New Insights into Clostridia Through Comparative Analyses of Their 40 Genomes
New Insights into Clostridia Through Comparative Analyses of Their 40 Genomes
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DOI：
10.1007/s12155-014-9486-9
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发表时间：
2014-06
影响因子：
3.6
通讯作者：
Chuan Zhou;Q. Ma;X. Mao;Bingqiang Liu;Yanbin Yin;Ying Xu
中科院分区：
文献类型：
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作者：
Chuan Zhou;Q. Ma;X. Mao;Bingqiang Liu;Yanbin Yin;Ying Xu
梭状芽胞杆菌属的细菌包含最广泛研究的生物燃料生产生物，如热胞梭状芽胞杆菌和一些人类病原体，以及一些不太常见的菌株。在这里，我们提出了40个完全测序的梭菌基因组的比较基因组分析，特别关注生物量降解的基因组。我们的分析表明，一些肉毒杆菌菌株在目前的分类中可能被错误地分类，因此应该根据16S核糖体RNA （rRNA）系统发育重新命名。核心基因组分析表明，所有菌株共有169个同源基因群，菌株特异性基因库由22,668个基因组成，这与这些细菌生活在非常多样化的环境中并进化出非常大量的菌株特异性基因以适应不同环境的事实相一致。在40个基因组中，1.4 - 5.8%的基因属于碳水化合物活性酶（CAZyme）家族，40个基因组中有20个可能编码纤维素体，每个基因组有1 - 76个基因携带纤维素体相关模块，如dockerins和cohesinins。系统发育足迹分析鉴定了CAZyme基因启动子中富集的顺式调控基序，从而产生了32个具有统计学意义的候选基序。
TheClostridiumgenus of bacteria contains the most widely studied biofuel-producing organisms such asClostridium thermocellumand 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 theClostridium botulinumstrains 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 identifiedcis-regulatory motifs that are enriched in the promoters of the CAZyme genes, giving rise to 32 statistically significant motif candidates.