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WO2009005564A3 - Cellulose- and hemicellulose-degradation enzyme -encoding nucleotide sequences with refined translational kinetics and methods of making same - Google Patents

Cellulose- and hemicellulose-degradation enzyme -encoding nucleotide sequences with refined translational kinetics and methods of making same Download PDF

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Publication number
WO2009005564A3
WO2009005564A3 PCT/US2008/006379 US2008006379W WO2009005564A3 WO 2009005564 A3 WO2009005564 A3 WO 2009005564A3 US 2008006379 W US2008006379 W US 2008006379W WO 2009005564 A3 WO2009005564 A3 WO 2009005564A3
Authority
WO
WIPO (PCT)
Prior art keywords
hemicellulose
cellulose
expression
degradation enzyme
encoding nucleotide
Prior art date
Application number
PCT/US2008/006379
Other languages
French (fr)
Other versions
WO2009005564A2 (en
Inventor
Kirsty A Salmon
David A Roth
Wesley G Hatfield
Yimeng Dou
Original Assignee
Univ California
Kirsty A Salmon
David A Roth
Wesley G Hatfield
Yimeng Dou
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Univ California, Kirsty A Salmon, David A Roth, Wesley G Hatfield, Yimeng Dou filed Critical Univ California
Publication of WO2009005564A2 publication Critical patent/WO2009005564A2/en
Publication of WO2009005564A3 publication Critical patent/WO2009005564A3/en

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/24—Hydrolases (3) acting on glycosyl compounds (3.2)
    • C12N9/2402—Hydrolases (3) acting on glycosyl compounds (3.2) hydrolysing O- and S- glycosyl compounds (3.2.1)
    • C12N9/2405—Glucanases
    • C12N9/2434—Glucanases acting on beta-1,4-glucosidic bonds
    • C12N9/2437—Cellulases (3.2.1.4; 3.2.1.74; 3.2.1.91; 3.2.1.150)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/52—Genes encoding for enzymes or proenzymes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/0004—Oxidoreductases (1.)
    • C12N9/0055—Oxidoreductases (1.) acting on diphenols and related substances as donors (1.10)
    • C12N9/0057—Oxidoreductases (1.) acting on diphenols and related substances as donors (1.10) with oxygen as acceptor (1.10.3)
    • C12N9/0061—Laccase (1.10.3.2)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/24—Hydrolases (3) acting on glycosyl compounds (3.2)
    • C12N9/2402—Hydrolases (3) acting on glycosyl compounds (3.2) hydrolysing O- and S- glycosyl compounds (3.2.1)
    • C12N9/2477—Hemicellulases not provided in a preceding group
    • C12N9/248—Xylanases
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y302/00—Hydrolases acting on glycosyl compounds, i.e. glycosylases (3.2)
    • C12Y302/01—Glycosidases, i.e. enzymes hydrolysing O- and S-glycosyl compounds (3.2.1)
    • C12Y302/01004—Cellulase (3.2.1.4), i.e. endo-1,4-beta-glucanase
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y302/00—Hydrolases acting on glycosyl compounds, i.e. glycosylases (3.2)
    • C12Y302/01—Glycosidases, i.e. enzymes hydrolysing O- and S-glycosyl compounds (3.2.1)
    • C12Y302/01091—Cellulose 1,4-beta-cellobiosidase (3.2.1.91)

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Wood Science & Technology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Zoology (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Biochemistry (AREA)
  • Biomedical Technology (AREA)
  • Biotechnology (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • Medicinal Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • Plant Pathology (AREA)
  • Preparation Of Compounds By Using Micro-Organisms (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)

Abstract

Provided are polynucleotide sequences and synthetic genes encoding cellulose- and hemicellulose-degradation enzymes for expression in a host organism with improved and/or refined translational kinetics, and methods of making same. The resultant cellulose- and hemicellulose-degradation enzyme-encoding nucleotide is predicted to be translated rapidly along its entire length. Expression of the resultant cellulose- and hemicellulose-degradation enzyme-encoding nucleotide is predicted to result in improved protein expression levels in cases where inappropriate or excessive translation pauses reduce protein expression. In addition, expression of the resultant cellulose- and hemicellulose-degradation enzyme-encoding nucleotide is predicted to result in improved levels of active and/or natively folded and functional polypeptide expression in cases where inappropriate or excessive translational pauses causes expression of inactive, insoluble, aggregated or somehow dysfunctional or minimally active cellulose- and hemicellulose-degradation enzyme.
PCT/US2008/006379 2007-06-29 2008-05-14 Cellulose- and hemicellulose-degradation enzyme -encoding nucleotide sequences with refined translational kinetics and methods of making same WO2009005564A2 (en)

Applications Claiming Priority (12)

Application Number Priority Date Filing Date Title
US94708607P 2007-06-29 2007-06-29
US94732907P 2007-06-29 2007-06-29
US94727707P 2007-06-29 2007-06-29
US60/947,086 2007-06-29
US60/947,329 2007-06-29
US60/947,277 2007-06-29
US94749607P 2007-07-02 2007-07-02
US94761707P 2007-07-02 2007-07-02
US60/947,496 2007-07-02
US60/947,617 2007-07-02
US94778407P 2007-07-03 2007-07-03
US60/947,784 2007-07-03

Publications (2)

Publication Number Publication Date
WO2009005564A2 WO2009005564A2 (en) 2009-01-08
WO2009005564A3 true WO2009005564A3 (en) 2009-03-05

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2008/006379 WO2009005564A2 (en) 2007-06-29 2008-05-14 Cellulose- and hemicellulose-degradation enzyme -encoding nucleotide sequences with refined translational kinetics and methods of making same

Country Status (1)

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WO (1) WO2009005564A2 (en)

Families Citing this family (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8686123B2 (en) * 2010-11-15 2014-04-01 Edeniq, Inc. Use of manganese peroxidase for enzymatic hydrolysis of lignocellulosic material
EP2885404B1 (en) * 2012-08-16 2018-04-25 Bangladesh Jute Research Institute Lignin degrading enzymes from macrophomina phaseolina and uses thereof
CN104388441B (en) * 2014-10-30 2017-11-14 上海市农业科学院 Laccase gene and its application from Colletotrichumlagenarium
CN104357414B (en) * 2014-11-28 2017-11-14 上海市农业科学院 Laccase gene and its application from Laccaria bicolor

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5082767A (en) * 1989-02-27 1992-01-21 Hatfield G Wesley Codon pair utilization
WO2003070957A2 (en) * 2002-02-20 2003-08-28 Novozymes A/S Plant polypeptide production
WO2007130606A2 (en) * 2006-05-04 2007-11-15 The Regents Of The University Of California Analyzing translational kinetics using graphical displays of translational kinetics values of codon pairs
WO2008000632A1 (en) * 2006-06-29 2008-01-03 Dsm Ip Assets B.V. A method for achieving improved polypeptide expression

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5082767A (en) * 1989-02-27 1992-01-21 Hatfield G Wesley Codon pair utilization
WO2003070957A2 (en) * 2002-02-20 2003-08-28 Novozymes A/S Plant polypeptide production
WO2007130606A2 (en) * 2006-05-04 2007-11-15 The Regents Of The University Of California Analyzing translational kinetics using graphical displays of translational kinetics values of codon pairs
WO2007130650A2 (en) * 2006-05-04 2007-11-15 The Regents Of The University Of California Methods for calculating codon pair-based translational kinetics values, and methods for generating polypeptide-encoding nucleotide sequences from such values
WO2008000632A1 (en) * 2006-06-29 2008-01-03 Dsm Ip Assets B.V. A method for achieving improved polypeptide expression

Non-Patent Citations (8)

* Cited by examiner, † Cited by third party
Title
DATABASE EMBL [online] 25 November 2003 (2003-11-25), "Pycnoporus sanguineus laccase mRNA, complete cds.", XP002496141, retrieved from EBI accession no. EMBL:AY458017 Database accession no. AY458017 *
GONZALEZ ET AL: "Identification of a new laccase gene and confirmation of genomic predictions by cDNA sequences of Trametes sp. I-62 laccase family", MYCOLOGICAL RESEARCH, ELSEVIER, GB, vol. 107, no. 6, 1 June 2003 (2003-06-01), pages 727 - 735, XP022443249, ISSN: 0953-7562 *
GUSTAFSSON C ET AL: "Codon bias and heterologous protein expression", TRENDS IN BIOTECHNOLOGY, ELSEVIER PUBLICATIONS, CAMBRIDGE, GB, vol. 22, no. 7, 1 July 2004 (2004-07-01), pages 346 - 353, XP004520507, ISSN: 0167-7799 *
HATFIELD G WESLEY ET AL: "Optimizing scaleup yield for protein production: Computationally Optimized DNA Assembly (CODA) and Translation Engineering(TM)", BIOTECHNOLOGY ANNUAL REVIEW, XX, XX, vol. 13, 1 January 2007 (2007-01-01), pages 27 - 42, XP009092735 *
HATFIELD G.W. ET AL.: "Codon pair utilization bias in bacteria, yeast and mammals", 1993, CRC PRESS, BOCA RATON, LA, XP002495824 *
IRWIN B ET AL: "codon pair utilization biases influence translational elongation step times", JOURNAL OF BIOLOGICAL CHEMISTRY, AMERICAN SOCIETY OF BIOLOCHEMICAL BIOLOGISTS, BIRMINGHAM,; US, vol. 270, no. 39, 29 September 1995 (1995-09-29), pages 22801 - 22806, XP002406003, ISSN: 0021-9258 *
KITTLE J.D., JR: "Radical Changes in the Engineering of Synthetic Genes for Protein Expression", BIOPHARM INTERNATIONAL, February 2006 (2006-02-01), XP002495822, Retrieved from the Internet <URL:http://www.codagenomics.com/technology/pubs/Biopharm_pdf_BP3-61-06e.pdf> [retrieved on 20080915] *
TRINH RYAN ET AL: "Optimization of codon pair use within the (GGGGS)3 linker sequence results in enhanced protein expression.", MOLECULAR IMMUNOLOGY, vol. 40, no. 10, January 2004 (2004-01-01), pages 717 - 722, XP002495823, ISSN: 0161-5890 *

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