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NCBI: 10-JUN-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL0019 [new locus tag: SACOL_RS00120 ]
  • pan locus tag?: SAUPAN000032000
  • symbol: yycF
  • pan gene symbol?: walR
  • synonym:
  • product: DNA-binding response regulator YycF

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SACOL0019 [new locus tag: SACOL_RS00120 ]
  • symbol: yycF
  • product: DNA-binding response regulator YycF
  • replicon: chromosome
  • strand: +
  • coordinates: 24952..25653
  • length: 702
  • essential: unknown other strains

⊟Accession numbers[edit | edit source]

⊟Phenotype[edit | edit source]

Share your knowledge and add information here. [edit]

⊟DNA sequence[edit | edit source]

  • 1
    61
    121
    181
    241
    301
    361
    421
    481
    541
    601
    661
    ATGGCTAGAAAAGTTGTTGTAGTTGATGATGAAAAACCGATTGCTGATATTTTAGAATTT
    AACTTAAAAAAAGAAGGATACGATGTGTACTGTGCATACGATGGTAATGATGCAGTCGAC
    TTAATTTATGAAGAAGAACCAGACATCGTATTACTAGATATCATGTTACCTGGTCGTGAT
    GGTATGGAAGTATGTCGTGAAGTGCGCAAAAAATACGAAATGCCAATAATAATGCTTACT
    GCTAAAGATTCAGAAATTGATAAAGTGCTTGGTTTAGAACTAGGTGCAGATGACTATGTA
    ACGAAACCGTTTAGTACGCGTGAATTAATCGCACGTGTGAAAGCGAACTTACGTCGTCAT
    TACTCACAACCAGCACAAGACACTGGAAATGTAACGAATGAAATCACAATTAAAGATATT
    GTGATTTATCCAGACGCATATTCTATTAAAAAACGTGGCGAAGATATTGAATTAACACAT
    CGTGAATTTGAATTGTTCCATTATTTATCAAAACATATGGGACAAGTAATGACACGTGAA
    CATTTATTACAAACAGTATGGGGCTATGATTACTTTGGCGATGTACGTACGGTCGATGTA
    ACGATTCGTCGTTTACGTGAAAAGATTGAAGATGATCCGTCACATCCTGAATATATTGTG
    ACGCGTAGAGGCGTTGGATATTTCCTCCAACAACATGAGTAG
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    702

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SACOL0019 [new locus tag: SACOL_RS00120 ]
  • symbol: YycF
  • description: DNA-binding response regulator YycF
  • length: 233
  • theoretical pI: 4.81211
  • theoretical MW: 27191.8
  • GRAVY: -0.475536

⊟Function[edit | edit source]

  • TIGRFAM:
    Signal transduction Regulatory functions DNA interactions phosphate regulon transcriptional regulatory protein PhoB (TIGR02154; HMM-score: 235.8)
    Signal transduction Signal transduction Two-component systems phosphate regulon transcriptional regulatory protein PhoB (TIGR02154; HMM-score: 235.8)
    Signal transduction Regulatory functions DNA interactions heavy metal response regulator (TIGR01387; HMM-score: 191.9)
    and 7 more
    proteobacterial dedicated sortase system response regulator (TIGR03787; HMM-score: 132.5)
    Metabolism Central intermediary metabolism Nitrogen metabolism nitrogen regulation protein NR(I) (TIGR01818; HMM-score: 70.6)
    Signal transduction Regulatory functions DNA interactions nitrogen regulation protein NR(I) (TIGR01818; HMM-score: 70.6)
    Signal transduction Signal transduction Two-component systems nitrogen regulation protein NR(I) (TIGR01818; HMM-score: 70.6)
    Cellular processes Cellular processes Sporulation and germination sporulation transcription factor Spo0A (TIGR02875; HMM-score: 69.4)
    Signal transduction Signal transduction Two-component systems TMAO reductase sytem sensor TorS (TIGR02956; EC 2.7.13.3; HMM-score: 41.1)
    Signal transduction Regulatory functions DNA interactions PEP-CTERM-box response regulator transcription factor (TIGR02915; HMM-score: 40.3)
  • TheSEED  :
    • Two-component response regulator SA14-24
    Iron acquisition and metabolism Iron acquisition and metabolism - no subcategory Heme, hemin uptake and utilization systems in GramPositives  Two-component response regulator SA14-24
  • PFAM:
    CheY (CL0304) Response_reg; Response regulator receiver domain (PF00072; HMM-score: 103.1)
    HTH (CL0123) Trans_reg_C; Transcriptional regulatory protein, C terminal (PF00486; HMM-score: 97)

