YmdB

• Description: phosphodiesterase, controls bistable gene expression
  
  

Gene name	ymdB
Synonyms
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
Get the DNA and protein sequences (Barbe et al., 2009)
Genetic context This image was kindly provided by SubtiList
Expression at a glance   PubMed

Categories containing this gene/protein

biofilm formation

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

Database entries

• DBTBS entry: no entry

• SubtiList entry: [1]

The protein

Basic information/ Evolution

• Catalyzed reaction/ biological activity: phosphatase activity toward phosphoenolpyruvate and phosphodiesterase activity toward 2',3'-cAMP (the Deinococcus ortholog) PubMed

• Protein family:

• Paralogous protein(s):

Extended information on the protein

• Kinetic information:

• Domains:

• Modification:

• Cofactor(s):

• Effectors of protein activity:

• Interactions:

• Localization:

Database entries

• Structure: 1T70 (the protein of Deinococcus radiodurans, 44% identity) PubMed

• UniProt: O31775

• KEGG entry: [2]

• E.C. number:

Expression and regulation

• Operon: rny-ymdB (weak readthrough transcription) PubMed

• Expression browser: ymdB PubMed

• Sigma factor:

• Regulation: constitutive

• Regulatory mechanism:

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

Biological materials

• Mutant:
  • GP583 (spc), available in Stülke lab
  • GP922 (cat), available in Stülke lab
  • GP921 (spc) NCIB3610 derivate, available in Stülke lab
  • GP969 (ymdB(E39Q)-cat) inactive enzyme, available in Stülke lab

• Expression vector:
  • for expression/ purification from B. subtilis with N-terminal Strep-tag, for SPINE, in pGP380: pGP1041, available in Stülke lab
  • for expression/ purification from B. subtilis with C-terminal Strep-tag, for SPINE, in pGP382: pGP1919, available in Stülke lab
  • for expression/ purification from E. coli with N-terminal His-tag, in pWH844: pGP1040, available in Stülke lab
  • for expression/ purification from E. coli with N-terminal Strep-tag, in pGP172: pGP1917, available in Stülke lab
  • GP970 (ymdB-Strep (cat)), purification from B. subtilis, for SPINE, available in Stülke lab

• lacZ fusion:

• GFP fusion:

• two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab

• FLAG-tag construct: GP1018 (spc, based on pGP1331), available in the Stülke lab

• Antibody:

Labs working on this gene/protein

Jörg Stülke, University of Göttingen, Germany Homepage

References

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)