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首页> 外文期刊>BMC Genomics >Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron : comparative genomics reconstruction of metabolic and regulatory networks
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Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron : comparative genomics reconstruction of metabolic and regulatory networks

机译：人体肠道细菌拟杆菌中的多糖利用：代谢和调控网络的比较基因组重建

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Background Bacteroides thetaiotaomicron , a predominant member of the human gut microbiota, is characterized by its ability to utilize a wide variety of polysaccharides using the extensive saccharolytic machinery that is controlled by an expanded repertoire of transcription factors (TFs). The availability of genomic sequences for multiple Bacteroides species opens an opportunity for their comparative analysis to enable characterization of their metabolic and regulatory networks. Results A comparative genomics approach was applied for the reconstruction and functional annotation of the carbohydrate utilization regulatory networks in 11 Bacteroides genomes. Bioinformatics analysis of promoter regions revealed putative DNA-binding motifs and regulons for 31 orthologous TFs in the Bacteroides . Among the analyzed TFs there are 4 SusR-like regulators, 16 AraC-like hybrid two-component systems (HTCSs), and 11 regulators from other families. Novel DNA motifs of HTCSs and SusR-like regulators in the Bacteroides have the common structure of direct repeats with a long spacer between two conserved sites. Conclusions The inferred regulatory network in B. thetaiotaomicron contains 308 genes encoding polysaccharide and sugar catabolic enzymes, carbohydrate-binding and transport systems, and TFs. The analyzed TFs control pathways for utilization of host and dietary glycans to monosaccharides and their further interconversions to intermediates of the central metabolism. The reconstructed regulatory network allowed us to suggest and refine specific functional assignments for sugar catabolic enzymes and transporters, providing a substantial improvement to the existing metabolic models for B. thetaiotaomicron . The obtained collection of reconstructed TF regulons is available in the RegPrecise database ( http://?regprecise.?lbl.?gov ).
机译：背景技术拟杆菌属细菌是人类肠道菌群的主要成员，其特征在于它能够利用广泛的糖酵解机制利用广泛的多糖，而糖化机制受转录因子（TFs）扩展库的控制。多种拟杆菌属的基因组序列的可获得性为其比较分析提供了机会，从而能够表征其代谢和调控网络。结果采用比较基因组学方法对11个拟杆菌属基因组中碳水化合物利用调节网络的重建和功能注释。启动子区域的生物信息学分析揭示了拟南芥中31个直系TF的假定的DNA结合基序和调节子。在已分析的TF中，有4个类似SusR的调节器，16个类似AraC的混合二元系统（HTCS）和其他家族的11个调节器。拟杆菌中的HTCS和SusR样调节剂的新型DNA图案具有直接重复的共同结构，在两个保守位点之间具有长间隔。结论B. thetaiotaomicron的推断调控网络包含308个编码多糖和糖分解代谢酶，碳水化合物结合和转运系统以及TF的基因。分析的TF控制宿主糖和膳食聚糖转化为单糖的途径，以及它们进一步相互转化为中央代谢中间体的途径。重建的监管网络使我们能够建议和完善糖分解代谢酶和转运蛋白的特定功能分配，从而大大改善了B. thetaiotaomicron的现有代谢模型。 RegPrecise数据库（http：//？regprecise。？lbl。？gov）中提供了获得的重构TF规则集的集合。

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