title: Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations.
abstract: We present here the complete 2.4-Mb genome of the cellulolytic actinobacterial thermophile Acidothermus cellulolyticus 11B. New secreted glycoside hydrolases and carbohydrate esterases were identified in the genome, revealing a diverse biomass-degrading enzyme repertoire far greater than previously characterized and elevating the industrial value of this organism. A sizable fraction of these hydrolytic enzymes break down plant cell walls, and the remaining either degrade components in fungal cell walls or metabolize storage carbohydrates such as glycogen and trehalose, implicating the relative importance of these different carbon sources. Several of the A. cellulolyticus secreted cellulolytic and xylanolytic enzymes are fused to multiple tandemly arranged carbohydrate binding modules (CBM), from families 2 and 3. For the most part, thermophilic patterns in the genome and proteome of A. cellulolyticus were weak, which may be reflective of the recent evolutionary history of A. cellulolyticus since its divergence from its closest phylogenetic neighbor Frankia, a mesophilic plant endosymbiont and soil dweller. However, ribosomal proteins and noncoding RNAs (rRNA and tRNAs) in A. cellulolyticus showed thermophilic traits suggesting the importance of adaptation of cellular translational machinery to environmental temperature. Elevated occurrence of IVYWREL amino acids in A. cellulolyticus orthologs compared to mesophiles and inverse preferences for G and A at the first and third codon positions also point to its ongoing thermoadaptation. Additional interesting features in the genome of this cellulolytic, hot-springs-dwelling prokaryote include a low occurrence of pseudogenes or mobile genetic elements, an unexpected complement of flagellar genes, and the presence of three laterally acquired genomic islands of likely ecophysiological value.
authors.affiliation: DOE Joint Genome Institute, Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.
authors.forename: Ravi D
authors.initials: RD
authors.lastname: Barabote
authors.forename: Gary
authors.initials: G
authors.lastname: Xie
authors.forename: David H
authors.initials: DH
authors.lastname: Leu
authors.forename: Philippe
authors.initials: P
authors.lastname: Normand
authors.forename: Anamaria
authors.initials: A
authors.lastname: Necsulea
authors.forename: Vincent
authors.initials: V
authors.lastname: Daubin
authors.forename: Claudine
authors.initials: C
authors.lastname: Médigue
authors.forename: William S
authors.initials: WS
authors.lastname: Adney
authors.forename: Xin Clare
authors.initials: XC
authors.lastname: Xu
authors.forename: Alla
authors.initials: A
authors.lastname: Lapidus
authors.forename: Rebecca E
authors.initials: RE
authors.lastname: Parales
authors.forename: Chris
authors.initials: C
authors.lastname: Detter
authors.forename: Petar
authors.initials: P
authors.lastname: Pujic
authors.forename: David
authors.initials: D
authors.lastname: Bruce
authors.forename: Celine
authors.initials: C
authors.lastname: Lavire
authors.forename: Jean F
authors.initials: JF
authors.lastname: Challacombe
authors.forename: Thomas S
authors.initials: TS
authors.lastname: Brettin
authors.forename: Alison M
authors.initials: AM
authors.lastname: Berry
mesh_terms: D000192:Actinomycetales / Q000235:genetics* / Q000254:growth & development; D000222:Adaptation, Physiological / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001482:Base Composition / Q000235:genetics; D002876:Chromosomes, Bacterial / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004463:Ecology; D019143:Evolution, Molecular; D005407:Flagella / Q000235:genetics / Q000502:physiology; D016680:Genome, Bacterial; D006358:Hot Temperature; D025341:Principal Component Analysis; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial