Difference between revisions of "Sandbox"

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−
* '''Description:''' transcriptional regulator of transition state genes <br/><br/>
+
* '''Description:''' citrate synthase <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''
+
|''citZ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''cpsX ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citA2 ''
 
|-
 
|-
−
|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''' || citrate synthase II
 
|-
 
|-
−
|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''' || TCA cycle
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 10 kDa, 6.57  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 5.451  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 288 bp, 96 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1116 bp, 372 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yabC]]'', ''[[metS]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytwI]], [[icd]]''
 
|-
 
|-
−
|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:CAB14874&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:abrB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:citZ_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 38: Line 38:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
+
glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]
−
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/citZ-icd-mdh.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10100]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10855]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 53:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' acetyl-CoA + oxaloacetate ---> citrate, the reaction is irreversible
−
 
 
−
* '''Protein family:'''
 
−
 
 
−
* '''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]]''
+
* '''Protein family:''' citrate synthase family
  
−
* ''' Repressed by AbrB:''' ''[[abrB]], [[aprE]], [[ftsA]]-[[ftsZ]], [[kinC]], [[motA]], [[nprE]], [[pbpE]], [[spo0H]], [[spoVG]], [[spo0E]], [[tycA]], [[sbo]]-[[alb]], [[yqxM]]-[[sipW]]-[[tasA]]''
+
* '''Paralogous protein(s):''' [[MmgD]], [[CitA]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 72: Line 65:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylation on Ser-284 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
  
 
* '''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:''' inhibited by ATP [http://www.ncbi.nlm.nih.gov/sites/entrez/4980242 PubMed]
  
−
* '''Interactions:''' [[AbrB]]-[[AbbA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
+
* '''Interactions:'''
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 84: Line 77:
 
=== 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:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2C6X 2C6X]
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P08874 P08874]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39120 P39120]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00370]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29140]
 +
 
 +
* '''E.C. number:'''  4.1.3.7
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''abrB'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
+
* '''Operon:''' ''[[citZ]]-[[icd]]-[[mdh]]''
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
+
* '''Sigma factor:''' [[SigA]]
  
−
* '''Regulation:''' expressed at the onset of stationary phase [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
+
* '''Regulation:''' repressed by glucose (6.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed], repression under anaerobic conditions [http://www.ncbi.nlm.nih.gov/pubmed/9642180 PubMed]
  
−
* '''Regulatory mechanism:''' repressed by [[Spo0A]]-P [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  [[CcpA]]: transcription repression, [[CcpC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 107: Line 101:
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' TT731 (aphA3)
+
* '''Mutant:''' GP678 (erm), available in [[Stülke]] lab
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 117: Line 111:
 
* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
  
−
* '''Antibody:'''
+
* '''Antibody:''' available in [[Linc Sonenshein]] lab
  
 
=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]
+
[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]
  
−
[[Mark Strauch]], Baltimore, USA [http://lifesciences.umaryland.edu/Pages/faculty_profile.aspx?ID=212 homepage]
+
[[Stülke|Jörg Stülke]], University of Göttingen, Germany
 +
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 129: Line 124:
 
=References=
 
=References=
  
−
# 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]
+
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 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]
+
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model  bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707  [http://www.ncbi.nlm.nih.gov/pubmed/17218307 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]
+
# Kim HJ, Roux A, Sonenshein AL (2002b) Direct and indirect roles of CcpA in regulation of ''Bacillus subtilis'' Krebs cycle genes. Mol Microbiol 45:179-190. [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 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]
+
# Nakano MM, Zuber P, Sonenshein AL (1998) Anaerobic regulation of ''Bacillus subtilis'' Krebs cycle genes. ''J Bacteriol.'' '''180:''' 3304-3311. [http://www.ncbi.nlm.nih.gov/pubmed/9642180 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
+
# Jin S, Sonenshein AL  (1994) Identification of two distinct ''Bacillus subtilis'' citrate synthase genes ''J Bacteriol.'' '''176:''' 4669-4679. [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]
−
# 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 22:33, 6 May 2009

  • Description: citrate synthase

Gene name citZ
Synonyms citA2
Essential no
Product citrate synthase II
Function TCA cycle
MW, pI 41 kDa, 5.451
Gene length, protein length 1116 bp, 372 aa
Immediate neighbours ytwI, icd
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
CitZ context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

glutamate auxotrophy and a defect in sporulation PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: acetyl-CoA + oxaloacetate ---> citrate, the reaction is irreversible
  • Protein family: citrate synthase family

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylation on Ser-284 PubMed
  • Cofactor(s):
  • Effectors of protein activity: inhibited by ATP PubMed
  • Interactions:
  • Localization:

Database entries

  • KEGG entry: [3]
  • E.C. number: 4.1.3.7

Additional information

Expression and regulation

  • Regulation: repressed by glucose (6.7-fold) (CcpA) PubMed, catabolite repression (CcpA), repression by glucose + glutamate (CcpC) PubMed, repression under anaerobic conditions PubMed
  • Regulatory mechanism: CcpA: transcription repression, CcpA: transcription repression, CcpC: transcription repression PubMed
  • Additional information:

Biological materials

  • Mutant: GP678 (erm), available in Stülke lab
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:

Labs working on this gene/protein

Linc Sonenshein, Tufts University, Boston, MA, USA Homepage

Jörg Stülke, University of Göttingen, Germany Homepage

Your additional remarks

References

  1. Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab Eng. 5: 133-149 PubMed
  2. Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed
  3. Kim HJ, Roux A, Sonenshein AL (2002b) Direct and indirect roles of CcpA in regulation of Bacillus subtilis Krebs cycle genes. Mol Microbiol 45:179-190. PubMed
  4. Nakano MM, Zuber P, Sonenshein AL (1998) Anaerobic regulation of Bacillus subtilis Krebs cycle genes. J Bacteriol. 180: 3304-3311. PubMed
  5. Jin S, Sonenshein AL (1994) Identification of two distinct Bacillus subtilis citrate synthase genes J Bacteriol. 176: 4669-4679. PubMed
  6. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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