Difference between revisions of "Sandbox"

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−
* '''Description:''' Transcriptional regulator Spx, involved in regulation of many genes. <br/><br/>
+
* '''Description:''' general stress protein, similar to L25 <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'''
−
|''spx''
+
|''ctc''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yjbD ''
+
|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 Spx
+
|style="background:#ABCDEF;" align="center"| '''Product''' || ribosomal protein
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || negative and positive regulator of many genes
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 15,5 kDa, 7.80
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 4.216 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 393 bp, 131 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 612 bp, 204 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yjbC]]'', ''[[yjbE]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[prs]]'', ''[[spoVC]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/spx_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ctc_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/spx_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ctc_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:spx_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ctc_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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<br/><br/>
 
<br/><br/>
−
 
  
 
=The gene=
 
=The gene=
Line 37: Line 36:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 1227010 - 1227402
+
* '''Coordinates:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
Loss of up-regulation of the methionine sulfoxide reductase (''[[mrsA]]-[[mrsB]]'') operon in response to thiol specific oxidative stress, also loss of ''[[trxA]]'' and ''[[trxB]]'' upregulation in response to thiol specific oxidative stress.
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yjbCD.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gcaD-prs-ctc.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13133 link]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10115]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 55: Line 53:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Transcriptional regulator of  many genes in response to thiol specific oxidative stress (transcription activator of'' [[trxA]]'' and ''[[trxB]]''). In addition, Spx inhibits transcription by binding to the C-terminal domain of the alpha subunit of RNAP ([[RpoA]]), disrupting complex formation between RNAP and certain transcriptional activator proteins like [[ResD]] and [[ComA]]. In response to thiol specific oxidative stress, Spx can also activate transcription, making it a general regulator that exerts both positive and negative control over transcription initiation.
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' Arsenate Reductase (ArsC) family, Spx subfamily
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[MgsR]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 65: Line 63:
 
* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:''' CXXC (10-13): Acts as a disulfide switch for the redox-sensitive transcriptional regulation of genes that function in thiol homeostasis.
+
* '''Domains:'''  
  
−
* '''Modification:''' Cysteine oxidation of the CXXC motif
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 73: Line 71:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[YjbH]]-[[Spx]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19074380 PubMed], [[Spx]]-[[RpoA]] (C-terminal domain [http://www.ncbi.nlm.nih.gov/sites/entrez/12642660 PubMed]
+
* '''Interactions:''' binds 5S rRNA [http://www.ncbi.nlm.nih.gov/sites/entrez/12432960 PubMed]
−
* '''Localization:'''
+
 
 +
* '''Localization:''' in the ribosome (large subunit) [http://www.ncbi.nlm.nih.gov/sites/entrez/12432960 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' complex with C-terminal domain of [[RpoA]] [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=35536 NCBI]
+
* '''Structure:'''
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU11500]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00520]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 88: Line 87:
 
=== Additional information===
 
=== Additional information===
  
−
 
+
:* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[yjbC]]-[[spx]]'', ''[[spx]]''
+
* '''Operon:''' ''[[gcaD]]-[[prs]]-[[ctc]]'', ''[[ctc]]''
  
−
* '''Sigma factor:''' four promoters upstream of ''[[yjbC]]'': [[SigW]], [[SigB]], [[SigX]], and unknown sigma [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+10913081 PubMed]
+
* '''Sigma factor:''' ''[[gcaD]]'': [[SigA]], ''[[ctc]]'': [[SigB]]
−
promoters upstream of ''spx'': [[SigA]], [[SigW]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+10913081 PubMed], [[SigM]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17434969 PubMed]
 
  
−
* '''Regulation:''' Transcription is represed by [[PerR]] and [[YodB ]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17158660 PubMed]
+
* '''Regulation:''' induced under stress conditions
  
−
* '''Regulatory mechanism:''' transcription repression
+
* '''Regulatory mechanism:''' alternative sigma factor, [[SigB]]
  
