ArticleBMC genomics2015
σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed, 17 citations in OpenAlex.
- Comparative Genomics of Sigma Factors inMicroorganisms · 2025Article
- High-resolution mapping of sigma factor DNA-binding sequences using artificial promoters, RNA aptamers, and deep sequencing.Nucleic acids research · 2025Article
- Analysis and comparison of the bacterial σ54 regulon: Evidence of phylogenetic trends in gene regulation.PloS one · 2025Article
- Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case ofFrontiers in microbiology · 2024Article
- Transcriptome-wide marker gene expression analysis of stress-responsive sulfate-reducing bacteria.Scientific reports · 2023Article
- OrpR is a σMolecular microbiology · 2021Article
- Gene Sets and Mechanisms of Sulfate-Reducing Bacteria Biofilm Formation and Quorum Sensing With Impact on Corrosion.Frontiers in microbiology · 2021Review
- Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in Yersinia pseudotuberculosis.mSystems · 2020Article
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7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 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.
resultsTo 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.
conclusionsThe 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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