Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough

Abstract

© 2015 Kazakov et al. 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 -dependentmore » 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.« less

Authors:
; ; ; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1618540
Alternate Identifier(s):
OSTI ID: 1256485; OSTI ID: 1378639
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Published Article
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Name: BMC Genomics Journal Volume: 16 Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer Science + Business Media
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; transcription factor; transcriptional regulation; sigma factor; Desulfovibrio vulgaris; enhancer binding

Citation Formats

Kazakov, Alexey E., Rajeev, Lara, Chen, Amy, Luning, Eric G., Dubchak, Inna, Mukhopadhyay, Aindrila, and Novichkov, Pavel S. σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough. United Kingdom: N. p., 2015. Web. doi:10.1186/s12864-015-2176-y.
Copy to clipboard
Kazakov, Alexey E., Rajeev, Lara, Chen, Amy, Luning, Eric G., Dubchak, Inna, Mukhopadhyay, Aindrila, & Novichkov, Pavel S. σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough. United Kingdom. https://doi.org/10.1186/s12864-015-2176-y
Copy to clipboard
Kazakov, Alexey E., Rajeev, Lara, Chen, Amy, Luning, Eric G., Dubchak, Inna, Mukhopadhyay, Aindrila, and Novichkov, Pavel S. Tue . "σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough". United Kingdom. https://doi.org/10.1186/s12864-015-2176-y.
Copy to clipboard
@article{osti_1618540,
title = {σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough},
author = {Kazakov, Alexey E. and Rajeev, Lara and Chen, Amy and Luning, Eric G. and Dubchak, Inna and Mukhopadhyay, Aindrila and Novichkov, Pavel S.},
abstractNote = {© 2015 Kazakov et al. 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.},
doi = {10.1186/s12864-015-2176-y},
journal = {BMC Genomics},
number = 1,
volume = 16,
place = {United Kingdom},
year = {Tue Nov 10 00:00:00 EST 2015},
month = {Tue Nov 10 00:00:00 EST 2015}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1186/s12864-015-2176-y
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Citation Metrics:
Cited by: 6 works
Citation information provided by
Web of Science

Figures / Tables:

Fig. 1 Fig. 1: The number of EBPs in the bacterial genomes of different sizes. Grey circles represent anaerobic Deltaproteobacteria, and black diamonds represent aerobic Deltaproteobacteria. D. vulgaris Hildenborough marked by a black ring. Grey triangles represent other bacterial genomes
All figures and tables (11 total)
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

MicrobesOnline: an integrated portal for comparative and functional genomics
journal, November 2009

  • Dehal, P. S.; Joachimiak, M. P.; Price, M. N.
  • Nucleic Acids Research, Vol. 38, Issue suppl_1, p. D396-D400
  • DOI: 10.1093/nar/gkp919

Energy metabolism in Desulfovibrio vulgaris Hildenborough: insights from transcriptome analysis
journal, December 2007

  • Pereira, Patrícia M.; He, Qiang; Valente, Filipa M. A.
  • Antonie van Leeuwenhoek, Vol. 93, Issue 4
  • DOI: 10.1007/s10482-007-9212-0

Compilation and analysis of  54-dependent promoter sequences
journal, November 1999

  • Barrios, H.; Valderrama, B.; Morett, E.
  • Nucleic Acids Research, Vol. 27, Issue 22
  • DOI: 10.1093/nar/27.22.4305

Transcription Factor Family-Based Reconstruction of Singleton Regulons and Study of the Crp/Fnr, ArsR, and GntR Families in Desulfovibrionales Genomes
journal, October 2012

  • Kazakov, A. E.; Rodionov, D. A.; Price, M. N.
  • Journal of Bacteriology, Vol. 195, Issue 1
  • DOI: 10.1128/JB.01977-12

Open source clustering software
journal, February 2004

The Bacterial Enhancer-Dependent sigma 54 (sigma N) Transcription Factor
journal, August 2000