⊟Structure, modifications & cofactors[edit | edit source]

  • domains:
  • modifications:
  • cofactors:
  • effectors:
  • genes regulated by WalR*, response regulator important in cell wall homeostasis: in NCTC8325

⊟Localization[edit | edit source]

  • PSORTb: Cytoplasmic
    • Cytoplasmic Score: 9.97
    • Cytoplasmic Membrane Score: 0
    • Cellwall Score: 0.01
    • Extracellular Score: 0.02
    • Internal Helices: 0
  • LocateP: Intracellular
    • Prediction by SwissProt Classification: Cytoplasmic
    • Pathway Prediction: No pathway
    • Intracellular possibility: 1
    • Signal peptide possibility: -1
    • N-terminally Anchored Score: 1
    • Predicted Cleavage Site: No CleavageSite
  • SignalP: no predicted signal peptide
    • SP(Sec/SPI): 0.004145
    • TAT(Tat/SPI): 0.000213
    • LIPO(Sec/SPII): 0.000302
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MARKVVVVDDEKPIADILEFNLKKEGYDVYCAYDGNDAVDLIYEEEPDIVLLDIMLPGRDGMEVCREVRKKYEMPIIMLTAKDSEIDKVLGLELGADDYVTKPFSTRELIARVKANLRRHYSQPAQDTGNVTNEITIKDIVIYPDAYSIKKRGEDIELTHREFELFHYLSKHMGQVMTREHLLQTVWGYDYFGDVRTVDVTIRRLREKIEDDPSHPEYIVTRRGVGYFLQQHE

⊟Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas
  • protein localization: Cytoplasmic [1] [2] [3] [4]
  • quantitative data / protein copy number per cell: 779 [5]
  • interaction partners:
    SACOL0557(cysK)cysteine synthase  [6] (data from MRSA252)
    SACOL2623(mqo2)malate:quinone oxidoreductase  [6] (data from MRSA252)
    SACOL1104(pdhC)branched-chain alpha-keto acid dehydrogenase E2  [6] (data from MRSA252)
    SACOL1516(rpsA)30S ribosomal protein S1  [6] (data from MRSA252)
    SACOL1274(rpsB)30S ribosomal protein S2  [6] (data from MRSA252)
    SACOL2233(rpsC)30S ribosomal protein S3  [6] (data from MRSA252)
    SACOL2104(upp)uracil phosphoribosyltransferase  [6] (data from MRSA252)
    SACOL0506ABC transporter substrate-binding protein  [6] (data from MRSA252)

⊟Expression & Regulation[edit | edit source]

⊟Operon[edit | edit source]

⊟Regulation[edit | edit source]

  • regulator: Rex* (repression) regulon
    Rex*(TF)important in Energy metabolism; RegPrecise 

⊟Transcription pattern[edit | edit source]

⊟Protein synthesis (provided by Aureolib)[edit | edit source]

⊟Protein stability[edit | edit source]

  • half-life: 38.27 h [7]

⊟Biological Material[edit | edit source]

⊟Mutants[edit | edit source]

⊟Expression vector[edit | edit source]

⊟lacZ fusion[edit | edit source]

⊟GFP fusion[edit | edit source]

⊟two-hybrid system[edit | edit source]

⊟FLAG-tag construct[edit | edit source]

⊟Antibody[edit | edit source]

⊟Other Information[edit | edit source]

You are kindly invited to share additional interesting facts.

