RhizoRegNet-A database of rhizobial transcription factors and regulatory networks

Krol E, Blom J, Winnebald J, Berhoerster A, Barnett MJ, Goesmann A, Baumbach J, Becker A (2011)
Journal of Biotechnology 155(1): 127-134.

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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. (C) 2010 Elsevier B. V. All rights reserved.
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Krol E, Blom J, Winnebald J, et al. RhizoRegNet-A database of rhizobial transcription factors and regulatory networks. Journal of Biotechnology. 2011;155(1):127-134.
Krol, E., Blom, J., Winnebald, J., Berhoerster, A., Barnett, M. J., Goesmann, A., Baumbach, J., et al. (2011). RhizoRegNet-A database of rhizobial transcription factors and regulatory networks. Journal of Biotechnology, 155(1), 127-134.
Krol, E., Blom, J., Winnebald, J., Berhoerster, A., Barnett, M. J., Goesmann, A., Baumbach, J., and Becker, A. (2011). RhizoRegNet-A database of rhizobial transcription factors and regulatory networks. Journal of Biotechnology 155, 127-134.
Krol, E., et al., 2011. RhizoRegNet-A database of rhizobial transcription factors and regulatory networks. Journal of Biotechnology, 155(1), p 127-134.
E. Krol, et al., “RhizoRegNet-A database of rhizobial transcription factors and regulatory networks”, Journal of Biotechnology, vol. 155, 2011, pp. 127-134.
Krol, E., Blom, J., Winnebald, J., Berhoerster, A., Barnett, M.J., Goesmann, A., Baumbach, J., Becker, A.: RhizoRegNet-A database of rhizobial transcription factors and regulatory networks. Journal of Biotechnology. 155, 127-134 (2011).
Krol, Elizaveta, Blom, Jochen, Winnebald, Jörn, Berhoerster, Alexander, Barnett, Melanie J., Goesmann, Alexander, Baumbach, Jan, and Becker, Anke. “RhizoRegNet-A database of rhizobial transcription factors and regulatory networks”. Journal of Biotechnology 155.1 (2011): 127-134.
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2 Citations in Europe PMC

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Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome.
Galardini M, Brilli M, Spini G, Rossi M, Roncaglia B, Bani A, Chiancianesi M, Moretto M, Engelen K, Bacci G, Pini F, Biondi EG, Bazzicalupo M, Mengoni A., PLoS Comput. Biol. 11(9), 2015
PMID: 26340565
Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti 1021.
Schluter JP, Reinkensmeier J, Barnett MJ, Lang C, Krol E, Giegerich R, Long SR, Becker A., BMC Genomics 14(), 2013
PMID: 23497287

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