Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.
J Biotechnol. 2011 Aug 20;155(1):127-34. doi: 10.1016/j.jbiotec.2010.11.004. Epub 2010 Nov 16.
Sinorhizobium meliloti is a symbiotic soil bacterium that forms nitrogen-fixing nodules on roots of leguminous plants, including Medicago truncatula (barrel medic), and M. sativa (alfalfa). The Sinorhizobium-Medicago symbiosis is an important symbiosis model system. Knowledge gained from this system can be extended to other agriculturally important "rhizobial" symbioses. Since the publication of the S. meliloti genome in 2001, many new genetic, biochemical and physiological data have been generated. Effective methods to organize, store, and mine this postgenome data are crucial for continued success of the S. meliloti model system. In 2009, we introduced a portal for rhizobial genomes, RhizoGATE (Becker et al., J. Biotechnol. 140, 45-50). The RhizoGATE portal combines continuously updated S. meliloti genome annotation with postgenome data resources. Here we report integration of a new component, RhizoRegNet, to RhizoGATE. RhizoRegNet combines transcriptome data and operon predictions with published data on regulatory interactions. By allowing searching and visualisation of complex transcriptional regulatory networks, RhizoRegNet advances our understanding of transcriptional regulation in S. meliloti. The current version of RhizoRegNet is divided into 13 functional modules containing information for 114 regulators, 475 regulated genes, and 178 transcription factor binding motifs. In this report, we provide an example of how RhizoRegNet facilitates visualisation and analysis of the regulatory network for exopolysaccharide biosynthesis and motility. Presently, RhizoRegNet contains regulatory network information for S. meliloti and the closely related bacterium, S. medicae, but can be expanded to include other rhizobial species.
根瘤菌属是一种共生土壤细菌，能在豆科植物的根部形成固氮结瘤，包括苜蓿属（截形苜蓿）和 Medicago sativa（紫花苜蓿）。根瘤菌属-苜蓿共生是一个重要的共生模型系统。从这个系统中获得的知识可以扩展到其他农业上重要的“根瘤菌”共生体。自 2001 年发表了 Sinorhizobium meliloti 基因组以来，已经产生了许多新的遗传、生化和生理数据。组织、存储和挖掘这些后基因组数据的有效方法对于继续成功地应用 Sinorhizobium meliloti 模型系统至关重要。2009 年，我们引入了一个根瘤菌基因组门户，RhizoGATE（Becker 等人，J. Biotechnol. 140，45-50）。RhizoGATE 门户将不断更新的 Sinorhizobium meliloti 基因组注释与后基因组数据资源相结合。在这里，我们报告了 RhizoRegNet 的一个新组件的整合到 RhizoGATE 中。RhizoRegNet 将转录组数据和操纵子预测与已发表的调控相互作用数据相结合。通过允许搜索和可视化复杂的转录调控网络，RhizoRegNet 推进了我们对 Sinorhizobium meliloti 中转录调控的理解。当前版本的 RhizoRegNet 分为 13 个功能模块，包含 114 个调节剂、475 个受调控基因和 178 个转录因子结合基序的信息。在本报告中，我们提供了一个示例，说明如何使用 RhizoRegNet 可视化和分析多糖生物合成和运动性的调控网络。目前，RhizoRegNet 包含了 Sinorhizobium meliloti 和密切相关的细菌 S. medicae 的调控网络信息，但可以扩展到包括其他根瘤菌物种。