 54-mediated control of the mannose phosphotransferase sytem in Lactobacillus plantarum impacts on carbohydrate metabolism
journal, November 2009

Transcription of glnA in E. coli is stimulated by activator bound to sites far from the promoter
journal, June 1986

GenBank
journal, November 2013

  • Benson, Dennis A.; Clark, Karen; Karsch-Mizrachi, Ilene
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1030

Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens
journal, January 2009

PspG, a New Member of the Yersinia enterocolitica Phage Shock Protein Regulon
journal, July 2004

The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough
journal, April 2004

  • Heidelberg, John F.; Seshadri, Rekha; Haveman, Shelley A.
  • Nature Biotechnology, Vol. 22, Issue 5
  • DOI: 10.1038/nbt959

Quantifying similarity between motifs
journal, January 2007

  • Gupta, Shobhit; Stamatoyannopoulos, John A.; Bailey, Timothy L.
  • Genome Biology, Vol. 8, Issue 2
  • DOI: 10.1186/gb-2007-8-2-r24

Comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior
journal, August 2011

  • Francke, Christof; Groot Kormelink, Tom; Hagemeijer, Yanick
  • BMC Genomics, Vol. 12, Issue 1
  • DOI: 10.1186/1471-2164-12-385

Global Analysis of Heat Shock Response in Desulfovibrio vulgaris Hildenborough
journal, February 2006

The σ 54 regulon (sigmulon) of Pseudomonas putida : σ
journal, November 2003

Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium
journal, January 2011

SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny
journal, November 2008

  • Wilson, Derek; Pethica, Ralph; Zhou, Yiduo
  • Nucleic Acids Research, Vol. 37, Issue suppl_1
  • DOI: 10.1093/nar/gkn762

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach
journal, June 2010

  • Novichkov, P. S.; Rodionov, D. A.; Stavrovskaya, E. D.
  • Nucleic Acids Research, Vol. 38, Issue Web Server
  • DOI: 10.1093/nar/gkq531

Pfam: the protein families database
journal, November 2013

  • Finn, Robert D.; Bateman, Alex; Clements, Jody
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1223

 54, a vital protein for Myxococcus xanthus
journal, March 1997

  • Keseler, I. M.; Kaiser, D.
  • Proceedings of the National Academy of Sciences, Vol. 94, Issue 5
  • DOI: 10.1073/pnas.94.5.1979

Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes
journal, August 2010

Evidence-Based Annotation of Transcripts and Proteins in the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough
journal, August 2011

  • Price, M. N.; Deutschbauer, A. M.; Kuehl, J. V.
  • Journal of Bacteriology, Vol. 193, Issue 20
  • DOI: 10.1128/JB.05563-11

Chromosomal organization is shaped by the transcription regulatory network
journal, March 2005

RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria
journal, January 2013

  • Novichkov, Pavel S.; Kazakov, Alexey E.; Ravcheev, Dmitry A.
  • BMC Genomics, Vol. 14, Issue 1
  • DOI: 10.1186/1471-2164-14-745
    Sort by:
    [ × clear filter / sort ]

    Works referencing / citing this record:

    Genome-Guided Identification of Organohalide-Respiring Deltaproteobacteria from the Marine Environment
    journal, December 2018

      Sort by:
      [ × clear filter / sort ]

      Figures / Tables found in this record:

      Fig. 1 (p. 2)figure
      Table 1 (p. 4)table
      Table 1 (Continued) (p. 5)table
      Fig. 2 (p. 6)figure
      Fig. 3 (p. 7)figure
      Fig. 4 (p. 8)figure
      Fig. 5 (p. 8)figure
      Table 2 (p. 9)table
      Fig. 6 (p. 10)figure
      Fig. 7 (p. 12)figure
      Fig. 8 (p. 13)figure
        [ × clear filter / sort ]
        Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.

        Similar Records in DOE PAGES and OSTI.GOV collections:

        Other research related to this record: