference values (100%). FIG. 22
shows that all cellulase treatments increased the detection of
eGFP-tagged crystalline celluloses. These results indicate that
enzymes expose previously buried crystalline celluloses at the
surface of pulp 1 handsheets compared to untreated handsheets.
[0106] The highest increase recorded was for the treatment of pulp
1 with cellulase C6 without refining. Cellulase C1 and C2
treatments led to the lowest increase of crystalline cellulose on
unrefined and refined pulp 1 at 3000 revolutions (vs untreated)
compared to the other enzyme samples. However, the use of more
intense refining (4500 revs) on treated pulp 1 with cellulase
sample C1, C2, and C3 lead to an increase of crystalline
celluloses. These observations might be explained by the
generations of microfibrils after refining and consequently an
increase exposition of crystalline cellulose at the surface of the
fibers. These results suggest that cellulase treatments of pulp 1
followed by mechanical treatment expose a larger quantity of
crystalline celluloses. In opposition to all other enzymes,
refining had no impact on C4-treated handsheet.
Example 10
[0107] This example demonstrates the prediction of the presence or
absence of changes in surface crystalline cellulose after refining
and xylanase treatments in accordance with the present invention.
Digestion of the xylan polymers by xylanases can uncover
crystalline cellulose and increase its detection on handsheet
surfaces when compared with the untreated controls. Probe 1 was
used to detect changes in crystalline cellulose at the surface of
paper after xylanase treatments. FIG. 23 depicts the quantification
(.mu.g/mm.sup.2) of Probe 1 bound on the surface of
xylanase-treated handsheets from plant 2 refined at 0, 3000 and
4500 PFI revolutions. Pulp 2 was used for sheet preparation. The
excitation wavelength was 488 nm. No xylanase treatments used here
had a significant impact on fluorescence detected. The quantity of
crystalline cellulose measured here suggests that xylanase
preparations used had no impact on cellulose fiber surface. This
result is in complete agreement with the analysis of paper physical
properties and fiber morphologies after xylanase treatments. The
probe 1 FPTM results reveal the absence of xylanase impact in a
much less time than involved for traditional TAPPI methods, thus
enabling a fast, high throughput protocol.
Example 11
[0108] This example demonstrates the detection of crystalline
cellulose after refining in accordance with the present invention.
Correlations were determined between Probe 1 detection and paper
physical properties using two different pulps. Two pulps (Pulp 1
and Pulp 2) were refined and analyzed by Probe 1 and by standard
TAPPI methods. The measurement of crystalline cellulose on
handsheet disks (60 g/m.sup.2) was performed by incubating the
paper disks with 250 .mu.g/ml of Probe 1. Probe 1 fluorescence was
used for recognition of crystalline cellulose on the surface of
handsheets after refining (various levels of energy). Using a
standardized curve, the measured fluorescence intensity is
converted into a quantity (m) of crystalline cellulose, which is
then divided by the surface (mm.sup.2) of the handsheets. The
results (.mu.g/mm.sup.2) enable the quantification of the
crystalline cellulose on the surface of the handsheets.
[0109] FIG. 24 depicts the quantification of crystalline cellulose
(.mu.g/mm.sup.2) on the surface of PFI refined handsheet (Pulp 1
(plant 1; left bar) vs Pulp 2 (plant 2; right bar). These FPTM
results support the concept that pulp refining partially
decrystallizes cellulose. In the case of the Pulp 2 handsheets, at
least three decrystallization events (or steps) are observed:
0-2000, 3000-4500 and at 6000 PFI revolutions. This effect is less
apparent than when using more than 3000 revs.
[0110] FIGS. 25A-25D depict correlations between crystalline
cellulose quantification using Probe 1 (.mu.g/mm.sup.2) and Pulp
2/paper physical properties as a function of refining energy (PFI
revolutions). FIG. 25A depicts tear index (mN m.sup.2/g), FIG. 25B
depicts tensile index (N m/g), FIG. 25C depicts internal bond
strength (J/m.sup.2), and FIG. 25D depicts fibers mean length (mm).
FIGS. 25A-25D show the correlations between Probe 1 signal and the
corresponding paper's physical properties for the Pulp 2
handsheets. An inverse correlation is observed with the tensile
index and the internal bond strength (FIG. 25B-25C). In contrast,
the tear index is directly correlated with the crystalline
cellulose quantification (FIG. 25A). These correlations can be used
for predicting the impact of various refining treatments on final
paper properties in a very short time (1 hour vs days) compared to
TAPPI pulp and paper analyses. The internal bond and fiber length
were further modified by refining past 3000 revs, at variance with
tear and tensile indices that stabilized under similar
conditions.
[0111] The changes in properties and crystalline cellulose detected
after treatment of pulp 1 are shown in FIGS. 26A-26D. Correlations
between crystalline cellulose quantification using Probe 1
(.mu.g/mm.sup.2) and pulp 1/paper physical properties as a function
of refining energy (PFI revolutions) are depicted. FIG. 26A depicts
tear index (mN m.sup.2/g), FIG. 26B depicts tensile index (N m/g),
FIG. 26C depicts internal bond strength (J/m.sup.2), and FIG. 26D
depicts fibers mean length (mm). The amount of cellulose detected
by Probe 1 decreased as refining energy increased in general, with
the exception of the value associated with 1500 revs. Except for
this particular value, all panels suggest the same correlations as
those observed with pulp 2 (FIGS. 25A-25B). The different content
in lignin of either pulp did not appear to affect the overall
correlations. Correlations were positive for tear index, and
reciprocal for internal bond and tensile index.
[0112] The four properties monitored continued to change when
refining was increased past 3000 revs. Thus, applying the method to
different pulp may result in subtle changes in correlations at high
refining energy. Independent of the physical properties and the
pulp studied here, the impact of refining on crystalline cellulose
was observed after a minimal degradation of fiber (i.e. when
treatment exceeded 1500 revs). The impact of refining past 3000
revs is no longer associated with changes in crystalline cellulose
at the surface (it is not changed by further refining).
Consequently, to improve and develop pulp/paper physical
properties, the refining intensity should minimally degrade the
crystalline matrix of the pulp.
[0113] The results demonstrate that the method is a diagnostic
indicator that can be taken into account when determining the
refining conditions for a given set of properties. Its simplicity
and high sensibility enable a fast and efficient diagnostic of the
best refining conditions used for a set of physical properties. The
results show that the method can be used to predict the impact of a
treatment on pulp and paper properties for tear, tensile and
internal bond strength, without performing actual measurements of
those properties on handsheets.
Example 12
[0114] This example demonstrates the detection of xylan on the
surface of paper disks in accordance with the present invention.
Pulp 5 (unbleached mechanical pulp), Pulp 6 (bleached mechanical
pulp, Pulp 3 (unbleached Kraft pulp), Pulp 4 (bleached Kraft pulp),
and Pulp 2 (unbleached Kraft pulp) were used in this example (as
described above in Table 5). The assay was performed in 96
well-microplates with each well containing a small handsheet disk
(60 g/m.sup.2). The specific detection of xylan on the surface of
such disks made from different pulps was achieved by binding Probe
3 (CBM15-mOrange2). The fluorescence intensity was measured after
incubating the paper disks with 200 .mu.l solution of Probe 3. The
excess Probe 3, as well as non-specific binding of the same adduct
to any other moieties, was removed by washing three times with a
TWEEN 20 solution (0.05%). Fluorescence intensity from bound Probe
3 was measured at a wavelength of 569 nm (excitation wavelength 549
nm) using a SYNERGY Mx microplate reader.
[0115] FIG. 27 depicts fluorescence intensity of Probe 3 bound to
xylan at the surface of five different paper disks--UBKPR
Unbleached Kraft pulp (Pulp 2), UBMP unbleached mechanical pulp
(Pulp 5), BMP bleached mechanical pulp (Pulp 6), UBKP unbleached
Kraft pulp (Pulp 3); and BKP bleached Kraft pulp (Pulp 4). These
results show that Probe 3 has a higher binding affinity towards BKP
derived disks compared to the other paper disks. These results may
be attributed to the lignin content on the surface of the paper
disks. In Kraft pulping, chemicals and heat are used to dissolve
the lignin, the binding agent that covers cellulose and
hemicellulose. The lignin content of unbleached chemical pulp is
approximately 3-5% and bleaching process removes practically all of
the remaining lignin, taking it towards 0% of the total content.
Mechanical pulping methods preserve most of the wood component so
that the lignin content is similar to that of wood (20-28%).
Bleached Kraft paper that contains the lowest amount of lignin has
been detected by the probe much more efficiently than the other
paper disks. This can be ascribed by the increased exposure of
xylan on the surface of bleached fibers. This analysis shows that
Probe 3 detect xylan on the surface of the paper disks and that it
can discriminate between paper surfaces made from different
pulps.
Example 13
[0116] This example demonstrates the detection of xylan removal
after enzymatic treatments in accordance with the present
invention. The ability to detect xylan was also tested for pulp
where xylan content was changed at the fiber surface. In order to
demonstrate binding of Probe 3 to xylan unambiguously, paper disks
(from bleached Kraft pulp (BKP)) were treated with a commercial
xylanase prior detection assay. Xylanase was used at two doses: 0.1
U per paper disk and 0.4 U per paper disk. Results are shown in
FIG. 28. FIG. 28 depicts fluorescence intensity of Probe 3 bound to
xylan at the surface of untreated and xylanase treated Pulp 4 (BKP)
paper. Treatment duration is indicated on the x axis. Untreated
indicates Pulp 4 paper disks without xylanase treatment. "O/N"
indicates paper treated with xylanase overnight at room
temperature. Binding of Probe 3 was reduced by almost 80% after
xylanase treatment, establishing that the method detects variations
in polymers at the surface of fibers.
Example 14
[0117] This example demonstrates the detection of mannan on the
surface of paper disks in accordance with the present invention. A
high content of mannan (and redeposition on the surface of
cellulose fiber during the Kraft pulping) may inhibit the bleaching
process. Accordingly, mannanase, in addition with xylanase, is used
for prebleaching. In order to optimize mannanase treatment, it is
useful to determine mannan content before and after
prebleaching.
[0118] Two different grades of pulp (Pulp 3: unbleached Kraft pulp
(UBKP) and pulp 4: bleached Kraft pulp (BKP)) were investigated
with respect to their mannan content. The assay was performed in 96
well-microplates with each well containing a small handsheet disk
(60 g/m2). The specific detection of mannan on the surface of such
disks made from different pulps was achieved by binding the
eCFP-CBM27 protein fusion, also named Probe 4. The fluorescence
intensity was measured after incubating the paper disks with 200
.mu.l solution of Probe 4. The excess Probe 4, as well as
non-specific binding of the same adduct to any other moieties, was
removed by washing 3 times with a TWEEN 20 solution (0.05%).
Fluorescence intensity from bound Probe 4 was measured at a
wavelength of 477 nm (excitation wavelength 434 nm) using a SYNERGY
Mx microplate reader. The fluorescence intensities of the bound
probes are presented in FIG. 29.
[0119] FIG. 29 depicts fluorescence intensity of Probe 4
(eCFP-CBM27) bound to mannan at the surface of two different paper
disks: unbleached Kraft pulp (Pulp 3, UBKP) and bleached Kraft pulp
(Pulp 4, BKP). These results show that Probe 4 has a higher binding
affinity towards Pulp 4 (BKP) derived disks compared to the pulp 3
(UBKP) paper disks. These results may be attributed to the
redeposit of the hemicelluloses and to the lignin content on the
surface of the paper disks of pulp 4 (BKP). In Kraft pulping,
chemicals and heat are used to dissolve lignin, the binding agent
that covers cellulose and hemicellulose. Thus the lignin content
drops from 3-5% down to nearly zero. So, mannan in bleached Kraft
paper (that contains the lowest amount of lignin) has been detected
by the probe much more efficiently than the other paper disks. This
result reflects the increased exposure of mannan on the surface of
bleached fibers.
Example 15
[0120] This example demonstrates the detection of mannan removal
after enzymatic treatment in accordance with the present invention.
The ability to detect mannan at the surface of fibers was tested.
In order to show the binding of Probe 4 to mannan unambiguously,
paper disks (from bleached Kraft pulp (Pulp 4, BKP)) were treated
with a commercial mannanase (MEGAZYME-E-BMANN) enzyme prior to
detection assay. Results are shown in FIG. 30. FIG. 30 depicts
fluorescence intensity of Probe 4 bound to mannan at the surface of
mannanase-treated bleached Kraft pulp (Pulp 4, BKP) paper. Binding
of Probe 4 was reduced by almost 44% after a 1 hour treatment with
mannanase. These results clearly demonstrate that the method
detects variations in polymers at the surface of fibers.
[0121] The present invention includes the following
aspects/embodiments/features in any order and/or in any
combination:
[0122] 1. A lignocellulosic polymer detection probe comprising a) a
binding module that specifically binds to at least one
lignocellulosic polymer and b) a reporter module that is
spectroscopically detectable.
[0123] 2. The probe of any preceding or following
embodiment/feature/aspect, wherein the lignocellulosic polymer
detection probe comprises a probe polypeptide.
[0124] 3. The probe of any preceding or following
embodiment/feature/aspect, wherein the binding module is a binding
module polypeptide and the reporter module is a reporter module
polypeptide.
[0125] 4. The probe of any preceding or following
embodiment/feature/aspect, wherein the binding module polypeptide
is fused directly to the reporter module polypeptide.
[0126] 5. The probe of any preceding or following
embodiment/feature/aspect, wherein the binding module polypeptide
is linked to the reporter polypeptide via a linker polypeptide.
[0127] 6. The probe of any preceding or following
embodiment/feature/aspect, wherein the probe polypeptide comprises
an amino acid sequence of any one of SEQ ID NOS: 2, 6, 8, 10, and
12.
[0128] 7. The probe of any preceding or following
embodiment/feature/aspect, wherein the binding module polypeptide
comprises an amino acid sequence of any one of SEQ ID NOS: 14, 16,
18, 20, and 22 and the reporter module polypeptide comprises an
amino acid sequence of any one of SEQ ID NOS: 24, 26, 28, and
30.
[0129] 8. The probe of any preceding or following
embodiment/feature/aspect, wherein the binding module polypeptide
is not an antibody or a fragment thereof.
[0130] 9. The probe of any preceding or following
embodiment/feature/aspect, wherein the reporter module is not an
antibody or a fragment thereof.
[0131] 10. The probe of any preceding or following
embodiment/feature/aspect, wherein the reporter module is not a
polypeptide.
[0132] 11. The probe of any preceding or following
embodiment/feature/aspect, wherein the reporter module is
fluorescent.
[0133] 12. The probe of any preceding or following
embodiment/feature/aspect, wherein the reporter module has a
fluorescence excitation peak (maximum) of from about 350 nm to
about 700 nm.
[0134] 13. The probe of any preceding or following
embodiment/feature/aspect, wherein the reporter module has a
fluorescence emission peak (maximum) of from about 400 nm to about
750 nm.
[0135] 14. The probe of any preceding or following
embodiment/feature/aspect, wherein the reporter module comprises a
fluorescent protein.
