Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' transcriptional regulator of transition state genes <br/><br/>
+
* '''Description:''' bacteriocin-like product <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'''
−
|''abrB''
+
|''sboX''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''cpsX ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
+
|style="background:#ABCDEF;" align="center"| '''Product''' || bacteriocin-like product
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of gene expression during the transition <br/>from growth to stationary phase
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 10 kDa, 6.57  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 5 kDa, 9.857  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 288 bp, 96 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 150 bp, 50 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yabC]]'', ''[[metS]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sboA]]'', ''[[albA]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11813&#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:CAE01468&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:abrB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:sboX_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>
 
|-
 
|-
Line 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00370
+
* '''Locus tag:''' BSU37360
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
No swarming motility on B medium. [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/abrB.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sboAX-albABCDEFG.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10100]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14182]
  
 
=== Additional information===
 
=== Additional information===
Line 58: Line 56:
 
* '''Protein family:'''
 
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[Abh]], [[SpoVT]] (only N-terminal domain)
+
* '''Paralogous protein(s):'''
−
 
 
−
=== Genes/ operons controlled by AbrB ===
 
−
 
 
−
* '''Activated by AbrB:''' ''[[citB]]'', ''[[comK]], [[hpr]]'', ''[[rbsR]]-[[rbsK]]-[[rbsD]]-[[rbsA]]-[[rbsC]]-[[rbsB]]''
 
−
 
 
−
* ''' Repressed by AbrB:''' ''[[abrB]], [[aprE]], [[ftsA]]-[[ftsZ]], [[kinC]], [[motA]], [[nprE]], [[pbpE]], [[spo0H]], [[spoVG]], [[spo0E]], [[tycA]], [[sbo]]-[[alb]], [[yqxM]]-[[sipW]]-[[tasA]]''
 
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 76: Line 68:
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:''' interaction with [[AbbA]] results in inactivation of AbrB [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
+
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[AbrB]]-[[AbbA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
+
* '''Interactions:'''
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 84: Line 76:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1Z0R 1Z0R] (N-terminal DNA recognition domain), 1Z0R (N-terminal DNA recognition domain)  [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=32611 NCBI] [http://www.ncbi.nlm.nih.gov/sites/entrez/16223496 PubMed]
+
* '''Structure:'''
 +
 
 +
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/Q7WY57 Q7WY57]
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P08874 P08874]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU37360]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00370]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''abrB'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
+
* '''Operon:''' ''[[sboA]]-[[sboX]]-[[albA]]-[[albB]]-[[albC]]-[[albD]]-[[albE]]-[[albF]]-[[albG]]''
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
+
* '''[[Sigma factor]]:''' [[SigA]]
  
−
* '''Regulation:''' repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/2504584, PubMed] expressed at the onset of stationary phase [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
+
* '''Regulation:''' repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10572140, 17720793 PubMed]  
  
−
* '''Regulatory mechanism:''' [[AbrB]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/2504584, PubMed] repressed by [[Spo0A]]-P [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
+
* '''Regulatory mechanism:''' [[AbrB]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10572140, 17720793 PubMed]  
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 107: Line 100:
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' TT731 (aphA3)
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 120: Line 113:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]
 
−
 
−
[[Mark Strauch]], Baltimore, USA [http://lifesciences.umaryland.edu/Pages/faculty_profile.aspx?ID=212 homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 129: Line 118:
 
=References=
 
=References=
  
−
<pubmed>18840696 3145384 8821944 8576231 11101897 11395475 11583849 11964117 11751836 12123659 12076816 12591885 15610005 16223496 16159768 16702211 17660417 17720793 19202088 7592460, 19465659  </pubmed>
 
−
# Banse et al. (2008) Parallel pathways of repression and antirepression governing the transition to stationary phase in ''Bacillus subtilis''.''Proc. Natl. Acad. Sci. USA'' '''105:''' 15547-15552. [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
 
−
# Perego et al. (1988) Structure of the gene for the transition state regulator, ''abrB'': regulator synthesis is controlled by the ''spo0A'' sporulation gene in ''Bacillus subtilis''. ''Mol. Microbiol.'' '''2:''' 689-699. [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
 
−
# Xu, K. and M.A. Strauch. (1996) In vitro selection of optimal AbrB-binding sites: comparison to known in vivo sites indicates flexibility in AbrB-binding and recognition of three-dimensional DNA structures. Molec. Microbiol. 19: 145-158 [http://www.ncbi.nlm.nih.gov/sites/entrez/8821944 PubMed]
 
−
# Xu, K., D. Clark and M.A. Strauch. (1996) Analysis of abrB mutations, mutant proteins, and why abrB does not utilize a perfect consensus in the –35 region of its sigmaA promoter.J. Biol. Chem. 271:2621-2626 [http://www.ncbi.nlm.nih.gov/sites/entrez/8576231 PubMed]
 
−
# Vaughn, J.L., Feher V., Naylor, S., Strauch, M.A. and J. Cavanagh. (2000) Novel DNA binding domain and genetic regulation model of Bacillus subtilis transition state regulator AbrB. Nature Structural Biology 7:1139-1146; [http://www.ncbi.nlm.nih.gov/sites/entrez/11101897 PubMed], Corrigendum appears in Nature Stuctural & Molecular Biology (2005) 12:380
 
