期刊
BIOENERGY RESEARCH
卷 7, 期 4, 页码 1481-1492出版社
SPRINGER
DOI: 10.1007/s12155-014-9486-9
关键词
Clostridium; Comparative genomics; Pan-genome; Phylogeny; CAZyme; Motif
资金
- National Science Foundation [NSF DEB-0830024, NSF MCB-0958172]
- US Department of Energy's BioEnergy Science Center (BESC) grant through the Office of Biological and Environmental Research
- National Science Foundation of China [NSFC 61272016, 61303084]
- Office of Biological and Environmental Research in the DOE Office of Science
- US Department of Energy's BioEnergy Science Center (BESC)
- Direct For Biological Sciences
- Division Of Environmental Biology [0830024] Funding Source: National Science Foundation
The Clostridium genus of bacteria contains the most widely studied biofuel-producing organisms such as Clostridium thermocellum and also some human pathogens, plus a few less characterized strains. Here, we present a comparative genomic analysis of 40 fully sequenced clostridial genomes, paying a particular attention to the biomass degradation ones. Our analysis indicates that some of the Clostridium botulinum strains may have been incorrectly classified in the current taxonomy and hence should be renamed according to the 16S ribosomal RNA (rRNA) phylogeny. A core-genome analysis suggests that only 169 orthologous gene groups are shared by all the strains, and the strain-specific gene pool consists of 22,668 genes, which is consistent with the fact that these bacteria live in very diverse environments and have evolved a very large number of strain-specific genes to adapt to different environments. Across the 40 genomes, 1.4-5.8 % of genes fall into the carbohydrate active enzyme (CAZyme) families, and 20 out of the 40 genomes may encode cellulosomes with each genome having 1 to 76 genes bearing the cellulosome-related modules such as dockerins and cohesins. A phylogenetic footprinting analysis identified cis-regulatory motifs that are enriched in the promoters of the CAZyme genes, giving rise to 32 statistically significant motif candidates.
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