[0136] 15. The probe of any preceding or following
embodiment/feature/aspect, wherein the fluorescent protein
comprises an ultraviolet fluorescent protein, a blue fluorescent
protein, a cyan fluorescent protein, a green fluorescent protein, a
yellow fluorescent protein, an orange fluorescent protein, a red
fluorescent protein, a far-red fluorescent protein, a near infrared
fluorescent protein, an infrared fluorescent protein, a
sapphire-type fluorescent protein, a long Stokes shift fluorescent
protein, a switchable fluorescent protein, or any combination
thereof.
[0137] 16. The probe of any preceding or following
embodiment/feature/aspect, wherein the fluorescent protein
comprises Sirius, TagBFP, mTagBFP2, Azurite, EBFP2, mKalama1,
Sirius, Sapphire, T-Sapphire, ECFP, mAmetrine, Cerulean,
mCerulean3, SCFP3A, CyPet, mTurguoise, mTurquoise2, monomeric
Midoriishi-Cyan, Aquamarine, eCFP, TagCFP, mTFP1, AmCyanl, EGFP,
Emerald, Superfolder GFP, monomeric Azami Green, TurboGFP, TagGFP2,
mUKG, mWasabi, Clover, mNeonGreen, eGFP, AcGFP1, ZGreen1,
ZsYellow1, mBanana, EYFP, Topaz, Citrine, Venus, SYFP2, Ypet,
IanRFP-deltaS83, mPapaya1, TagYFP, mOrange, mOrange2, monomeric
Kusabira-Orange, mKOk, mKO2, mTangerine, mNectarine, TagRFP,
TagRFP-T, mApple, mRuby, mRuby2, DsRed-Express2, DsRed-Express,
tdTomato, DsRed-Monomer, DsRed-Monomer, DsRed2, AsRed2,
mStrawberry, mCherry, HcRed1, FusionRed, mRaspberry, E2-Crimson,
mPlum, HcRed-Tandem, mKate2, mNeptune, NirFP, TagRFP657, TagRFP675,
iFP1.4, iRFP(iRFP713), iRFP670, iRFP682, iRFP702, iRFP720, iFP2.0,
mIFP, mKeima Red, LSS-mKate1, LSS-mKate2, LSSmOrange, mBeRFP,
PA-GFP, PATag RFP, Dendra2, Timer, PAmCherry, Kaede (green), Kaeda
(red), KikGR1 (green), KikGR1 (red), PS-CFP2, mEos2 (green), mEos2
(red), mEos3.2 (green), mEos3.2(red), PSmOrange, Dropna, or any
combination thereof.
[0138] 17. The probe of any preceding or following
embodiment/feature/aspect, wherein binding module is a
carbohydrate-binding module (CBM) comprising CBM1, CBM2, CBM3,
CBM3a CBM4, CBM5, CBM6, CBM9, CBM10, CBM11, CBM12, CBM14, CBM15,
CBM17, CBM18, CBM19, CBM20, CBM21, CBM25, CBM27, CBM28, CBM33,
CBM48, CBM49, or any combination thereof.
[0139] 18. The probe of any preceding or following
embodiment/feature/aspect, wherein the binding module specifically
binds to cellulose, hemicellulose, lignin, xylan, mannan, or any
combination thereof.
[0140] 19. The probe of any preceding or following
embodiment/feature/aspect, wherein the binding module specifically
binds to crystallized cellulose.
[0141] 20. The probe of any preceding or following
embodiment/feature/aspect, wherein the lignocellulosic polymer
detection probe comprises a plurality of lignocellulosic polymer
detection probes, each lignocellulosic polymer detection probe
specifically binding to a different lignocellulosic polymer.
[0142] 21. The probe of any preceding or following
embodiment/feature/aspect, wherein each lignocellulosic polymer
detection probe comprises a different reporter module.
[0143] 22. The probe of any preceding or following
embodiment/feature/aspect, wherein each reporter module has a
different fluorescence signature.
[0144] 23. The probe of any preceding or following
embodiment/feature/aspect, wherein the reporter modules comprise
one or more of eGFP, mCherry, mOrange2, and eCFP.
[0145] 24. The probe of any preceding or following
embodiment/feature/aspect, wherein the binding modules comprise one
or more of CBM3a, CBM4-1, CBM15, and CBM27.
[0146] 25. The probe of any preceding or following
embodiment/feature/aspect, wherein the lignocellulosic polymer
detection probe comprises eGFP-CBM3a, mCherry-CBM4-1,
mOrange2-CBM15, eCFP-CBM27, or any combination thereof.
[0147] 26. The probe of any preceding or following
embodiment/feature/aspect, wherein the lignocellulosic polymer
detection probe is detectable at a distinct wavelength.
[0148] 27. A complex comprising the probe of any preceding or
following embodiment/feature/aspect specifically bound to a pulp or
paper product comprising at least one surface available
lignocellulosic polymer.
[0149] 28. A pulp or paper product comprising at least one surface
available lignocellulosic polymer and at least one probe of any
preceding or following embodiment/feature/aspect specifically bound
thereto.
[0150] 29. A method of detecting a lignocellulosic polymer, the
method comprising:
[0151] contacting the probe of any one of any preceding or
following embodiment/feature/aspect with a biomass material;
and
[0152] measuring a property associated with the reporter module to
determine the presence or absence of at least one lignocellulosic
polymer in the biomass material based on specific binding of the
probe to the at least one lignocellulosic polymer.
[0153] 30. The method of any preceding or following
embodiment/feature/aspect, wherein the property measured is
fluorescence.
[0154] 31. The method of any preceding or following
embodiment/feature/aspect, further comprising calculating the
amount of the at least one lignocellulosic polymer, determining the
type of the at least one lignocellulosic polymer, or both.
[0155] 32. The method of any preceding or following
embodiment/feature/aspect, wherein the biomass material comprises a
wood biomass material.
[0156] 33. The method of any preceding or following
embodiment/feature/aspect, wherein the wood biomass material is
pulp, furnish, paper, or any combination thereof.
[0157] 34. The method of any preceding or following
embodiment/feature/aspect, further comprising forming at least one
handsheet from the wood biomass product, wherein the measuring is
performed on the handsheet.
[0158] 35. The method of any preceding or following
embodiment/feature/aspect, wherein the measuring is performed
before treatment, during treatment, or after treatment, or any
combination thereof.
[0159] 36. The method of any preceding or following
embodiment/feature/aspect, wherein the treatment comprises an
enzymatic treatment, bleaching, amorphogenesis, milling, or PFI
refining, or any combination thereof.
[0160] 37. The method of any preceding or following
embodiment/feature/aspect, wherein the treatment comprises
enzymatic treatment with at least one enzyme comprising a
cellulase, a xylanase, a mannase, a lignase, or any combination
thereof.
[0161] 38. The method of any preceding or following
embodiment/feature/aspect, further comprising performing at least
one treatment of the biomass material based on the amount of the at
least one lignocellulosic polymer measured, the type of
lignocellulosic polymer measured, or both.
[0162] 39. The method of any preceding or following
embodiment/feature/aspect, wherein the amount of lignocellulosic
polymer measured correlates negatively or positively with at least
one physical property of the biomass product.
[0163] 40. The method of any preceding or following
embodiment/feature/aspect, wherein the at least one physical
property comprises burst index, drainage rate, tear index, tensile
index, or internal bond strength, or any combination thereof.
[0164] 41. The method of any preceding or following
embodiment/feature/aspect, further comprising dosing at least one
enzyme based on the amount of lignocellulosic polymer measured, the
type of lignocellulosic polymer measured, or both.
[0165] 42. The method of any preceding or following
embodiment/feature/aspect, further comprising adjusting mill speed
based on the amount of lignocellulosic polymer measured, the type
of lignocellulosic polymer measured, or both.
[0166] 43. The method of any preceding or following
embodiment/feature/aspect, further comprising adjusting total water
content of the biomass material based on the amount of
lignocellulosic polymer measured, the type of lignocellulosic
polymer measured, or both.
[0167] 44. The method of any preceding or following
embodiment/feature/aspect, wherein the probe comprises a plurality
of probes.
[0168] 45. A method of determining the effectiveness of an
industrial treatment on pulp or a paper product comprising:
[0169] contacting the lignocellulosic polymer detection probe of
any one of any preceding or following embodiment/feature/aspect
with pulp or a paper product;
[0170] detecting the specific binding of the probe to the pulp or
the paper product;
[0171] calculating the amount of at least one lignocellulosic
polymer on a surface of the pulp or the paper product; and
[0172] determining the effectiveness of an industrial treatment on
the pulp or paper product based on the amount of the at least one
lignocellulosic polymer detected.
[0173] 46. The method of any preceding or following
embodiment/feature/aspect, wherein the industrial treatment
comprises an enzymatic treatment, a chemical treatment, or a
physical treatment, or any combination thereof.
[0174] 47. The method of any preceding or following
embodiment/feature/aspect, wherein the method is performed before
the industrial treatment, during the industrial treatment, or after
the industrial treatment, or any combination thereof.
[0175] 48. The method of any preceding or following
embodiment/feature/aspect, wherein the lignocellulosic polymer
detection probe is detectable at a distinct wavelength.
[0176] 49. A method of determining a physical property of pulp or a
paper product comprising:
[0177] contacting the lignocellulosic polymer detection probe of
any preceding or following embodiment/feature/aspect with pulp or a
paper product;
[0178] detecting the specific binding of the probe to the pulp or
the paper product;
[0179] calculating the amount of at least one lignocellulosic
polymer on a surface of the pulp or the paper product; and
[0180] determining at least one physical property of the pulp or
paper product based on the amount of the at least one
lignocellulosic polymer detected.
[0181] 50. The method of any preceding or following
embodiment/feature/aspect, wherein the at least one physical
property comprises burst index, drainage rate, tear index, tensile
index, or internal bond strength, or any combination thereof.
[0182] 51. A polymer detection probe comprising a) a binding module
that specifically binds to at least one polymer and b) a reporter
module that is spectroscopically detectable.
[0183] 52. The probe of any preceding or following
embodiment/feature/aspect, wherein the polymer detection probe
comprises a probe polypeptide.
[0184] 53. The probe of any preceding or following
embodiment/feature/aspect, wherein the reporter module is
fluorescent.
[0185] 54. The probe of any preceding or following
embodiment/feature/aspect, wherein the reporter module comprises a
fluorescent protein.
[0186] 55. The probe of any preceding or following
embodiment/feature/aspect, wherein the fluorescent protein
comprises an ultraviolet fluorescent protein, a blue fluorescent
protein, a cyan fluorescent protein, a green fluorescent protein, a
yellow fluorescent protein, an orange fluorescent protein, a red
fluorescent protein, a far-red fluorescent protein, a near infrared
fluorescent protein, an infrared fluorescent protein, a
sapphire-type fluorescent protein, a long Stokes shift fluorescent
protein, a switchable fluorescent protein, or any combination
thereof.
[0187] 56. The probe of any preceding or following
embodiment/feature/aspect, wherein binding module is a
carbohydrate-binding module (CBM).
[0188] 57. The probe of any preceding or following
embodiment/feature/aspect, wherein the binding module specifically
binds to cellulose, hemicellulose, lignin, xylan, mannan,
glucuronoxylan, arabinoxylan, glucomannan, xyloglucan, or any
combination thereof or a linear fragment thereof, or a branched
fragment thereof, or an oligomer thereof, or a monomer and/or
macromer thereof, for example, glucose, D-glucose, mannose, xylose,
galactose, rhamnose, arabinose, monolignol, p-coumaryl alcohol,
coniferyl alcohol, sinapyl alcohol, p-hydroxyphenyl
phenylpropanoid, guaiacyl phenylpropanoid, or syringyl
phenylpropanoid, or a combination thereof.
[0189] 58. The probe of any preceding or following
embodiment/feature/aspect, wherein the binding module specifically
binds to a glycoprotein, carbohydrate, or both, specific to a
particular blood antigen, type, group, or subgroup.
[0190] 59. The probe of any preceding or following
embodiment/feature/aspect, wherein the binding module specifically
binds to a polyaryletherketone (PAEK), a polyether ether ketone
(PEEK), a polyethylene, a polypropylene, a polystyrene, a
polytetrfluoroethylene, a polyvinylchloride, a polyamide, a
para-aramid, a polyethylene terephthalate, a polyimide, a
polycarbonate, a polypeptide, a polynucleotide, a glycoprotein, a
protein, a phosphorylated protein, a modified protein, a lipid, a
surfactant, lecithin, or a biosurfactant, or any combination
thereof.
[0191] 60. The probe of any preceding or following
embodiment/feature/aspect, wherein the polymer detection probe
comprises a plurality of polymer detection probes, each polymer
detection probe specifically binding to a different polymer.
[0192] 61. The probe of any preceding or following
embodiment/feature/aspect, wherein each polymer detection probe
comprises a different reporter module.
[0193] 62. The probe of any preceding or following
embodiment/feature/aspect, wherein each reporter module has a
different fluorescence signature.
[0194] 63. The probe of any preceding or following
embodiment/feature/aspect, wherein the polymer detection probe is
detectable at a distinct wavelength.
[0195] 64. A complex comprising the probe of any preceding or
following embodiment/feature/aspect specifically bound to a
material comprising at least one surface available polymer.
[0196] 65. A method of detecting a polymer, the method
comprising:
[0197] contacting the probe of any preceding or following
embodiment/feature/aspect with a material; and
[0198] measuring a property associated with the reporter module to
determine the presence or absence of at least one polymer in the
material based on specific binding of the probe to the at least one
polymer.
[0199] 66. The method of any preceding or following
embodiment/feature/aspect, wherein the property measured is
fluorescence.
[0200] 67. The method of any preceding or following
embodiment/feature/aspect, further comprising calculating the
amount of the at least one polymer, determining the type of the at
least one polymer, or both.
[0201] 68. The method of any preceding or following
embodiment/feature/aspect, wherein the material comprises a blood
sample.
[0202] 69. The method of any preceding or following
embodiment/feature/aspect, further comprising determining at least
one of a blood antigen, type, group, and subgroup of the blood
sample.
[0203] 70. The method of any preceding or following
embodiment/feature/aspect, wherein the probe comprises a plurality
of probes.
[0204] 71. The probe of any preceding or following
embodiment/feature/aspect, wherein said polymer is at least one
saccharide polymer.
[0205] 72. The probe of any preceding or following
embodiment/feature/aspect, wherein said polymer is at least one
oligosaccharide polymer.
[0206] The present invention can include any combination of these
various features or embodiments above and/or below as set forth in
sentences and/or paragraphs. Any combination of disclosed features
herein is considered part of the present invention and no
limitation is intended with respect to combinable features.
[0207] The following references are incorporated by reference
herein in their entireties: [0208] Linder, M. et al. (1996) J Biol
Chem 271, 21268-21272. [0209] McLean, B. W. et al. (2002) J Biol
Chem 277, 50245-50254. [0210] Hilden, L. et al. (2003)
Biotechnology letters 25, 553-558. [0211] Lehtio, J. et al. (2003)
Proc Natl Acad Sci USA 100, 484-489. [0212] Czjzek et al., J Biol
Chem. 2001 Dec. 21; 276(51):48580-7. Epub 2001 Oct. 22. [0213]
Ding, S.-Y. et al. (2006) BioTechniques 41, 435-443. [0214]
McCartney, L. et al. (2006) Proc Natl Acad Sci USA 103, 4765-4770.
[0215] Hong, J. et al. (2007) Langmuir: the ACS journal of surfaces
and colloids 23, 12535-12540. [0216] Herve, C. et al. (2010) Proc
Natl Acad Sci USA 107, 15293-15298. [0217] Gourlay, K. et al.
