Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium

Rajeev, Lara; Luning, Eric G.; Dehal, Paramvir S.; Price, Morgan N.; Arkin, Adam P.; Mukhopadhyay, Aindrila

doi:10.1186/gb-2011-12-10-r99

Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium

Journal Article · Sat Jan 01 00:00:00 EST 2011 · GenomeBiology.com

DOI:https://doi.org/10.1186/gb-2011-12-10-r99· OSTI ID:1626736

Rajeev, Lara ^[1]; Luning, Eric G. ^[2]; Dehal, Paramvir S. ^[2]; Price, Morgan N. ^[2]; Arkin, Adam P. ^[2]; Mukhopadhyay, Aindrila ^[2]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division; DOE/OSTI
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division

Background: Two component regulatory systems are the primary form of signal transduction in bacteria. Although genomic binding sites have been determined for several eukaryotic and bacterial transcription factors, comprehensive identification of gene targets of two component response regulators remains challenging due to the lack of knowledge of the signals required for their activation. We focused our study on Desulfovibrio vulgaris Hildenborough, a sulfate reducing bacterium that encodes unusually diverse and largely uncharacterized two component signal transduction systems. Results: We report the first systematic mapping of the genes regulated by all transcriptionally acting response regulators in a single bacterium. Our results enabled functional predictions for several response regulators and include key processes of carbon, nitrogen and energy metabolism, cell motility and biofilm formation, and responses to stresses such as nitrite, low potassium and phosphate starvation. Our study also led to the prediction of new genes and regulatory networks, which found corroboration in a compendium of transcriptome data available for D. vulgaris. For several regulators we predicted and experimentally verified the binding site motifs, most of which were discovered as part of this study. Conclusions: The gene targets identified for the response regulators allowed strong functional predictions to be made for the corresponding two component systems. By tracking the D. vulgaris regulators and their motifs outside the Desulfovibrio spp. we provide testable hypotheses regarding the functions of orthologous regulators in other organisms. The in vitro array based method optimized here is generally applicable for the study of such systems in all organisms.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1626736

Journal Information:: GenomeBiology.com, Journal Name: GenomeBiology.com Journal Issue: 10 Vol. 12; ISSN 1465-6906

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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