Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks.
Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks.
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DOI：
10.1186/1471-2164-14-873
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发表时间：
2013-12-12
期刊：
影响因子：
4.4
通讯作者：
Rodionov DA
中科院分区：
文献类型：
--
作者：
Ravcheev DA;Godzik A;Osterman AL;Rodionov DA
拟杆菌（Bacteroides thetaiotaomicron）是人类肠道微生物群的主要成员，其特点是能够利用各种各样的多糖，利用广泛的糖分解机制，这是由扩展的转录因子（tf）库控制的。多种拟杆菌属物种基因组序列的可用性为它们的比较分析提供了机会，从而能够表征它们的代谢和调节网络。采用比较基因组学方法对11个拟杆菌基因组的碳水化合物利用调控网络进行了重建和功能注释。启动子区域的生物信息学分析揭示了拟杆菌中31个同源TFs的推定dna结合基序和调控。在分析的tf中，有4个类似susr的调节器，16个类似arac的混合双组分系统（htcs），以及11个来自其他家族的调节器。拟杆菌中HTCSs和susr样调节因子的新型DNA基序具有直接重复序列的共同结构，两个保守位点之间有一个长间隔。由此推断，该调控网络包含308个基因，编码多糖和糖分解代谢酶、碳水化合物结合和运输系统以及tf。分析了TFs控制宿主和膳食聚糖转化为单糖的途径，以及它们进一步转化为中枢代谢中间体的途径。重建的调控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，为现有的b.s thetaiotaomicron代谢模型提供实质性的改进。得到的重构TF规则集合可以在RegPrecise数据库（http://regprecise.lbl.gov）中找到。
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. 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. 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).
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聚糖代谢如何塑造人类肠道微生物群。
DOI：
10.1038/nrmicro2746
发表时间：
2012-04-11
期刊：
Nature reviews. Microbiology
影响因子：
--
作者：
通讯作者：
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影响因子：
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作者：
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通讯作者：
Bork, Peer
影响因子：
3.2
作者：
Leyn, Semen A.;Kazanov, Marat D.;Rodionov, Dmitry A.
通讯作者：
Rodionov, Dmitry A.
DOI：
10.1073/pnas.0506687102
发表时间：
2005-12-06
影响因子：
11.1
作者：
Grainger, DC;Hurd, D;Busby, SJW
通讯作者：
Busby, SJW
影响因子：
12.3
作者：
Kinross JM;Darzi AW;Nicholson JK
通讯作者：
Nicholson JK