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Title: Genome Sequence and Analysis of the Soil Cellulolytic Actinomycete Thermobifida fusca YX

Abstract

Thermobifida fusca is a moderately thermophilic soil bacterium that belongs to Actinobacteria. It is a major degrader of plant cell walls and has been used as a model organism for the study of secreted, thermostable cellulases. The complete genome sequence showed that T. fusca has a single circular chromosome of 3,642,249 bp predicted to encode 3,117 proteins and 65 RNA species with a coding density of 85%. Genome analysis revealed the existence of 29 putative glycoside hydrolases in addition to the previously identified cellulases and xylanases. The glycosyl hydrolases include enzymes predicted to exhibit mainly dextran/starch- and xylan-degrading functions. T. fusca possesses two protein secretion systems: the sec general secretion system and the twin-arginine translocation system. Several of the secreted cellulases have sequence signatures indicating their secretion may be mediated by the twin-arginine translocation system. T. fusca has extensive transport systems for import of carbohydrates coupled to transcriptional regulators controlling the expression of the transporters and glycosylhydrolases. In addition to providing an overview of the physiology of a soil actinomycete, this study presents insights on the transcriptional regulation and secretion of cellulases which may facilitate the industrial exploitation of these systems.

Authors:
 [1];  [1];  [1];  [1];  [2];  [1];  [1];  [1];  [1];  [1];  [1];  [3];  [1]
  1. U.S. Department of Energy, Joint Genome Institute
  2. ORNL
  3. Cornell University
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
931550
DOE Contract Number:
DE-AC05-00OR22725
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Bacteriology; Journal Volume: 189; Journal Issue: 6
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; GLYCOSYL HYDROLASES; PLANT CELLS; SECRETION; SOILS; CELLULASE

Citation Formats

Lykidis, A, Mavromatis, K, Ivanova, N, Anderson, Iain, Land, Miriam L, DiBartolo, Genevieve, Martinez, Michele, Lapidus, Alla L., Lucas, Susan, Copeland, A, Richardson, P M, Wilson, David B, and Kyrpides, Nikos C. Genome Sequence and Analysis of the Soil Cellulolytic Actinomycete Thermobifida fusca YX. United States: N. p., 2007. Web. doi:10.1128/JB.01899-06.
Lykidis, A, Mavromatis, K, Ivanova, N, Anderson, Iain, Land, Miriam L, DiBartolo, Genevieve, Martinez, Michele, Lapidus, Alla L., Lucas, Susan, Copeland, A, Richardson, P M, Wilson, David B, & Kyrpides, Nikos C. Genome Sequence and Analysis of the Soil Cellulolytic Actinomycete Thermobifida fusca YX. United States. doi:10.1128/JB.01899-06.
Lykidis, A, Mavromatis, K, Ivanova, N, Anderson, Iain, Land, Miriam L, DiBartolo, Genevieve, Martinez, Michele, Lapidus, Alla L., Lucas, Susan, Copeland, A, Richardson, P M, Wilson, David B, and Kyrpides, Nikos C. Mon . "Genome Sequence and Analysis of the Soil Cellulolytic Actinomycete Thermobifida fusca YX". United States. doi:10.1128/JB.01899-06.
@article{osti_931550,
title = {Genome Sequence and Analysis of the Soil Cellulolytic Actinomycete Thermobifida fusca YX},
author = {Lykidis, A and Mavromatis, K and Ivanova, N and Anderson, Iain and Land, Miriam L and DiBartolo, Genevieve and Martinez, Michele and Lapidus, Alla L. and Lucas, Susan and Copeland, A and Richardson, P M and Wilson, David B and Kyrpides, Nikos C},
abstractNote = {Thermobifida fusca is a moderately thermophilic soil bacterium that belongs to Actinobacteria. It is a major degrader of plant cell walls and has been used as a model organism for the study of secreted, thermostable cellulases. The complete genome sequence showed that T. fusca has a single circular chromosome of 3,642,249 bp predicted to encode 3,117 proteins and 65 RNA species with a coding density of 85%. Genome analysis revealed the existence of 29 putative glycoside hydrolases in addition to the previously identified cellulases and xylanases. The glycosyl hydrolases include enzymes predicted to exhibit mainly dextran/starch- and xylan-degrading functions. T. fusca possesses two protein secretion systems: the sec general secretion system and the twin-arginine translocation system. Several of the secreted cellulases have sequence signatures indicating their secretion may be mediated by the twin-arginine translocation system. T. fusca has extensive transport systems for import of carbohydrates coupled to transcriptional regulators controlling the expression of the transporters and glycosylhydrolases. In addition to providing an overview of the physiology of a soil actinomycete, this study presents insights on the transcriptional regulation and secretion of cellulases which may facilitate the industrial exploitation of these systems.},
doi = {10.1128/JB.01899-06},
journal = {Journal of Bacteriology},
number = 6,
volume = 189,
place = {United States},
year = {Mon Jan 01 00:00:00 EST 2007},
month = {Mon Jan 01 00:00:00 EST 2007}
}
  • Thermobifida fusca is a moderately thermophilic soilbacterium that belongs to Actinobacteria. 3 It is a major degrader ofplant cell walls and has been used as a model organism for the study of 4secreted, thermostable cellulases. The complete genome sequence showedthat T. fusca has a 5 single circular chromosome of 3642249 bp predictedto encode 3117 proteins and 65 RNA6 species with a coding densityof 85percent. Genome analysis revealed the existence of 29 putative 7glycoside hydrolases in addition to the previously identified cellulasesand xylanases. The 8 glycosyl hydrolases include enzymes predicted toexhibit mainly dextran/starch and xylan 9 degrading functions. T. fuscapossesses twomore » protein secretion systems: the sec general secretion 10system and the twin-arginine translocation system. Several of thesecreted cellulases have 11 sequence signatures indicating theirsecretion may be mediated by the twin-arginine12 translocation system. T.fusca has extensive transport systems for import of carbohydrates 13coupled to transcriptional regulators controlling the expression of thetransporters and14 glycosylhydrolases. In addition to providing anoverview of the physiology of a soil 15 actinomycete, this study presentsinsights on the transcriptional regulation and secretion of16 cellulaseswhich may facilitate the industrial exploitation of thesesystems.« less
  • Thermobifida fusca is a moderately thermophilic soilbacterium that belongs to Actinobacteria. It is a major degrader of plantcell walls and has been used as a model organism for the study ofsecreted, thermostable cellulases. The complete genome sequence showedthat T. fusca has a single circular chromosome of 3642249 bp predicted toencode 3117 proteins and 65 RNA species with a coding density of 85percent. Genome analysis revealed the existence of 29 putative glycosidehydrolases in addition to the previously identified cellulases andxylanases. The glycosyl hydrolases include enzymes predicted to exhibitmainly dextran/starch and xylan degrading functions. T. fusca possessestwo protein secretion systems: the secmore » general secretion system and thetwin-arginine translocation system. Several of the secreted cellulaseshave sequence signatures indicating their secretion may be mediated bythe twin-arginine translocation system. T. fusca has extensive transportsystems for import of carbohydrates coupled to transcriptional regulatorscontrolling the expression of the transporters and glycosylhydrolases. Inaddition to providing an overview of the physiology of a soilactinomycete, this study presents insights on the transcriptionalregulation and secretion of cellulases which may facilitate theindustrial exploitation of these systems.« less