(2012) Biotechnology for biofuels 5, 51. [0218] Knox, J. P. (2012)
Methods in enzymology 510, 233-245. [0219] Ruel, K. et al. (2012)
Plant science: an international journal of experimental plant
biology 193-194, 48-61. [0220] Luis, A. S. et al. (2013) J. Biol.
Chem. 288, 4799-4809 [0221] Zhang, M. et al. (2013) Physical
chemistry chemical physics: PCCP 15, 6508-6515. [0222] Mou et al.
(2013) Bioresources 8, 2325-2336. [0223] Machado et al., (2009)
Cellulose 16, 817-824. [0224] Kim et al. (2010) Planta 232,
817-824. [0225] Kim et al. (2012) Planta 236, 35-50. [0226] irok et
al. (2012) Carbohyd. Polym. 89, 213-221. [0227] Gao et al., (2014)
Biotechnology for biofuels 7, 24. [0228] Filonova et al. (2007)
Biomacromolecules 8, 91-97. [0229]
http://www.cazy.org/Carbohydrate-Binding-Modules.html on Mar. 30,
2015 [0230] U.S. Pat. Nos. 5,856,201; 5,837,814; 5,738,984;
5,719,044; 5,670,623; 6,174,700; 5,962,289; 7,361,487; 5,928,917
[0231] Boraston et al., Biochem J., 382: 769-781 (2004) [0232]
Shoseyov et al., Microbiology and Molecular Biology Reviews, 70(2):
283-295 (2006) [0233] Christiansen et al., FEBS Journal,
276:5006-5029 (2009).
[0234] Applicants specifically incorporate the entire contents of
all cited references in this disclosure. Further, when an amount,
concentration, or other value or parameter is given as either a
range, preferred range, or a list of upper preferable values and
lower preferable values, this is to be understood as specifically
disclosing all ranges formed from any pair of any upper range limit
or preferred value and any lower range limit or preferred value,
regardless of whether ranges are separately disclosed. Where a
range of numerical values is recited herein, unless otherwise
stated, the range is intended to include the endpoints thereof, and
all integers and fractions within the range. It is not intended
that the scope of the invention be limited to the specific values
recited when defining a range.
[0235] Other embodiments of the present invention will be apparent
to those skilled in the art from consideration of the present
specification and practice of the present invention disclosed
herein. It is intended that the present specification and examples
be considered as exemplary only with a true scope and spirit of the
invention being indicated by the following claims and equivalents
thereof.
TABLE-US-00006 SEQUENCE LISTING SEQ ID NO: 1 (nucleic acid) for
eGFP-CBM3a (Probe 1). The underlined text represents the thrombin
cleavage site which link eGFP to CBM3a.
ATGGGTCATCACCATCACCATCACGGTGTGAGCAAGGGCGAGGAGCTGTTCACCGG
GGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCG
TGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATC
TGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTAC
GGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAG
TCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGG
CAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCA
TCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTG
GAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGG
CATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCG
CCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGAC
AACCACTACCTGAGCACCCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGA
TCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGA
GCTGTACAAAAGTTCCGGTCTGGTGCCGCGTGGTAGCACACCGGTATCAGGCAATTT
GAAGGTTGAATTCTACAACAGCAATCCTTCAGATACTACTAACTCAATCAATCCTCA
GTTCAAGGTTACTAATACCGGAAGCAGTGCAATTGATTTGTCCAAACTCACATTGAG
ATATTATTATACAGTAGACGGACAGAAAGATCAGACCTTCTGGTGTGACCATGCTGC
AATAATCGGCAGTAACGGCAGCTACAACGGAATTACTTCAAATGTAAAAGGAACAT
TTGTAAAAATGAGTTCCTCAACAAATAACGCAGACACCTACCTTGAAATTAGCTTTA
CAGGCGGAACTCTTGAACCGGGTGCACATGTTCAGATACAAGGTAGATTTGCAAAG
AATGACTGGAGTAACTATACACAGTCAAATGACTACTCATTCAAGTCTGCTTCACAG
TTTGTTGAATGGGATCAGGTAACAGCATACTTGAACGGTGTTCTTGTATGGGGTAAA GAATAA
SEQ ID NO: 2 (amino acid) for eGFP-CBM3a (Probe 1). The underlined
text represents the thrombin cleavage site which link eGFP to
CBM3a. MGHEIHHHHGVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICT
TGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYK
TRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFK
IRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVT
AAGITLGMDELYKSSGLVPRGSTPVSGNLKVEFYNSNPSDTTNSINPQFKVTNTGSSAID
LSKLTLRYYYTVDGQKDQTFWCDHAAIIGSNGSYNGITSNVKGTFVKMSSSTNNADTYL
EISFTGGTLEPGAHVQIQGRFAKNDWSNYTQSNDYSFKSASQFVEWDQVTAYLNGVLV WGKE SEQ
ID NO: 3 for Probe 1 linker. AGTTCCGGTCTGGTGCCGCGTGGTAGC SEQ ID NO:
4 (amino acid) for Probe 1 linker. SSGLVPRGS SEQ ID NO: 5 (nucleic
acid) for mCherry-CBM4-1 (Probe 2a). The underlined text represents
the glycine which link mCherry to CBM4-1.
ATGGGTCATCACCATCACCATCACGGTGTGAGCAAGGGCGAGGAGGATAACATGGC
CATCATCAAGGAGTTCATGCGCTTCAAGGTGCACATGGAGGGCTCCGTGAACGGCC
ACGAGTTCGAGATCGAGGGCGAGGGCGAGGGCCGCCCCTACGAGGGCACCCAGAC
CGCCAAGCTGAAGGTGACCAAGGGTGGCCCCCTGCCCTTCGCCTGGGACATCCTGTC
CCCTCAGTTCATGTACGGCTCCAAGGCCTACGTGAAGCACCCCGCCGACATCCCCGA
CTACTTGAAGCTGTCCTTCCCCGAGGGCTTCAAGTGGGAGCGCGTGATGAACTTCGA
GGACGGCGGCGTGGTGACCGTGACCCAGGACTCCTCCCTGCAGGACGGCGAGTTCA
TCTACAAGGTGAAGCTGCGCGGCACCAACTTCCCCTCCGACGGCCCCGTAATGCAG
AAGAAGACCATGGGCTGGGAGGCCTCCTCCGAGCGGATGTACCCCGAGGACGGCGC
CCTGAAGGGCGAGATCAAGCAGAGGCTGAAGCTGAAGGACGGCGGCCACTACGAC
GCTGAGGTCAAGACCACCTACAAGGCCAAGAAGCCCGTGCAGCTGCCCGGCGCCTA
CAACGTCAACATCAAGTTGGACATCACCTCCCACAACGAGGACTACACCATCGTGG
AACAGTACGAACGCGCCGAGGGCCGCCACTCCACCGGCGGCATGGACGAGCTGTAC
AAGGGTGCGTCGCCGATCGGGGAGGGAACGTTCGACGACGGGCCCGAGGGGTGGGT
CGCGTACGGCACCGACGGCCCCCTCGACACGAGCACGGGCGCGCTGTGCGTCGCCG
TGCCGGCCGGCTCCGCGCAGTACGGCGTCGGCGTCGTGCTCAACGGCGTCGCGATC
GAGGAAGGGACCACCTACACGCTCCGGTACACCGCGACGGCCTCGACCGACGTCAC
CGTGCGGGCGCTCGTCGGGCAGAACGGCGCCCCCTACGGCACCGTGCTCGACACGA
GCCCGGCCCTGACGTCCGAGCCGCGGCAGGTGACCGAGACGTTCACGGCCTCGGCG
ACGTACCCCGCGACACCCGCCGCCGACGACCCCGAGGGGCAGATCGCCTTCCAGCT
CGGCGGGTTCAGCGCCGACGCGTGGACGTTCTGCCTCGACGACGTCGCGCTCGACTC
CGAGGTCGAGCTCTAA SEQ ID NO: 6 (amino acid) for mCherry-CBM4-1
(Probe 2a). The underlined text represents the glycine which link
mCherry to CBM4-1.
MGHEIHHHHGVSKGEEDNMAIIKEFIVIRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAK
LKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGG
VVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASSERMYPEDGALKGEI
KQRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNIKLDITSHNEDYTIVEQYERAEG
RHSTGGMDELYKGASPIGEGTFDDGPEGWVAYGTDGPLDTSTGALCVAVPAGSAQYG
VGVVLNGVAIEEGTTYTLRYTATASTDVTVRALVGQNGAPYGTVLDTSPALTSEPRQVT
ETFTASATYPATPAADDPEGQIAFQLGGFSADAWTFCLDDVALDSEVEL SEQ ID NO: 7
(nucleic acid) for mCherry-CBM17 (Probe 2b). The underlined text
represents the glycine codon that link mCherry to CBM17.
ATGGGTCATCACCATCACCATCACGGTGTGAGCAAGGGCGAGGAGGATAACATGGC
CATCATCAAGGAGTTCATGCGCTTCAAGGTGCACATGGAGGGCTCCGTGAACGGCC
ACGAGTTCGAGATCGAGGGCGAGGGCGAGGGCCGCCCCTACGAGGGCACCCAGAC
CGCCAAGCTGAAGGTGACCAAGGGTGGCCCCCTGCCCTTCGCCTGGGACATCCTGTC
CCCTCAGTTCATGTACGGCTCCAAGGCCTACGTGAAGCACCCCGCCGACATCCCCGA
CTACTTGAAGCTGTCCTTCCCCGAGGGCTTCAAGTGGGAGCGCGTGATGAACTTCGA
GGACGGCGGCGTGGTGACCGTGACCCAGGACTCCTCCCTGCAGGACGGCGAGTTCA
TCTACAAGGTGAAGCTGCGCGGCACCAACTTCCCCTCCGACGGCCCCGTAATGCAG
AAGAAGACCATGGGCTGGGAGGCCTCCTCCGAGCGGATGTACCCCGAGGACGGCGC
CCTGAAGGGCGAGATCAAGCAGAGGCTGAAGCTGAAGGACGGCGGCCACTACGAC
GCTGAGGTCAAGACCACCTACAAGGCCAAGAAGCCCGTGCAGCTGCCCGGCGCCTA
CAACGTCAACATCAAGTTGGACATCACCTCCCACAACGAGGACTACACCATCGTGG
AACAGTACGAACGCGCCGAGGGCCGCCACTCCACCGGCGGCATGGACGAGCTGTAC
AAGGGTTTATGGGCAGATAATGAATTAACCACTTCAGGTCAATATGTACGTGCTCGT
ATTAAGGGAGCTTATTATGCTACACCAGTTGATCCTGTAACAAACCAACCAACAGCA
CCGAAAGACTTTTCTTCAGGCTTTTGGGACTTTAATGACGGTACTACACAAGGTTTT
GGTGTAAATCCAGATAGTCCAATAACTGCTATTAATGTTGAAAATGCTAACAATGCT
TTAAAAATCAGCAATCTTAATAGTAAGGGTAGTAATGATTTATCTGAAGGAAACTTT
TGGGCCAATGTCCGCATTTCAGCTGATATCTGGGGACAAAGTATAAATATATATGGA
GACACAAAACTAACAATGGATGTTATAGCTCCAACACCTGTAAATGTATCAATCGCA
GCTATCCCACAAAGTAGTACTCACGGTTGGGGAAATCCTACAAGAGCTATACGTGTT
TGGACAAACAACTTTGTAGCACAAACTGATGGAACCTATAAAGCAACTTTGACCATT
TCTACAAACGATAGTCCAAATTTCAATACTATAGCTACAGATGCTGCTGATAGTGTA
GTAACAAATATGATTCTATTTGTTGGTTCAAATTCAGATAATATTTCTTTAGACAATA
TAAAGTTTACTAAATAAGGATCCGGCTGCTAACAAAGCCCGAAAGGAAGCTGAGTT
GGCTGCTGCCACCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAA SEQ ID NO: 8
(amino acid) for mCherry-CBM17 (Probe 2b). The underlined text
represents the glycine codon that link mCherry to CBM17.
MGHHIREIHHGVSKGEEDNMAIIKEFIVIRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAK
LKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGG
VVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASSERMYPEDGALKGEI
KQRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNIKLDITSHNEDYTIVEQYERAEG
RHSTGGMDELYKGLWADNELTTSGQYVRARIKGAYYATPVDPVTNQPTAPKDFSSGF
WDFNDGTTQGFGVNPDSPITAINVENANNALKISNLNSKGSNDLSEGNFWANVRISADI
WGQSINIYGDTKLTMDVIAPTPVNVSIAAIPQSSTHGWGNPTRAIRVWTNNFVAQTDGT
YKATLTISTNDSPNFNTIATDAADSVVTNMILFVGSNSDNISLDNIKFTK SEQ ID NO: 9
(nucleic acid) for mOrange2-CBM15 (Probe 3). The underlined text
represents the glycine codon that link mOrange2 to CBM15.
ATGGGTCATCACCATCACCATCACGGTGTGAGCAAGGGCGAGGAGAATAACATGGC
CATCATCAAGGAGTTCATGCGCTTCAAGGTGCGCATGGAGGGCTCCGTGAACGGCC
ACGAGTTCGAGATCGAGGGCGAGGGCGAGGGCCGCCCCTACGAGGGCTTTCAGACC
GCTAAGCTGAAGGTGACCAAGGGTGGCCCCCTGCCCTTCGCCTGGGACATCCTGTCC
CCTCATTTCACCTACGGCTCCAAGGCCTACGTGAAGCACCCCGCCGACATCCCCGAC
TACTTCAAGCTGTCCTTCCCCGAGGGCTTCAAGTGGGAGCGCGTGATGAACTACGAG
GACGGCGGCGTGGTGACCGTGACCCAGGACTCCTCCCTGCAGGACGGCGAGTTCAT
CTACAAGGTGAAGCTGCGCGGCACCAACTTCCCCTCCGACGGCCCCGTGATGCAGA
AGAAGACCATGGGCTGGGAGGCCTCCTCCGAGCGGATGTACCCCGAGGACGGTGCC
CTGAAGGGCAAGATCAAGATGAGGCTGAAGCTGAAGGACGGCGGCCACTACACCTC
CGAGGTCAAGACCACCTACAAGGCCAAGAAGCCCGTGCAGCTGCCCGGCGCCTACA
TCGTCGACATCAAGTTGGACATCACCTCCCACAACGAGGACTACACCATCGTGGAA
CAGTACGAACGCGCCGAGGGCCGCCACTCCACCGGCGGCATGGACGAGCTGTACAA
GGGTGTCGCTGCCAGCGAGGGCAATGTTGTTATAGAGGTGGACATGGCAAATGGCT
GGAGAGGCAACGCATCAGGCAGTACCAGCCATTCCGGTATTACCTACAGTGCCGAT
GGCGTTACCTTTGCCGCACTGGGCGATGGCGTGGGCGCTGTTTTTGATATTGCCCGA
CCAACCACACTGGAAGATGCTGTGATAGCAATGGTTGTTAATGTCAGCGCTGAATTT
AAGGCCAGTGAAGCCAACTTGCAGATATTTGCCCAGTTAAAAGAAGACTGGTCAAA
GGGCGAATGGGATTGTCTGGCGGCCAGCAGCGAACTCACTGCGGATACTGACCTAA
CCCTGACCTGCACCATTGATGAAGACGACGATAAATTCAACCAAACGGCGCGCGAT
GTGCAAGTCGGTATCCAGGCCAAGGGAACACCCGCCGGAACTATCACCATTAAAAG
CGTCACCATTACACTCGCACAGGAAGCCTATTCAGCCAATTAA SEQ ID NO: 10 (amino
acid) for mOrange2-CBM15 (Probe 3). The underlined text represents
the glycine codon that link mOrange2 to CBM15.
MGHHHHHHGVSKGEENNMAIIKEFIVIRFKVRMEGSVNGHEFEIEGEGEGRPYEGFQTAK
LKVTKGGPLPFAWDILSPHFTYGSKAYVKHPADIPDYFKLSFPEGFKWERVMNYEDGG
VVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASSERMYPEDGALKGKI
KMRLKLKDGGHYTSEVKTTYKAKKPVQLPGAYIVDIKLDITSHNEDYTIVEQYERAEGR
HSTGGMDELYKGVAASEGNVVIEVDMANGWRGNASGSTSHSGITYSADGVTFAALGD
GVGAVFDIARPTTLEDAVIAMVVNVSAEFKASEANLQIFAQLKEDWSKGEWDCLAASS
ELTADTDLTLTCTIDEDDDKFNQTARDVQVGIQAKGTPAGTITIKSVTITLAQEAYSAN SEQ ID
NO: 11 (nucleic acid) for eCFP-CBM27 (Probe 4). The underlined text
represents the glycine codon that link eCFP to CBM27.
ATGGGTCATCACCATCACCATCACGGTGTGAGCAAGGGCGAGGAGCTGTTCACCGG
GGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCG
TGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATC
TGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTGG
GGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAG
TCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGG
CAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCA
TCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTG
GAGTACAACTACATCAGCCACAACGTCTATATCACCGCCGACAAGCAGAAGAACGG
CATCAAGGCCAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCG
CCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGAC
AACCACTACCTGAGCACCCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGA
TCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGA
GCTGTACAAGGGTAACGAAGCACGGTACGTGCTCGCAGAGGAAGTTGATTTTTCCTC
TCCAGAAGAGGTGAAAAACTGGTGGAACAGCGGAACCTGGCAGGCAGAGTTCGGGT
CACCTGACATTGAATGGAACGGTGAGGTGGGAAATGGAGCACTGCAGCTGAACGTG
AAACTGCCCGGAAAGAGCGACTGGGAAGAAGTGAGAGTAGCAAGGAAGTTCGAAA
GACTCTCAGAATGTGAGATCCTCGAGTACGACATCTACATTCCAAACGTCGAGGGAC
TCAAGGGAAGGTTGAGGCCGTACGCGGTTCTGAACCCCGGCTGGGTGAAGATAGGC
CTCGACATGAACAACGCGAACGTGGAAAGTGCGGAGATCATCACTTTCGGCGGAAA
AGAGTACAGAAGATTCCATGTAAGAATTGAGTTCGACAGAACAGCGGGGGTGAAAG
AACTTCACATAGGAGTTGTCGGTGATCATCTGAGGTACGATGGACCGATTTTCATCG
ATAATGTGAGACTTTATAAAAGAACAGGAGGTATGTAA SEQ ID NO: 12 (amino acid)
for eCFP-CBM27 (Probe 4). The underlined text represents the
glycine codon that link eCFP to CBM27.
MGHHHHHHGVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICT
TGKLPVPWPTLVTTLTWGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYK
TRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYISHNVYITADKQKNGIKANFKI
RHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTA
AGITLGMDELYKGNEARYVLAEEVDFSSPEEVKNWWNSGTWQAEFGSPDIEWNGEVG
NGALQLNVKLPGKSDWEEVRVARKFERLSECEILEYDIYIPNVEGLKGRLRPYAVLNPG
WVKIGLDMNNANVESAEIITFGGKEYRRFHVRIEFDRTAGVKELHIGVVGDHLRYDGPIF
IDNVRLYKRTGGM SEQ ID NO: 13 (nucleic acid) for CBM3a.
ATGGGTCATCACCATCACCATCACGGTACACCGACCAAGGGAGCAACACCAACAAA
TACAGCTACGCCGACAAAATCAGCTACGGCTACGCCCACCAGGCCATCGGTACCGA
CAAACACACCGACAAACACACCGGCAAATACACCGGTATCAGGCAATTTGAAGGTT
GAATTCTACAACAGCAATCCTTCAGATACTACTAACTCAATCAATCCTCAGTTCAAG
GTTACTAATACCGGAAGCAGTGCAATTGATTTGTCCAAACTCACATTGAGATATTAT
TATACAGTAGACGGACAGAAAGATCAGACCTTCTGGTGTGACCATGCTGCAATAAT
CGGCAGTAACGGCAGCTACAACGGAATTACTTCAAATGTAAAAGGAACATTTGTAA
AAATGAGTTCCTCAACAAATAACGCAGACACCTACCTTGAAATTAGCTTTACAGGCG
GAACTCTTGAACCGGGTGCACATGTTCAGATACAAGGTAGATTTGCAAAGAATGAC
TGGAGTAACTATACACAGTCAAATGACTACTCATTCAAGTCTGCTTCACAGTTTGTT
GAATGGGATCAGGTAACAGCATACTTGAACGGTGTTCTTGTATGGGGTAAAGAATA A SEQ ID
NO: 14 (amino acid) for CBM3a.
MGHEIHHHHGTPTKGATPTNTATPTKSATATPTRPSVPTNTPTNTPANTPVSGNLKVEFY
NSNPSDTTNSINPQFKVTNTGSSAIDLSKLTLRYYYTVDGQKDQTFWCDHAAIIGSNGSY
NGITSNVKGTFVKMSSSTNNADTYLEISFTGGTLEPGAHVQIQGRFAKNDWSNYTQSND
YSFKSASQFVEWDQVTAYLNGVLVWGKE SEQ ID NO: 15 (nucleic acid) for
CBM4-1. ATGGGTCATCACCATCACCATCACGGTGCGTCGCCGATCGGGGAGGGAACGTTCGA
CGACGGGCCCGAGGGGTGGGTCGCGTACGGCACCGACGGCCCCCTCGACACGAGCA
CGGGCGCGCTGTGCGTCGCCGTGCCGGCCGGCTCCGCGCAGTACGGCGTCGGCGTC
GTGCTCAACGGCGTCGCGATCGAGGAAGGGACCACCTACACGCTCCGGTACACCGC
GACGGCCTCGACCGACGTCACCGTGCGGGCGCTCGTCGGGCAGAACGGCGCCCCCT
ACGGCACCGTGCTCGACACGAGCCCGGCCCTGACGTCCGAGCCGCGGCAGGTGACC
GAGACGTTCACGGCCTCGGCGACGTACCCCGCGACACCCGCCGCCGACGACCCCGA
GGGGCAGATCGCCTTCCAGCTCGGCGGGTTCAGCGCCGACGCGTGGACGTTCTGCCT
CGACGACGTCGCGCTCGACTCCGAGGTCGAGCTCTAA SEQ ID NO: 16 (amino acid)
for CBM4-1. MGHREIRHHGASPIGEGTFDDGPEGWVAYGTDGPLDT
STGALCVAVPAGSAQYGVGVV
LNGVAIEEGTTYTLRYTATASTDVTVRALVGQNGAPYGTVLDTSPALTSEPRQVTETFT
ASATYPATPAADDPEGQIAFQLGGFSADAWTFCLDDVALDSEVEL SEQ ID NO: 17
(nucleic acid) for CBM17.
ATGGGTCATCACCATCACCATCACGGTTTATGGGCAGATAATGAATTAACCACTTCA
GGTCAATATGTACGTGCTCGTATTAAGGGAGCTTATTATGCTACACCAGTTGATCCT
GTAACAAACCAACCAACAGCACCGAAAGACTTTTCTTCAGGCTTTTGGGACTTTAAT
GACGGTACTACACAAGGTTTTGGTGTAAATCCAGATAGTCCAATAACTGCTATTAAT
GTTGAAAATGCTAACAATGCTTTAAAAATCAGCAATCTTAATAGTAAGGGTAGTAAT
GATTTATCTGAAGGAAACTTTTGGGCCAATGTCCGCATTTCAGCTGATATCTGGGGA
CAAAGTATAAATATATATGGAGACACAAAACTAACAATGGATGTTATAGCTCCAAC
ACCTGTAAATGTATCAATCGCAGCTATCCCACAAAGTAGTACTCACGGTTGGGGAAA
TCCTACAAGAGCTATACGTGTTTGGACAAACAACTTTGTAGCACAAACTGATGGAAC
CTATAAAGCAACTTTGACCATTTCTACAAACGATAGTCCAAATTTCAATACTATAGC
TACAGATGCTGCTGATAGTGTAGTAACAAATATGATTCTATTTGTTGGTT CAAATTC
AGATAATATTTCTTTAGACAATATAAAGTTTACTAAATAA SEQ ID NO: 18 (amino acid)
for CBM17.
MGHREIHHHGLWADNELTTSGQYVRARIKGAYYATPVDPVTNQPTAPKDFSSGFWDFN
DGTTQGFGVNPDSPITAINVENANNALKISNLNSKGSNDLSEGNFWANVRISADIWGQSI
NIYGDTKLTMDVIAPTPVNVSIAAIPQSSTHGWGNPTRAIRVWTNNFVAQTDGTYKATL
TISTNDSPNFNTIATDAADSVVTNMILFVGSNSDNISLDNIKFTK SEQ ID NO: 19
(nucleic acid) for CBM15.
ATGGGTCATCACCATCACCATCACGGTGTCGCTGCCAGCGAGGGCAATGTTGTTATA
GAGGTGGACATGGCAAATGGCTGGAGAGGCAACGCATCAGGCAGTACCAGCCATTC
CGGTATTACCTACAGTGCCGATGGCGTTACCTTTGCCGCACTGGGCGATGGCGTGGG
CGCTGTTTTTGATATTGCCCGACCAACCACACTGGAAGATGCTGTGATAGCAATGGT
TGTTAATGTCAGCGCTGAATTTAAGGCCAGTGAAGCCAACTTGCAGATATTTGCCCA
GTTAAAAGAAGACTGGTCAAAGGGCGAATGGGATTGTCTGGCGGCCAGCAGCGAAC
TCACTGCGGATACTGACCTAACCCTGACCTGCACCATTGATGAAGACGACGATAAAT
TCAACCAAACGGCGCGCGATGTACAAGTCGGTATCCAGGCCAAGGGAACACCCGCC
GGAACTATCACCATTAAAAGCGTCACCATTACACTCGCACAGGAAGCCTATTCAGCC AATTAA
SEQ ID NO: 20 (amino acid) for CBM15.
MGHHHHHHGVAASEGNVVIEVDMANGWRGNASGSTSHSGITYSADGVTFAALGDGV
GAVFDTARPTTLEDAVIAMVVNVSAEFKASEANLQIFAQLKEDWSKGEWDCLAASSELT
ADTDLTLTCTIDEDDDKFNQTARDVQVGIQAKGTPAGTITIKSVTITLAQEAYSAN SEQ ID NO:
21 (nucleic acid) for CBM27.
ATGGGTCATCACCATCACCATCACGGTAACGAAGCACGGTACGTGCTCGCAGAGGA
AGTTGATTTTTCCTCTCCAGAAGAGGTGAAAAACTGGTGGAACAGCGGAACCTGGC
AGGCAGAGTTCGGGTCACCTGACATTGAATGGAACGGTGAGGTGGGAAATGGAGCA
CTGCAGCTGAACGTGAAACTGCCCGGAAAGAGCGACTGGGAAGAAGTGAGAGTAG
CAAGGAAGTTCGAAAGACTCTCAGAATGTGAGATCCTCGAGTACGACATCTACATTC
CAAACGTCGAGGGACTCAAGGGAAGGTTGAGGCCGTACGCGGTTCTGAACCCCGGC
TGGGTGAAGATAGGCCTCGACATGAACAACGCGAACGTGGAAAGTGCGGAGATCAT
CACTTTCGGCGGAAAAGAGTACAGAAGATTCCATGTAAGAATTGAGTTCGACAGAA
CAGCGGGGGTGAAAGAACTTCACATAGGAGTTGTCGGTGATCATCTGAGGTACGAT
GGACCGATTTTCATCGATAATGTGAGACTTTATAAAAGAACAGGAGGTATGTAA SEQ ID NO:
22 (amino acid) for CBM27.
MGHHHHHHGNEARYVLAEEVDFSSPEEVKNWWNSGTWQAEFGSPDIEWNGEVGNGA
LQLNVKLPGKSDWEEVRVARKFERLSECEILEYDIYIPNVEGLKGRLRPYAVLNPGWVK
IGLDMNNANVESAEIITFGGKEYRRFHVRIEFDRTAGVKELHIGVVGDHLRYDGPIFIDN
VRLYKRTGGM SEQ ID NO: 23 (nucleic acid) for eGFP.
ATGGGTCATCACCATCACCATCACGGTGTGAGCAAGGGCGAGGAGCTGTTCACCGG
GGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCG
TGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATC
TGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTAC
GGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAG
TCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGG
CAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCA
TCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTG
GAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGG
CATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCG
CCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGAC
AACCACTACCTGAGCACCCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGA
TCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGA
GCTGTACAAGTAA SEQ ID NO: 24 (amino acid) for eGFP.
MGHHHHHHGVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICT
TGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYK
TRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFK
IRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVT
AAGITLGMDELYK SEQ ID NO: 25 (nucleic acid) for mCherry.
ATGGGTCATCACCATCACCATCACGGTGTGAGCAAGGGCGAGGAGGATAACATGGC
CATCATCAAGGAGTTCATGCGCTTCAAGGTGCACATGGAGGGCTCCGTGAACGGCC
ACGAGTTCGAGATCGAGGGCGAGGGCGAGGGCCGCCCCTACGAGGGCACCCAGAC
CGCCAAGCTGAAGGTGACCAAGGGTGGCCCCCTGCCCTTCGCCTGGGACATCCTGTC
CCCTCAGTTCATGTACGGCTCCAAGGCCTACGTGAAGCACCCCGCCGACATCCCCGA
CTACTTGAAGCTGTCCTTCCCCGAGGGCTTCAAGTGGGAGCGCGTGATGAACTTCGA
GGACGGCGGCGTGGTGACCGTGACCCAGGACTCCTCCCTGCAGGACGGCGAGTTCA
TCTACAAGGTGAAGCTGCGCGGCACCAACTTCCCCTCCGACGGCCCCGTAATGCAG
AAGAAGACCATGGGCTGGGAGGCCTCCTCCGAGCGGATGTACCCCGAGGACGGCGC
CCTGAAGGGCGAGATCAAGCAGAGGCTGAAGCTGAAGGACGGCGGCCACTACGAC
GCTGAGGTCAAGACCACCTACAAGGCCAAGAAGCCCGTGCAGCTGCCCGGCGCCTA
CAACGTCAACATCAAGTTGGACATCACCTCCCACAACGAGGACTACACCATCGTGG
AACAGTACGAACGCGCCGAGGGCCGCCACTCCACCGGCGGCATGGACGAGCTGTAC AAGTAA SEQ
ID NO: 26 (amino acid) for mCherry.
MGHEIREIHHGVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAK
LKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGG
VVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASSERMYPEDGALKGEI
KQRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNIKLDITSHNEDYTIVEQYERAEG
RHSTGGMDELYK SEQ ID NO: 27 (nucleic acid) for mOrange2.
ATGGGTCATCACCATCACCATCACGGTGTGAGCAAGGGCGAGGAGAATAACATGGC
CATCATCAAGGAGTTCATGCGCTTCAAGGTGCGCATGGAGGGCTCCGTGAACGGCC
ACGAGTTCGAGATCGAGGGCGAGGGCGAGGGCCGCCCCTACGAGGGCTTTCAGACC
GCTAAGCTGAAGGTGACCAAGGGTGGCCCCCTGCCCTTCGCCTGGGACATCCTGTCC
CCTCATTTCACCTACGGCTCCAAGGCCTACGTGAAGCACCCCGCCGACATCCCCGAC
TACTTCAAGCTGTCCTTCCCCGAGGGCTTCAAGTGGGAGCGCGTGATGAACTACGAG
GACGGCGGCGTGGTGACCGTGACCCAGGACTCCTCCCTGCAGGACGGCGAGTTCAT
CTACAAGGTGAAGCTGCGCGGCACCAACTTCCCCTCCGACGGCCCCGTGATGCAGA
AGAAGACCATGGGCTGGGAGGCCTCCTCCGAGCGGATGTACCCCGAGGACGGTGCC
CTGAAGGGCAAGATCAAGATGAGGCTGAAGCTGAAGGACGGCGGCCACTACACCTC
CGAGGTCAAGACCACCTACAAGGCCAAGAAGCCCGTGCAGCTGCCCGGCGCCTACA
TCGTCGACATCAAGTTGGACATCACCTCCCACAACGAGGACTACACCATCGTGGAA
CAGTACGAACGCGCCGAGGGCCGCCACTCCACCGGCGGCATGGACGAGCTGTACAA GTAA SEQ
ID NO: 28 (amino acid) for mOrange2.
MGHEIHHHHGVSKGEENNMAIIKEFMRFKVRMEGSVNGHEFEIEGEGEGRPYEGFQTAK
LKVTKGGPLPFAWDILSPHFTYGSKAYVKHPADIPDYFKLSFPEGFKWERVMNYEDGG
VVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASSERMYPEDGALKGKI
KMRLKLKDGGHYTSEVKTTYKAKKPVQLPGAYIVDIKLDITSHNEDYTIVEQYERAEGR
HSTGGMDELYK SEQ ID NO: 29 (nucleic acid) for eCFP.
ATGGGTCATCACCATCACCATCACGGTGTGAGCAAGGGCGAGGAGCTGTTCACCGG
GGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCG
TGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATC
TGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTGG
GGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAG
TCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGG
CAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCA
TCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTG
GAGTACAACTACATCAGCCACAACGTCTATATCACCGCCGACAAGCAGAAGAACGG
CATCAAGGCCAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCG
CCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGAC
AACCACTACCTGAGCACCCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGA
TCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGA
GCTGTACAAGTAA SEQ ID NO: 30 (amino acid) for eCFP.
MGHHHHHHGVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICT
TGKLPVPWPTLVTTLTWGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYK
TRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYISHNVYITADKQKNGIKANFKI
RHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTA
AGITLGMDELYK
Sequence CWU 1
1
3011248DNAArtificial SequenceNucleic acid sequence for eGFP-CBM3a
(Probe 1).misc_feature(742)..(768)Thrombin cleavage site that links
eGFP to CBM3a. 1atgggtcatc accatcacca tcacggtgtg agcaagggcg
aggagctgtt caccggggtg 60gtgcccatcc tggtcgagct ggacggcgac gtaaacggcc
acaagttcag cgtgtccggc 120gagggcgagg gcgatgccac ctacggcaag
ctgaccctga agttcatctg caccaccggc 180aagctgcccg tgccctggcc
caccctcgtg accaccctga cctacggcgt gcagtgcttc 240agccgctacc
ccgaccacat gaagcagcac gacttcttca agtccgccat gcccgaaggc
300tacgtccagg agcgcaccat cttcttcaag gacgacggca actacaagac
ccgcgccgag 360gtgaagttcg agggcgacac cctggtgaac cgcatcgagc
tgaagggcat cgacttcaag 420gaggacggca acatcctggg gcacaagctg
gagtacaact acaacagcca caacgtctat 480atcatggccg acaagcagaa
gaacggcatc aaggtgaact tcaagatccg ccacaacatc 540gaggacggca
gcgtgcagct cgccgaccac taccagcaga acacccccat cggcgacggc
600cccgtgctgc tgcccgacaa ccactacctg agcacccagt ccgccctgag
caaagacccc 660aacgagaagc gcgatcacat ggtcctgctg gagttcgtga
ccgccgccgg gatcactctc 720ggcatggacg agctgtacaa aagttccggt
ctggtgccgc gtggtagcac accggtatca 780ggcaatttga aggttgaatt
ctacaacagc aatccttcag atactactaa ctcaatcaat 840cctcagttca
aggttactaa taccggaagc agtgcaattg atttgtccaa actcacattg
900agatattatt atacagtaga cggacagaaa gatcagacct tctggtgtga
ccatgctgca 960ataatcggca gtaacggcag ctacaacgga attacttcaa
atgtaaaagg aacatttgta 1020aaaatgagtt cctcaacaaa taacgcagac
acctaccttg aaattagctt tacaggcgga 1080actcttgaac cgggtgcaca
tgttcagata caaggtagat ttgcaaagaa tgactggagt 1140aactatacac
agtcaaatga ctactcattc aagtctgctt cacagtttgt tgaatgggat
1200caggtaacag catacttgaa cggtgttctt gtatggggta aagaataa
12482415PRTArtificial SequenceAmino acid sequence for eGFP-CBM3a
(Probe 1).misc_feature(248)..(256)Thrombin cleavage site that links
eGFP to CBM3a. 2Met Gly His His His His His His Gly Val Ser Lys Gly
Glu Glu Leu1 5 10 15Phe Thr Gly Val Val Pro Ile Leu Val Glu Leu Asp
Gly Asp Val Asn 20 25 30Gly His Lys Phe Ser Val Ser Gly Glu Gly Glu
Gly Asp Ala Thr Tyr 35 40 45Gly Lys Leu Thr Leu Lys Phe Ile Cys Thr
Thr Gly Lys Leu Pro Val 50 55 60Pro Trp Pro Thr Leu Val Thr Thr Leu
Thr Tyr Gly Val Gln Cys Phe65 70 75 80Ser Arg Tyr Pro Asp His Met
Lys Gln His Asp Phe Phe Lys Ser Ala 85 90 95Met Pro Glu Gly Tyr Val
Gln Glu Arg Thr Ile Phe Phe Lys Asp Asp 100 105 110Gly Asn Tyr Lys
Thr Arg Ala Glu Val Lys Phe Glu Gly Asp Thr Leu 115 120 125Val Asn
Arg Ile Glu Leu Lys Gly Ile Asp Phe Lys Glu Asp Gly Asn 130 135
140Ile Leu Gly His Lys Leu Glu Tyr Asn Tyr Asn Ser His Asn Val
Tyr145 150 155 160Ile Met Ala Asp Lys Gln Lys Asn Gly Ile Lys Val
Asn Phe Lys Ile 165 170 175Arg His Asn Ile Glu Asp Gly Ser Val Gln
Leu Ala Asp His Tyr Gln 180 185 190Gln Asn Thr Pro Ile Gly Asp Gly
Pro Val Leu Leu Pro Asp Asn His 195 200 205Tyr Leu Ser Thr Gln Ser
Ala Leu Ser Lys Asp Pro Asn Glu Lys Arg 210 215 220Asp His Met Val
Leu Leu Glu Phe Val Thr Ala Ala Gly Ile Thr Leu225 230 235 240Gly
Met Asp Glu Leu Tyr Lys Ser Ser Gly Leu Val Pro Arg Gly Ser 245 250
255Thr Pro Val Ser Gly Asn Leu Lys Val Glu Phe Tyr Asn Ser Asn Pro
260 265 270Ser Asp Thr Thr Asn Ser Ile Asn Pro Gln Phe Lys Val Thr
Asn Thr 275 280 285Gly Ser Ser Ala Ile Asp Leu Ser Lys Leu Thr Leu
Arg Tyr Tyr Tyr 290 295 300Thr Val Asp Gly Gln Lys Asp Gln Thr Phe
Trp Cys Asp His Ala Ala305 310 315 320Ile Ile Gly Ser Asn Gly Ser
Tyr Asn Gly Ile Thr Ser Asn Val Lys 325 330 335Gly Thr Phe Val Lys
Met Ser Ser Ser Thr Asn Asn Ala Asp Thr Tyr 340 345 350Leu Glu Ile
Ser Phe Thr Gly Gly Thr Leu Glu Pro Gly Ala His Val 355 360 365Gln
Ile Gln Gly Arg Phe Ala Lys Asn Asp Trp Ser Asn Tyr Thr Gln 370 375
380Ser Asn Asp Tyr Ser Phe Lys Ser Ala Ser Gln Phe Val Glu Trp
Asp385 390 395 400Gln Val Thr Ala Tyr Leu Asn Gly Val Leu Val Trp
Gly Lys Glu 405 410 415327DNAArtificial SequenceNucleic acid
sequence for probe 1 linker. 3agttccggtc tggtgccgcg tggtagc
2749PRTArtificial SequenceAmino acid sequence for Probe 1 linker.
4Ser Ser Gly Leu Val Pro Arg Gly Ser1 551194DNAArtificial
SequenceNucleic acid sequence for mCherry-CBM4-1 (Probe
2a).misc_feature(733)..(735)Glycine codon that links mCherry to
CBM4-1. 5atgggtcatc accatcacca tcacggtgtg agcaagggcg aggaggataa
catggccatc 60atcaaggagt tcatgcgctt caaggtgcac atggagggct ccgtgaacgg
ccacgagttc 120gagatcgagg gcgagggcga gggccgcccc tacgagggca
cccagaccgc caagctgaag 180gtgaccaagg gtggccccct gcccttcgcc
tgggacatcc tgtcccctca gttcatgtac 240ggctccaagg cctacgtgaa
gcaccccgcc gacatccccg actacttgaa gctgtccttc 300cccgagggct
tcaagtggga gcgcgtgatg aacttcgagg acggcggcgt ggtgaccgtg
360acccaggact cctccctgca ggacggcgag ttcatctaca aggtgaagct
gcgcggcacc 420aacttcccct ccgacggccc cgtaatgcag aagaagacca
tgggctggga ggcctcctcc 480gagcggatgt accccgagga cggcgccctg
aagggcgaga tcaagcagag gctgaagctg 540aaggacggcg gccactacga
cgctgaggtc aagaccacct acaaggccaa gaagcccgtg 600cagctgcccg
gcgcctacaa cgtcaacatc aagttggaca tcacctccca caacgaggac
660tacaccatcg tggaacagta cgaacgcgcc gagggccgcc actccaccgg
cggcatggac 720gagctgtaca agggtgcgtc gccgatcggg gagggaacgt
tcgacgacgg gcccgagggg 780tgggtcgcgt acggcaccga cggccccctc
gacacgagca cgggcgcgct gtgcgtcgcc 840gtgccggccg gctccgcgca
gtacggcgtc ggcgtcgtgc tcaacggcgt cgcgatcgag 900gaagggacca
cctacacgct ccggtacacc gcgacggcct cgaccgacgt caccgtgcgg
960gcgctcgtcg ggcagaacgg cgccccctac ggcaccgtgc tcgacacgag
cccggccctg 1020acgtccgagc cgcggcaggt gaccgagacg ttcacggcct
cggcgacgta ccccgcgaca 1080cccgccgccg acgaccccga ggggcagatc
gccttccagc tcggcgggtt cagcgccgac 1140gcgtggacgt tctgcctcga
cgacgtcgcg ctcgactccg aggtcgagct ctaa 11946397PRTArtificial
SequenceAmino acid sequence for mCherry-CBM4-1 (Probe
2a).misc_feature(245)..(245)Glycine that links mCherry to CBM4-1.
6Met Gly His His His His His His Gly Val Ser Lys Gly Glu Glu Asp1 5
10 15Asn Met Ala Ile Ile Lys Glu Phe Met Arg Phe Lys Val His Met
Glu 20 25 30Gly Ser Val Asn Gly His Glu Phe Glu Ile Glu Gly Glu Gly
Glu Gly 35 40 45Arg Pro Tyr Glu Gly Thr Gln Thr Ala Lys Leu Lys Val
Thr Lys Gly 50 55 60Gly Pro Leu Pro Phe Ala Trp Asp Ile Leu Ser Pro
Gln Phe Met Tyr65 70 75 80Gly Ser Lys Ala Tyr Val Lys His Pro Ala
Asp Ile Pro Asp Tyr Leu 85 90 95Lys Leu Ser Phe Pro Glu Gly Phe Lys
Trp Glu Arg Val Met Asn Phe 100 105 110Glu Asp Gly Gly Val Val Thr
Val Thr Gln Asp Ser Ser Leu Gln Asp 115 120 125Gly Glu Phe Ile Tyr
Lys Val Lys Leu Arg Gly Thr Asn Phe Pro Ser 130 135 140Asp Gly Pro
Val Met Gln Lys Lys Thr Met Gly Trp Glu Ala Ser Ser145 150 155
160Glu Arg Met Tyr Pro Glu Asp Gly Ala Leu Lys Gly Glu Ile Lys Gln
165 170 175Arg Leu Lys Leu Lys Asp Gly Gly His Tyr Asp Ala Glu Val
Lys Thr 180 185 190Thr Tyr Lys Ala Lys Lys Pro Val Gln Leu Pro Gly
Ala Tyr Asn Val 195 200 205Asn Ile Lys Leu Asp Ile Thr Ser His Asn
Glu Asp Tyr Thr Ile Val 210 215 220Glu Gln Tyr Glu Arg Ala Glu Gly
Arg His Ser Thr Gly Gly Met Asp225 230 235 240Glu Leu Tyr Lys Gly
Ala Ser Pro Ile Gly Glu Gly Thr Phe Asp Asp 245 250 255Gly Pro Glu
Gly Trp Val Ala Tyr Gly Thr Asp Gly Pro Leu Asp Thr 260 265 270Ser
Thr Gly Ala Leu Cys Val Ala Val Pro Ala Gly Ser Ala Gln Tyr 275 280
285Gly Val Gly Val Val Leu Asn Gly Val Ala Ile Glu Glu Gly Thr Thr
290 295 300Tyr Thr Leu Arg Tyr Thr Ala Thr Ala Ser Thr Asp Val Thr
Val Arg305 310 315 320Ala Leu Val Gly Gln Asn Gly Ala Pro Tyr Gly
Thr Val Leu Asp Thr 325 330 335Ser Pro Ala Leu Thr Ser Glu Pro Arg
Gln Val Thr Glu Thr Phe Thr 340 345 350Ala Ser Ala Thr Tyr Pro Ala
Thr Pro Ala Ala Asp Asp Pro Glu Gly 355 360 365Gln Ile Ala Phe Gln
Leu Gly Gly Phe Ser Ala Asp Ala Trp Thr Phe 370 375 380Cys Leu Asp
Asp Val Ala Leu Asp Ser Glu Val Glu Leu385 390
39571464DNAArtificial SequenceNucleic acid sequence for
mCherry-CBM17 (Probe 2b).misc_feature(733)..(735)Glycine codon that
links mCherry to CBM17. 7atgggtcatc accatcacca tcacggtgtg
agcaagggcg aggaggataa catggccatc 60atcaaggagt tcatgcgctt caaggtgcac
atggagggct ccgtgaacgg ccacgagttc 120gagatcgagg gcgagggcga
gggccgcccc tacgagggca cccagaccgc caagctgaag 180gtgaccaagg
gtggccccct gcccttcgcc tgggacatcc tgtcccctca gttcatgtac
240ggctccaagg cctacgtgaa gcaccccgcc gacatccccg actacttgaa
gctgtccttc 300cccgagggct tcaagtggga gcgcgtgatg aacttcgagg
acggcggcgt ggtgaccgtg 360acccaggact cctccctgca ggacggcgag
ttcatctaca aggtgaagct gcgcggcacc 420aacttcccct ccgacggccc
cgtaatgcag aagaagacca tgggctggga ggcctcctcc 480gagcggatgt
accccgagga cggcgccctg aagggcgaga tcaagcagag gctgaagctg
540aaggacggcg gccactacga cgctgaggtc aagaccacct acaaggccaa
gaagcccgtg 600cagctgcccg gcgcctacaa cgtcaacatc aagttggaca
tcacctccca caacgaggac 660tacaccatcg tggaacagta cgaacgcgcc
gagggccgcc actccaccgg cggcatggac 720gagctgtaca agggtttatg
ggcagataat gaattaacca cttcaggtca atatgtacgt 780gctcgtatta
agggagctta ttatgctaca ccagttgatc ctgtaacaaa ccaaccaaca
840gcaccgaaag acttttcttc aggcttttgg gactttaatg acggtactac
acaaggtttt 900ggtgtaaatc cagatagtcc aataactgct attaatgttg
aaaatgctaa caatgcttta 960aaaatcagca atcttaatag taagggtagt
aatgatttat ctgaaggaaa cttttgggcc 1020aatgtccgca tttcagctga
tatctgggga caaagtataa atatatatgg agacacaaaa 1080ctaacaatgg
atgttatagc tccaacacct gtaaatgtat caatcgcagc tatcccacaa
1140agtagtactc acggttgggg aaatcctaca agagctatac gtgtttggac
aaacaacttt 1200gtagcacaaa ctgatggaac ctataaagca actttgacca
tttctacaaa cgatagtcca 1260aatttcaata ctatagctac agatgctgct
gatagtgtag taacaaatat gattctattt 1320gttggttcaa attcagataa
tatttcttta gacaatataa agtttactaa ataaggatcc 1380ggctgctaac
aaagcccgaa aggaagctga gttggctgct gccaccgctg agcaataact
1440agcataaccc cttggggcct ctaa 14648457PRTArtificial SequenceAmino
acid sequence for mCherry-CBM17 (Probe
2b).misc_feature(245)..(245)Glycine that links mCherry to CBM17.
8Met Gly His His His His His His Gly Val Ser Lys Gly Glu Glu Asp1 5
10 15Asn Met Ala Ile Ile Lys Glu Phe Met Arg Phe Lys Val His Met
Glu 20 25 30Gly Ser Val Asn Gly His Glu Phe Glu Ile Glu Gly Glu Gly
Glu Gly 35 40 45Arg Pro Tyr Glu Gly Thr Gln Thr Ala Lys Leu Lys Val
Thr Lys Gly 50 55 60Gly Pro Leu Pro Phe Ala Trp Asp Ile Leu Ser Pro
Gln Phe Met Tyr65 70 75 80Gly Ser Lys Ala Tyr Val Lys His Pro Ala
Asp Ile Pro Asp Tyr Leu 85 90 95Lys Leu Ser Phe Pro Glu Gly Phe Lys
Trp Glu Arg Val Met Asn Phe 100 105 110Glu Asp Gly Gly Val Val Thr
Val Thr Gln Asp Ser Ser Leu Gln Asp 115 120 125Gly Glu Phe Ile Tyr
Lys Val Lys Leu Arg Gly Thr Asn Phe Pro Ser 130 135 140Asp Gly Pro
Val Met Gln Lys Lys Thr Met Gly Trp Glu Ala Ser Ser145 150 155
160Glu Arg Met Tyr Pro Glu Asp Gly Ala Leu Lys Gly Glu Ile Lys Gln
165 170 175Arg Leu Lys Leu Lys Asp Gly Gly His Tyr Asp Ala Glu Val
Lys Thr 180 185 190Thr Tyr Lys Ala Lys Lys Pro Val Gln Leu Pro Gly
Ala Tyr Asn Val 195 200 205Asn Ile Lys Leu Asp Ile Thr Ser His Asn
Glu Asp Tyr Thr Ile Val 210 215 220Glu Gln Tyr Glu Arg Ala Glu Gly
Arg His Ser Thr Gly Gly Met Asp225 230 235 240Glu Leu Tyr Lys Gly
Leu Trp Ala Asp Asn Glu Leu Thr Thr Ser Gly 245 250 255Gln Tyr Val
Arg Ala Arg Ile Lys Gly Ala Tyr Tyr Ala Thr Pro Val 260 265 270Asp
Pro Val Thr Asn Gln Pro Thr Ala Pro Lys Asp Phe Ser Ser Gly 275 280
285Phe Trp Asp Phe Asn Asp Gly Thr Thr Gln Gly Phe Gly Val Asn Pro
290 295 300Asp Ser Pro Ile Thr Ala Ile Asn Val Glu Asn Ala Asn Asn
Ala Leu305 310 315 320Lys Ile Ser Asn Leu Asn Ser Lys Gly Ser Asn
Asp Leu Ser Glu Gly 325 330 335Asn Phe Trp Ala Asn Val Arg Ile Ser
Ala Asp Ile Trp Gly Gln Ser 340 345 350Ile Asn Ile Tyr Gly Asp Thr
Lys Leu Thr Met Asp Val Ile Ala Pro 355 360 365Thr Pro Val Asn Val
Ser Ile Ala Ala Ile Pro Gln Ser Ser Thr His 370 375 380Gly Trp Gly
Asn Pro Thr Arg Ala Ile Arg Val Trp Thr Asn Asn Phe385 390 395
400Val Ala Gln Thr Asp Gly Thr Tyr Lys Ala Thr Leu Thr Ile Ser Thr
405 410 415Asn Asp Ser Pro Asn Phe Asn Thr Ile Ala Thr Asp Ala Ala
Asp Ser 420 425 430Val Val Thr Asn Met Ile Leu Phe Val Gly Ser Asn
Ser Asp Asn Ile 435 440 445Ser Leu Asp Asn Ile Lys Phe Thr Lys 450
45591224DNAArtificial SequenceNucleic acid sequence for
mOrange2-CBM15 (Probe 3).misc_feature(733)..(735)Glycine codon that
links mOrange2 to CBM15. 9atgggtcatc accatcacca tcacggtgtg
agcaagggcg aggagaataa catggccatc 60atcaaggagt tcatgcgctt caaggtgcgc
atggagggct ccgtgaacgg ccacgagttc 120gagatcgagg gcgagggcga
gggccgcccc tacgagggct ttcagaccgc taagctgaag 180gtgaccaagg
gtggccccct gcccttcgcc tgggacatcc tgtcccctca tttcacctac
240ggctccaagg cctacgtgaa gcaccccgcc gacatccccg actacttcaa
gctgtccttc 300cccgagggct tcaagtggga gcgcgtgatg aactacgagg
acggcggcgt ggtgaccgtg 360acccaggact cctccctgca ggacggcgag
ttcatctaca aggtgaagct gcgcggcacc 420aacttcccct ccgacggccc
cgtgatgcag aagaagacca tgggctggga ggcctcctcc 480gagcggatgt
accccgagga cggtgccctg aagggcaaga tcaagatgag gctgaagctg
540aaggacggcg gccactacac ctccgaggtc aagaccacct acaaggccaa
gaagcccgtg 600cagctgcccg gcgcctacat cgtcgacatc aagttggaca
tcacctccca caacgaggac 660tacaccatcg tggaacagta cgaacgcgcc
gagggccgcc actccaccgg cggcatggac 720gagctgtaca agggtgtcgc
tgccagcgag ggcaatgttg ttatagaggt ggacatggca 780aatggctgga
gaggcaacgc atcaggcagt accagccatt ccggtattac ctacagtgcc
840gatggcgtta cctttgccgc actgggcgat ggcgtgggcg ctgtttttga
tattgcccga 900ccaaccacac tggaagatgc tgtgatagca atggttgtta
atgtcagcgc tgaatttaag 960gccagtgaag ccaacttgca gatatttgcc
cagttaaaag aagactggtc aaagggcgaa 1020tgggattgtc tggcggccag
cagcgaactc actgcggata ctgacctaac cctgacctgc 1080accattgatg
aagacgacga taaattcaac caaacggcgc gcgatgtgca agtcggtatc
1140caggccaagg gaacacccgc cggaactatc accattaaaa gcgtcaccat
tacactcgca 1200caggaagcct attcagccaa ttaa 122410407PRTArtificial
SequenceAmino acid sequence for mOrange2-CBM15 (Probe
3).misc_feature(245)..(245)Glycine that links mOrange2 to CBM15.
10Met Gly His His His His His His Gly Val Ser Lys Gly Glu Glu Asn1
5 10 15Asn Met Ala Ile Ile Lys Glu Phe Met Arg Phe Lys Val Arg Met
Glu 20 25 30Gly Ser Val Asn Gly His Glu Phe Glu Ile Glu Gly Glu Gly
Glu Gly 35 40 45Arg Pro Tyr Glu Gly Phe Gln Thr Ala Lys Leu Lys Val
Thr Lys Gly 50 55 60Gly Pro Leu Pro Phe Ala Trp Asp Ile Leu Ser Pro
His Phe Thr Tyr65 70 75 80Gly Ser Lys Ala Tyr Val Lys His Pro Ala
Asp Ile Pro Asp Tyr Phe 85 90 95Lys Leu Ser Phe Pro Glu Gly Phe Lys
Trp Glu Arg Val Met Asn Tyr 100 105 110Glu Asp Gly Gly Val Val Thr
Val Thr Gln Asp Ser Ser Leu Gln Asp 115 120 125Gly Glu Phe Ile Tyr
Lys Val Lys Leu Arg Gly Thr Asn Phe Pro Ser 130 135 140Asp Gly Pro
Val Met Gln Lys Lys
Thr Met Gly Trp Glu Ala Ser Ser145 150 155 160Glu Arg Met Tyr Pro
Glu Asp Gly Ala Leu Lys Gly Lys Ile Lys Met 165 170 175Arg Leu Lys
Leu Lys Asp Gly Gly His Tyr Thr Ser Glu Val Lys Thr 180 185 190Thr
Tyr Lys Ala Lys Lys Pro Val Gln Leu Pro Gly Ala Tyr Ile Val 195 200
205Asp Ile Lys Leu Asp Ile Thr Ser His Asn Glu Asp Tyr Thr Ile Val
210 215 220Glu Gln Tyr Glu Arg Ala Glu Gly Arg His Ser Thr Gly Gly
Met Asp225 230 235 240Glu Leu Tyr Lys Gly Val Ala Ala Ser Glu Gly
Asn Val Val Ile Glu 245 250 255Val Asp Met Ala Asn Gly Trp Arg Gly
Asn Ala Ser Gly Ser Thr Ser 260 265 270His Ser Gly Ile Thr Tyr Ser
Ala Asp Gly Val Thr Phe Ala Ala Leu 275 280 285Gly Asp Gly Val Gly
Ala Val Phe Asp Ile Ala Arg Pro Thr Thr Leu 290 295 300Glu Asp Ala
Val Ile Ala Met Val Val Asn Val Ser Ala Glu Phe Lys305 310 315
320Ala Ser Glu Ala Asn Leu Gln Ile Phe Ala Gln Leu Lys Glu Asp Trp
325 330 335Ser Lys Gly Glu Trp Asp Cys Leu Ala Ala Ser Ser Glu Leu
Thr Ala 340 345 350Asp Thr Asp Leu Thr Leu Thr Cys Thr Ile Asp Glu
Asp Asp Asp Lys 355 360 365Phe Asn Gln Thr Ala Arg Asp Val Gln Val
Gly Ile Gln Ala Lys Gly 370 375 380Thr Pro Ala Gly Thr Ile Thr Ile
Lys Ser Val Thr Ile Thr Leu Ala385 390 395 400Gln Glu Ala Tyr Ser
Ala Asn 405111275DNAArtificial SequenceNucleic acid sequence for
eCFP-CBM27 (Probe 4).misc_feature(742)..(744)Glycine codon that
links eCFP to CBM27. 11atgggtcatc accatcacca tcacggtgtg agcaagggcg
aggagctgtt caccggggtg 60gtgcccatcc tggtcgagct ggacggcgac gtaaacggcc
acaagttcag cgtgtccggc 120gagggcgagg gcgatgccac ctacggcaag
ctgaccctga agttcatctg caccaccggc 180aagctgcccg tgccctggcc
caccctcgtg accaccctga cctggggcgt gcagtgcttc 240agccgctacc
ccgaccacat gaagcagcac gacttcttca agtccgccat gcccgaaggc
300tacgtccagg agcgcaccat cttcttcaag gacgacggca actacaagac
ccgcgccgag 360gtgaagttcg agggcgacac cctggtgaac cgcatcgagc
tgaagggcat cgacttcaag 420gaggacggca acatcctggg gcacaagctg
gagtacaact acatcagcca caacgtctat 480atcaccgccg acaagcagaa
gaacggcatc aaggccaact tcaagatccg ccacaacatc 540gaggacggca
gcgtgcagct cgccgaccac taccagcaga acacccccat cggcgacggc
600cccgtgctgc tgcccgacaa ccactacctg agcacccagt ccgccctgag
caaagacccc 660aacgagaagc gcgatcacat ggtcctgctg gagttcgtga
ccgccgccgg gatcactctc 720ggcatggacg agctgtacaa gggtaacgaa
gcacggtacg tgctcgcaga ggaagttgat 780ttttcctctc cagaagaggt
gaaaaactgg tggaacagcg gaacctggca ggcagagttc 840gggtcacctg
acattgaatg gaacggtgag gtgggaaatg gagcactgca gctgaacgtg
900aaactgcccg gaaagagcga ctgggaagaa gtgagagtag caaggaagtt
cgaaagactc 960tcagaatgtg agatcctcga gtacgacatc tacattccaa
acgtcgaggg actcaaggga 1020aggttgaggc cgtacgcggt tctgaacccc
ggctgggtga agataggcct cgacatgaac 1080aacgcgaacg tggaaagtgc
ggagatcatc actttcggcg gaaaagagta cagaagattc 1140catgtaagaa
ttgagttcga cagaacagcg ggggtgaaag aacttcacat aggagttgtc
1200ggtgatcatc tgaggtacga tggaccgatt ttcatcgata atgtgagact
ttataaaaga 1260acaggaggta tgtaa 127512424PRTArtificial
SequenceAmino acid sequence for eCFP-CBM27 (Probe
4).misc_feature(248)..(248)Glycine that links eCFP to CBM27. 12Met
Gly His His His His His His Gly Val Ser Lys Gly Glu Glu Leu1 5 10
15Phe Thr Gly Val Val Pro Ile Leu Val Glu Leu Asp Gly Asp Val Asn
20 25 30Gly His Lys Phe Ser Val Ser Gly Glu Gly Glu Gly Asp Ala Thr
Tyr 35 40 45Gly Lys Leu Thr Leu Lys Phe Ile Cys Thr Thr Gly Lys Leu
Pro Val 50 55 60Pro Trp Pro Thr Leu Val Thr Thr Leu Thr Trp Gly Val
Gln Cys Phe65 70 75 80Ser Arg Tyr Pro Asp His Met Lys Gln His Asp
Phe Phe Lys Ser Ala 85 90 95Met Pro Glu Gly Tyr Val Gln Glu Arg Thr
Ile Phe Phe Lys Asp Asp 100 105 110Gly Asn Tyr Lys Thr Arg Ala Glu
Val Lys Phe Glu Gly Asp Thr Leu 115 120 125Val Asn Arg Ile Glu Leu
Lys Gly Ile Asp Phe Lys Glu Asp Gly Asn 130 135 140Ile Leu Gly His
Lys Leu Glu Tyr Asn Tyr Ile Ser His Asn Val Tyr145 150 155 160Ile
Thr Ala Asp Lys Gln Lys Asn Gly Ile Lys Ala Asn Phe Lys Ile 165 170
175Arg His Asn Ile Glu Asp Gly Ser Val Gln Leu Ala Asp His Tyr Gln
180 185 190Gln Asn Thr Pro Ile Gly Asp Gly Pro Val Leu Leu Pro Asp
Asn His 195 200 205Tyr Leu Ser Thr Gln Ser Ala Leu Ser Lys Asp Pro
Asn Glu Lys Arg 210 215 220Asp His Met Val Leu Leu Glu Phe Val Thr
Ala Ala Gly Ile Thr Leu225 230 235 240Gly Met Asp Glu Leu Tyr Lys
Gly Asn Glu Ala Arg Tyr Val Leu Ala 245 250 255Glu Glu Val Asp Phe
Ser Ser Pro Glu Glu Val Lys Asn Trp Trp Asn 260 265 270Ser Gly Thr
