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ymdB [Tue Dec 13 2016 11:16:33 GMT+0100 (CET)]
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ymdB [Tue Dec 13 2016 11:16:33 GMT+0100 (CET)]

phosphodiesterase, controls bistable gene expression, required for nanotube formation
locus
BSU16970
pI
6.00
mw
29.00 kDa
function
control of bistable gene expression
product
phosphodiesterase
essential
no
synonyms

Genomic Context

      

categories

  • [category|SW 4|Lifestyles] → [category|SW 4.1|Exponential and early post-exponential lifestyles] → [category|SW 4.1.2|Biofilm formation]
  • [category|SW 4|Lifestyles] → [category|SW 4.1|Exponential and early post-exponential lifestyles] → [category|SW 4.1.2|Biofilm formation] → [category|SW 4.1.2.4|Regulation]
  • [SW|Categories] containing this gene/protein

  • [SW|biofilm formation], [SW|sporulation/ other]
  • Gene

    Coordinates on the chromosome (coding sequence)
    1,768,941 -> 1,769,735

    Phenotypes of a mutant

  • strong overexpression of ''[protein|search|hag]'' [Pubmed|21856853]
  • defective in [SW|biofilm formation] [Pubmed|21856853,22113911]
  • the phenotypes of the ''ymdB'' mutant can be suppressed by overexpression of ''[protein|search|slrR]'' [Pubmed|21856853]
  • inactivation of ''[protein|search|ymdB]'' restores beta-lactam resistance in a ''[protein|search|sigM]'' mutant [Pubmed|22211522]
  • increased expression of genes encoding small acid-soluble proteins [Pubmed|24163345]
  • increased intracellular levels of cyclic AMP [Pubmed|26904951]
  • abberant colony development, reduced colony size [Pubmed|26904951]
  • reduced formation of nanotubes [Pubmed|26906740]
  • inactivation of ''[SW|ymdB]'' reduces sporulation efficiency to 11.4% that of wild type cells [Pubmed|26735940]
  • The protein

    Catalyzed reaction/ biological activity

  • phosphodiesterase activity toward 2',3'-cAMP [Pubmed|24163345]
  • Structure

  • [PDB|4B2O] [Pubmed|24163345]
  • [SW|Interactions]

  • forms tetramers [Pubmed|24163345]
  • Expression and Regulation

    Operon

  • ''[protein|search|rny]-[protein|search|ymdB]'' (weak readthrough transcription) [Pubmed|21856853]
  • Regulation

  • constitutive
  • Additional information

  • there is a terminator between ''[SW|rny]'' and ''[SW|ymdB]'', most transcripts terminate there [PubMed|21856853]
  • the [SW|transcription] terminator between ''[SW|rny]'' and ''[SW|ymdB]'' is strong and [SW|NusA]-independent [http://www.nature.com/articles/nmicrobiol20157 Reference]
  • Biological materials

    Mutant

  • GP583 (spc), available in [SW|Jörg Stülke]'s lab [Pubmed|21856853]
  • GP922 (cat), available in [SW|Jörg Stülke]'s lab [Pubmed|21856853]
  • GP921 (spc) NCIB3610 derivate, available in [SW|Jörg Stülke]'s lab [Pubmed|21856853]
  • GP969 (''[protein|search|ymdB]''(E39Q)-cat) inactive enzyme, available in [SW|Jörg Stülke]'s lab [Pubmed|24163345]
  • GP1558 (aphA3; cassette w/o terminator), available in [SW|Jörg Stülke]'s lab
  • GP1573 (aphA3), available in [SW|Jörg Stülke]'s lab
  • GP1848 (replacement of ''[SW|ymdB]-[SW|spoVS]'' by a ''spc'' cassette), available in [SW|Jörg Stülke]'s lab
  • Expression vector

  • for expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [SW|SPINE], in [SW|pGP380]: pGP1041, available in [SW|Jörg Stülke]'s lab
  • for expression/ purification from ''B. subtilis'' with C-terminal Strep-tag, for [SW|SPINE], in [SW|pGP382]: pGP1919, available in [SW|Jörg Stülke]'s lab
  • for expression/ purification from ''E. coli'' with N-terminal His-tag, in [SW|pWH844]: pGP1040, available in [SW|Jörg Stülke]'s lab
  • for expression/ purification from ''E. coli'' with N-terminal Strep-tag, in [SW|pGP172]: pGP1917, available in [SW|Jörg Stülke]'s lab [Pubmed|24163345]
  • GP970 (''[protein|search|ymdB]''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [SW|SPINE], available in [SW|Jörg Stülke]'s lab
  • two-hybrid system

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

  • GP1018 (spc, based on [SW|pGP1331]), available in [SW|Jörg Stülke]'s lab
  • Labs working on this gene/protein

  • [SW|Jörg Stülke], University of Göttingen, Germany
  • [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
  • References

    Reviews

  • 25837850
  • Original Publications

  • 21856853,22211522,22113911,24163345,26904951,26906740,26735940
  • Functional and structural analysis of orthologs in other organisms

  • 19376879,17847097