The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota
The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota
复制标题
DOI：
10.1101/gr.7136508
复制
发表时间：
2008-03-01
期刊：
影响因子：
7
通讯作者：
Watanabe, Kazuya
中科院分区：
文献类型：
--
作者：
Kosaka, Tomoyuki;Kato, Souichiro;Watanabe, Kazuya
有机物的厌氧生物降解是通过不同生态位的微生物的顺序互养分解代谢来完成的。 Pelotomaculum thermopropionicum 是一种代表性的互养细菌，可催化厌氧生物降解过程中的中间瓶颈步骤，从而将上游发酵细菌产生的挥发性脂肪酸 (VFA) 和醇转化为乙酸盐、氢气和二氧化碳（下游产甲烷古菌的底物）。为了揭示有助于我们了解热丙酸杆菌生态位和进化的基因组特征，我们对其 3,025,375 个基因组进行了测序，并与数据库中其他群落成员的基因组进行了比较分析。在基因组中，鉴定出了 2920 个编码序列 (CDS)。这些CD在直系同源群数据库的功能类别中显示出独特的分布模式，这被认为反映了该生物体的生态位。热丙酸丙酸杆菌具有简单的分解代谢途径，其中丙酸氧化甲基丙二酸单酰辅酶A途径构成主链，并与多个外周途径相连。大多数重要分解代谢酶的基因与含有 PAS 结构域的调节因子的基因物理相连，这表明分解代谢途径是根据环境条件和/或整体细胞情况而不是特定底物进行调节的。密码子使用的比较分析揭示了热丙酸杆菌与其他生态位成员之间密切的进化关系，而它与系统发育相关的糖发酵细菌相距甚远。这些分析表明，热丙酸丙酸杆菌通过与生态位相关微生物相互作用，已进化为一种共养专家。
The anaerobic biodegradation of organic matter is accomplished by sequential syntrophic catabolism by microbes in different niches. Pelotomaculum thermopropionicum is a representative syntrophic bacterium that catalyzes the intermediate bottleneck step in the anaerobic-biodegradation process, whereby volatile fatty acids (VFAs) and alcohols produced by upstream fermenting bacteria are converted to acetate, hydrogen, and carbon dioxide (substrates for downstream methanogenic archaea). To reveal genomic features that contribute to our understanding of the ecological niche and evolution of P, thermopropionicum, we sequenced its 3,025,375-by genome and performed comparative analyses with genomes of other community members available in the databases. In the genome, 2920 coding sequences (CDSs) were identified. These CD's showed a distinct distribution pattern in the functional categories of the Clusters of Orthologous Groups database, which is considered to reflect the niche of this organism. P. thermopropionicum has simple catabolic pathways, in which the propionate-oxidizing methylmalonyl-CoA pathway constitutes the backbone and is linked to several peripheral pathways. Genes for most of the important catabolic enzymes are physically linked to those for PAS-domain-containing regulators, suggesting that the catabolic pathways are regulated in response to environmental conditions and/or global cellular situations rather than specific substrates. Comparative analyses of codon usages revealed close evolutionary relationships between P. thermopropionicum and other niche members, while it was distant from phylogenetically related sugar-fermenting bacteria. These analyses suggest that P. thermopropionicum has evolved as a syntrophy specialist by interacting with niche-associated microbes.