title: RhizoRegNet--a database of rhizobial transcription factors and regulatory networks.
abstract: 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.
authors.affiliation: Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.
authors.forename: Elizaveta
authors.initials: E
authors.lastname: Krol
authors.forename: Jochen
authors.initials: J
authors.lastname: Blom
authors.forename: Jörn
authors.initials: J
authors.lastname: Winnebald
authors.forename: Alexander
authors.initials: A
authors.lastname: Berhörster
authors.forename: Melanie J
authors.initials: MJ
authors.lastname: Barnett
authors.forename: Alexander
authors.initials: A
authors.lastname: Goesmann
authors.forename: Jan
authors.initials: J
authors.lastname: Baumbach
authors.forename: Anke
authors.initials: A
authors.lastname: Becker
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D003628:Database Management Systems; D016208:Databases, Factual; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks / Q000235:genetics*; D005798:Genes, Bacterial; D029902:Medicago; D009586:Nitrogen Fixation; D016962:Sinorhizobium meliloti / Q000235:genetics* / Q000378:metabolism; D012984:Software; D013559:Symbiosis; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D014584:User-Computer Interface
chemical_list: D001426:Bacterial Proteins; D014157:Transcription Factors