Difference between revisions of "Easter egg"

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(→‎RNA switches)
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'''Name of the page???'''
+
* '''Description:''' amino acid racemase, production of D-amino acids, control of [[biofilm formation]] <br/><br/>
  
−
= [[Sigma factors]] =
+
{| align="right" border="1" cellpadding="2"
 +
|-
 +
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 +
|''racX''
 +
|-
 +
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 +
|-
 +
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 +
|-
 +
|style="background:#ABCDEF;" align="center"| '''Product''' || amino acid racemase
 +
|-
 +
|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[biofilm formation]]
 +
|-
 +
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 5.396 
 +
|-
 +
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 681 bp, 227 aa
 +
|-
 +
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yveF]]'', ''[[pbpE]]''
 +
|-
 +
|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>
 +
|-
 +
|}
  
−
* [[SigB regulon]]
+
__TOC__
−
* [[SigD regulon]]
 
−
* [[SigE regulon]]
 
−
* [[SigF regulon]]
 
−
* [[SigG regulon]]
 
−
* [[SigH regulon]]
 
−
* [[SigI regulon]]
 
−
* [[SigK regulon]]
 
−
* [[SigL regulon]]
 
−
* [[SigM regulon]]
 
−
* [[SigW regulon]]
 
−
* [[SigX regulon]]
 
−
* [[SigY regulon]]
 
−
* [[Xpf regulon]]
 
−
* [[YlaC regulon]]
 
−
* [[YvrI-YvrHa regulon]]
 
  
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= DNA-binding regulators =
+
<br/><br/>
  
−
* [[Abh regulon]]
+
= [[Categories]] containing this gene/protein =
−
* [[AbrB regulon]]
+
{{SubtiWiki category|[[biofilm formation]]}},
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* [[AcoR regulon]]
+
{{SubtiWiki category|[[cell envelope stress proteins (controlled by SigM, W, X, Y)]]}}
−
* [[AdaA regulon]]
 
−
* [[AdhR regulon]]
 
−
* [[AhrC regulon]]
 
−
* [[AlsR regulon]]
 
−
* [[AnsR regulon]]
 
−
* [[AraR regulon]]
 
−
* [[ArsR regulon]]
 
−
* [[AseR regulon]]
 
−
* [[AzlB regulon]]
 
−
* [[BceR regulon]]
 
−
* [[BirA regulon]]
 
−
* [[BkdR regulon]]
 
−
* [[BltR regulon]]
 
−
* [[BmrR regulon]]
 
−
* [[BsdA regulon]]
 
−
* [[Btr regulon]]
 
−
* [[CatR regulon]]
 
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* [[CcpA regulon]]
 
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* [[CcpC regulon]]
 
−
* [[CcpN regulon]]
 
−
* [[CggR regulon]]
 
−
* [[CitR regulon]]
 
−
* [[CitT regulon]]
 
−
* [[CodY regulon]]
 
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* [[ComA regulon]]
 
−
* [[ComK regulon]]
 
−
* [[Cso regulon]]
 
−
* [[CsoR regulon]]
 
−
* [[CssR regulon]]
 
−
* [[CtsR regulon]]
 
−
* [[CymR regulon]]
 
−
* [[CysL regulon]]
 
−
* [[CzrA regulon]]
 
−
* [[DegU regulon]]
 
−
* [[DeoR regulon]]
 
−
* [[DesR regulon]]
 
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* [[DnaA regulon]]
 
−
* [[ExuR regulon]]
 
−
* [[FadR regulon]]
 
−
* [[FapR regulon]]
 
−
* [[FatR regulon]]
 
−
* [[Fnr regulon]]
 
−
* [[FruR regulon]]
 
−
* [[Fur regulon]]
 
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* [[GabR regulon]]
 
−
* [[GerE regulon]]
 
−
* [[GerR regulon]]
 
−
* [[GlnL regulon]]
 
−
* [[GlnR regulon]]
 
−
* [[GltC regulon]]
 
−
* [[GltR regulon]]
 
−
* [[GlvR regulon]]
 