Trp Gln Ala Glu Phe Gly Ser Pro Asp Ile Glu Trp Asn 275 280 285Gly
Glu Val Gly Asn Gly Ala Leu Gln Leu Asn Val Lys Leu Pro Gly 290 295
300Lys Ser Asp Trp Glu Glu Val Arg Val Ala Arg Lys Phe Glu Arg
Leu305 310 315 320Ser Glu Cys Glu Ile Leu Glu Tyr Asp Ile Tyr Ile
Pro Asn Val Glu 325 330 335Gly Leu Lys Gly Arg Leu Arg Pro Tyr Ala
Val Leu Asn Pro Gly Trp 340 345 350Val Lys Ile Gly Leu Asp Met Asn
Asn Ala Asn Val Glu Ser Ala Glu 355 360 365Ile Ile Thr Phe Gly Gly
Lys Glu Tyr Arg Arg Phe His Val Arg Ile 370 375 380Glu Phe Asp Arg
Thr Ala Gly Val Lys Glu Leu His Ile Gly Val Val385 390 395 400Gly
Asp His Leu Arg Tyr Asp Gly Pro Ile Phe Ile Asp Asn Val Arg 405 410
415Leu Tyr Lys Arg Thr Gly Gly Met 42013621DNAArtificial
SequenceNucleic acid sequence for CBM3a. 13atgggtcatc accatcacca
tcacggtaca ccgaccaagg gagcaacacc aacaaataca 60gctacgccga caaaatcagc
tacggctacg cccaccaggc catcggtacc gacaaacaca 120ccgacaaaca
caccggcaaa tacaccggta tcaggcaatt tgaaggttga attctacaac
180agcaatcctt cagatactac taactcaatc aatcctcagt tcaaggttac
taataccgga 240agcagtgcaa ttgatttgtc caaactcaca ttgagatatt
attatacagt agacggacag 300aaagatcaga ccttctggtg tgaccatgct
gcaataatcg gcagtaacgg cagctacaac 360ggaattactt caaatgtaaa
aggaacattt gtaaaaatga gttcctcaac aaataacgca 420gacacctacc
ttgaaattag ctttacaggc ggaactcttg aaccgggtgc acatgttcag
480atacaaggta gatttgcaaa gaatgactgg agtaactata cacagtcaaa
tgactactca 540ttcaagtctg cttcacagtt tgttgaatgg gatcaggtaa
cagcatactt gaacggtgtt 600cttgtatggg gtaaagaata a
62114206PRTArtificial SequenceAmino acid sequence for CBM3a. 14Met
Gly His His His His His His Gly Thr Pro Thr Lys Gly Ala Thr1 5 10
15Pro Thr Asn Thr Ala Thr Pro Thr Lys Ser Ala Thr Ala Thr Pro Thr
20 25 30Arg Pro Ser Val Pro Thr Asn Thr Pro Thr Asn Thr Pro Ala Asn
Thr 35 40 45Pro Val Ser Gly Asn Leu Lys Val Glu Phe Tyr Asn Ser Asn
Pro Ser 50 55 60Asp Thr Thr Asn Ser Ile Asn Pro Gln Phe Lys Val Thr
Asn Thr Gly65 70 75 80Ser Ser Ala Ile Asp Leu Ser Lys Leu Thr Leu
Arg Tyr Tyr Tyr Thr 85 90 95Val Asp Gly Gln Lys Asp Gln Thr Phe Trp
Cys Asp His Ala Ala Ile 100 105 110Ile Gly Ser Asn Gly Ser Tyr Asn
Gly Ile Thr Ser Asn Val Lys Gly 115 120 125Thr Phe Val Lys Met Ser
Ser Ser Thr Asn Asn Ala Asp Thr Tyr Leu 130 135 140Glu Ile Ser Phe
Thr Gly Gly Thr Leu Glu Pro Gly Ala His Val Gln145 150 155 160Ile
Gln Gly Arg Phe Ala Lys Asn Asp Trp Ser Asn Tyr Thr Gln Ser 165 170
175Asn Asp Tyr Ser Phe Lys Ser Ala Ser Gln Phe Val Glu Trp Asp Gln
180 185 190Val Thr Ala Tyr Leu Asn Gly Val Leu Val Trp Gly Lys Glu
195 200 20515486DNAArtificial SequenceNucleic acid sequence for
CBM4-1. 15atgggtcatc accatcacca tcacggtgcg tcgccgatcg gggagggaac
gttcgacgac 60gggcccgagg ggtgggtcgc gtacggcacc gacggccccc tcgacacgag
cacgggcgcg 120ctgtgcgtcg ccgtgccggc cggctccgcg cagtacggcg
tcggcgtcgt gctcaacggc 180gtcgcgatcg aggaagggac cacctacacg
ctccggtaca ccgcgacggc ctcgaccgac 240gtcaccgtgc gggcgctcgt
cgggcagaac ggcgccccct acggcaccgt gctcgacacg 300agcccggccc
tgacgtccga gccgcggcag gtgaccgaga cgttcacggc ctcggcgacg
360taccccgcga cacccgccgc cgacgacccc gaggggcaga tcgccttcca
gctcggcggg 420ttcagcgccg acgcgtggac gttctgcctc gacgacgtcg
cgctcgactc cgaggtcgag 480ctctaa 48616161PRTArtificial SequenceAmino
acid sequence for CBM4-1. 16Met Gly His His His His His His Gly Ala
Ser Pro Ile Gly Glu Gly1 5 10 15Thr Phe Asp Asp Gly Pro Glu Gly Trp
Val Ala Tyr Gly Thr Asp Gly 20 25 30Pro Leu Asp Thr Ser Thr Gly Ala
Leu Cys Val Ala Val Pro Ala Gly 35 40 45Ser Ala Gln Tyr Gly Val Gly
Val Val Leu Asn Gly Val Ala Ile Glu 50 55 60Glu Gly Thr Thr Tyr Thr
Leu Arg Tyr Thr Ala Thr Ala Ser Thr Asp65 70 75 80Val Thr Val Arg
Ala Leu Val Gly Gln Asn Gly Ala Pro Tyr Gly Thr 85 90 95Val Leu Asp
Thr Ser Pro Ala Leu Thr Ser Glu Pro Arg Gln Val Thr 100 105 110Glu
Thr Phe Thr Ala Ser Ala Thr Tyr Pro Ala Thr Pro Ala Ala Asp 115 120
125Asp Pro Glu Gly Gln Ile Ala Phe Gln Leu Gly Gly Phe Ser Ala Asp
130 135 140Ala Trp Thr Phe Cys Leu Asp Asp Val Ala Leu Asp Ser Glu
Val Glu145 150 155 160Leu17666DNAArtificial SequenceNucleic acid
sequence for CBM17. 17atgggtcatc accatcacca tcacggttta tgggcagata
atgaattaac cacttcaggt 60caatatgtac gtgctcgtat taagggagct tattatgcta
caccagttga tcctgtaaca 120aaccaaccaa cagcaccgaa agacttttct
tcaggctttt gggactttaa tgacggtact 180acacaaggtt ttggtgtaaa
tccagatagt ccaataactg ctattaatgt tgaaaatgct 240aacaatgctt
taaaaatcag caatcttaat agtaagggta gtaatgattt atctgaagga
300aacttttggg ccaatgtccg catttcagct gatatctggg gacaaagtat
aaatatatat 360ggagacacaa aactaacaat ggatgttata gctccaacac
ctgtaaatgt atcaatcgca 420gctatcccac aaagtagtac tcacggttgg
ggaaatccta caagagctat acgtgtttgg 480acaaacaact ttgtagcaca
aactgatgga acctataaag caactttgac catttctaca 540aacgatagtc
caaatttcaa tactatagct acagatgctg ctgatagtgt agtaacaaat
600atgattctat ttgttggttc aaattcagat aatatttctt tagacaatat
aaagtttact 660aaataa 66618221PRTArtificial SequenceAmino acid
sequence for CBM17. 18Met Gly His His His His His His Gly Leu Trp
Ala Asp Asn Glu Leu1 5 10 15Thr Thr Ser Gly Gln Tyr Val Arg Ala Arg
Ile Lys Gly Ala Tyr Tyr 20 25 30Ala Thr Pro Val Asp Pro Val Thr Asn
Gln Pro Thr Ala Pro Lys Asp 35 40 45Phe Ser Ser Gly Phe Trp Asp Phe
Asn Asp Gly Thr Thr Gln Gly Phe 50 55 60Gly Val Asn Pro Asp Ser Pro
Ile Thr Ala Ile Asn Val Glu Asn Ala65 70 75 80Asn Asn Ala Leu Lys
Ile Ser Asn Leu Asn Ser Lys Gly Ser Asn Asp 85 90 95Leu Ser Glu Gly
Asn Phe Trp Ala Asn Val Arg Ile Ser Ala Asp Ile 100 105 110Trp Gly
Gln Ser Ile Asn Ile Tyr Gly Asp Thr Lys Leu Thr Met Asp 115 120
125Val Ile Ala Pro Thr Pro Val Asn Val Ser Ile Ala Ala Ile Pro Gln
130 135 140Ser Ser Thr His Gly Trp Gly Asn Pro Thr Arg Ala Ile Arg
Val Trp145 150 155 160Thr Asn Asn Phe Val Ala Gln Thr Asp Gly Thr
Tyr Lys Ala Thr Leu 165 170 175Thr Ile Ser Thr Asn Asp Ser Pro Asn
Phe Asn Thr Ile Ala Thr Asp 180 185 190Ala Ala Asp Ser Val Val Thr
Asn Met Ile Leu Phe Val Gly Ser Asn 195 200 205Ser Asp Asn Ile Ser
Leu Asp Asn Ile Lys Phe Thr Lys 210 215 22019516DNAArtificial
SequenceNucleic acid sequence for CBM15. 19atgggtcatc accatcacca
tcacggtgtc gctgccagcg agggcaatgt tgttatagag 60gtggacatgg caaatggctg
gagaggcaac gcatcaggca gtaccagcca ttccggtatt 120acctacagtg
ccgatggcgt tacctttgcc gcactgggcg atggcgtggg cgctgttttt
180gatattgccc gaccaaccac actggaagat gctgtgatag caatggttgt
taatgtcagc 240gctgaattta aggccagtga agccaacttg cagatatttg
cccagttaaa agaagactgg 300tcaaagggcg aatgggattg tctggcggcc
agcagcgaac tcactgcgga tactgaccta 360accctgacct gcaccattga
tgaagacgac gataaattca accaaacggc gcgcgatgta 420caagtcggta
tccaggccaa gggaacaccc gccggaacta tcaccattaa aagcgtcacc
480attacactcg cacaggaagc ctattcagcc aattaa 51620171PRTArtificial
SequenceAmino acid sequence for CBM15. 20Met Gly His His His His
His His Gly Val Ala Ala Ser Glu Gly Asn1 5 10 15Val Val Ile Glu Val
Asp Met Ala Asn Gly Trp Arg Gly Asn Ala Ser 20 25 30Gly Ser Thr Ser
His Ser Gly Ile Thr Tyr Ser Ala Asp Gly Val Thr 35 40 45Phe Ala Ala
Leu Gly Asp Gly Val Gly Ala Val Phe Asp Ile Ala Arg 50 55 60Pro Thr
Thr Leu Glu Asp Ala Val Ile Ala Met Val Val Asn Val Ser65 70 75
80Ala Glu Phe Lys Ala Ser Glu Ala Asn Leu Gln Ile Phe Ala Gln Leu
85 90 95Lys Glu Asp Trp Ser Lys Gly Glu Trp Asp Cys Leu Ala Ala Ser
Ser 100 105 110Glu Leu Thr Ala Asp Thr Asp Leu Thr Leu Thr Cys Thr
Ile Asp Glu 115 120 125Asp Asp Asp Lys Phe Asn Gln Thr Ala Arg Asp
Val Gln Val Gly Ile 130 135 140Gln Ala Lys Gly Thr Pro Ala Gly Thr
Ile Thr Ile Lys Ser Val Thr145 150 155 160Ile Thr Leu Ala Gln Glu
Ala Tyr Ser Ala Asn 165 17021558DNAArtificial SequenceNucleic acid
sequence for CBM27. 21atgggtcatc accatcacca tcacggtaac gaagcacggt
acgtgctcgc agaggaagtt 60gatttttcct ctccagaaga ggtgaaaaac tggtggaaca
gcggaacctg gcaggcagag 120ttcgggtcac ctgacattga atggaacggt
gaggtgggaa atggagcact gcagctgaac 180gtgaaactgc ccggaaagag
cgactgggaa gaagtgagag tagcaaggaa gttcgaaaga 240ctctcagaat
gtgagatcct cgagtacgac atctacattc caaacgtcga gggactcaag
300ggaaggttga ggccgtacgc ggttctgaac cccggctggg tgaagatagg
cctcgacatg 360aacaacgcga acgtggaaag tgcggagatc atcactttcg
gcggaaaaga gtacagaaga 420ttccatgtaa gaattgagtt cgacagaaca
gcgggggtga aagaacttca cataggagtt 480gtcggtgatc atctgaggta
cgatggaccg attttcatcg ataatgtgag actttataaa 540agaacaggag gtatgtaa
55822185PRTArtificial SequenceAmino acid sequence for CBM27. 22Met
Gly His His His His His His Gly Asn Glu Ala Arg Tyr Val Leu1 5 10
15Ala Glu Glu Val Asp Phe Ser Ser Pro Glu Glu Val Lys Asn Trp Trp
20 25 30Asn Ser Gly Thr Trp Gln Ala Glu Phe Gly Ser Pro Asp Ile Glu
Trp 35 40 45Asn Gly Glu Val Gly Asn Gly Ala Leu Gln Leu Asn Val Lys
Leu Pro 50 55 60Gly Lys Ser Asp Trp Glu Glu Val Arg Val Ala Arg Lys
Phe Glu Arg65 70 75 80Leu Ser Glu Cys Glu Ile Leu Glu Tyr Asp Ile
Tyr Ile Pro Asn Val 85 90 95Glu Gly Leu Lys Gly Arg Leu Arg Pro Tyr
Ala Val Leu Asn Pro Gly 100 105 110Trp Val Lys Ile Gly Leu Asp Met
Asn Asn Ala Asn Val Glu Ser Ala 115 120 125Glu Ile Ile Thr Phe Gly
