Difference between revisions of "Easter egg"

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−
* '''Description:''' amino acid racemase, production of D-amino acids, control of [[biofilm formation]] <br/><br/>
+
* '''Description:''' 4.5 S RNA<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'''
−
|''racX''
+
|''scr''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || amino acid racemase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || small cytoplasmic RNA (scRNA, 4.5S RNA),
 +
 
 +
signal recognition particle-like (SRP) component
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[biofilm formation]]
+
|style="background:#ABCDEF;" align="center"|'''Function''' || presecretory protein translocation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 5.396 
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaJ]]'', ''[[dnaX]]''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 681 bp, 227 aa
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/scr_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
 +
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/scr_protein.txt Protein sequence]'''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yveF]]'', ''[[pbpE]]''
+
|colspan="2" | '''Genetic context''' <br/> [[Image:scr_context.gif]]
−
|-
 
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15448&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:racX_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 28:
 
__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/><br/><br/><br/>
  
 
= [[Categories]] containing this gene/protein =
 
= [[Categories]] containing this gene/protein =
−
{{SubtiWiki category|[[biofilm formation]]}},
+
{{SubtiWiki category|[[protein secretion]]}},
−
{{SubtiWiki category|[[cell envelope stress proteins (controlled by SigM, W, X, Y)]]}}
+
{{SubtiWiki category|[[ncRNA]]}}
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
Line 42: Line 41:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU34430
+
* '''Locus tag:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 48: Line 47:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pbpE-racX.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10391]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG00095]
 +
 
 +
* '''Structure:'''
  
 
=== Additional information===
 
=== Additional information===
Line 56: Line 57:
  
  
−
 
+
=The RNA=
−
=The protein=
 
  
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
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* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' aspartate/glutamate racemases family (according to Swiss-Prot)
+
=== Extended information on the RNA===
−
 
 
−
* '''Paralogous protein(s):'''
 
  
−
=== Extended information on the protein ===
+
* '''Kinetic information'''
  
−
* '''Kinetic information:'''
+
* '''Interactions:''' [[Scr]]-[[Ffh]]
  
−
* '''Domains:'''
+
* '''Localization'''
−
 
 
−
* '''Modification:'''
 
−
 
 
−
* '''Cofactor(s):'''
 
−
 
 
−
* '''Effectors of protein activity:'''
 
−
 
 
−
* '''Interactions:'''
 
−
 
 
−
* '''Localization:'''
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure''':  
−
 
 
−
* '''UniProt:''' [http://www.uniprot.org/uniprot/P32960 P32960]
 
−
 
 
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34430]
 
−
 
 
−
* '''E.C. number:'''
 
  
 
=== Additional information===
 
=== Additional information===
  
 
=Expression and regulation=
 
=Expression and regulation=
−
* '''Operon:''' ''[[pbpE]]-[[racX]]'' {{PubMed|8491712}}
 
  
−
* '''[[Sigma factor]]:''' [[SigW]] {{PubMed|8491712,12207695}}
+
* '''Operon:''' ''[[yaaJ]]-[[scr]],  [[scr]]''
 +
 
 +
* '''Sigma factor:''' [[SigA]] (both promoters)
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
−
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/7592498 PubMed]
 
−
** induced by cell wall stress ([[SigW]]) {{PubMed|8491712,12207695}}
 
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
−
** [[AbrB]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/7592498 PubMed]
 
  
−
* '''Additional information:'''
+
* '''Additional information:''' transcribed as 354 nt precursor, cleaved at the 5' end by [[rnc| RNase III]] and at the 3' site by [[rnjA| RNase J1]] to yield a 275 nt molecule, final trimming to 271 nt sc RNA by [[rph| RNase PH]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17576666 PubMed]
  
 
=Biological materials =
 
=Biological materials =
Line 117: Line 97:
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
−
* '''GFP fusion:'''
+
=Labs working on this gene/protein=
−
 
 
−
* '''two-hybrid system:'''
 
−
 
 
−
* '''Antibody:'''
 
  
−
=Labs working on this gene/protein=
+
[[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]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 129: Line 105:
 
=References=
 
=References=
  
−
<pubmed>8491712,19063962,9987136, 20431016,7592498, </pubmed>
+
<pubmed>9346318,2468993,17576666, </pubmed>
  
−
[[Category:Protein-coding genes]]
+
[[Category:small RNA]]

Revision as of 13:48, 8 December 2010

  • Description: 4.5 S RNA

Gene name scr
Synonyms
Essential no
Product small cytoplasmic RNA (scRNA, 4.5S RNA),

signal recognition particle-like (SRP) component

Function presecretory protein translocation
Immediate neighbours yaaJ, dnaX
Gene sequence (+200bp) Protein sequence
Genetic context
Scr context.gif
This image was kindly provided by SubtiList







Categories containing this gene/protein

protein secretion, ncRNA

This gene is a member of the following regulons

The gene

Basic information

  • Locus tag:

Phenotypes of a mutant

Database entries

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

Additional information

The RNA

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:

Extended information on the RNA

  • Kinetic information
  • Localization

Database entries

  • Structure:

Additional information

Expression and regulation

  • Sigma factor: SigA (both promoters)
  • Regulation:
  • Regulatory mechanism:
  • Additional information: transcribed as 354 nt precursor, cleaved at the 5' end by RNase III and at the 3' site by RNase J1 to yield a 275 nt molecule, final trimming to 271 nt sc RNA by RNase PH PubMed

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:

Labs working on this gene/protein

David Bechhofer, Mount Sinai School, New York, USA Homepage

Your additional remarks

References

Shiyi Yao, Joshua B Blaustein, David H Bechhofer
Processing of Bacillus subtilis small cytoplasmic RNA: evidence for an additional endonuclease cleavage site.
Nucleic Acids Res: 2007, 35(13);4464-73
[PubMed:17576666] [WorldCat.org] [DOI] (I p)

H Takamatsu, K Bunai, T Horinaka, A Oguro, K Nakamura, K Watabe, K Yamane
Identification of a region required for binding to presecretory protein in Bacillus subtilis Ffh, a homologue of the 54-kDa subunit of mammalian signal recognition particle.
Eur J Biochem: 1997, 248(2);575-82
[PubMed:9346318] [WorldCat.org] [DOI] (P p)

J C Struck, R K Hartmann, H Y Toschka, V A Erdmann
Transcription and processing of Bacillus subtilis small cytoplasmic RNA.
Mol Gen Genet: 1989, 215(3);478-82
[PubMed:2468993] [WorldCat.org] [DOI] (P p)

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