Difference between revisions of "Sandbox"

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* '''Description:''' RNase J1<br/><br/>
+
* '''Description:''' low affinity potassium  transporter KtrCD, peripheric membrane component <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'''
−
|''rnjA ''
+
|''ktrC ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykqC''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ylxV, yzaC, ykqB ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || RNase J1
+
|style="background:#ABCDEF;" align="center"| '''Product''' || low affinity potassium  transporter KtrCD, peripheric membrane component (proton symport)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA processing
+
|style="background:#ABCDEF;" align="center"|'''Function''' || potassium uptake
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 61 kDa, 5.902  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 24 kDa, 5.63  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1665 bp, 555 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 663 bp, 221 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[adeC]]'', ''[[ykzG]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykqA]]'', ''[[adeC]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ykqC_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ykqB_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 ===
−
 
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
Line 45: Line 43:
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11813]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10991]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' endonuclease and 5'-3' exonuclease
+
* '''Catalyzed reaction/ biological activity:'''  
  
 
* '''Protein family:'''
 
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[RnjB]]
+
* '''Paralogous protein(s):''' [[KtrA]]
−
 
 
−
=== RNAs  affected by ''rnjA'' ===
 
−
 
 
−
''[[hbs]]'', ''[[thrS]]''
 
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 76: Line 70:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[RnjA]]-[[RnjB]], [[RnjA]]-[[PfkA]], [[RnjA]]-[[PnpA]], [[RnjA]]-[[Rny]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
+
* '''Interactions:''' [[KtrC]]-[[KtrD]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12562800 PubMed]
  
−
* '''Localization:'''
+
* '''Localization:''' peripheral membrane protein [http://www.ncbi.nlm.nih.gov/sites/entrez/12562800 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do;jsessionid=8B071C0C81B11ADEBA3DDC3FF3395811?structureId=3BK1 3BK1] (RNase J from ''Thermus thermophilus'') [http://www.pdb.org/pdb/explore/explore.do?structureId=3BK2 3BK2] (RNase J from ''Thermus thermophilus'', complex with UMP)
+
* '''Structure:'''
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14530]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14510]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
  
 
=== 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]
 
−
 
−
required for ''[[thrS]]'' RNA processing, involved in maturation of the 5’-end of the16S rRNA, 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:'''  
+
* '''Operon:''' ''ktrC'' [http://www.ncbi.nlm.nih.gov/sites/entrez/12562800 PubMed]
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 106: Line 96:
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''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],  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]
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 118: Line 108:
 
* '''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:'''
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
  
−
[[Harald Putzer]], IBPC Paris, France [http://www.ibpc.fr/UPR9073/putzer/recherches_harald.htm Homepage]
+
[[Erhard Bremer]], University of Marburg, Germany [http://www.uni-marburg.de/fb17/fachgebiete/mikrobio/molmibi homepage]
−
 
 
−
[[David Bechhofer]], Mount Sinai School, New York, USA [http://www.mountsinai.org/Research/Centers%20Laboratories%20and%20Programs/Bechhofer%20Laboratory?citype=Physician&ciid=Bechhofer%20David%20H%201255565 Homepage]
 
−
 
 
−
[[Ciaran Condon]], IBPC, Paris, France [http://www.ibpc.fr/UPR9073/condon/index_en.html Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
# 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]
 
−
# Even, S., Pellegrini, O., Zig, L., Labas, V., Vinh, J., Brechemmier-Baey, D., and Putzer, H. (2005) Ribonucleases J1 and J2: Two novel endoribonucleases in B. subtilis with functional  homology to E. coli RNase E. Nucl Acids Res 33, 2141-2152. [http://www.ncbi.nlm.nih.gov/sites/entrez/15831787 PubMed]
 
−
# de la Sierra-Gallay IL, Zig L, Jamalli A, Putzer H. (2008 Structural insights into the dual activity of RNase J. Nat. Struct. Mol. Biol. 15:206-212. [http://www.ncbi.nlm.nih.gov/sites/entrez/18204464 PubMed]
 
−
# Mäder, U., Zig, L., Kretschmer, J., Homuth, G., and Putzer, H. (2008) mRNA processing by RNases J1 and J2 affects Bacillus subtilis gene expression on a global scale. Mol Microbiol 70, 183-196. [http://www.ncbi.nlm.nih.gov/sites/entrez/18713320 PubMed]
 
−
# Commichau, F. M., Rothe, F. M., Herzberg, C., Wagner, E., Hellwig, D., Lehnik-Habrink, M., Hammer, E., Völker, U. & Stülke, J. (2009) Novel activities of glycolytic enzymes in Bacillus subtilis: Interactions with essential proteins involved in mRNA processing. Mol. Cell. Proteomics in press [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
 
−
# Hunt, A., Rawlins, J. P., Thomaides, H. B., and Errington, J. (2006) Functional analysis of 11 putative essential genes in Bacillus subtilis. Microbiology 152, 2895-2907. [http://www.ncbi.nlm.nih.gov/sites/entrez/17005971 PubMed]
 
−
# Deikus, G., Condon, C. & Bechhofer, D. H. (2008). Role of ''Bacillus subtilis'' RNase J1 endonuclease and 5'-exonuclease activities in ''trp'' leader RNA turnover. J Biol Chem. 283:17158-17167. [http://www.ncbi.nlm.nih.gov/sites/entrez/18445592 PubMed]
 
−
# Mathy, N., Bénard, L., Pellegrini, O., Daou, R., Wen, T. & Condon, C. (2007). 5'-to-3' exoribonuclease activity in bacteria: role of RNase J1 in rRNA maturation and 5' stability of mRNA. Cell 129:681-692. [http://www.ncbi.nlm.nih.gov/sites/entrez/17512403 PubMed]
 
−
# Britton et al. (2007) Maturation of the 5' end of Bacillus subtilis 16S rRNA by the essential ribonuclease YkqC/RNase J1. Mol. Microbiol. 63: 127-138. [http://www.ncbi.nlm.nih.gov/sites/entrez/17229210 PubMed]
 
−
# Yao, S., Blaustein, J. B. & Bechhofer, D. H. (2007). Processing of ''Bacillus subtilis'' small cytoplasmic RNA: evidence for an additional endonuclease cleavage site. Nucleic Acids Res. 35:4464-4473. [http://www.ncbi.nlm.nih.gov/sites/entrez/17576666 PubMed]
 
−
# Daou-Chabo R, Mathy N, Bénard L, Condon C. (2009) Ribosomes initiating translation of the ''hbs'' mRNA protect it from 5'-to-3' exoribonucleolytic degradation by RNase J1.  ''Mol. Microbiol.'' '''71:''' 1538-1550. [http://www.ncbi.nlm.nih.gov/sites/entrez/19210617 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 20:02, 15 April 2009

  • Description: low affinity potassium transporter KtrCD, peripheric membrane component

Gene name ktrC
Synonyms ylxV, yzaC, ykqB
Essential no
Product low affinity potassium transporter KtrCD, peripheric membrane component (proton symport)
Function potassium uptake
MW, pI 24 kDa, 5.63
Gene length, protein length 663 bp, 221 aa
Immediate neighbours ykqA, adeC
Hier soll was neues rein
Genetic context
YkqB context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

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): KtrA

Extended information on the protein

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

Database entries

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

Additional information

Expression and regulation

  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Erhard Bremer, University of Marburg, Germany homepage

Your additional remarks

References

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