title: σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough.
abstract: BACKGROUND
  The σ(54) subunit controls a unique class of promoters in bacteria. Such promoters, without exception, require enhancer binding proteins (EBPs) for transcription initiation. Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, has a high number of EBPs, more than most sequenced bacteria. The cellular processes regulated by many of these EBPs remain unknown.
  
  
  RESULTS
  To characterize the σ(54)-dependent regulome of D. vulgaris Hildenborough, we identified EBP binding motifs and regulated genes by a combination of computational and experimental techniques. These predictions were supported by our reconstruction of σ(54)-dependent promoters by comparative genomics. We reassessed and refined the results of earlier studies on regulation in D. vulgaris Hildenborough and consolidated them with our new findings. It allowed us to reconstruct the σ(54) regulome in D. vulgaris Hildenborough. This regulome includes 36 regulons that consist of 201 coding genes and 4 non-coding RNAs, and is involved in nitrogen, carbon and energy metabolism, regulation, transmembrane transport and various extracellular functions. To the best of our knowledge, this is the first report of direct regulation of alanine dehydrogenase, pyruvate metabolism genes and type III secretion system by σ(54)-dependent regulators.
  
  
  CONCLUSIONS
  The σ(54)-dependent regulome is an important component of transcriptional regulatory network in D. vulgaris Hildenborough and related free-living Deltaproteobacteria. Our study provides a representative collection of σ(54)-dependent regulons that can be used for regulation prediction in Deltaproteobacteria and other taxa.
authors.affiliation: Lawrence Berkeley National Laboratory, Berkeley, CA, 94710, USA. aekazakov@lbl.gov.
authors.forename: Alexey E
authors.initials: AE
authors.lastname: Kazakov
authors.affiliation: Lawrence Berkeley National Laboratory, Berkeley, CA, 94710, USA. lrajeev@lbl.gov.
authors.forename: Lara
authors.initials: L
authors.lastname: Rajeev
authors.affiliation: Lawrence Berkeley National Laboratory, Berkeley, CA, 94710, USA. amychenn@gmail.com.
authors.forename: Amy
authors.initials: A
authors.lastname: Chen
authors.affiliation: Lawrence Berkeley National Laboratory, Berkeley, CA, 94710, USA. eluning4@gmail.com.
authors.forename: Eric G
authors.initials: EG
authors.lastname: Luning
authors.affiliation: Lawrence Berkeley National Laboratory, Berkeley, CA, 94710, USA. ildubchak@lbl.gov.|Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. ildubchak@lbl.gov.
authors.forename: Inna
authors.initials: I
authors.lastname: Dubchak
authors.affiliation: Lawrence Berkeley National Laboratory, Berkeley, CA, 94710, USA. amukhopadhyay@lbl.gov.
authors.forename: Aindrila
authors.initials: A
authors.lastname: Mukhopadhyay
authors.affiliation: Lawrence Berkeley National Laboratory, Berkeley, CA, 94710, USA. psnovichkov@lbl.gov.
authors.forename: Pavel S
authors.initials: PS
authors.lastname: Novichkov
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D016000:Cluster Analysis; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D016969:Desulfovibrio vulgaris / Q000235:genetics* / Q000378:metabolism*; D004742:Enhancer Elements, Genetic; D015964:Gene Expression Regulation, Bacterial; D059372:Nucleotide Motifs; D010802:Phylogeny; D056510:Position-Specific Scoring Matrices; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D012808:Sigma Factor / Q000235:genetics / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism; D000069296:Type III Secretion Systems / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D012808:Sigma Factor; D014157:Transcription Factors; D000069296:Type III Secretion Systems