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
Sequences	Protein DNA DNA_with_flanks
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
• increased expression of genes encoding small acid-soluble proteins PubMed

Database entries

• DBTBS entry: no entry

• SubtiList entry: [1]

• GEO entry: GSE39142 (ymdB mutant vs. wild type) PubMed

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:

• Domains:

• Modification:

• Cofactors:

• Effectors of protein activity:

• Interactions:
  • forms tetramers PubMed

• Localization:

Database entries

• Structure: 4B2O 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 Jörg Stülke's lab PubMed
  • GP922 (cat), available in Jörg Stülke's lab PubMed
  • GP921 (spc) NCIB3610 derivate, available in Jörg Stülke's lab PubMed
  • GP969 (ymdB(E39Q)-cat) inactive enzyme, available in Jörg Stülke's lab PubMed
  • GP1558 (aphA3; cassette w/o terminator), available in Jörg Stülke's lab
  • GP1573 (aphA3), available in Jörg Stülke's lab

• 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

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

• Antibody:

Labs working on this gene/protein

Jörg Stülke, University of Göttingen, Germany Homepage

References

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)