YvyD

• Description: general stress protein, required for ribosome dimerization in the stationary phase, required for protection against paraquat stress
  
  

Gene name	yvyD
Synonyms	yviI
Essential	no
Product	unknown
Function	dimerization of ribosomes in the stationary phase, protection against paraquat stress
Gene expression levels in SubtiExpress: yvyD
MW, pI	21 kDa, 5.184
Gene length, protein length	567 bp, 189 aa
Immediate neighbours	secA, smiA
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

general stress proteins (controlled by SigB), resistance against oxidative and electrophile stress, membrane proteins, phosphoproteins

This gene is a member of the following regulons

SigB regulon, SigH regulon

The gene

Basic information

• Locus tag: BSU35310

Phenotypes of a mutant

• the mutant is cold-sensitive
• delayed recovery from stationary phase and delayed germination

Database entries

• BsubCyc: BSU35310

• DBTBS entry: [1]

• SubtiList entry: [2]

The protein

Basic information/ Evolution

• Catalyzed reaction/ biological activity:

• Protein family: ribosomal protein S30Ae family (according to Swiss-Prot)

• Paralogous protein(s):

Extended information on the protein

• Kinetic information:

• Domains:

• Modification:
  • phosphorylated on Arg-6 PubMed

• Cofactor(s):

• Effectors of protein activity:

• Interactions:
  • YvyD-ribosome (for ribosome dimerization) PubMed
• Localization:
  • membrane protein

Database entries

• BsubCyc: BSU35310

• Structure:

• UniProt: P28368

• KEGG entry: [3]

• E.C. number:

Expression and regulation

• Operon: yvyD PubMed

• Expression browser: yvyD PubMed

• Sigma factor: SigB PubMed, SigH PubMed

• Regulation:
  • repressed by casamino acids PubMed
  • induced by stress (SigB) PubMed

• Regulatory mechanism:

• Additional information:
  • number of protein molecules per cell (minimal medium with glucose and ammonium): 2138 PubMed
  • number of protein molecules per cell (complex medium with amino acids, without glucose): 3361 PubMed

Biological materials

• Mutant:

• Expression vector:

• lacZ fusion:

• GFP fusion:

• two-hybrid system:

• Antibody:

References

Kazumi Tagami, Hideaki Nanamiya, Yuka Kazo, Marie Maehashi, Shota Suzuki, Eri Namba, Masahiro Hoshiya, Ryo Hanai, Yuzuru Tozawa, Takuya Morimoto, Naotake Ogasawara, Yasushi Kageyama, Katsutoshi Ara, Katsuya Ozaki, Masaki Yoshida, Haruko Kuroiwa, Tsuneyoshi Kuroiwa, Yoshiaki Ohashi, Fujio Kawamura
Expression of a small (p)ppGpp synthetase, YwaC, in the (p)ppGpp(0) mutant of Bacillus subtilis triggers YvyD-dependent dimerization of ribosome.
Microbiologyopen: 2012, 1(2);115-34
[PubMed:22950019] [WorldCat.org] [DOI] (I p)

Alexander Reder, Dirk Höper, Ulf Gerth, Michael Hecker
Contributions of individual σB-dependent general stress genes to oxidative stress resistance of Bacillus subtilis.
J Bacteriol: 2012, 194(14);3601-10
[PubMed:22582280] [WorldCat.org] [DOI] (I p)

Alexander K W Elsholz, Kürsad Turgay, Stephan Michalik, Bernd Hessling, Katrin Gronau, Dan Oertel, Ulrike Mäder, Jörg Bernhardt, Dörte Becher, Michael Hecker, Ulf Gerth
Global impact of protein arginine phosphorylation on the physiology of Bacillus subtilis.
Proc Natl Acad Sci U S A: 2012, 109(19);7451-6
[PubMed:22517742] [WorldCat.org] [DOI] (I p)

Dirk Höper, Uwe Völker, Michael Hecker
Comprehensive characterization of the contribution of individual SigB-dependent general stress genes to stress resistance of Bacillus subtilis.
J Bacteriol: 2005, 187(8);2810-26
[PubMed:15805528] [WorldCat.org] [DOI] (P p)

Ulrike Mäder, Georg Homuth, Christian Scharf, Knut Büttner, Rüdiger Bode, Michael Hecker
Transcriptome and proteome analysis of Bacillus subtilis gene expression modulated by amino acid availability.
J Bacteriol: 2002, 184(15);4288-95
[PubMed:12107147] [WorldCat.org] [DOI] (P p)

Christine Eymann, Georg Homuth, Christian Scharf, Michael Hecker
Bacillus subtilis functional genomics: global characterization of the stringent response by proteome and transcriptome analysis.
J Bacteriol: 2002, 184(9);2500-20
[PubMed:11948165] [WorldCat.org] [DOI] (P p)

H Antelmann, C Scharf, M Hecker
Phosphate starvation-inducible proteins of Bacillus subtilis: proteomics and transcriptional analysis.
J Bacteriol: 2000, 182(16);4478-90
[PubMed:10913081] [WorldCat.org] [DOI] (P p)

K Drzewiecki, C Eymann, G Mittenhuber, M Hecker
The yvyD gene of Bacillus subtilis is under dual control of sigmaB and sigmaH.
J Bacteriol: 1998, 180(24);6674-80
[PubMed:9852014] [WorldCat.org] [DOI] (P p)

Publications on the homologous proteins from other bacteria

Pranav Puri, Thomas H Eckhardt, Linda E Franken, Fabrizia Fusetti, Marc C A Stuart, Egbert J Boekema, Oscar P Kuipers, Jan Kok, Bert Poolman
Lactococcus lactis YfiA is necessary and sufficient for ribosome dimerization.
Mol Microbiol: 2014, 91(2);394-407
[PubMed:24279750] [WorldCat.org] [DOI] (I p)

Yury S Polikanov, Gregor M Blaha, Thomas A Steitz
How hibernation factors RMF, HPF, and YfiA turn off protein synthesis.
Science: 2012, 336(6083);915-8
[PubMed:22605777] [WorldCat.org] [DOI] (I p)