−
# Xu, K. and M.A. Strauch. (2001) DNA-binding activity of amino-terminal domains of the Bacillus subtilis AbrB protein. J. Bacteriol. 183:4094-4098 [http://www.ncbi.nlm.nih.gov/sites/entrez/11395475 PubMed]
 
−
# Phillips, Z. E.V. and M.A. Strauch. (2001) Role of Cys54 in AbrB multimerization and DNA-binding activity. FEMS Microbiol. Letters. 203:207-210 [http://www.ncbi.nlm.nih.gov/sites/entrez/11583849 PubMed]
 
−
# Phillips, Z.E.V. and M.A. Strauch. (2002) Bacillus subtilis sporulation and stationary phase gene expression. Cellular and Molecular Life Sciences 59:392-402 [http://www.ncbi.nlm.nih.gov/sites/entrez/11964117 PubMed]
 
−
# Shafikhani, S.H., Mandic-Mulec, I., Strauch, M.A., Smith, I. and T. Leighton. (2002) Postexponential regulation of sin operon expression in Bacillus subtilis. J. Bacteriol. 184:564-571 [http://www.ncbi.nlm.nih.gov/sites/entrez/11751836 PubMed]
 
−
# Benson, L. M., Vaughn, J. L., Strauch, M. A., Bobay, B. G., Thompson, R., Naylor, S. and J. Cavanagh (2002). Macromolecular assembly of the transition state regulator AbrB in its unbound and complexed states probed by microelectrospray ionization mass spectrometry. Analytical Biochemistry 306:222-227 [http://www.ncbi.nlm.nih.gov/sites/entrez/12123659 PubMed]
 
−
# Qian, Q., Lee, C.Y., Helmann, J. and M.A. Strauch. (2002) AbrB regulation of the sigmaW regulon of Bacillus subtilis. FEMS Microbiol. Letters 211:219-223. [http://www.ncbi.nlm.nih.gov/sites/entrez/12076816 PubMed]
 
−
# Kim, H. J., S. I. Kim, M. Ratnayake-Lecamwasam, K. Tachikawa, A. L. Sonenshein, and M. Strauch. (2003) Complex regulation of the Bacillus subtilis aconitase gene. J. Bacteriol. 185:1672-1680. [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed]
 
−
# Bobay, B.G., Benson, L., Naylor, S., Feeney, B., Clark, A.C., Goshe, M.B., Strauch, M.A., Thompson, R., and J.Cavanagh. (2004) Evaluation of the DNA binding tendencies of the transition state regulator AbrB. Biochemistry. 43:16106-16118. [http://www.ncbi.nlm.nih.gov/sites/entrez/15610005 PubMed]
 
−
# Bobay et al.(2005) Revised structure of the AbrB N-terminal domain unifies a diverse superfamily of putative DNA-binding proteins. FEBS Lett. 579:5669-5674. [http://www.ncbi.nlm.nih.gov/sites/entrez/16223496 PubMed]
 
−
# Yao, F and M.A. Strauch (2005) Independent and Interchangeable Multimerization Domains of the AbrB, Abh and SpoVT Global Regulatory Proteins. J. Bacteriol. 187:6354-6362 [http://www.ncbi.nlm.nih.gov/sites/entrez/16159768 PubMed]
 
−
# Bobay, B.G., Mueller, G.A., Thompson, R.J., Venters, R.A., Murzin, A.G., Strauch, M.A. & J. Cavanagh (2006) NMR structure of AbhN and comparison with AbrBN: First Insights into the DNA-binding Promiscuity and Specificity of AbrB-like Transition-state Regulator Proteins. J. Biol. Chem. 281:21399-21409  [http://www.ncbi.nlm.nih.gov/sites/entrez/16702211 PubMed]
 
−
# Jordan S. Rietkötter E. Strauch MA. Kalamorz F. Butcher BG. Helmann JD. Mascher T. (2007) LiaRS-dependent gene expression is embedded in transition state regulation in Bacillus subtilis. Microbiology. 153: 2530-2540. [http://www.ncbi.nlm.nih.gov/sites/entrez/17660417 PubMed]
 
−
# Strauch MA. Bobay BG. Cavanagh J. Yao F. Wilson A. Le Breton Y. (2007) Abh and AbrB control of Bacillus subtilis antimicrobial gene expression. J. of Bacteriol. 189:7720-7732. [http://www.ncbi.nlm.nih.gov/sites/entrez/17720793 PubMed]
 
−
# Hamze et al. (2009) Identification of genes required for different stages of dendritic swarming in ''Bacillus subtilis'', with a novel role for ''phrC''.  ''Microbiology'' '''155:''' 398-412. [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 PubMed]
 
−
# Strauch MA. (1995) AbrB modulates expression and catabolite repression of a Bacillus subtilis ribose transport operon. ''J Bacteriol.'' '''Dec;177(23):'''6727-31. [http://www.ncbi.nlm.nih.gov/sites/entrez/7592460 PubMed]
 
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 07:09, 11 June 2009

  • Description: bacteriocin-like product

Gene name sboX
Synonyms
Essential no
Product bacteriocin-like product
Function unknown
MW, pI 5 kDa, 9.857
Gene length, protein length 150 bp, 50 aa
Immediate neighbours sboA, albA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
SboX context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU37360

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • 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:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • 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

  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "http://subtiwiki-test.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=90312"