Evidence map›Paper›PMID 25880922›Full record

ArticleBMC microbiology2015

Hyperphosphorylation of DegU cancels CcpA-dependent catabolite repression of rocG in Bacillus subtilis.

Kosei Tanaka, Kana Iwasaki, Takuya Morimoto, Takatsugu Matsuse, Tomohisa Hasunuma, Shinji Takenaka, Onuma Chumsakul, Shu Ishikawa, Naotake Ogasawara, Ken-ichi Yoshida

Open access · goldAbstract read
In one paragraph

Article in BMC microbiology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.5field-weighted citation impact, top 27% 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

3 citing papers in PubMed, 10 citations in OpenAlex.

  1. Article
  2. DegU-mediated suppression of carbohydrate uptake inApplied and environmental microbiology · 2023
    Article
  3. ComX-Induced Exoproteases Degrade ComX inFrontiers in microbiology · 2018
    Article
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

10 authors at 3 institutions in 1 country.

Kosei TanakaOrganization of Advanced Science and Technology, Kobe University, Kobe, Hyogo, Japan. ktanaka@people.kobe-u.ac.jp.
Kana IwasakiDepartment of Agrobioscience, Kobe University, Kobe, Hyogo, Japan. kana_smileday_o53o@yahoo.co.jp.
Takuya MorimotoBiological Science Laboratories, Kao Corporation, Haga, Tochigi, Japan. morimoto.takuya@kao.co.jp.
Takatsugu MatsuseDepartment of Agrobioscience, Kobe University, Kobe, Hyogo, Japan. takatugu_m_8@yahoo.co.jp.
Tomohisa HasunumaOrganization of Advanced Science and Technology, Kobe University, Kobe, Hyogo, Japan. hasunuma@port.kobe-u.ac.jp.
Shinji TakenakaOrganization of Advanced Science and Technology, Kobe University, Kobe, Hyogo, Japan. stakenaka@people.kobe-u.ac.jp.
Onuma ChumsakulGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan. c-onuma@bs.naist.jp.
Shu IshikawaGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan. shu@bs.naist.jp.
Naotake OgasawaraGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan. nogasawa@bs.naist.jp.
Ken-ichi YoshidaOrganization of Advanced Science and Technology, Kobe University, Kobe, Hyogo, Japan. kenyoshi@kobe-u.ac.jp.
Kobe University · JPNara Institute of Science and Technology · JPKao Corporation (Japan) · JP

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundThe two-component regulatory system, involving the histidine sensor kinase DegS and response regulator DegU, plays an important role to control various cell processes in the transition phase of Bacillus subtilis. The degU32 allele in strain 1A95 is characterized by the accumulation of phosphorylated form of DegU (DegU-P).

resultsGrowing 1A95 cells elevated the pH of soytone-based medium more than the parental strain 168 after the onset of the transition phase. The rocG gene encodes a catabolic glutamate dehydrogenase that catalyzes one of the main ammonia-releasing reactions. Inactivation of rocG abolished 1A95-mediated increases in the pH of growth media. Thus, transcription of the rocG locus was examined, and a novel 3.7-kb transcript covering sivA, rocG, and rocA was found in 1A95 but not 168 cells. Increased intracellular fructose 1,6-bisphosphate (FBP) levels are known to activate the HPr kinase HPrK, and to induce formation of the P-Ser-HPr/CcpA complex, which binds to catabolite responsive elements (cre) and exerts CcpA-dependent catabolite repression. A putative cre found within the intergenic region between sivA and rocG, and inactivation of ccpA led to creation of the 3.7-kb transcript in 168 cells. Analyses of intermediates in central carbon metabolism revealed that intracellular FBP levels were lowered earlier in 1A95 than in 168 cells. A genome wide transcriptome analysis comparing 1A95 and 168 cells suggested similar events occurring in other catabolite repressive loci involving induction of lctE encoding lactate dehydrogenase.

conclusionsUnder physiological conditions the 3.7-kb rocG transcript may be tightly controlled by a roadblock mechanism involving P-Ser-HPr/CcpA in 168 cells, while in 1A95 cells abolished repression of the 3.7-kb transcript. Accumulation of DegU-P in 1A95 affects central carbon metabolism involving lctE enhanced by unknown mechanisms, downregulates FBP levels earlier, and inactivates HPrK to allow the 3.7-kb transcription, and thus similar events may occur in other catabolite repressive loci.

Indexed as

Gene Expression Regulation, BacterialOperonBacillus subtilisBacterial ProteinsBase SequenceCarbonCatabolite RepressionGenetic LociGlutamate DehydrogenaseHydrogen-Ion ConcentrationL-Lactate DehydrogenaseMolecular Sequence DataPhosphorylationPromoter Regions, GeneticRNA, MessengerSpecies SpecificityBacterial ProteinsCarbonDegU protein, BacteriaGlutamate DehydrogenaseL-Lactate DehydrogenaseRNA, Messenger

Identifiers

PMID25880922
PMCPMC4348106
OpenAlexW2058920872

What OpenQuestion holds

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LicenceCC BY
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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.