Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' transcriptional pleiotropic regulator invoved in global nitrogen regulation <br/><br/>
+
* '''Description:''' RNA polymerase sigma factor SigI <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'''
−
|''tnrA''
+
|''sigI''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''scgR ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykoZ ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || transcription activator/ repressor
+
|style="background:#ABCDEF;" align="center"| '''Product''' || RNA polymerase sigma factor SigI
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' ||regulation of nitrogen assimilation <br/>(positive regulation of nrgAB, nasBCDEF, gabP,<br/> ureABC, guaD; negative regulation of glnRA, gltAB)
+
|style="background:#ABCDEF;" align="center"|'''Function''' || control of a class of heat shock genes
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 12 kDa, 10.235  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 8.306  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 330 bp, 110 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 753 bp, 251 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mgtE]]'', ''[[ykzB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykoY]]'', ''[[rsgI]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13188&#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:CAB13218&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:tnrA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:sigI_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 29:
 
__TOC__
 
__TOC__
  
−
<br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
Line 38: Line 38:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
temperature-sensitive growth on agar plates [http://www.ncbi.nlm.nih.gov/sites/entrez/11157964 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/tnrA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sigI-rsgI.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11805]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13269]
  
 
=== Additional information===
 
=== Additional information===
Line 58: Line 60:
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
  
−
=== Genes/ operons controlled by TnrA ===
+
=== Members of the SigI regulon ===
  
−
* '''Activation by TnrA:''' ''[[nrgA]]-[[nrgB]]''
+
''[[gsiB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/11157964 PubMed], ''[[mreBH]], [[bcrC]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/18156261 PubMed]
−
 
 
−
* '''Repression by TnrA:''' ''[[degS]]-[[degU]]'', ''[[gltA]]-[[gltB]]''
 
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 74: Line 74:
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:''' feedback-inhibited [[GlnA]] prevents TnrA from DNA binding
+
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[TnrA]]-[[GlnA]],  [[TnrA]]-[[NrgB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17001076 PubMed], [[TnrA]]-[[GlnA]], this interaction results in loss of TnrA DNA-binding activity
+
* '''Interactions:''' [[RsgI]]-[[SigI]],  [[RsgI]]-[[SigI]], the interaction inhibits SigI activity [http://www.ncbi.nlm.nih.gov/sites/entrez/17185538 PubMed]
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 86: Line 86:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU13310]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU13450]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 95: Line 95:
  
 
* '''Operon:'''  
 
* '''Operon:'''  
 +
* '''Operon:''' ''[[sigI]]-[[rsgI]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/17185538 PubMed]
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:''' [[SigI]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17185538 PubMed]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' induced by heat [http://www.ncbi.nlm.nih.gov/sites/entrez/17185538 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 116: Line 117:
 
* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
  
−
* '''Antibody:''' available in the [[Karl Forchhammer]] lab
+
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Susan Fisher]], Boston, USA [http://www.bumc.bu.edu/microbiology/research/susan-h-fisher-phd/ homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 126: Line 125:
 
=References=
 
=References=
  
−
# Wray LV Jr, Ferson AE, Rohrer K, Fisher SH (1996) TnrA, a transcription factor required for global nitrogen regulation in Bacillus subtilis. Proc Natl Acad Sci USA 93:8841-8845. [http://www.ncbi.nlm.nih.gov/sites/entrez/8799114 PubMed]
+
# Asai K, Ootsuji T, Obata K, Matsumoto T, Fujita Y, Sadaie Y. (2007) Regulatory role of RsgI in ''sigI'' expression in ''Bacillus subtilis''. ''Microbiology'' '''153:''' 92-101. [http://www.ncbi.nlm.nih.gov/sites/entrez/17185538 PubMed]
−
# Yoshida K, et al. (2003) Identification of additional TnrA-regulated genes of ''Bacillus subtilis'' associated with a TnrA box. ''Mol Microbiol'' '''49:''' 157-65. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12823818 PubMed]
+
# Zuber, U., K. Drzewiecki, and M. Hecker (2001) Putative sigma factor SigI (YkoZ) of ''Bacillus subtilis'' is induced by heat shock ''J. Bacteriol.'' '''183:''' 1472-1475. [http://www.ncbi.nlm.nih.gov/sites/entrez/11157964 PubMed]
−
# Wray LV Jr, Zalieckas JM, Fisher SH. (2001) ''Bacillus subtilis'' glutamine synthetase controls gene expression through protein-protein interaction with transcription factor TnrA. Cell 107:427-435. [http://www.ncbi.nlm.nih.gov/sites/entrez/11719184 PubMed]
+
# Tseng, C. L., and Shaw, G. C. (2008) Genetic evidence for the actin homolog gene ''mreBH'' and the bacitracin resistance gene ''bcrC'' as targets of the alternative sigma factor SigI of ''Bacillus subtilis''. ''J. Bacteriol.'' '''190:''' 1561-1567. [http://www.ncbi.nlm.nih.gov/sites/entrez/18156261 PubMed]
−
# Belitsky, B. R., and Sonenshein, A. L. (2004) Modulation of activity of ''Bacillus subtilis'' regulatory proteins GltC and TnrA by glutamate dehydrogenase. J Bacteriol 186: 3399-3407.[http://www.ncbi.nlm.nih.gov/sites/entrez/15150225 PubMed]
 
−
# Belitsky, B. R., Wray, L. V., Jr., Fisher, S. H., Bohannon, D. E. & Sonenshein, A. L. (2000). Role of TnrA in nitrogen source-dependent repression of ''Bacillus subtilis'' glutamate synthase gene expression. J Bacteriol 182, 5939-5947. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11029411 PubMed]
 
−
# Heinrich, A., Woyda, K., Brauburger, K., Meiss, G., Detsch, C., Stülke, J. & Forchhammer, K. (2006) Interaction of the membrane-bound GlnK-AmtB complex with the master regulator of nitrogen metabolism TnrA in ''Bacillus subtilis''. J. Biol. Chem. 281: 34909-34917. [http://www.ncbi.nlm.nih.gov/sites/entrez/17001076 PubMed]
 
−
# Tojo S, Satomura T, Morisaki K, Yoshida KI, Hirooka K, Fujita Y: Negative transcriptional regulation of the ''ilv-leu'' operon for biosynthesis of branched-chain amino acids through the ''Bacillus subtilis'' global regulator TnrA. J Bacteriol 2004, 186:7971-7979. [http://www.ncbi.nlm.nih.gov/sites/entrez/15547269 PubMed]
 
−
# Fisher, S. H., Brandenburg, J. L. & Wray, L. V. (2002). Mutations in ''Bacillus subtilis'' glutamine synthetase that block its interaction with transcription factor TnrA. Mol Microbiol 45, 627-635. [http://www.ncbi.nlm.nih.gov/sites/entrez/12139611 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 23:56, 27 April 2009

  • Description: RNA polymerase sigma factor SigI

Gene name sigI
Synonyms ykoZ
Essential no
Product RNA polymerase sigma factor SigI
Function control of a class of heat shock genes
MW, pI 29 kDa, 8.306
Gene length, protein length 753 bp, 251 aa
Immediate neighbours ykoY, rsgI
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
SigI context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

temperature-sensitive growth on agar plates 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):

Members of the SigI regulon

gsiB PubMed, mreBH, bcrC PubMed

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Localization:

Database entries

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

Additional information

Expression and regulation

  • Regulation: induced by heat PubMed
  • Regulatory mechanism:
  • 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. Asai K, Ootsuji T, Obata K, Matsumoto T, Fujita Y, Sadaie Y. (2007) Regulatory role of RsgI in sigI expression in Bacillus subtilis. Microbiology 153: 92-101. PubMed
  2. Zuber, U., K. Drzewiecki, and M. Hecker (2001) Putative sigma factor SigI (YkoZ) of Bacillus subtilis is induced by heat shock J. Bacteriol. 183: 1472-1475. PubMed
  3. Tseng, C. L., and Shaw, G. C. (2008) Genetic evidence for the actin homolog gene mreBH and the bacitracin resistance gene bcrC as targets of the alternative sigma factor SigI of Bacillus subtilis. J. Bacteriol. 190: 1561-1567. PubMed
  4. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=62451"