−
* [[GmuR regulon]]
 
−
* [[GntR regulon]]
 
−
* [[GutR regulon]]
 
−
* [[HrcA regulon]]
 
−
* [[HxlR regulon]]
 
−
* [[ImmR regulon]]
 
−
* [[IolR regulon]]
 
−
* [[KdgR regulon]]
 
−
* [[KipR regulon]]
 
−
* [[LacR regulon]]
 
−
* [[LevR regulon]]
 
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* [[LexA regulon]]
 
−
* [[LiaR regulon]]
 
−
* [[LicR regulon]]
 
−
* [[LmrA regulon]]
 
−
* [[LutR regulon]]
 
−
* [[LytR regulon]]
 
−
* [[MalR regulon]]
 
−
* [[ManR regulon]]
 
−
* [[MdtR regulon]]
 
−
* [[MhqR regulon]]
 
−
* [[MntR regulon]]
 
−
* [[Mta regulon]]
 
−
* [[MsmR regulon]]
 
−
* [[MtlR regulon]]
 
−
* [[NadR regulon]]
 
−
* [[NatR regulon]]
 
−
* [[NsrR regulon]]
 
−
* [[NtdR regulon]]
 
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* [[OhrR regulon]]
 
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* [[PadR regulon]]
 
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* [[PerR regulon]]
 
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* [[PhoP regulon]]
 
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* [[PucR regulon]]
 
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* [[PurR regulon]]
 
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* [[ResD regulon]]
 
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* [[Rex regulon]]
 
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* [[RghR regulon]]
 
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* [[RocR regulon]]
 
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* [[Rok regulon]]
 
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* [[RsfA regulon]]
 
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* [[SalA regulon]]
 
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* [[ScoC regulon]]
 
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* [[SdpR regulon]]
 
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* [[SenS regulon]]
 
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* [[SinR regulon]]
 
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* [[SlrR regulon]]
 
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* [[Spo0A regulon]]
 
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* [[SpoIIID regulon]]
 
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* [[Spx regulon]]
 
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* [[TnrA regulon]]
 
−
* [[TreR regulon]]
 
−
* [[WalR regulon]]
 
−
* [[Xre regulon]]
 
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* [[XylR regulon]]
 
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* [[YcbG regulon]]
 
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* [[YclJ regulon]]
 
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* [[YcnK regulon]]
 
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* [[YdfI regulon]]
 
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* [[YesS regulon]]
 
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* [[YetL regulon]]
 
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* [[YfhP regulon]]
 
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* [[YfmP regulon]]
 
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* [[YkrP regulon]]
 
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* [[YodB regulon]]
 
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* [[YofA regulon]]
 
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* [[YrkP regulon]]
 
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* [[YtlI regulon]]
 
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* [[YtrA regulon]]
 
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* [[YvoA regulon]]
 
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* [[YvrHb regulon]]
 
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* [[YwcC regulon]]
 
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* [[YxaF regulon]]
 
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* [[YxdJ regulon]]
 
−
* [[Zur regulon]]
 
  
−
= [[RNA switch|RNA switches]] =
+
= This gene is a member of the following [[regulons]] =
 +
{{SubtiWiki regulon|[[AbrB regulon]]}},
 +
{{SubtiWiki regulon|[[SigW regulon]]}}
  
−
* [[A-box]]
+
=The gene=
−
* [[EAR riboswitch]]
 
−
* [[FMN-box]]
 
−
* [[G-box]]
 
−
* [[GlcT riboswitch]]
 
−
* [[glmS ribozyme]]
 
−
* [[GlpP riboswitch]]
 
−
* [[HutP riboswitch]]
 
−
* [[L-box]]
 
−
* [[LicT riboswitch]]
 
−
* [[M-box]]
 
−
* [[preQ1 riboswitch]]
 
−
* [[PyrR riboswitch]]
 
−
* [[RplT riboswitch]]
 
−
* [[SacT riboswitch]]
 
−
* [[SacY riboswitch]]
 
−
* [[S-box]]
 
−
* [[T-box]]
 
−
* [[Thi-box]]
 
−
* [[TRAP riboswitch]]
 
−
* [[YdaO riboswitch]]
 
−
* [[RNA switch/ other]]
 
  
−
= Additional regulatory mechanisms =
+
=== Basic information ===
  
−
* [[CitB regulon]]
+
* '''Locus tag:''' BSU34430
−
* [[ComN regulon]]
+
 
−
* [[CsrA regulon]]
+
===Phenotypes of a mutant ===
−
* [[FsrA regulon]]
+
 
−
* [[MifM regulon]]
+
=== Database entries ===
−
* [[ratA regulon]]
+
 
−
* [[SR1 regulon]]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pbpE-racX.html]
−
* [[Stringent response]]
+
 
 +
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10391]
 +
 
 +
=== Additional information===
 +
 
 +
 
 +
 
 +
 
 +
=The protein=
 +
 
 +
=== Basic information/ Evolution ===
 +
 
 +
* '''Catalyzed reaction/ biological activity:'''
 +
 
 +
* '''Protein family:''' aspartate/glutamate racemases 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:'''
 +
 
 +
* '''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===
 +
 
 +
=Expression and regulation=
 +
* '''Operon:''' ''[[pbpE]]-[[racX]]'' {{PubMed|8491712}}
 +
 
 +
* '''[[Sigma factor]]:''' [[SigW]] {{PubMed|8491712,12207695}}
 +
 
 +
* '''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:'''
 +
** [[AbrB]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/7592498 PubMed]
 +
 
 +
* '''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=
 +
 
 +
<pubmed>8491712,19063962,9987136, 20431016,7592498, </pubmed>
 +
 
 +
[[Category:Protein-coding genes]]

Revision as of 13:27, 8 December 2010

  • Description: amino acid racemase, production of D-amino acids, control of biofilm formation

Gene name racX
Synonyms
Essential no
Product amino acid racemase
Function control of biofilm formation
MW, pI 25 kDa, 5.396
Gene length, protein length 681 bp, 227 aa
Immediate neighbours yveF, pbpE
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
RacX context.gif
This image was kindly provided by SubtiList



Categories containing this gene/protein

biofilm formation, cell envelope stress proteins (controlled by SigM, W, X, Y)

This gene is a member of the following regulons

AbrB regulon, SigW regulon

The gene

Basic information

  • Locus tag: BSU34430

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: aspartate/glutamate racemases 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:
  • KEGG entry: [3]
  • 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

Your additional remarks

References

Ilana Kolodkin-Gal, Diego Romero, Shugeng Cao, Jon Clardy, Roberto Kolter, Richard Losick
D-amino acids trigger biofilm disassembly.
Science: 2010, 328(5978);627-9
[PubMed:20431016] [WorldCat.org] [DOI] (I p)

María Mercedes Palomino, Carmen Sanchez-Rivas, Sandra M Ruzal
High salt stress in Bacillus subtilis: involvement of PBP4* as a peptidoglycan hydrolase.
Res Microbiol: 2009, 160(2);117-24
[PubMed:19063962] [WorldCat.org] [DOI] (P p)

X Huang, A Gaballa, M Cao, J D Helmann
Identification of target promoters for the Bacillus subtilis extracytoplasmic function sigma factor, sigma W.
Mol Microbiol: 1999, 31(1);361-71
[PubMed:9987136] [WorldCat.org] [DOI] (P p)

M A Strauch
Delineation of AbrB-binding sites on the Bacillus subtilis spo0H, kinB, ftsAZ, and pbpE promoters and use of a derived homology to identify a previously unsuspected binding site in the bsuB1 methylase promote.
J Bacteriol: 1995, 177(23);6999-7002
[PubMed:7592498] [WorldCat.org] [DOI] (P p)

D L Popham, P Setlow
Cloning, nucleotide sequence, and regulation of the Bacillus subtilis pbpE operon, which codes for penicillin-binding protein 4* and an apparent amino acid racemase.
J Bacteriol: 1993, 175(10);2917-25
[PubMed:8491712] [WorldCat.org] [DOI] (P p)

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