Gly Lys Glu Tyr Arg Arg Phe His Val Arg 130 135 140Ile Glu Phe Asp
Arg Thr Ala Gly Val Lys Glu Leu His Ile Gly Val145 150 155 160Val
Gly Asp His Leu Arg Tyr Asp Gly Pro Ile Phe Ile Asp Asn Val 165 170
175Arg Leu Tyr Lys Arg Thr Gly Gly Met 180
18523744DNAArtificial
SequenceNucleic acid sequence for eGFP. 23atgggtcatc accatcacca
tcacggtgtg agcaagggcg aggagctgtt caccggggtg 60gtgcccatcc tggtcgagct
ggacggcgac gtaaacggcc acaagttcag cgtgtccggc 120gagggcgagg
gcgatgccac ctacggcaag ctgaccctga agttcatctg caccaccggc
180aagctgcccg tgccctggcc caccctcgtg accaccctga cctacggcgt
gcagtgcttc 240agccgctacc ccgaccacat gaagcagcac gacttcttca
agtccgccat gcccgaaggc 300tacgtccagg agcgcaccat cttcttcaag
gacgacggca actacaagac ccgcgccgag 360gtgaagttcg agggcgacac
cctggtgaac cgcatcgagc tgaagggcat cgacttcaag 420gaggacggca
acatcctggg gcacaagctg gagtacaact acaacagcca caacgtctat
480atcatggccg acaagcagaa gaacggcatc aaggtgaact tcaagatccg
ccacaacatc 540gaggacggca gcgtgcagct cgccgaccac taccagcaga
acacccccat cggcgacggc 600cccgtgctgc tgcccgacaa ccactacctg
agcacccagt ccgccctgag caaagacccc 660aacgagaagc gcgatcacat
ggtcctgctg gagttcgtga ccgccgccgg gatcactctc 720ggcatggacg
agctgtacaa gtaa 74424247PRTArtificial SequenceAmino acid sequence
for eGFP. 24Met Gly His His His His His His Gly Val Ser Lys Gly Glu
Glu Leu1 5 10 15Phe Thr Gly Val Val Pro Ile Leu Val Glu Leu Asp Gly
Asp Val Asn 20 25 30Gly His Lys Phe Ser Val Ser Gly Glu Gly Glu Gly
Asp Ala Thr Tyr 35 40 45Gly Lys Leu Thr Leu Lys Phe Ile Cys Thr Thr
Gly Lys Leu Pro Val 50 55 60Pro Trp Pro Thr Leu Val Thr Thr Leu Thr
Tyr Gly Val Gln Cys Phe65 70 75 80Ser Arg Tyr Pro Asp His Met Lys
Gln His Asp Phe Phe Lys Ser Ala 85 90 95Met Pro Glu Gly Tyr Val Gln
Glu Arg Thr Ile Phe Phe Lys Asp Asp 100 105 110Gly Asn Tyr Lys Thr
Arg Ala Glu Val Lys Phe Glu Gly Asp Thr Leu 115 120 125Val Asn Arg
Ile Glu Leu Lys Gly Ile Asp Phe Lys Glu Asp Gly Asn 130 135 140Ile
Leu Gly His Lys Leu Glu Tyr Asn Tyr Asn Ser His Asn Val Tyr145 150
155 160Ile Met Ala Asp Lys Gln Lys Asn Gly Ile Lys Val Asn Phe Lys
Ile 165 170 175Arg His Asn Ile Glu Asp Gly Ser Val Gln Leu Ala Asp
His Tyr Gln 180 185 190Gln Asn Thr Pro Ile Gly Asp Gly Pro Val Leu
Leu Pro Asp Asn His 195 200 205Tyr Leu Ser Thr Gln Ser Ala Leu Ser
Lys Asp Pro Asn Glu Lys Arg 210 215 220Asp His Met Val Leu Leu Glu
Phe Val Thr Ala Ala Gly Ile Thr Leu225 230 235 240Gly Met Asp Glu
Leu Tyr Lys 24525735DNAArtificial SequenceNucleic acid sequence for
mCherry. 25atgggtcatc accatcacca tcacggtgtg agcaagggcg aggaggataa
catggccatc 60atcaaggagt tcatgcgctt caaggtgcac atggagggct ccgtgaacgg
ccacgagttc 120gagatcgagg gcgagggcga gggccgcccc tacgagggca
cccagaccgc caagctgaag 180gtgaccaagg gtggccccct gcccttcgcc
tgggacatcc tgtcccctca gttcatgtac 240ggctccaagg cctacgtgaa
gcaccccgcc gacatccccg actacttgaa gctgtccttc 300cccgagggct
tcaagtggga gcgcgtgatg aacttcgagg acggcggcgt ggtgaccgtg
360acccaggact cctccctgca ggacggcgag ttcatctaca aggtgaagct
gcgcggcacc 420aacttcccct ccgacggccc cgtaatgcag aagaagacca
tgggctggga ggcctcctcc 480gagcggatgt accccgagga cggcgccctg
aagggcgaga tcaagcagag gctgaagctg 540aaggacggcg gccactacga
cgctgaggtc aagaccacct acaaggccaa gaagcccgtg 600cagctgcccg
gcgcctacaa cgtcaacatc aagttggaca tcacctccca caacgaggac
660tacaccatcg tggaacagta cgaacgcgcc gagggccgcc actccaccgg
cggcatggac 720gagctgtaca agtaa 73526244PRTArtificial SequenceAmino
acid sequence for mCherry. 26Met Gly His His His His His His Gly
Val Ser Lys Gly Glu Glu Asp1 5 10 15Asn Met Ala Ile Ile Lys Glu Phe
Met Arg Phe Lys Val His Met Glu 20 25 30Gly Ser Val Asn Gly His Glu
Phe Glu Ile Glu Gly Glu Gly Glu Gly 35 40 45Arg Pro Tyr Glu Gly Thr
Gln Thr Ala Lys Leu Lys Val Thr Lys Gly 50 55 60Gly Pro Leu Pro Phe
Ala Trp Asp Ile Leu Ser Pro Gln Phe Met Tyr65 70 75 80Gly Ser Lys
Ala Tyr Val Lys His Pro Ala Asp Ile Pro Asp Tyr Leu 85 90 95Lys Leu
Ser Phe Pro Glu Gly Phe Lys Trp Glu Arg Val Met Asn Phe 100 105
110Glu Asp Gly Gly Val Val Thr Val Thr Gln Asp Ser Ser Leu Gln Asp
115 120 125Gly Glu Phe Ile Tyr Lys Val Lys Leu Arg Gly Thr Asn Phe
Pro Ser 130 135 140Asp Gly Pro Val Met Gln Lys Lys Thr Met Gly Trp
Glu Ala Ser Ser145 150 155 160Glu Arg Met Tyr Pro Glu Asp Gly Ala
Leu Lys Gly Glu Ile Lys Gln 165 170 175Arg Leu Lys Leu Lys Asp Gly
Gly His Tyr Asp Ala Glu Val Lys Thr 180 185 190Thr Tyr Lys Ala Lys
Lys Pro Val Gln Leu Pro Gly Ala Tyr Asn Val 195 200 205Asn Ile Lys
Leu Asp Ile Thr Ser His Asn Glu Asp Tyr Thr Ile Val 210 215 220Glu
Gln Tyr Glu Arg Ala Glu Gly Arg His Ser Thr Gly Gly Met Asp225 230
235 240Glu Leu Tyr Lys27735DNAArtificial SequenceNucleic acid
sequence for mOrange2. 27atgggtcatc accatcacca tcacggtgtg
agcaagggcg aggagaataa catggccatc 60atcaaggagt tcatgcgctt caaggtgcgc
atggagggct ccgtgaacgg ccacgagttc 120gagatcgagg gcgagggcga
gggccgcccc tacgagggct ttcagaccgc taagctgaag 180gtgaccaagg
gtggccccct gcccttcgcc tgggacatcc tgtcccctca tttcacctac
240ggctccaagg cctacgtgaa gcaccccgcc gacatccccg actacttcaa
gctgtccttc 300cccgagggct tcaagtggga gcgcgtgatg aactacgagg
acggcggcgt ggtgaccgtg 360acccaggact cctccctgca ggacggcgag
ttcatctaca aggtgaagct gcgcggcacc 420aacttcccct ccgacggccc
cgtgatgcag aagaagacca tgggctggga ggcctcctcc 480gagcggatgt
accccgagga cggtgccctg aagggcaaga tcaagatgag gctgaagctg
540aaggacggcg gccactacac ctccgaggtc aagaccacct acaaggccaa
gaagcccgtg 600cagctgcccg gcgcctacat cgtcgacatc aagttggaca
tcacctccca caacgaggac 660tacaccatcg tggaacagta cgaacgcgcc
gagggccgcc actccaccgg cggcatggac 720gagctgtaca agtaa
73528244PRTArtificial SequenceAmino acid sequence for mOrange2.
28Met Gly His His His His His His Gly Val Ser Lys Gly Glu Glu Asn1
5 10 15Asn Met Ala Ile Ile Lys Glu Phe Met Arg Phe Lys Val Arg Met
Glu 20 25 30Gly Ser Val Asn Gly His Glu Phe Glu Ile Glu Gly Glu Gly
Glu Gly 35 40 45Arg Pro Tyr Glu Gly Phe Gln Thr Ala Lys Leu Lys Val
Thr Lys Gly 50 55 60Gly Pro Leu Pro Phe Ala Trp Asp Ile Leu Ser Pro
His Phe Thr Tyr65 70 75 80Gly Ser Lys Ala Tyr Val Lys His Pro Ala
Asp Ile Pro Asp Tyr Phe 85 90 95Lys Leu Ser Phe Pro Glu Gly Phe Lys
Trp Glu Arg Val Met Asn Tyr 100 105 110Glu Asp Gly Gly Val Val Thr
Val Thr Gln Asp Ser Ser Leu Gln Asp 115 120 125Gly Glu Phe Ile Tyr
Lys Val Lys Leu Arg Gly Thr Asn Phe Pro Ser 130 135 140Asp Gly Pro
Val Met Gln Lys Lys Thr Met Gly Trp Glu Ala Ser Ser145 150 155
160Glu Arg Met Tyr Pro Glu Asp Gly Ala Leu Lys Gly Lys Ile Lys Met
165 170 175Arg Leu Lys Leu Lys Asp Gly Gly His Tyr Thr Ser Glu Val
Lys Thr 180 185 190Thr Tyr Lys Ala Lys Lys Pro Val Gln Leu Pro Gly
Ala Tyr Ile Val 195 200 205Asp Ile Lys Leu Asp Ile Thr Ser His Asn
Glu Asp Tyr Thr Ile Val 210 215 220Glu Gln Tyr Glu Arg Ala Glu Gly
Arg His Ser Thr Gly Gly Met Asp225 230 235 240Glu Leu Tyr
Lys29744DNAArtificial SequenceNucleic acid sequence for eCFP.
29atgggtcatc accatcacca tcacggtgtg agcaagggcg aggagctgtt caccggggtg
60gtgcccatcc tggtcgagct ggacggcgac gtaaacggcc acaagttcag cgtgtccggc
120gagggcgagg gcgatgccac ctacggcaag ctgaccctga agttcatctg
caccaccggc 180aagctgcccg tgccctggcc caccctcgtg accaccctga
cctggggcgt gcagtgcttc 240agccgctacc ccgaccacat gaagcagcac
gacttcttca agtccgccat gcccgaaggc 300tacgtccagg agcgcaccat
cttcttcaag gacgacggca actacaagac ccgcgccgag 360gtgaagttcg
agggcgacac cctggtgaac cgcatcgagc tgaagggcat cgacttcaag
420gaggacggca acatcctggg gcacaagctg gagtacaact acatcagcca
caacgtctat 480atcaccgccg acaagcagaa gaacggcatc aaggccaact
tcaagatccg ccacaacatc 540gaggacggca gcgtgcagct cgccgaccac
taccagcaga acacccccat cggcgacggc 600cccgtgctgc tgcccgacaa
ccactacctg agcacccagt ccgccctgag caaagacccc 660aacgagaagc
gcgatcacat ggtcctgctg gagttcgtga ccgccgccgg gatcactctc
720ggcatggacg agctgtacaa gtaa 74430247PRTArtificial SequenceAmino
acid sequence for eCFP. 30Met Gly His His His His His His Gly Val
Ser Lys Gly Glu Glu Leu1 5 10 15Phe Thr Gly Val Val Pro Ile Leu Val
Glu Leu Asp Gly Asp Val Asn 20 25 30Gly His Lys Phe Ser Val Ser Gly
Glu Gly Glu Gly Asp Ala Thr Tyr 35 40 45Gly Lys Leu Thr Leu Lys Phe
Ile Cys Thr Thr Gly Lys Leu Pro Val 50 55 60Pro Trp Pro Thr Leu Val
Thr Thr Leu Thr Trp Gly Val Gln Cys Phe65 70 75 80Ser Arg Tyr Pro
Asp His Met Lys Gln His Asp Phe Phe Lys Ser Ala 85 90 95Met Pro Glu
Gly Tyr Val Gln Glu Arg Thr Ile Phe Phe Lys Asp Asp 100 105 110Gly
Asn Tyr Lys Thr Arg Ala Glu Val Lys Phe Glu Gly Asp Thr Leu 115 120
125Val Asn Arg Ile Glu Leu Lys Gly Ile Asp Phe Lys Glu Asp Gly Asn
130 135 140Ile Leu Gly His Lys Leu Glu Tyr Asn Tyr Ile Ser His Asn
Val Tyr145 150 155 160Ile Thr Ala Asp Lys Gln Lys Asn Gly Ile Lys
Ala Asn Phe Lys Ile 165 170 175Arg His Asn Ile Glu Asp Gly Ser Val
Gln Leu Ala Asp His Tyr Gln 180 185 190Gln Asn Thr Pro Ile Gly Asp
Gly Pro Val Leu Leu Pro Asp Asn His 195 200 205Tyr Leu Ser Thr Gln
Ser Ala Leu Ser Lys Asp Pro Asn Glu Lys Arg 210 215 220Asp His Met
Val Leu Leu Glu Phe Val Thr Ala Ala Gly Ile Thr Leu225 230 235
240Gly Met Asp Glu Leu Tyr Lys 245
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References