⊟Literature[edit | edit source]

⊟References[edit | edit source]

  1. ↑ Dörte Becher, Kristina Hempel, Susanne Sievers, Daniela Zühlke, Jan Pané-Farré, Andreas Otto, Stephan Fuchs, Dirk Albrecht, Jörg Bernhardt, Susanne Engelmann, Uwe Völker, Jan Maarten van Dijl, Michael Hecker
    A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome.
    PLoS One: 2009, 4(12);e8176
    [PubMed:19997597] [WorldCat.org] [DOI] (I e)
  2. ↑ Kristina Hempel, Jan Pané-Farré, Andreas Otto, Susanne Sievers, Michael Hecker, Dörte Becher
    Quantitative cell surface proteome profiling for SigB-dependent protein expression in the human pathogen Staphylococcus aureus via biotinylation approach.
    J Proteome Res: 2010, 9(3);1579-90
    [PubMed:20108986] [WorldCat.org] [DOI] (I p)
  3. ↑ Kristina Hempel, Florian-Alexander Herbst, Martin Moche, Michael Hecker, Dörte Becher
    Quantitative proteomic view on secreted, cell surface-associated, and cytoplasmic proteins of the methicillin-resistant human pathogen Staphylococcus aureus under iron-limited conditions.
    J Proteome Res: 2011, 10(4);1657-66
    [PubMed:21323324] [WorldCat.org] [DOI] (I p)
  4. ↑ Andreas Otto, Jan Maarten van Dijl, Michael Hecker, Dörte Becher
    The Staphylococcus aureus proteome.
    Int J Med Microbiol: 2014, 304(2);110-20
    [PubMed:24439828] [WorldCat.org] [DOI] (I p)
  5. ↑ Daniela Zühlke, Kirsten Dörries, Jörg Bernhardt, Sandra Maaß, Jan Muntel, Volkmar Liebscher, Jan Pané-Farré, Katharina Riedel, Michael Lalk, Uwe Völker, Susanne Engelmann, Dörte Becher, Stephan Fuchs, Michael Hecker
    Costs of life - Dynamics of the protein inventory of Staphylococcus aureus during anaerobiosis.
    Sci Rep: 2016, 6;28172
    [PubMed:27344979] [WorldCat.org] [DOI] (I e)
  6. ↑ 6.0 6.1 6.2 6.3 6.4 6.5 6.6 6.7 Artem Cherkasov, Michael Hsing, Roya Zoraghi, Leonard J Foster, Raymond H See, Nikolay Stoynov, Jihong Jiang, Sukhbir Kaur, Tian Lian, Linda Jackson, Huansheng Gong, Rick Swayze, Emily Amandoron, Farhad Hormozdiari, Phuong Dao, Cenk Sahinalp, Osvaldo Santos-Filho, Peter Axerio-Cilies, Kendall Byler, William R McMaster, Robert C Brunham, B Brett Finlay, Neil E Reiner
    Mapping the protein interaction network in methicillin-resistant Staphylococcus aureus.
    J Proteome Res: 2011, 10(3);1139-50
    [PubMed:21166474] [WorldCat.org] [DOI] (I p)
  7. ↑ Stephan Michalik, Jörg Bernhardt, Andreas Otto, Martin Moche, Dörte Becher, Hanna Meyer, Michael Lalk, Claudia Schurmann, Rabea Schlüter, Holger Kock, Ulf Gerth, Michael Hecker
    Life and death of proteins: a case study of glucose-starved Staphylococcus aureus.
    Mol Cell Proteomics: 2012, 11(9);558-70
    [PubMed:22556279] [WorldCat.org] [DOI] (I p)

⊟Relevant publications[edit | edit source]

Sarah Dubrac, Tarek Msadek
Identification of genes controlled by the essential YycG/YycF two-component system of Staphylococcus aureus.
J Bacteriol: 2004, 186(4);1175-81
[PubMed:14762013] [WorldCat.org] [DOI] (P p)Sarah Dubrac, Ivo Gomperts Boneca, Olivier Poupel, Tarek Msadek
New insights into the WalK/WalR (YycG/YycF) essential signal transduction pathway reveal a major role in controlling cell wall metabolism and biofilm formation in Staphylococcus aureus.
J Bacteriol: 2007, 189(22);8257-69
[PubMed:17827301] [WorldCat.org] [DOI] (I p)Aurélia Delauné, Sarah Dubrac, Charlène Blanchet, Olivier Poupel, Ulrike Mäder, Aurélia Hiron, Aurélie Leduc, Catherine Fitting, Pierre Nicolas, Jean-Marc Cavaillon, Minou Adib-Conquy, Tarek Msadek
The WalKR system controls major staphylococcal virulence genes and is involved in triggering the host inflammatory response.
Infect Immun: 2012, 80(10);3438-53
[PubMed:22825451] [WorldCat.org] [DOI] (I p)

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