Difference between revisions of "Sandbox"

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* '''Description:''' two-component sensor kinase for exoenzyme and competence regulation <br/><br/>
+
* '''Description:''' two-component response regulator, regulation of degradative enzyme and genetic competence, involved in activation of capsule biosynthetic operon expression (together with [[SwrAA]]), non-phosphorylated DegU is required for swarming motility [http://www3.interscience.wiley.com/journal/122328658/abstract PubMed] <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''degS''
+
|''degU''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''sacU ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''sacU, iep ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || two-component sensor kinase (NarL family)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || two-component response regulator
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of degradative enzyme and genetic competence
 
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of degradative enzyme and genetic competence
 +
of genetic competence
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 44 kDa, 5.988  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 5.602  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1155 bp, 385 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 687 bp, 229 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[degU]]'', ''[[yvyE]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yviA]]'', ''[[degS]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15567&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15566&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:degS_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:degU_context.gif]]
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU35500
+
* '''Locus tag:''' BSU35490
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 44:
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/degSU.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/degSU.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10392]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10393]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 53:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' ATP + protein L-histidine = ADP + protein N-phospho-L-histidine (according to Swiss-Prot) autophosphorylation, autodephosphorylation, phosphorylation of [[DegU]] on Asp-56 [http://www.ncbi.nlm.nih.gov/sites/entrez/1901568 PubMed]
+
* '''Catalyzed reaction/ biological activity:''' transcription activator of degradative enzyme genes (''[[sacB]]'' and ''[[degQ]]'') and of ''[[comK]]'' expression
  
 
* '''Protein family:'''
 
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
 +
 +
=== Genes controlled by DegU ===
 +
 +
* '''Activation by DegU-P:''' ''[[degS]]-[[degU]]''
 +
 +
* '''Activation by DegU:''' ''[[epr]]'' [http://www3.interscience.wiley.com/journal/122328658/abstract PubMed]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 64: Line 71:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
** aa  12 ... 170: unknown DegS domain
+
* '''Modification:''' phosphorylated by [[DegS]] on Asp-56 [http://www.ncbi.nlm.nih.gov/sites/entrez/1901568 PubMed], this modulates DNA-binding activity
−
** aa 180 ... 248: HisKA_3 domain (autophosphorylation)
 
−
** aa 289 ... 384: HATPase_c
 
−
 
 
−
* '''Modification:''' phosphorylation on Ser-76 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], autophosphorylation on His-189
 
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:''' [[DegQ]]
+
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[DegS]]-[[DegU]], [[DegS]]-[[DegQ]]
+
* '''Interactions:''' [[DegU]]-[[RapG]], [[DegS]]-[[DegU]]
  
−
* '''Localization:''' Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
+
* '''Localization:''' cytoplasm (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
Line 82: Line 85:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P13799 P13799]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P13800 P13800]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU35500]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU35490]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 97: Line 100:
  
 
* '''Regulation:''' induced in the presence of ammonium ([[TnrA]])
 
* '''Regulation:''' induced in the presence of ammonium ([[TnrA]])
 +
** repressed in the absence of good nitrogen sources (glutamine or ammonium) ([[TnrA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/18502860 PubMed]
  
 
* '''Regulatory mechanism:''' [[TnrA]]: repression, [[DegU]]: positive autoregulation
 
* '''Regulatory mechanism:''' [[TnrA]]: repression, [[DegU]]: positive autoregulation
 +
** [[TnrA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/18502860 PubMed]
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 117: Line 122:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Tarek Msadek]], Institut Pasteur, Paris, France
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 124: Line 127:
 
=References=
 
=References=
  
−
<pubmed>17850253,12471443,14563871,1459944,1901568,10094672,,16479537, 17218307 </pubmed>
+
<pubmed>17850253,12471443,8878039,14563871,1901568,1321152,1459944,18194340,10908654,18502860,10094672,19389763,18414485,19420703,2428811,7746142,,18502860, 19389763, 19416356, 19118340 </pubmed>
−
 
 
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 

Revision as of 09:03, 13 June 2009

  • Description: two-component response regulator, regulation of degradative enzyme and genetic competence, involved in activation of capsule biosynthetic operon expression (together with SwrAA), non-phosphorylated DegU is required for swarming motility PubMed

Gene name degU
Synonyms sacU, iep
Essential no
Product two-component response regulator
Function regulation of degradative enzyme and genetic competence

of genetic competence

MW, pI 25 kDa, 5.602
Gene length, protein length 687 bp, 229 aa
Immediate neighbours yviA, degS
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
DegU context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU35490

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: transcription activator of degradative enzyme genes (sacB and degQ) and of comK expression
  • Protein family:
  • Paralogous protein(s):

Genes controlled by DegU

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylated by DegS on Asp-56 PubMed, this modulates DNA-binding activity
  • Cofactor(s):
  • Effectors of protein activity:
  • Localization: cytoplasm (according to Swiss-Prot)

Database entries

  • Structure:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation: induced in the presence of ammonium (TnrA)
    • repressed in the absence of good nitrogen sources (glutamine or ammonium) (TnrA) PubMed
  • Regulatory mechanism: TnrA: repression, DegU: positive autoregulation
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

