Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations

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.Efforts are under way worldwide to develop renewable energy sources as alternatives to fossil fuels. Microorganisms capable of breaking down lignocellulosic plant matter, a bioenergy source, are of enormous interest in the global quest to identify enzymes that can convert biomass into biofuels. Acidothermus cellulolyticus was first isolated in enrichment cultures from acidic hot springs in Yellowstone National Park, in a screen for microorganisms that carry out efficient cellulose degradation at high temperature (Mohagheghi et al. 1986). A. cellulolyticus 11B is acid-tolerant (pH 4–6, with optimal pH 5.5) and thermophilic (growth between 37°C and 70°C; the optimal growth temperature [OGT] is 55°C). It produces many thermostable cellulose-degrading enzymes (Tucker et al. 1989; Baker et al. 1994; Adney et al. 1995; Ding et al. 2003). One of the endoglucanases, E1, which has been crystallized, is highly thermostable to 81°C and has very high specific activity on carboxymethylcellulose (Thomas et al. 1995; Sakon et al. 1996). E1 has been expressed in several plants and shows promise for generating genetically improved feedstock for the production of affordable cellulosic ethanol (Sticklen 2008). Hydrolytic enzymes from A. cellulolyticus have great potential in the biofuels industry because of their thermostability and activity at low pH (Rubin 2008).A. cellulolyticus is a member of the Frankineae, a high G+C, primarily Gram-positive Actinobacterial group (Rainey and Stackebrandt 1993). All of the characterized strains of A. cellulolyticus are thermophilic and do not grow below 37°C (Mohagheghi et al. 1986). This makes the evolutionary context of A. cellulolyticus interesting, because its closest known phylogenetic neighbor is the mesophilic actinobacterium Frankia, based on the analysis of the 16S rRNA, recA, and shc nucleotide sequences (Supplemental Fig. S1; Normand et al. 1996; Marechal et al. 2000; Alloisio et al. 2005). Frankia is a mesophilic (OGT 25°C–28°C), nitrogen-fixing soil organism that forms symbiotic root nodule associations with plants (Benson 1988). The genetic distance between A. cellulolyticus and three Frankia strains—ACN14a, CcI3, and EAN1pec—is very small and comparable to that found between certain strains within the Frankia species. Thus, although Acidothermus and Frankia share a close phylogenetic relationship at the DNA sequence level, they have evolved to live in dramatically diverse environments over the last 200–250 million years (Myr) since their last common ancestor (Normand et al. 2007). Complete genome sequences of three Frankia strains—ACN14a, CcI3, and EAN1pec—as well as those of other close relatives of A. cellulolyticus are now available, including the mesophilic Streptomyces avermitilis, Streptomyces coelicolor, and the terrestrial thermophilic Thermobifida fusca (Omura et al. 2001; Bentley et al. 2002; Ikeda et al. 2003; Lykidis et al. 2007; Normand et al. 2007). Genomic comparison of A. cellulolyticus with the mesophilic as well as thermophilic actinobacteria could provide insight into the nature of adaptation of this aquatic thermophile and add to our understanding of evolution within the actinobacteria.We present analysis of the complete genome of Acidothermus cellulolyticus 11B (ATCC 43068; GenBank accession {"type":"entrez-nucleotide","attrs":{"text":"NC_008578","term_id":"117927211","term_text":"NC_008578"}}NC_008578). Insights into the biomass degradation capabilities of the organism as well as thermophilic features of its genome and proteome are discussed. In addition, we discuss three laterally acquired genomic islands with genes of likely ecophysiological value, as well as the unexpected presence of flagellar genes in the genome.