Evidence map›Paper›PMID 30964892›Full record

ArticlePloS one2019

LurR is a regulator of the central lactate oxidation pathway in sulfate-reducing Desulfovibrio species.

Lara Rajeev, Eric G Luning, Grant M Zane, Thomas R Juba, Alexey E Kazakov, Pavel S Novichkov, Judy D Wall, Aindrila Mukhopadhyay

Open access · goldAbstract read
In one paragraph

Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.5field-weighted citation impact, top 31% 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

2 citing papers in PubMed, 3 citations in OpenAlex.

  1. Article
  2. Review
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

8 authors at 2 institutions in 1 country.

Lara RajeevBiological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
Eric G LuningBiological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
Grant M ZaneDepartment of Biochemistry, University of Missouri, Columbia, Missouri, United States of America.
Thomas R JubaDepartment of Biochemistry, University of Missouri, Columbia, Missouri, United States of America.
Alexey E KazakovEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.ORCID 0000-0001-7245-857X
Pavel S NovichkovEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
Judy D WallDepartment of Biochemistry, University of Missouri, Columbia, Missouri, United States of America.
Aindrila MukhopadhyayBiological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.ORCID 0000-0002-6513-7425
Lawrence Berkeley National Laboratory · USUniversity of Missouri · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The central carbon/lactate utilization pathway in the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough, is encoded by the highly conserved operon DVU3025-3033. Our earlier in vitro genome-wide study had suggested a network of four two-component system regulators that target this large operon; however, how these four regulators control this operon was not known. Here, we probe the regulation of the lactate utilization operon with mutant strains and DNA-protein binding assays. We show that the LurR response regulator is required for optimal growth and complete lactate utilization, and that it activates the DVU3025-3033 lactate oxidation operon as well as DVU2451, a lactate permease gene, in the presence of lactate. We show by electrophoretic mobility shift assays that LurR binds to three sites in the upstream region of DVU3025, the first gene of the operon. NrfR, a response regulator that is activated under nitrite stress, and LurR share similar binding site motifs and bind the same sites upstream of DVU3025. The DVU3025 promoter also has a binding site motif (Pho box) that is bound by PhoB, a two-component response regulator activated under phosphate limitation. The lactate utilization operon, the regulator LurR, and LurR binding sites are conserved across the order Desulfovibrionales whereas possible modulation of the lactate utilization genes by additional regulators such as NrfR and PhoB appears to be limited to D. vulgaris.

Indexed as

Bacterial ProteinsDesulfovibrio vulgarisOperonResponse ElementsTranscription FactorsGenome-Wide Association StudyLactic AcidNucleotide MotifsOxidation-ReductionSpecies SpecificityBacterial ProteinsLactic AcidTranscription Factors

Identifiers

PMID30964892
PMCPMC6456213
OpenAlexW2935930767

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

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.