Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations
- Ravi D Barabote1,
- Gary Xie2,
- David H Leu1,
- Philippe Normand3,
- Anamaria Necsulea4,
- Vincent Daubin4,
- Claudine Medigue5,
- William S Adney6,
- Xin Clare Xu1,
- Alla Lapidus7,
- Chris Detter2,
- Petar Pujic4,
- David R Bruce2,
- Celine Lavire3,
- Jean F Challacombe2,
- Thomas S. Brettin2 and
- Alison M Berry8,9
- 1 University of California, Davis;
- 2 Los Alamos National Laboratory;
- 3 CNRS, University of Lyon 1;
- 4 CNRS/University of Lyon 1;
- 5 CNRS/CEA/DSV/IG/Genoscope;
- 6 National Renewable Energy Laboratory;
- 7 DOE Joint Genome Institute;
- 8 University of California
- E-mail: amberry{at}ucdavis.edu
Abstract
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 significantly 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. A novel feature of the A. cellulolyticus secreted cellulolytic and xylanolytic enzymes is that they are fused to multiple tandemly arranged carbohydrate binding modules (CBM), from families 2 and 3. Interestingly, CBM3 was found to be always N-terminal to CBM2, suggesting a functional constraint driving this organization. While the catalytic domains of these modular enzymes are either diverse or unrelated, the CBMs were found to be highly conserved in sequence and may suggest selective substrate-binding interactions. 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 non-coding 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 presence of three laterally-acquired genomic islands of likely ecophysiological value.
Footnotes
-
- Received August 13, 2008.
- Accepted February 24, 2009.
- Copyright © 2009, Cold Spring Harbor Laboratory Press
