Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

被引：832

作者：

Martinez, Diego ^{[1
,15
]}

Berka, Randy M. ^{[2
]}

Henrissat, Bernard ^{[3
,4
]}

Saloheimo, Markku ^{[5
]}

Arvas, Mikko ^{[5
]}

Baker, Scott E. ^{[6
]}

Chapman, Jarod ^{[7
]}

Chertkov, Olga ^{[1
]}

Coutinho, Pedro M. ^{[3
,4
]}

Cullen, Dan ^{[8
]}

Danchin, Etienne G. J. ^{[3
,4
]}

Grigoriev, Igor V. ^{[7
]}

Harris, Paul ^{[2
]}

Jackson, Melissa ^{[1
]}

Kubicek, Christian P. ^{[9
]}

Han, Cliff S. ^{[1
]}

Ho, Isaac ^{[7
]}

Larrondo, Luis F. ^{[10
,11
]}

de Leon, Alfredo Lopez ^{[2
]}

Magnuson, Jon K. ^{[6
]}

Merino, Sandy ^{[2
]}

Misra, Monica ^{[1
]}

Nelson, Beth ^{[2
]}

Putnam, Nicholas ^{[7
]}

Robbertse, Barbara ^{[12
]}

Salamov, Asaf A. ^{[7
]}

Schmoll, Monika ^{[9
]}

Terry, Astrid ^{[7
]}

Thayer, Nina ^{[1
]}

Westerholm-Parvinen, Ann ^{[5
]}

Schoch, Conrad L. ^{[12
]}

Yao, Jian ^{[13
]}

Barbote, Ravi ^{[1
]}

Nelson, Mary Anne ^{[15
]}

Detter, Chris ^{[1
]}

Bruce, David ^{[1
]}

Kuske, Cheryl R. ^{[1
]}

Xie, Gary ^{[1
]}

Richardson, Paul ^{[7
]}

Rokhsar, Daniel S. ^{[7
]}

Lucas, Susan M. ^{[7
]}

Rubin, Edward M. ^{[7
]}

Dunn-Coleman, Nigel ^{[14
]}

Ward, Michael ^{[13
]}

Brettin, Thomas S. ^{[7
]}

机构：

[1] Los Alamos Natl Lab, Joint Genome Inst, Los Alamos, NM 87545 USA

[2] Novozymes Inc, Davis, CA 95618 USA

[3] Univ Aix Marseille 1, AFMB, CNRS, UMR 6098,Case 932, F-13288 Marseille, France

[4] Univ Aix Marseille 2, AFMB, CNRS, UMR 6098,Case 932, F-13288 Marseille, France

[5] VTT Tech Res Ctr Finland, Espoo 02044, Finland

[6] Pacific NW Natl Lab, Richland, WA 99352 USA

[7] Joint Genome Inst, Dept Energy, Walnut Creek, CA 94598 USA

[8] US Forest Serv, USDA, Forest Prod Lab, Madison, WI 53726 USA

[9] Vienna Univ Technol, Inst Chem Engn, Res Area Gene Technol & Appl Biochem, A-1060 Vienna, Austria

[10] Pontificia Univ Catolica Chile, Fac Ciencias Biol, Dept Mol Genet & Microbiol, Santiago, Chile

[11] Millenium Inst Fundamental & Appl Biol, Santiago, Chile

[12] Oregon State Univ, Dept Bot & Plant Pathol, Corvallis, OR 97331 USA

[13] Genencor Int, Palo Alto, CA 94304 USA

[14] AlerGenetiCa SL, Tenerife, Spain

[15] Univ New Mexico, Dept Biol, Albuquerque, NM 87131 USA

来源：

NATURE BIOTECHNOLOGY | 2008年 / 26卷 / 05期

关键词：

D O I：

10.1038/nbt1403

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to depolymerize biomass to simple sugars that are converted to chemical intermediates and biofuels, such as ethanol. We assembled 89 scaffolds (sets of ordered and oriented contigs) to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models. Unexpectedly, considering the industrial utility and effectiveness of the carbohydrate-active enzymes of T. reesei, its genome encodes fewer cellulases and hemicellulases than any other sequenced fungus able to hydrolyze plant cell wall polysaccharides. Many T. reesei genes encoding carbohydrate-active enzymes are distributed nonrandomly in clusters that lie between regions of synteny with other Sordariomycetes. Numerous genes encoding biosynthetic pathways for secondary metabolites may promote survival of T. reesei in its competitive soil habitat, but genome analysis provided little mechanistic insight into its extraordinary capacity for protein secretion. Our analysis, coupled with the genome sequence data, provides a roadmap for constructing enhanced T. reesei strains for industrial applications such as biofuel production.

引用

页码：553 / 560

页数：8

共 53 条

[1]

ARORA DK, 2006, BIOINFORMATICS

[2] Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[3]

Bashkirova EV, 2005, APPL MYCOL BIOTECH, V5, P275

[4] Using GeneWise in the Drosophila annotation experiment [J].

Birney, E ;

Durbin, R .

GENOME RESEARCH, 2000, 10 (04) :547-548

[5] The yeast cell wall and septum as paradigms of cell growth and morphogenesis [J].

Cabib, E ;

Roh, DH ;

Schmidt, M ;

Crotti, LB ;

Varma, A .

JOURNAL OF BIOLOGICAL CHEMISTRY, 2001, 276 (23) :19679-19682

[6] CHROMOSOMAL AND GENETIC-ANALYSIS OF THE ELECTROPHORETIC KARYOTYPE OF TRICHODERMA-REESEI - MAPPING OF THE CELLULASE AND XYLANASE GENES [J].

CARTER, GL ;

ALLISON, D ;

REY, MW ;

DUNNCOLEMAN, NS .

MOLECULAR MICROBIOLOGY, 1992, 6 (15) :2167-2174

[7] Directed evolution of industrial enzymes: an update [J].

Cherry, JR ;

Fidantsef, AL .

CURRENT OPINION IN BIOTECHNOLOGY, 2003, 14 (04) :438-443

[8]

Coutinho PM, 1999, ROY SOC CH, P3

[9] The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization [J].

Cuomo, Christina A. ;

Gueldener, Ulrich ;

Xu, Jin-Rong ;

Trail, Frances ;

Turgeon, B. Gillian ;

Di Pietro, Antonio ;

Walton, Jonathan D. ;

Ma, Li-Jun ;

Baker, Scott E. ;

Rep, Martijn ;

Adam, Gerhard ;

Antoniw, John ;

Baldwin, Thomas ;

Calvo, Sarah ;

Chang, Yueh-Long ;

DeCaprio, David ;

Gale, Liane R. ;

Gnerre, Sante ;

Goswami, Rubella S. ;

Hammond-Kosack, Kim ;

Harris, Linda J. ;

Hilburn, Karen ;

Kennell, John C. ;

Kroken, Scott ;

Magnuson, Jon K. ;

Mannhaupt, Gertrud ;

Mauceli, Evan ;

Mewes, Hans-Werner ;

Mitterbauer, Rudolf ;

Muehlbauer, Gary ;

Muensterkoetter, Martin ;

Nelson, David ;

O'Donnell, Kerry ;

Ouellet, Thérèse ;

Qi, Weihong ;

Quesneville, Hadi ;

Roncero, M. Isabel G. ;

Seong, Kye-Yong ;

Tetko, Igor V. ;

Urban, Martin ;

Waalwijk, Cees ;

Ward, Todd J. ;

Yao, Jiqiang ;

Birren, Bruce W. ;

Kistler, H. Corby .

SCIENCE, 2007, 317 (5843) :1400-1402

[10] The genome sequence of the rice blast fungus Magnaporthe grisea [J].

Dean, RA ;

Talbot, NJ ;

Ebbole, DJ ;

Farman, ML ;

Mitchell, TK ;

Orbach, MJ ;

Thon, M ;

Kulkarni, R ;

Xu, JR ;

Pan, HQ ;

Read, ND ;

Lee, YH ;

Carbone, I ;

Brown, D ;

Oh, YY ;

Donofrio, N ;

Jeong, JS ;

Soanes, DM ;

Djonovic, S ;

Kolomiets, E ;

Rehmeyer, C ;

Li, WX ;

Harding, M ;

Kim, S ;

Lebrun, MH ;

Bohnert, H ;

Coughlan, S ;

Butler, J ;

Calvo, S ;

Ma, LJ ;

Nicol, R ;

Purcell, S ;

Nusbaum, C ;

Galagan, JE ;

Birren, BW .

NATURE, 2005, 434 (7036) :980-986

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