SubtiBank SubtiBank

Categories containing this gene/protein


carbon core metabolism, essential genes, membrane proteins, phosphoproteins, most abundant proteins

This gene is a member of the following regulons


CggR regulon

Gene


  • Coordinates on the chromosome (coding sequence): 3,481,698 -> 3,482,705
  • Phenotypes of a mutant

  • Essential PubMed
  • The protein


    Catalyzed reaction/ biological activity

  • D-glyceraldehyde 3-phosphate phosphate NAD = 3-phospho-D-glyceroyl phosphate NADH (according to Swiss-Prot)
  • This reaction is part of the glycolysis.
  • Protein family

  • glyceraldehyde-3-phosphate dehydrogenase family (according to Swiss-Prot)
  • Paralogous protein(s)

  • GapB
  • Kinetic information

  • Michaelis-Menten PubMed
  • Domains

    Modification

  • phosphorylated on Arg-199 PubMed
  • Phosphorylation on (Ser-148 OR Ser-151 OR Thr-153 OR Thr-154) PubMed1, PubMed2
  • Reversible thiol modifications after exposure to toxic quinones PubMed
  • Cys152-Cys156 form intramolecular disulfide in response to disulfide stress (diamide, NaOCl-stress) PubMed
  • Cofactors

  • NAD (does not accept NADP ) PubMed
  • Effectors of protein activity

    Structure

  • 1GD1 (from Geobacillus stearothermophilus)
  • 1NQO (from Geobacillus stearothermophilus, mutant with cys 149 replaced by ser, complex with NAD und D-Glyceraldehyde-3-Phosphate)
  • Localization

  • cytoplasm (Homogeneous) PubMed PubMed
  • loosely membrane associated PubMed
  • Interactions

  • GapA-PtsH: HPr(Ser-46-P) binds GapA resulting in a slight inhibition of enzymatic activity PubMed
  • GapA-Crh: Crh(Ser-46-P) binds GapA resulting in a slight inhibition of enzymatic activity.PubMed
  • GapA-YkzW PubMed
  • GapA-RnjA PubMed, about 1% of all GapA molecules participate in this interaction PubMed, this interaction is stabilized in the presence of YkzW PubMed
  • GapA-Rny PubMed, about 2% of all GapA molecules participate in this interaction PubMed
  • Additional information

  • GAP dehydrogenases from different sources (incl. Geobacillus stearothermophilus) were shown to cleave RNA (PubMed)
  • Moreover, mutations in gapA from B. subtilis can suppress mutations in genes involved in DNA replication (PubMed).
  • extensive information on the structure and enzymatic properties of GapA can be found at Proteopedia
  • Expression and Regulation


    Operon

  • cggR-gapA-pgk-tpi-pgm-eno PubMed
  • cggR-gapA PubMed
  • Sigma factor

  • SigA PubMed
  • Regulation

  • expression activated by glucose (10 fold) (CggR) PubMed
  • Regulatory mechanism

  • CggR: transcription repression PubMed
  • Additional information

  • In the presence of glucose, there are about 25,000 GapA molecules per cell PubMed
  • belongs to the 100 most abundant proteins PubMed
  • The primary mRNAs of the operon are highly unstable. The primary mRNA is subject to processing at the very end of the cggR open reading frame. This results in stable mature gapA and gapA-pgk-tpiA-pgm-eno mRNAs. PubMed The processing event requires the RNase Y PubMed.
  • The accumulation of the cggR-gapA mRNA is strongly dependent on the presence of the YkzW peptide, due to stabilization of the mRNA PubMed.
  • the mRNA is substantially stabilized upon depletion of RNase Y PubMed
  • the mature 1.2 kb gapA mRNA segment is degraded by RNase J1 and RNase J2 PubMed
  • Biological materials


    Mutant

  • GP592 (gapA::cat), available in Jörg Stülke's lab, PubMed
  • GP597 (gapA::erm), available in Jörg Stülke's lab, PubMed
  • GP703 (gapA::cat gapB::spec), available in Jörg Stülke's lab, PubMed
  • GM1501 (under p(spac) control), available in Stephane Aymerich's lab
  • 1A1003 ( gapA::erm), available at BGSC
  • Expression vector

  • pGP1424 (expression in B. subtilis, in pBQ200) (available in Jörg Stülke's lab)
  • pGP90 (N-terminal Strep-tag, for SPINE, purification from B. subtilis, in pGP380) (available in Jörg Stülke's lab)
  • pGP704 (N-terminal His-tag, in pWH844) (available in Jörg Stülke's lab)
  • lacZ fusion

