title: Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1.
abstract: BACKGROUND
  Ruminococcus flavefaciens is a predominant cellulolytic rumen bacterium, which forms a multi-enzyme cellulosome complex that could play an integral role in the ability of this bacterium to degrade plant cell wall polysaccharides. Identifying the major enzyme types involved in plant cell wall degradation is essential for gaining a better understanding of the cellulolytic capabilities of this organism as well as highlighting potential enzymes for application in improvement of livestock nutrition and for conversion of cellulosic biomass to liquid fuels.
  
  
  RESULTS
  The R. flavefaciens FD-1 genome was sequenced to 29x-coverage, based on pulsed-field gel electrophoresis estimates (4.4 Mb), and assembled into 119 contigs providing 4,576,399 bp of unique sequence. As much as 87.1% of the genome encodes ORFs, tRNA, rRNAs, or repeats. The GC content was calculated at 45%. A total of 4,339 ORFs was detected with an average gene length of 918 bp. The cellulosome model for R. flavefaciens was further refined by sequence analysis, with at least 225 dockerin-containing ORFs, including previously characterized cohesin-containing scaffoldin molecules. These dockerin-containing ORFs encode a variety of catalytic modules including glycoside hydrolases (GHs), polysaccharide lyases, and carbohydrate esterases. Additionally, 56 ORFs encode proteins that contain carbohydrate-binding modules (CBMs). Functional microarray analysis of the genome revealed that 56 of the cellulosome-associated ORFs were up-regulated, 14 were down-regulated, 135 were unaffected, when R. flavefaciens FD-1 was grown on cellulose versus cellobiose. Three multi-modular xylanases (ORF01222, ORF03896, and ORF01315) exhibited the highest levels of up-regulation.
  
  
  CONCLUSIONS
  The genomic evidence indicates that R. flavefaciens FD-1 has the largest known number of fiber-degrading enzymes likely to be arranged in a cellulosome architecture. Functional analysis of the genome has revealed that the growth substrate drives expression of enzymes predicted to be involved in carbohydrate metabolism as well as expression and assembly of key cellulosomal enzyme components.
authors.affiliation: Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
authors.forename: Margret E
authors.initials: ME
authors.lastname: Berg Miller
authors.forename: Dionysios A
authors.initials: DA
authors.lastname: Antonopoulos
authors.forename: Marco T
authors.initials: MT
authors.lastname: Rincon
authors.forename: Mark
authors.initials: M
authors.lastname: Band
authors.forename: Albert
authors.initials: A
authors.lastname: Bari
authors.forename: Tatsiana
authors.initials: T
authors.lastname: Akraiko
authors.forename: Alvaro
authors.initials: A
authors.lastname: Hernandez
authors.forename: Jyothi
authors.initials: J
authors.lastname: Thimmapuram
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
authors.forename: Pedro M
authors.initials: PM
authors.lastname: Coutinho
authors.forename: Ilya
authors.initials: I
authors.lastname: Borovok
authors.forename: Sadanari
authors.initials: S
authors.lastname: Jindou
authors.forename: Raphael
authors.initials: R
authors.lastname: Lamed
authors.forename: Harry J
authors.initials: HJ
authors.lastname: Flint
authors.forename: Edward A
authors.initials: EA
authors.lastname: Bayer
authors.forename: Bryan A
authors.initials: BA
authors.lastname: White
mesh_terms: D000595:Amino Acid Sequence; D055162:Biocatalysis; D002473:Cell Wall / Q000378:metabolism*; D004798:Enzymes / Q000737:chemistry / Q000378:metabolism*; D020869:Gene Expression Profiling; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames; D010802:Phylogeny; D020133:Reverse Transcriptase Polymerase Chain Reaction; D045857:Ruminococcus / Q000201:enzymology* / Q000235:genetics; D013045:Species Specificity
chemical_list: D004798:Enzymes
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