−
* '''Additional information:'''Post-translational control by [[ClpX]]-[[ClpP]]: Spx naturally contains a C-terminal sequence that resembles the [[SsrA]] tag and targets the protein for degradation. [http://www.ncbi.nlm.nih.gov/pubmed/12642660?ordinalpos=27&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed]
+
* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
−
 
 
−
Proteolysis is enhanced by [[YjbH]]. [http://www.ncbi.nlm.nih.gov/pubmed/19074380?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed]
 
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' ORB6781 (spc), ORB6876 (tet), available in [[Zuber]] lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
−
+
       
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
+
* '''two-hybrid system:'''  
  
−
* '''Antibody:'''
+
* '''Antibody:''' available in [[Stülke]] lab
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Peter Zuber]], Oregon Health and Science University, USA
 
−
[http://www.ogi.edu/people/dsp_person.cfm?person_id=411D6801-2A56-D16D-58A06B4480EDB9C7 Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 127: Line 120:
 
=References=
 
=References=
  
−
# H�per et al. (2005)Comprehensive Characterization of the Contribution of Individual ''[[SigB]]''-Dependent General Stress Genes to Stress Resistance of ''Bacillus subtilis''. J. Bact. '''187:''' 2810-2826  [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
+
# HU+00F6per et al. (2005)Comprehensive Characterization of the Contribution of Individual ''[[SigB]]''-Dependent General Stress Genes to Stress Resistance of ''Bacillus subtilis''. J. Bact. '''187:''' 2810-2826  [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
−
# Choi, S. Y., D. Reyes, M. Leelakriangsak, and P. Zuber. 2006. The global regulator Spx functions in the control of organosulfur metabolism in Bacillus subtilis. J. Bacteriol. 188:5741-5751. [http://www.ncbi.nlm.nih.gov/sites/entrez/16885442 PubMed]
+
# Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
−
# Eiamphungporn, W., and J. D. Helmann. 2008. The Bacillus subtilis sigma(M) regulon and its contribution to cell envelope stress responses. Mol. Microbiol. 67:830-848. [http://www.ncbi.nlm.nih.gov/sites/entrez/18179421 PubMed]
+
# Schmalisch, M., Langbein, I. & Stülke, J. (2002) The general stress protein Ctc of ''Bacillus subtilis'' is a ribosomal protein. J. Mol. Microbiol. Biotechnol. 4: 495-501. [http://www.ncbi.nlm.nih.gov/sites/entrez/12432960 PubMed]
−
# Garg et al. 2009. The YjbH protein of Bacillus subtilis enhances ClpXP-catalyzed proteolysis of Spx. J. Bacteriol. 191: 1268-1277. [http://www.ncbi.nlm.nih.gov/sites/entrez/19074380 PubMed]
+
# Ollington, J. F., Haldenwang, W. G., Huynh, T. V. and Losick, R. 1981. Developmentally regulated transcription in a cloned segment of the ''Bacillus subtilis'' chromosome. J. Bacteriol. 147: 432-442. [http://www.ncbi.nlm.nih.gov/sites/entrez/6790515 PubMed]
−
# Jervis et al. 2007. SigM-responsive genes of ''Bacillus subtilis'' and their promoters. J. Bacteriol. 189: 4534-4538. [http://www.ncbi.nlm.nih.gov/sites/entrez/17434969 PubMed]
+
# Truitt, C. L., Weaver, E. A. and Haldenwang, W. G. 1988. Effects on growth and sporulation of inactivation of a ''Bacillus subtilis'' gene (''ctc'') transcribed in vitro by minor vegetative cell RNA polymerases (E-sigma(37), E-sigma(32)). Mol. Gen. Genet. 212: 166-171. [http://www.ncbi.nlm.nih.gov/sites/entrez/2836704 PubMed]
−
# Larsson, J. T., A. Rogstam, and C. von Wachenfeldt. 2007. YjbH is a novel negative effector of the disulphide stress regulator, Spx, in Bacillus subtilis. Mol. Microbiol. 66:669-684. [http://www.ncbi.nlm.nih.gov/sites/entrez/17908206 PubMed]
+
# Haldenwang, W. G. & Losick, R. (1979). A modified RNA polymerase transcribes a cloned gene under sporulation control in ''Bacillus subtilis''. Nature 282, 256-260 [http://www.ncbi.nlm.nih.gov/pubmed/116131 PubMed]
−
# Leelakriangsak, M., K. Kobayashi, and P. Zuber. 2007. Dual negative control of spx transcription initiation from the P3 promoter by repressors PerR and YodB in Bacillus subtilis. J. Bacteriol. 189:1736-1744. [http://www.ncbi.nlm.nih.gov/sites/entrez/17158660 PubMed]
+
# Gongadze GM, Korepanov AP, Korobeinikova AV, Garber MB (2008) Bacterial 5S rRNA-binding proteins of the CTC family. ''Biochemistry (Moscow)'' '''73:''' 1405-1417. [http://www.ncbi.nlm.nih.gov/sites/entrez/19216708 PubMed]
−
# Nakano, M. M., F. Hajarizadeh, Y. Zhu, and P. Zuber. 2001. Loss-of-function mutations in yjbD result in ClpX- and ClpP-independent competence development of Bacillus subtilis. Mol. Microbiol. 42:383-394.[http://www.ncbi.nlm.nih.gov/sites/entrez/11703662 PubMed]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Nakano, S., K. N. Erwin, M. Ralle, and P. Zuber. 2005. Redox-sensitive transcriptional control by a thiol/disulphide switch in the global regulator, Spx. Mol. Microbiol. 55:498-510. [http://www.ncbi.nlm.nih.gov/sites/entrez/15659166 PubMed]
 
−
# Nakano, S., E. Küster-Schöck, A. D. Grossman, and P. Zuber. 2003. Spx dependent global transcriptional control is induced by thiol-specific oxidative stress in Bacillus subtilis. Proc. Natl. Acad. Sci. USA 100:13603-13608. [http://www.ncbi.nlm.nih.gov/sites/entrez/14597697 PubMed]
 
−
# Nakano, S., M. M. Nakano, Y. Zhang, M. Leelakriangsak, and P. Zuber. 2003. A regulatory protein that interferes with activator-stimulated transcription in bacteria. Proc. Natl. Acad. Sci. USA 100:4233-4238. [http://www.ncbi.nlm.nih.gov/sites/entrez/12642660 PubMed]
 
−
# Nakano, S., G. Zheng, M. M. Nakano, and P. Zuber. 2002. Multiple pathways of Spx (YjbD) proteolysis in Bacillus subtilis. J. Bacteriol. 184:3664-3670. [http://www.ncbi.nlm.nih.gov/sites/entrez/12057962 PubMed]
 
−
# Newberry, K. J., S. Nakano, P. Zuber, and R. G. Brennan. 2005. Crystal structure of the Bacillus subtilis anti-alpha, global transcriptional regulator, Spx, in complex with the alpha C-terminal domain of RNA polymerase. Proc. Natl. Acad. Sci. USA 102:15839-15844. [http://www.ncbi.nlm.nih.gov/sites/entrez/16249335 PubMed]
 
−
# Petersohn, A., J. Bernhardt, U. Gerth, D. Hoper, T. Koburger, U. Volker, and M. Hecker. 1999. Identification of sigma(B)-dependent genes in Bacillus subtilis using a promoter consensus-directed search and oligonucleotide hybridization. J. Bacteriol. 181:5718-5724. [http://www.ncbi.nlm.nih.gov/sites/entrez/10482513 PubMed]
 
−
# Reyes, D. Y. and P. Zuber. 2008. Activation of transcription initiation by Spx: formation of a transcription complex and identification of a cis-acting element required for transcriptional activation. Mol. Microbiol. 69:765-779. [http://www.ncbi.nlm.nih.gov/sites/entrez/18687074 PubMed]
 
−
# Thackray, P. D., and A. Moir. 2003. SigM, an extracytoplasmic function sigma factor of Bacillus subtilis, is activated in response to cell wall antibiotics, ethanol, heat, acid, and superoxide stress. J. Bacteriol. 185:3491-3498. [http://www.ncbi.nlm.nih.gov/sites/entrez/12775685 PubMed]
 
−
# Zhang, Y., S. Nakano, S. Y. Choi, and P. Zuber. 2006. Mutational analysis of the Bacillus subtilis RNA polymerase alpha C-terminal domain supports the interference model of Spx-dependent repression. J. Bacteriol. 188:4300-4311. [http://www.ncbi.nlm.nih.gov/sites/entrez/16740936 PubMed]
 
−
# Zhang, Y., and P. Zuber. 2007. Requirement of the zinc-binding domain of ClpX for Spx proteolysis in Bacillus subtilis and effects of disulfide stress on ClpXP activity. J. Bacteriol. 189:7669-7680. [http://www.ncbi.nlm.nih.gov/sites/entrez/17827297 PubMed]
 
−
# Zuber, P. 2004. Spx-RNA polymerase interaction and global transcriptional control during oxidative stress. J. Bacteriol. 186:1911-1918. [http://www.ncbi.nlm.nih.gov/sites/entrez/15028674 PubMed]
 

Revision as of 15:21, 27 March 2009

  • Description: general stress protein, similar to L25

Gene name ctc
Synonyms
Essential no
Product ribosomal protein
Function unknown
MW, pI 21 kDa, 4.216
Gene length, protein length 612 bp, 204 aa
Immediate neighbours prs, spoVC
Gene sequence (+200bp) Protein sequence
Genetic context
Ctc context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

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: binds 5S rRNA PubMed
  • Localization: in the ribosome (large subunit) PubMed

Database entries

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

Additional information

  • subject to Clp-dependent proteolysis upon glucose starvation PubMed

Expression and regulation

  • Regulation: induced under stress conditions
  • Regulatory mechanism: alternative sigma factor, SigB
  • Additional information: subject to Clp-dependent proteolysis upon glucose starvation PubMed

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody: available in Stülke lab

Labs working on this gene/protein

Your additional remarks

References

  1. HU+00F6per et al. (2005)Comprehensive Characterization of the Contribution of Individual SigB-Dependent General Stress Genes to Stress Resistance of Bacillus subtilis. J. Bact. 187: 2810-2826 PubMed
  2. Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 PubMed
  3. Schmalisch, M., Langbein, I. & Stülke, J. (2002) The general stress protein Ctc of Bacillus subtilis is a ribosomal protein. J. Mol. Microbiol. Biotechnol. 4: 495-501. PubMed
  4. Ollington, J. F., Haldenwang, W. G., Huynh, T. V. and Losick, R. 1981. Developmentally regulated transcription in a cloned segment of the Bacillus subtilis chromosome. J. Bacteriol. 147: 432-442. PubMed
  5. Truitt, C. L., Weaver, E. A. and Haldenwang, W. G. 1988. Effects on growth and sporulation of inactivation of a Bacillus subtilis gene (ctc) transcribed in vitro by minor vegetative cell RNA polymerases (E-sigma(37), E-sigma(32)). Mol. Gen. Genet. 212: 166-171. PubMed
  6. Haldenwang, W. G. & Losick, R. (1979). A modified RNA polymerase transcribes a cloned gene under sporulation control in Bacillus subtilis. Nature 282, 256-260 PubMed
  7. Gongadze GM, Korepanov AP, Korobeinikova AV, Garber MB (2008) Bacterial 5S rRNA-binding proteins of the CTC family. Biochemistry (Moscow) 73: 1405-1417. PubMed
  8. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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