PDF(Pubmed)
Abstract：
Glycoside hydrolases (GHs) are carbohydrate-active enzymes essential for many environmental (e.g., carbon cycling) and biotechnological (e.g., biofuels) processes. The complete processing of carbohydrates by bacteria requires many enzymes acting synergistically. Here, I investigated the clustered or scattered distribution of 406,337 GH-genes and their association with transporter genes identified in 15,640 completely sequenced bacterial genomes. Different bacterial lineages displayed conserved levels of clustered or scattered GH-genes, but overall, the GH-genes clustering was generally higher than in randomized genomes. In lineages with highly clustered GH-genes (e.g., Bacteroides, Paenibacillus), clustered genes shared the same orientation. These codirectional gene clusters potentially facilitate the genes\' co-expression by allowing transcriptional read-through and, at least in some cases, forming operons. In several taxa, the GH-genes clustered with distinct types of transporter genes. The type of transporter genes and the distribution of the so-called GH:TR-genes clusters were conserved in selected lineages. Globally, the phylogenetically conserved clustering of the GH-genes with transporter genes highlights the central function of carbohydrate processing across bacterial lineages. In addition, in bacteria with the most identified GH-genes, the genomic adaptations for carbohydrate processing also mirrored the broad environmental origin of the sequenced strains (e.g., soil and mammal gut) suggesting that a combination of evolutionary history and the environment selects for the specific supragenic organization of the GH-genes supporting the carbohydrate processing in bacterial genomes.
摘要：
糖苷水解酶(GHs)是许多环境必需的碳水化合物活性酶(例如，碳循环)和生物技术(例如，生物燃料)过程。细菌对碳水化合物的完全处理需要许多酶协同作用。这里,我调查了406,337个GH基因的聚集或分散分布及其与15,640个完全测序的细菌基因组中鉴定的转运蛋白基因的关联。不同的细菌谱系显示出聚集或分散的GH基因的保守水平，但总的来说,GH基因聚类通常高于随机基因组。在具有高度聚集的GH基因的谱系中(例如，拟杆菌,拟杆菌)，成簇的基因具有相同的取向。这些共向基因簇可能通过允许转录通读和促进基因共表达，至少在某些情况下,形成操纵子。在几个分类单元中，GH基因与不同类型的转运蛋白基因聚集在一起。在选定的谱系中，转运蛋白基因的类型和所谓的GH：TR基因簇的分布是保守的。全球范围内,GH基因与转运蛋白基因的系统发育保守聚类突出了碳水化合物加工在细菌谱系中的中心功能。此外,在具有最明确GH基因的细菌中，碳水化合物加工的基因组适应也反映了测序菌株的广泛环境起源(例如，土壤和哺乳动物的肠道），表明进化史和环境的结合选择了支持细菌基因组中碳水化合物加工的GH基因的特定顺化组织。
