Evidence map›Paper›PMID 25313388›Full record

ArticleJournal of bacteriology2015

Rex (encoded by DVU_0916) in Desulfovibrio vulgaris Hildenborough is a repressor of sulfate adenylyl transferase and is regulated by NADH.

G A Christensen, G M Zane, A E Kazakov, X Li, D A Rodionov, P S Novichkov, I Dubchak, A P Arkin, J D Wall

Open access · bronzeAbstract read
In one paragraph

Article in Journal of bacteriology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing papers in PubMed
2.8field-weighted citation impact, top 11% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

13 citing papers in PubMed, 31 citations in OpenAlex.

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  8. NADH-Mediated Gene Expression inFrontiers in microbiology · 2018
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors at 4 institutions in 2 countries.

G A ChristensenDepartment of Biochemistry, University of Missouri, Columbia, Missouri, USA Ecosystems and Networks Integrated with Genes and Molecular Assemblies, Berkeley, California, USA.
G M ZaneDepartment of Biochemistry, University of Missouri, Columbia, Missouri, USA Ecosystems and Networks Integrated with Genes and Molecular Assemblies, Berkeley, California, USA.
A E KazakovEcosystems and Networks Integrated with Genes and Molecular Assemblies, Berkeley, California, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
X LiSanford-Burnham Medical Research Institute, La Jolla, California, USA.
D A RodionovSanford-Burnham Medical Research Institute, La Jolla, California, USA A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
P S NovichkovEcosystems and Networks Integrated with Genes and Molecular Assemblies, Berkeley, California, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
I DubchakEcosystems and Networks Integrated with Genes and Molecular Assemblies, Berkeley, California, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
A P ArkinEcosystems and Networks Integrated with Genes and Molecular Assemblies, Berkeley, California, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
J D WallDepartment of Biochemistry, University of Missouri, Columbia, Missouri, USA Ecosystems and Networks Integrated with Genes and Molecular Assemblies, Berkeley, California, USA wallj@missouri.edu.
Lawrence Berkeley National Laboratory · USUniversity of Missouri · USInstitute for Information Transmission Problems · RUSanford Burnham Prebys Medical Discovery Institute · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Although the enzymes for dissimilatory sulfate reduction by microbes have been studied, the mechanisms for transcriptional regulation of the encoding genes remain unknown. In a number of bacteria the transcriptional regulator Rex has been shown to play a key role as a repressor of genes producing proteins involved in energy conversion. In the model sulfate-reducing microbe Desulfovibrio vulgaris Hildenborough, the gene DVU_0916 was observed to resemble other known Rex proteins. Therefore, the DVU_0916 protein has been predicted to be a transcriptional repressor of genes encoding proteins that function in the process of sulfate reduction in D. vulgaris Hildenborough. Examination of the deduced DVU_0916 protein identified two domains, one a winged helix DNA-binding domain common for transcription factors, and the other a Rossman fold that could potentially interact with pyridine nucleotides. A deletion of the putative rex gene was made in D. vulgaris Hildenborough, and transcript expression studies of sat, encoding sulfate adenylyl transferase, showed increased levels in the D. vulgaris Hildenborough Rex (RexDvH) mutant relative to the parental strain. The RexDvH-binding site upstream of sat was identified, confirming RexDvH to be a repressor of sat. We established in vitro that the presence of elevated NADH disrupted the interaction between RexDvH and DNA. Examination of the 5' transcriptional start site for the sat mRNA revealed two unique start sites, one for respiring cells that correlated with the RexDvH-binding site and a second for fermenting cells. Collectively, these data support the role of RexDvH as a transcription repressor for sat that senses the redox status of the cell.

Indexed as

Bacterial ProteinsBase SequenceBinding SitesDesulfovibrio vulgarisGene DeletionGene Expression Regulation, BacterialGene Expression Regulation, EnzymologicNADSulfate AdenylyltransferaseBacterial ProteinsNADSulfate Adenylyltransferase

Identifiers

PMID25313388
PMCPMC4288696
OpenAlexW2040293788

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.