Difference between revisions of "Sandbox"

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* '''Description:''' MreD is a cell shape determining protein and is associated with the MreB cytoskeleton in B. subtilis and other rod shaped bacteria. <br/><br/>
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* '''Description:''' ribosomal protein <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'''
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|''mreD''
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|''rpsD''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''rodB ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Essential''' || yes  
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || cell-shape determining protein
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|style="background:#ABCDEF;" align="center"| '''Product''' || ribosomal protein S4 (BS4)
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || cell-shape determation
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|style="background:#ABCDEF;" align="center"|'''Function''' || translation
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 19 kDa, 7.906  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 10.243  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 516 bp, 172 aa  
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 600 bp, 200 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[minC]]'', ''[[mreC]]''
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytrP]]'', ''[[tyrS]]''
 
|-
 
|-
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|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14761&#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:CAB14944&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
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|colspan="2" | '''Genetic context''' <br/> [[Image:mreD_context.gif]]
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|colspan="2" | '''Genetic context''' <br/> [[Image:rpsD_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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=== Basic information ===
 
=== Basic information ===
  
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* '''Locus tag:''' BSU28010
+
* '''Locus tag:''' BSU29660
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
  
−
the phenotype of ''mreD'' is similar to that of ''[[mreC]]''.  ''mreD'' is essential under normal conditions [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed].  Depletion of MreD leads to a progressive increase in the width and a decrease in the length of the cell and cells become lytic. In the depletion strain, lysis can be prevented and cell growth, but not cell shape, can be recovered by inculaion of Magnesium in the media.  This shape defect is consistent with a role for ''mreD'' in cell wall synthesis during elongation and has a similar phenotype to other genes with roles in elongation.
+
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
−
 
 
  
 
=== Database entries ===
 
=== Database entries ===
  
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* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/mreBCD-minCD.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rpsD.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10328]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10372]
  
−
= Additional information=
+
=== Additional information===
−
 
 
−
 
 
−
===Function===
 
−
 
 
−
MreD functions in cell wall synthesis by, together with the MreB cytoskeleton, localizing the cell wall synthetic machinery to the correct part of the cell.  As a transmembrane protein MreD is thought to provide a patch on the membrane that MreB inteacts with.  MreC therefore ensures that the cell wall is made in the correct way to maintain the proper shape of the cell.
 
−
 
 
−
===''mreD'' and the mapping of ''mre-min'' operon===
 
  
−
The ''mre-min'' operon was first sequenced by levin et al in 1992.  The temperature sentitive ''rodB1'' mutation mapperd to that region.
 
  
 
=The protein=
 
=The protein=
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' None/ structural
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' mreD family (according to Swiss-Prot) COG2891
+
* '''Protein family:''' ribosomal protein S4P family (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):''' None
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' None
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1C06 1C06] (Geobacillus stearothermophilus)
  
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* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/Q01467 Q01467]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P21466 P21466]
  
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* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28010]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29660]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
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* '''Operon:''' ''[[mreB]]''-''[[mreC]]''-'''mreD'''-''[[minC]]''-''[[minD]]''
+
* '''Operon:'''  
  
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* '''[[Sigma factor]]:''' [[SigH]] [http://www.ncbi.nlm.nih.gov/sites/entrez/8459776 PubMed]
+
* '''Sigma factor:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
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* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' A conditional mutant with an inframe deletion of ''mreD'' complemented by a xylose inducible copy at an ectopic locus (strain named 4352) is avaliable from the Errington Group.
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
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* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
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* '''GFP fusion:''' A functional N-terminal GFP fusion has been made where the fusion protein is the only copy of the gene in the cell: strain 3416 [http://www.ncbi.nlm.nih.gov/pubmed/16101995 PubMed].
+
* '''GFP fusion:'''
−
 
 
  
 
* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Peter Graumann]], Freiburg University, Germany [http://www.biologie.uni-freiburg.de/data/bio2/graumann/index.htm homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed>1400224,18156271,16101995,, </pubmed>
+
<pubmed>1699930,2121712,6420647,1400226,1906866,, </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 09:00, 13 June 2009

  • Description: ribosomal protein

Gene name rpsD
Synonyms
Essential yes PubMed
Product ribosomal protein S4 (BS4)
Function translation
MW, pI 22 kDa, 10.243
Gene length, protein length 600 bp, 200 aa
Immediate neighbours ytrP, tyrS
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
RpsD context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU29660

Phenotypes of a mutant

essential PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: ribosomal protein S4P family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • Structure: 1C06 (Geobacillus stearothermophilus)
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • 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

F J Grundy, T M Henkin
Characterization of the Bacillus subtilis rpsD regulatory target site.
J Bacteriol: 1992, 174(21);6763-70
[PubMed:1400226] [WorldCat.org] [DOI] (P p)

F J Grundy, T M Henkin
The rpsD gene, encoding ribosomal protein S4, is autogenously regulated in Bacillus subtilis.
J Bacteriol: 1991, 173(15);4595-602
[PubMed:1906866] [WorldCat.org] [DOI] (P p)

T M Henkin, G H Chambliss, F J Grundy
Bacillus subtilis mutants with alterations in ribosomal protein S4.
J Bacteriol: 1990, 172(11);6380-5
[PubMed:2121712] [WorldCat.org] [DOI] (P p)

F J Grundy, T M Henkin
Cloning and analysis of the Bacillus subtilis rpsD gene, encoding ribosomal protein S4.
J Bacteriol: 1990, 172(11);6372-9
[PubMed:1699930] [WorldCat.org] [DOI] (P p)

T M Henkin, G H Chambliss
Genetic mapping of a mutation causing an alteration in Bacillus subtilis ribosomal protein S4.
Mol Gen Genet: 1984, 193(2);364-9
[PubMed:6420647] [WorldCat.org] [DOI] (P p)

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