Keitarou Kimura, Lam-Son Phan Tran, Thi-Huyen Do, Yoshifumi Itoh
Expression of the pgsB encoding the poly-gamma-DL-glutamate synthetase of Bacillus subtilis (natto).
Biosci Biotechnol Biochem: 2009, 73(5);1149-55
[PubMed:19420703] [WorldCat.org] [DOI] (I p)

Monica Gupta, Kestur Krishnamurthy Rao
Epr plays a key role in DegU-mediated swarming motility of Bacillus subtilis.
FEMS Microbiol Lett: 2009, 295(2);187-94
[PubMed:19416356] [WorldCat.org] [DOI] (I p)

Cecilia Osera, Giuseppe Amati, Cinzia Calvio, Alessandro Galizzi
SwrAA activates poly-gamma-glutamate synthesis in addition to swarming in Bacillus subtilis.
Microbiology (Reading): 2009, 155(Pt 7);2282-2287
[PubMed:19389763] [WorldCat.org] [DOI] (P p)

Ewan J Murray, Taryn B Kiley, Nicola R Stanley-Wall
A pivotal role for the response regulator DegU in controlling multicellular behaviour.
Microbiology (Reading): 2009, 155(Pt 1);1-8
[PubMed:19118340] [WorldCat.org] [DOI] (P p)

Ayako Yasumura, Sadanobu Abe, Teruo Tanaka
Involvement of nitrogen regulation in Bacillus subtilis degU expression.
J Bacteriol: 2008, 190(15);5162-71
[PubMed:18502860] [WorldCat.org] [DOI] (I p)

Jan-Willem Veening, Oleg A Igoshin, Robyn T Eijlander, Reindert Nijland, Leendert W Hamoen, Oscar P Kuipers
Transient heterogeneity in extracellular protease production by Bacillus subtilis.
Mol Syst Biol: 2008, 4;184
[PubMed:18414485] [WorldCat.org] [DOI] (I p)

Kensuke Tsukahara, Mitsuo Ogura
Characterization of DegU-dependent expression of bpr in Bacillus subtilis.
FEMS Microbiol Lett: 2008, 280(1);8-13
[PubMed:18194340] [WorldCat.org] [DOI] (P p)

Kazuo Kobayashi
Gradual activation of the response regulator DegU controls serial expression of genes for flagellum formation and biofilm formation in Bacillus subtilis.
Mol Microbiol: 2007, 66(2);395-409
[PubMed:17850253] [WorldCat.org] [DOI] (P p)

Leif Steil, Tamara Hoffmann, Ina Budde, Uwe Völker, Erhard Bremer
Genome-wide transcriptional profiling analysis of adaptation of Bacillus subtilis to high salinity.
J Bacteriol: 2003, 185(21);6358-70
[PubMed:14563871] [WorldCat.org] [DOI] (P p)

U Mäder, H Antelmann, T Buder, M K Dahl, M Hecker, G Homuth
Bacillus subtilis functional genomics: genome-wide analysis of the DegS-DegU regulon by transcriptomics and proteomics.
Mol Genet Genomics: 2002, 268(4);455-67
[PubMed:12471443] [WorldCat.org] [DOI] (P p)

L W Hamoen, A F Van Werkhoven, G Venema, D Dubnau
The pleiotropic response regulator DegU functions as a priming protein in competence development in Bacillus subtilis.
Proc Natl Acad Sci U S A: 2000, 97(16);9246-51
[PubMed:10908654] [WorldCat.org] [DOI] (P p)

C Fabret, V A Feher, J A Hoch
Two-component signal transduction in Bacillus subtilis: how one organism sees its world.
J Bacteriol: 1999, 181(7);1975-83
[PubMed:10094672] [WorldCat.org] [DOI] (P p)

J Hahn, A Luttinger, D Dubnau
Regulatory inputs for the synthesis of ComK, the competence transcription factor of Bacillus subtilis.
Mol Microbiol: 1996, 21(4);763-75
[PubMed:8878039] [WorldCat.org] [DOI] (P p)

B J Haijema, L W Hamoen, J Kooistra, G Venema, D van Sinderen
Expression of the ATP-dependent deoxyribonuclease of Bacillus subtilis is under competence-mediated control.
Mol Microbiol: 1995, 15(2);203-11
[PubMed:7746142] [WorldCat.org] [DOI] (P p)

K Mukai, M Kawata-Mukai, T Tanaka
Stabilization of phosphorylated Bacillus subtilis DegU by DegR.
J Bacteriol: 1992, 174(24);7954-62
[PubMed:1459944] [WorldCat.org] [DOI] (P p)

M K Dahl, T Msadek, F Kunst, G Rapoport
The phosphorylation state of the DegU response regulator acts as a molecular switch allowing either degradative enzyme synthesis or expression of genetic competence in Bacillus subtilis.
J Biol Chem: 1992, 267(20);14509-14
[PubMed:1321152] [WorldCat.org] (P p)

M K Dahl, T Msadek, F Kunst, G Rapoport
Mutational analysis of the Bacillus subtilis DegU regulator and its phosphorylation by the DegS protein kinase.
J Bacteriol: 1991, 173(8);2539-47
[PubMed:1901568] [WorldCat.org] [DOI] (P p)

H Shimotsu, D J Henner
Modulation of Bacillus subtilis levansucrase gene expression by sucrose and regulation of the steady-state mRNA level by sacU and sacQ genes.
J Bacteriol: 1986, 168(1);380-8
[PubMed:2428811] [WorldCat.org] [DOI] (P p)

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