RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria

Novichkov, Pavel S.; Kazakov, Alexey E.; Ravcheev, Dmitry A.; Leyn, Semen A.; Kovaleva, Galina Y.; Sutormin, Roman A.; Kazanov, Marat D.; Riehl, William; Arkin, Adam P.; Dubchak, Inna; Rodionov, Dmitry A.

doi:10.1186/1471-2164-14-745

Title: RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria

Journal Article · Tue Jan 01 00:00:00 EST 2013 · BMC Genomics

DOI:https://doi.org/10.1186/1471-2164-14-745· OSTI ID:1626423

Novichkov, Pavel S. ^[1]; Kazakov, Alexey E. ^[1]; Ravcheev, Dmitry A. ^[2]; Leyn, Semen A. ^[3]; Kovaleva, Galina Y. ^[4]; Sutormin, Roman A. ^[5]; Kazanov, Marat D. ^[3]; Riehl, William ^[1]; Arkin, Adam P. ^[1]; Dubchak, Inna ^[1]; Rodionov, Dmitry A. ^[2]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Russian Academy of Sciences (RAS), Moscow (Russian Federation). Inst. for Information Transmission Problems (IITP); Sanford-Burnham Medical Research Inst., La Jolla, CA (United States)
Russian Academy of Sciences (RAS), Moscow (Russian Federation). Inst. for Information Transmission Problems (IITP)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Russian Academy of Sciences (RAS), Moscow (Russian Federation). Inst. for Information Transmission Problems (IITP)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Lomonosov Moscow State Univ. (Russia). Dept. of Bioengineering and Bioinformatics

Background: Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in prokaryotes is one of the critical tasks of modern genomics. Bacteria from different taxonomic groups, whose lifestyles and natural environments are substantially different, possess highly diverged transcriptional regulatory networks. The comparative genomics approaches are useful for in silico reconstruction of bacterial regulons and networks operated by both transcription factors (TFs) and RNA regulatory elements (riboswitches). Description: RegPrecise (http://regprecise.lbl.gov) is a web resource for collection, visualization and analysis of transcriptional regulons reconstructed by comparative genomics. We significantly expanded a reference collection of manually curated regulons we introduced earlier. RegPrecise 3.0 provides access to inferred regulatory interactions organized by phylogenetic, structural and functional properties. Taxonomy-specific collections include 781 TF regulogs inferred in more than 160 genomes representing 14 taxonomic groups of Bacteria. TF-specific collections include regulogs for a selected subset of 40 TFs reconstructed across more than 30 taxonomic lineages. Novel collections of regulons operated by RNA regulatory elements (riboswitches) include near 400 regulogs inferred in 24 bacterial lineages. RegPrecise 3.0 provides four classifications of the reference regulons implemented as controlled vocabularies: 55 TF protein families; 43 RNA motif families; ~150 biological processes or metabolic pathways; and ~200 effectors or environmental signals. Genome-wide visualization of regulatory networks and metabolic pathways covered by the reference regulons are available for all studied genomes. A separate section of RegPrecise 3.0 contains draft regulatory networks in 640 genomes obtained by an conservative propagation of the reference regulons to closely related genomes. Conclusions: RegPrecise 3.0 gives access to the transcriptional regulons reconstructed in bacterial genomes. Analytical capabilities include exploration of: regulon content, structure and function; TF binding site motifs; conservation and variations in genome-wide regulatory networks across all taxonomic groups of Bacteria. RegPrecise 3.0 was selected as a core resource on transcriptional regulation of the Department of Energy Systems Biology Knowledgebase, an emerging software and data environment designed to enable researchers to collaboratively generate, test and share new hypotheses about gene and protein functions, perform large-scale analyses, and model interactions in microbes, plants, and their communities.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA (United States)

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

Grant/Contract Number:: AC02-05CH11231; SC0004999

OSTI ID:: 1626423

Journal Information:: BMC Genomics, Vol. 14, Issue 1; ISSN 1471-2164

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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