σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough

Kazakov, Alexey E.; Rajeev, Lara; Chen, Amy; Luning, Eric G.; Dubchak, Inna; Mukhopadhyay, Aindrila; Novichkov, Pavel S.

doi:10.1186/s12864-015-2176-y

Title: σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough

Journal Article · Tue Nov 10 00:00:00 EST 2015 · BMC Genomics

DOI:https://doi.org/10.1186/s12864-015-2176-y· OSTI ID:1618540

Kazakov, Alexey E.; Rajeev, Lara; Chen, Amy; Luning, Eric G.; Dubchak, Inna; Mukhopadhyay, Aindrila; Novichkov, Pavel S.

© 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.

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

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

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1618540

Alternate ID(s):: OSTI ID: 1256485; OSTI ID: 1378639

Journal Information:: BMC Genomics, Journal Name: BMC Genomics Vol. 16 Journal Issue: 1; ISSN 1471-2164

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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Cited by: 6 works

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Fig. 1(p. 2)

Table 1(p. 4)

Table 1 (Continued)(p. 5)

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
transcription factor
transcriptional regulation
sigma factor
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enhancer binding

σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough [Supplemental Data] Kazakov, Alexey; Rajeev, Lara; Chen, Amy https://doi.org/10.6084/m9.figshare.c.3615395 The current record is supplemented by this dataset	dataset	November 2015
Additional file 5: of Ď 54-dependent regulome in Desulfovibrio vulgaris Hildenborough Kazakov, Alexey; Rajeev, Lara; Chen, Amy https://doi.org/10.6084/M9.FIGSHARE.C.3615395_D1 The current record is supplemented by this dataset	dataset	January 2015
Additional file 5: of σ⁵⁴-dependent regulome in Desulfovibrio vulgaris Hildenborough Kazakov, Alexey; Rajeev, Lara; Chen, Amy https://doi.org/10.6084/m9.figshare.c.3615395_d1.v1 The current record is supplemented by this dataset	dataset	November 2015
Additional file 4: of Ď 54-dependent regulome in Desulfovibrio vulgaris Hildenborough Kazakov, Alexey; Rajeev, Lara; Chen, Amy https://doi.org/10.6084/M9.FIGSHARE.C.3615395_D2 The current record is supplemented by this dataset	dataset	January 2015
Additional file 4: of σ⁵⁴-dependent regulome in Desulfovibrio vulgaris Hildenborough Kazakov, Alexey; Rajeev, Lara; Chen, Amy https://doi.org/10.6084/m9.figshare.c.3615395_d2.v1 The current record is supplemented by this dataset	dataset	November 2015
Additional file 2: of σ⁵⁴-dependent regulome in Desulfovibrio vulgaris Hildenborough Kazakov, Alexey; Rajeev, Lara; Chen, Amy https://doi.org/10.6084/m9.figshare.c.3615395_d3.v1 The current record is supplemented by this dataset	dataset	November 2015
Additional file 1: of Ď 54-dependent regulome in Desulfovibrio vulgaris Hildenborough Kazakov, Alexey; Rajeev, Lara; Chen, Amy https://doi.org/10.6084/M9.FIGSHARE.C.3615395_D4 The current record is supplemented by this dataset	dataset	January 2015
Additional file 1: of σ⁵⁴-dependent regulome in Desulfovibrio vulgaris Hildenborough Kazakov, Alexey; Rajeev, Lara; Chen, Amy https://doi.org/10.6084/m9.figshare.c.3615395_d4.v1 The current record is supplemented by this dataset	dataset	November 2015
Additional file 3: of σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough Kazakov, Alexey; Rajeev, Lara; Chen, Amy https://doi.org/10.6084/m9.figshare.c.3615395_d5.v1 The current record is supplemented by this dataset	dataset	November 2015
Additional file 6: of σ⁵⁴-dependent regulome in Desulfovibrio vulgaris Hildenborough Kazakov, Alexey; Rajeev, Lara; Chen, Amy https://doi.org/10.6084/m9.figshare.c.3615395_d6.v1 The current record is supplemented by this dataset	dataset	November 2015
σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough Kazakov, Alexey; Rajeev, Lara; Chen, Amy https://doi.org/10.6084/m9.figshare.c.3615395.v1 The current record is supplemented by this dataset	dataset	November 2015