Difference between revisions of "Sandbox"

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* '''Description:''' Transcriptional regulator Spx, involved in regulation of many genes. <br/><br/>
+
* '''Description:''' NAD kinase <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''
+
|''nadF''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yjbD ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yjbN, ppnK''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator Spx
+
|style="background:#ABCDEF;" align="center"| '''Product''' || inorganic polyphosphate/ATP-NAD kinase
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || negative and positive regulator of many genes
+
|style="background:#ABCDEF;" align="center"|'''Function''' || generation of NADP from NAD
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 15,5 kDa, 7.80
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.991 
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 393 bp, 131 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 798 bp, 266 aa
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yjbC]]'', ''[[yjbE]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yjbM]]'', ''[[yjbO]]''
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13007&#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:CAB13018&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:spx_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yjbN_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 36: Line 35:
 
=== 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.
+
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yjbCD.html]
+
* '''DBTBS entry:''' no entry
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13133 link]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13143]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 54: Line 54:
 
=== 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 64: Line 64:
 
* '''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):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
* '''Interactions:''' [[Spx]]-[[YjbH]],  [[RpoA]]-[[Spx]],  [[Spx]]-[[YjbH]],  [[RpoA]]-[[Spx]],  [[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:'''
 +
 
 
* '''Localization:''' Cytoplasm
 
* '''Localization:''' Cytoplasm
  
 
=== 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+BSU11610]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
* '''Operon:''' ''[[yjbC]]-[[spx]]'', ''[[spx]]''
+
* '''Operon:'''  
  
* '''[[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]]:'''  
:::: 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:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed], Transcription is represed by [[PerR]] and [[YodB ]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17158660 PubMed]
+
* '''Regulation:'''  
  
* '''Regulatory mechanism:''' transcription repression
+
* '''Regulatory mechanism:'''  
  
* '''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:'''  
 
 
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:'''
  
 
=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]
 
 
[[Richard Brennan]], Houston, Texas, USA [http://www.mdanderson.org/departments/biochem/display.cfm?id=556ef368-6c81-4043-b74f350d41dd06cb&method=displayfull&pn=a8427ebd-d0ff-11d4-80fd00508b603a14 Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 128: Line 120:
 
=References=
 
=References=
  
# H&ouml;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]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID 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]
 
# 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]
 
# 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]
 
# 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]
 
# 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]
 
# 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]
 
# 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]
 
# 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 01:58, 30 April 2009

  • Description: NAD kinase

Gene name nadF
Synonyms yjbN, ppnK
Essential yes PubMed
Product inorganic polyphosphate/ATP-NAD kinase
Function generation of NADP from NAD
MW, pI 29 kDa, 5.991
Gene length, protein length 798 bp, 266 aa
Immediate neighbours yjbM, yjbO
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YjbN context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

essential PubMed

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

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: Cytoplasm

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation:
  • 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. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed