Difference between revisions of "YmdB"

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(Biological materials)
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** GP921 (spc) NCIB3610 derivate, available in [[Jörg Stülke]]'s lab {{PubMed|21856853}}
** GP921 (spc) NCIB3610 derivate, available in [[Jörg Stülke]]'s lab {{PubMed|21856853}}
** GP969 (''[[ymdB]]''(E39Q)-cat) inactive enzyme, available in [[Jörg Stülke]]'s lab {{PubMed|24163345}}
** GP969 (''[[ymdB]]''(E39Q)-cat) inactive enzyme, available in [[Jörg Stülke]]'s lab {{PubMed|24163345}}
** GP1558 (aphA3; cassette w/o terminator), available in [[Jörg Stülke]]'s lab
** GP1573 (aphA3), available in [[Jörg Stülke]]'s lab
* '''Expression vector:'''  
* '''Expression vector:'''  

Revision as of 17:03, 27 January 2014

  • Description: phosphodiesterase, controls bistable gene expression

Gene name ymdB
Essential no
Product phosphodiesterase
Function control of bistable gene expression
Gene expression levels in SubtiExpress: ymdB
MW, pI 29,1 kDa, 6.50
Gene length, protein length 792 bp, 264 amino acids
Immediate neighbours rny, spoVS
Sequences Protein DNA DNA_with_flanks
Genetic context
YmdB context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
YmdB expression.png

Categories containing this gene/protein

biofilm formation

This gene is a member of the following regulons

The gene

Basic information

  • Locus tag: BSU16970

Phenotypes of a mutant

  • strong overexpression of hag PubMed
  • defective in biofilm formation PubMed
  • the phenotypes of the ymdB mutant can be suppressed by overexpression of slrR PubMed
  • inactivation of ymdB restores beta-lactam resistance in a sigM mutant PubMed
  • increased expression of genes encoding small acid-soluble proteins PubMed

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
    • phosphodiesterase activity toward 2',3'-cAMP PubMed
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Modification:
  • Effectors of protein activity:

Database entries

  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation: constitutive
  • Regulatory mechanism:
  • Additional information: there is a terminator between rny and ymdB, most transcripts terminate there PubMed

Biological materials

  • Expression vector:
    • for expression/ purification from B. subtilis with N-terminal Strep-tag, for SPINE, in pGP380: pGP1041, available in Jörg Stülke's lab
    • for expression/ purification from B. subtilis with C-terminal Strep-tag, for SPINE, in pGP382: pGP1919, available in Jörg Stülke's lab
    • for expression/ purification from E. coli with N-terminal His-tag, in pWH844: pGP1040, available in Jörg Stülke's lab
    • for expression/ purification from E. coli with N-terminal Strep-tag, in pGP172: pGP1917, available in Jörg Stülke's lab PubMed
    • GP970 (ymdB-Strep (cat)), purification from B. subtilis, for SPINE, available in Jörg Stülke's lab
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Jörg Stülke's lab
  • Antibody:

Labs working on this gene/protein

Jörg Stülke, University of Göttingen, Germany Homepage

Your additional remarks


Christine Diethmaier, Joseph A Newman, Akos T Kovács, Volkhard Kaever, Christina Herzberg, Cecilia Rodrigues, Mirjam Boonstra, Oscar P Kuipers, Richard J Lewis, Jörg Stülke
The YmdB phosphodiesterase is a global regulator of late adaptive responses in Bacillus subtilis.
J. Bacteriol.: 2014, 196(2);265-75
[PubMed:24163345] [WorldCat.org] [DOI] (I p)

Yun Luo, John D Helmann
Analysis of the role of Bacillus subtilis σ(M) in β-lactam resistance reveals an essential role for c-di-AMP in peptidoglycan homeostasis.
Mol. Microbiol.: 2012, 83(3);623-39
[PubMed:22211522] [WorldCat.org] [DOI] (I p)

Eric R Pozsgai, Kris M Blair, Daniel B Kearns
Modified mariner transposons for random inducible-expression insertions and transcriptional reporter fusion insertions in Bacillus subtilis.
Appl. Environ. Microbiol.: 2012, 78(3);778-85
[PubMed:22113911] [WorldCat.org] [DOI] (I p)

Christine Diethmaier, Nico Pietack, Katrin Gunka, Christoph Wrede, Martin Lehnik-Habrink, Christina Herzberg, Sebastian Hübner, Jörg Stülke
A novel factor controlling bistability in Bacillus subtilis: the YmdB protein affects flagellin expression and biofilm formation.
J. Bacteriol.: 2011, 193(21);5997-6007
[PubMed:21856853] [WorldCat.org] [DOI] (I p)

Functional and structural analysis of orthologs in other organisms

Jason Zemansky, Benjamin C Kline, Joshua J Woodward, Jess H Leber, Hélène Marquis, Daniel A Portnoy
Development of a mariner-based transposon and identification of Listeria monocytogenes determinants, including the peptidyl-prolyl isomerase PrsA2, that contribute to its hemolytic phenotype.
J. Bacteriol.: 2009, 191(12);3950-64
[PubMed:19376879] [WorldCat.org] [DOI] (I p)

Dong Hae Shin, Michael Proudfoot, Hyo Jin Lim, In-Kyu Choi, Hisao Yokota, Alexander F Yakunin, Rosalind Kim, Sung-Hou Kim
Structural and enzymatic characterization of DR1281: A calcineurin-like phosphoesterase from Deinococcus radiodurans.
Proteins: 2008, 70(3);1000-9
[PubMed:17847097] [WorldCat.org] [DOI] (I p)