title: Global gene expression patterns in Clostridium thermocellum as determined by microarray analysis of chemostat cultures on cellulose or cellobiose.
abstract: A microarray study of chemostat growth on insoluble cellulose or soluble cellobiose has provided substantial new information on Clostridium thermocellum gene expression. This is the first comprehensive examination of gene expression in C. thermocellum under defined growth conditions. Expression was detected from 2,846 of 3,189 genes, and regression analysis revealed 348 genes whose changes in expression patterns were growth rate and/or substrate dependent. Successfully modeled genes included those for scaffoldin and cellulosomal enzymes, intracellular metabolic enzymes, transcriptional regulators, sigma factors, signal transducers, transporters, and hypothetical proteins. Unique genes encoding glycolytic pathway and ethanol fermentation enzymes expressed at high levels simultaneously with previously established maximal ethanol production were also identified. Ranking of normalized expression intensities revealed significant changes in transcriptional levels of these genes. The pattern of expression of transcriptional regulators, sigma factors, and signal transducers indicates that response to growth rate is the dominant global mechanism used for control of gene expression in C. thermocellum.
authors.affiliation: DOE Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin 53706, USA.
authors.forename: Allison
authors.initials: A
authors.lastname: Riederer
authors.forename: Taichi E
authors.initials: TE
authors.lastname: Takasuka
authors.forename: Shin-ichi
authors.initials: S
authors.lastname: Makino
authors.forename: David M
authors.initials: DM
authors.lastname: Stevenson
authors.forename: Yury V
authors.initials: YV
authors.lastname: Bukhman
authors.forename: Nathaniel L
authors.initials: NL
authors.lastname: Elsen
authors.forename: Brian G
authors.initials: BG
authors.lastname: Fox
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D002352:Carrier Proteins / Q000235:genetics; D002475:Cellobiose / Q000378:metabolism*; D002480:Cellulase / Q000235:genetics; D002482:Cellulose / Q000378:metabolism*; D048013:Acetivibrio thermocellus / Q000201:enzymology / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D003470:Culture Media; D000431:Ethanol / Q000378:metabolism; D005285:Fermentation / Q000235:genetics; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D006019:Glycolysis; D046228:Microarray Analysis; D009097:Multienzyme Complexes / Q000235:genetics; D005810:Multigene Family; D050436:Regulatory Elements, Transcriptional; D012808:Sigma Factor / Q000235:genetics; D015398:Signal Transduction; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D002352:Carrier Proteins; D003470:Culture Media; D009097:Multienzyme Complexes; D012808:Sigma Factor; C473132:cellulosome, Clostridium; C074074:cellulose binding protein A, Clostridium cellulovorans; D002475:Cellobiose; D000431:Ethanol; D002482:Cellulose; D002480:Cellulase