  • pGP506 (in pAC7), pGP512 (in pAC6) (available in Jörg Stülke's lab)
  • GFP fusion

    two-hybrid system

  • B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Jörg Stülke's lab
  • FLAG-tag construct

    Antibody

  • available in Jörg Stülke's lab
  • Labs working on this gene/protein


  • Stephane Aymerich, Microbiology and Molecular Genetics, INRA Paris-Grignon, France
  • Jörg Stülke, University of Göttingen, Germany
  • homepage
  • References


    Reviews

    Gimpel M, Brantl S

    Dual-function small regulatory RNAs in bacteria

    Mol Microbiol. 2017 Feb;103(3):387-397. doi: 10.1111/mmi.13558. Review. PubMed PMID: 27750368.
    Nagradova NK

    Interdomain interactions in oligomeric enzymes: creation of asymmetry in homo-oligomers and role in metabolite channeling between active centers of hetero-oligomers

    FEBS Lett. 2001 Jan 5;487(3):327-32. Review. PubMed PMID: 11163353.

    Original publications

    Gimpel M, Brantl S

    Dual-function sRNA encoded peptide SR1P modulates moonlighting activity of B

    subtilis GapA. RNA Biol. 2016 Sep;13(9):916-26. doi: 10.1080/15476286.2016.1208894. PubMed PMID: 27449348; PubMed Central PMCID: PMC5013986.
    Commichau FM, Pietack N, Stülke J

    Essential genes in Bacillus subtilis: a re-evaluation after ten years

    Mol Biosyst. 2013 Jun;9(6):1068-75. doi: 10.1039/c3mb25595f. Review. PubMed PMID: 23420519.
    Gimpel M, Preis H, Barth E, Gramzow L, Brantl S

    SR1--a small RNA with two remarkably conserved functions

    Nucleic Acids Res. 2012 Dec;40(22):11659-72. doi: 10.1093/nar/gks895. PubMed PMID: 23034808; PubMed Central PMCID: PMC3526287.
    Rühl M, Le Coq D, Aymerich S, Sauer U

    13C-flux analysis reveals NADPH-balancing transhydrogenation cycles in stationary phase of nitrogen-starving Bacillus subtilis

    J Biol Chem. 2012 Aug 10;287(33):27959-70. doi: 10.1074/jbc.M112.366492. PubMed PMID: 22740702; PubMed Central PMCID: PMC3431622.
    Elsholz AK, Turgay K, Michalik S, Hessling B, Gronau K, Oertel D, Mäder U, Bernhardt J, Becher D, Hecker M, Gerth U

    Global impact of protein arginine phosphorylation on the physiology of Bacillus subtilis

    Proc Natl Acad Sci U S A. 2012 May 8;109(19):7451-6. doi: 10.1073/pnas.1117483109. PubMed PMID: 22517742; PubMed Central PMCID: PMC3358850.
    Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Herzberg C, Stülke J

    RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y

    Mol Microbiol. 2011 Sep;81(6):1459-73. doi: 10.1111/j.1365-2958.2011.07777.x. PubMed PMID: 21815947.
    Chi BK, Gronau K, Mäder U, Hessling B, Becher D, Antelmann H

    S-bacillithiolation protects against hypochlorite stress in Bacillus subtilis as revealed by transcriptomics and redox proteomics

    Mol Cell Proteomics. 2011 Nov;10(11):M111.009506. doi: 10.1074/mcp.M111.009506. PubMed PMID: 21749987; PubMed Central PMCID: PMC3226405.
    Gimpel M, Heidrich N, Mäder U, Krügel H, Brantl S

    A dual-function sRNA from B

    subtilis: SR1 acts as a peptide encoding mRNA on the gapA operon. Mol Microbiol. 2010 May;76(4):990-1009. doi: 10.1111/j.1365-2958.2010.07158.x. PubMed PMID: 20444087.
    Commichau FM, Rothe FM, Herzberg C, Wagner E, Hellwig D, Lehnik-Habrink M, Hammer E, Völker U, Stülke J

    Novel activities of glycolytic enzymes in Bacillus subtilis: interactions with essential proteins involved in mRNA processing

    Mol Cell Proteomics. 2009 Jun;8(6):1350-60. doi: 10.1074/mcp.M800546-MCP200. PubMed PMID: 19193632; PubMed Central PMCID: PMC2690492.
    Liebeke M, Pöther DC, van Duy N, Albrecht D, Becher D, Hochgräfe F, Lalk M, Hecker M, Antelmann H

