Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria

Ravcheev, Dmitry A.; Best, Aaron A.; Sernova, Natalia V.; Kazanov, Marat D.; Novichkov, Pavel S.; Rodionov, Dmitry A.

doi:10.1186/1471-2164-14-94

Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria

Journal Article · Mon Dec 31 23:00:00 EST 2012 · BMC Genomics

DOI:https://doi.org/10.1186/1471-2164-14-94· OSTI ID:1626426

Ravcheev, Dmitry A. ^[1]; Best, Aaron A. ^[2]; Sernova, Natalia V. ^[3]; Kazanov, Marat D. ^[3]; Novichkov, Pavel S. ^[4]; Rodionov, Dmitry A. ^[5]

Sanford-Burnham Medical Research Institute, La Jolla, CA (United States); Russian Academy of Sciences (RAS), Moscow (Russian Federation). A.A. Kharkevich Inst. for Information Transmission Problems; DOE/OSTI
Hope College, Holland, MI (United States). Dept. of Biology
Russian Academy of Sciences (RAS), Moscow (Russian Federation). A.A. Kharkevich Inst. for Information Transmission Problems
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sanford-Burnham Medical Research Institute, La Jolla, CA (United States); Russian Academy of Sciences (RAS), Moscow (Russian Federation). A.A. Kharkevich Inst. for Information Transmission Problems

Background: Genome scale annotation of regulatory interactions and reconstruction of regulatory networks are the crucial problems in bacterial genomics. The Lactobacillales order of bacteria collates various microorganisms having a large economic impact, including both human and animal pathogens and strains used in the food industry. Nonetheless, no systematic genome-wide analysis of transcriptional regulation has been previously made for this taxonomic group. Results: A comparative genomics approach was used for reconstruction of transcriptional regulatory networks in 30 selected genomes of lactic acid bacteria. The inferred networks comprise regulons for 102 orthologous transcription factors (TFs), including 47 novel regulons for previously uncharacterized TFs. Numerous differences between regulatory networks of the Streptococcaceae and Lactobacillaceae groups were described on several levels. The two groups are characterized by substantially different sets of TFs encoded in their genomes. Content of the inferred regulons and structure of their cognate TF binding motifs differ for many orthologous TFs between the two groups. Multiple cases of non-orthologous displacements of TFs that control specific metabolic pathways were reported. Conclusions: The reconstructed regulatory networks substantially expand the existing knowledge of transcriptional regulation in lactic acid bacteria. In each of 30 studied genomes the obtained regulatory network contains on average 36 TFs and 250 target genes that are mostly involved in carbohydrate metabolism, stress response, metal homeostasis and amino acids biosynthesis. The inferred networks can be used for genetic experiments, functional annotations of genes, metabolic reconstruction and evolutionary analysis. All reconstructed regulons are captured within the Streptococcaceae and Lactobacillaceae collections in the RegPrecise database (http://regprecise.lbl.gov).

View Accepted Manuscript (DOE)

Research Organization:: 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:: SC0004999

OSTI ID:: 1626426

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

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Biotechnology & Applied Microbiology
Carbohydrate metabolism
Comparative genomics
Genetics & Heredity
Lactic acid bacteria
Lactobacillaceae
Regulon
Streptococcaceae
Transcription factor
Transcriptional regulatory network

Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria

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