Difference between revisions of "Sandbox"

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−
* '''Description:''' competence transcription factor (CTF) <br/><br/>
+
* '''Description:''' transcriptional regulator of transition state genes <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'''
−
|''comK''
+
|''abrB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''cpsX ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || competence transcription factor (CTF)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of competence and DNA uptake
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of gene expression during the transition <br/>from growth to stationary phase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 7.669 
+
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 576 bp, 192 aa
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 10 kDa, 6.57 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhzC]]'', ''[[yhxD]]''
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 288 bp, 96 aa
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12882&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yabC]]'', ''[[metS]]''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:comK_context.gif]]
+
|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" | '''Genetic context''' <br/> [[Image:abrB_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 29: Line 31:
 
__TOC__
 
__TOC__
  
−
<br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
Line 35: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU10420
+
* '''Locus tag:''' BSU00370
  
 
===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/comK.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/abrB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11059]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10100]
  
 
=== Additional information===
 
=== Additional information===
Line 56: Line 60:
 
* '''Protein family:'''
 
* '''Protein family:'''
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[Abh]], [[SpoVT]] (only N-terminal domain)
 +
 
 +
=== 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 68: Line 78:
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:'''
+
* '''Effectors of protein activity:''' interaction with [[AbbA]] results in inactivation of AbrB [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
  
−
* '''Interactions:''' [[MecA]]-[[ComK]] [http://www.ncbi.nlm.nih.gov/sites/entrez/10447896 PubMed]
+
* '''Interactions:''' [[AbrB]]-[[AbbA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 76: Line 86:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''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]
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P40396 P40396]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P08874 P08874]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU10420]
+
* '''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:'''  
+
* '''Operon:''' ''abrB'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
  
−
* '''Regulation:''' repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
+
* '''Regulation:''' expressed at the onset of stationary phase [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
−
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12586407 PubMed]
+
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/2504584 PubMed]** repressed during logrithmic growth ([[AbrB]])
−
* '''Regulatory mechanism:'''  
+
 
−
** [[AbrB]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12586407 PubMed]
+
* '''Regulatory mechanism:''' repressed by [[Spo0A]]-P [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
−
* '''Additional information:'''  
+
** [[AbrB]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/2504584 PubMed]
 +
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' TT731 (aphA3)
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 114: Line 124:
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
  
−
[[Oscar Kuipers]], University of Groningen, The Netherlands
+
[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]
−
[http://molgen.biol.rug.nl/molgen/index.php Homepage]
+
 
 +
[[Mark Strauch]], Baltimore, USA [http://lifesciences.umaryland.edu/Pages/faculty_profile.aspx?ID=212 homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 121: Line 132:
 
=References=
 
=References=
  
−
<pubmed> 10447896, 12028382, 8016067, 10361283, 11703662, 12107147, 17581123, 17493123,16391071,16436435 </pubmed>
+
<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 11:24, 11 June 2009

  • Description: transcriptional regulator of transition state genes

Gene name abrB
Synonyms cpsX
Essential no
Product transcriptional regulator
Function regulation of gene expression during the transition
from growth to stationary phase
Metabolic function and regulation of this protein in SubtiPathways:
Sugar catabolism
MW, pI 10 kDa, 6.57
Gene length, protein length 288 bp, 96 aa
Immediate neighbours yabC, metS
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
AbrB context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU00370

Phenotypes of a mutant

No swarming motility on B medium. PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family:
  • Paralogous protein(s): Abh, SpoVT (only N-terminal domain)

Genes/ operons controlled by AbrB

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity: interaction with AbbA results in inactivation of AbrB PubMed
  • Localization:

Database entries

  • Structure: 1Z0R (N-terminal DNA recognition domain), 1Z0R (N-terminal DNA recognition domain) NCBI PubMed
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Regulation: expressed at the onset of stationary phase PubMed
    • repressed during logrithmic growth (AbrB) PubMed** repressed during logrithmic growth (AbrB)
  • Regulatory mechanism: repressed by Spo0A-P PubMed
  • Additional information:

Biological materials

  • Mutant: TT731 (aphA3)
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Richard Losick, Harvard Univ., Cambridge, USA homepage

Mark Strauch, Baltimore, USA homepage

Your additional remarks

References

  1. 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. PubMed
  2. 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. PubMed
  3. 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 PubMed
  4. 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 PubMed
  5. 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; PubMed, Corrigendum appears in Nature Stuctural & Molecular Biology (2005) 12:380
  6. 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 PubMed
  7. 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 PubMed
  8. 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 PubMed
  9. 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 PubMed
  10. 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 PubMed
  11. 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. PubMed
  12. 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. PubMed
  13. 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. PubMed
  14. 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. PubMed
  15. 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 PubMed
  16. 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 PubMed
  17. 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. PubMed
  18. 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. PubMed
  19. 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. PubMed
  20. Strauch MA. (1995) AbrB modulates expression and catabolite repression of a Bacillus subtilis ribose transport operon. J Bacteriol. Dec;177(23):6727-31. PubMed
  21. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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