    Depletion of thiol-containing proteins in response to quinones in Bacillus subtilis

    Mol Microbiol. 2008 Sep;69(6):1513-29. doi: 10.1111/j.1365-2958.2008.06382.x. PubMed PMID: 18673455.
    Eymann C, Becher D, Bernhardt J, Gronau K, Klutzny A, Hecker M

    Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis

    Proteomics. 2007 Oct;7(19):3509-26. PubMed PMID: 17726680.
    Jannière L, Canceill D, Suski C, Kanga S, Dalmais B, Lestini R, Monnier AF, Chapuis J, Bolotin A, Titok M, Le Chatelier E, Ehrlich SD

    Genetic evidence for a link between glycolysis and DNA replication

    PLoS One. 2007 May 16;2(5):e447. PubMed PMID: 17505547; PubMed Central PMCID: PMC1866360.
    Macek B, Mijakovic I, Olsen JV, Gnad F, Kumar C, Jensen PR, Mann M

    The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis

    Mol Cell Proteomics. 2007 Apr;6(4):697-707. PubMed PMID: 17218307.
    Pompeo F, Luciano J, Galinier A

    Interaction of GapA with HPr and its homologue, Crh: Novel levels of regulation of a key step of glycolysis in Bacillus subtilis

    J Bacteriol. 2007 Feb;189(3):1154-7. PubMed PMID: 17142398; PubMed Central PMCID: PMC1797305.
    Thomaides HB, Davison EJ, Burston L, Johnson H, Brown DR, Hunt AC, Errington J, Czaplewski L

    Essential bacterial functions encoded by gene pairs

    J Bacteriol. 2007 Jan;189(2):591-602. PubMed PMID: 17114254; PubMed Central PMCID: PMC1797375.
    Meile JC, Wu LJ, Ehrlich SD, Errington J, Noirot P

    Systematic localisation of proteins fused to the green fluorescent protein in Bacillus subtilis: identification of new proteins at the DNA replication factory

    Proteomics. 2006 Apr;6(7):2135-46. PubMed PMID: 16479537.
    Eymann C, Dreisbach A, Albrecht D, Bernhardt J, Becher D, Gentner S, Tam le T, Büttner K, Buurman G, Scharf C, Venz S, Völker U, Hecker M

    A comprehensive proteome map of growing Bacillus subtilis cells

    Proteomics. 2004 Oct;4(10):2849-76. PubMed PMID: 15378759.
    Blencke HM, Homuth G, Ludwig H, Mäder U, Hecker M, Stülke J

    Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways

    Metab Eng. 2003 Apr;5(2):133-49. PubMed PMID: 12850135.
    Meinken C, Blencke HM, Ludwig H, Stülke J

    Expression of the glycolytic gapA operon in Bacillus subtilis: differential syntheses of proteins encoded by the operon

    Microbiology. 2003 Mar;149(Pt 3):751-61. PubMed PMID: 12634343.
    Evguenieva-Hackenberg E, Schiltz E, Klug G

    Dehydrogenases from all three domains of life cleave RNA

    J Biol Chem. 2002 Nov 29;277(48):46145-50. PubMed PMID: 12359717.
    Ludwig H, Rebhan N, Blencke HM, Merzbacher M, Stülke J

    Control of the glycolytic gapA operon by the catabolite control protein A in Bacillus subtilis: a novel mechanism of CcpA-mediated regulation

    Mol Microbiol. 2002 Jul;45(2):543-53. PubMed PMID: 12123463.
    Ludwig H, Homuth G, Schmalisch M, Dyka FM, Hecker M, Stülke J

    Transcription of glycolytic genes and operons in Bacillus subtilis: evidence for the presence of multiple levels of control of the gapA operon

    Mol Microbiol. 2001 Jul;41(2):409-22. PubMed PMID: 11489127.
    Fillinger S, Boschi-Muller S, Azza S, Dervyn E, Branlant G, Aymerich S

    Two glyceraldehyde-3-phosphate dehydrogenases with opposite physiological roles in a nonphotosynthetic bacterium

    J Biol Chem. 2000 May 12;275(19):14031-7. PubMed PMID: 10799476.
    Tobisch S, Zühlke D, Bernhardt J, Stülke J, Hecker M

    Role of CcpA in regulation of the central pathways of carbon catabolism in Bacillus subtilis

    J Bacteriol. 1999 Nov;181(22):6996-7004. PubMed PMID: 10559165; PubMed Central PMCID: PMC94174.
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