Difference between revisions of "YydF"

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(Extended information on the protein)
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|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[LiaR]]-[[LiaS]] activity
 
|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[LiaR]]-[[LiaS]] activity
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU40180 yydF]
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|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU40180 yydF]
 
|-
 
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|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/YydF YydF]
 
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/YydF YydF]
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yydG]]'', ''[[fbp]]''
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yydG]]'', ''[[fbp]]''
 
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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:CAB16055&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
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|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU40180 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU40180 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU40180 Advanced_DNA]
 
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|colspan="2" | '''Genetic context''' <br/> [[Image:yydF_context.gif]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:yydF_context.gif]]

Revision as of 14:18, 13 May 2013

  • Description: secreted peptide, controls LiaR-LiaS activity

Gene name yydF
Synonyms
Essential no
Product secreted peptide
Function control of LiaR-LiaS activity
Gene expression levels in SubtiExpress: yydF
Interactions involving this protein in SubtInteract: YydF
MW, pI 5 kDa, 9.567
Gene length, protein length 147 bp, 49 aa
Immediate neighbours yydG, fbp
Sequences Protein DNA Advanced_DNA
Genetic context
YydF context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
500px















Categories containing this gene/protein

transcription factors and their control

This gene is a member of the following regulons

AbrB regulon

The gene

Basic information

  • Locus tag: BSU40180

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:
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • Structure:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation:
    • activated after transition to stationary phase(AbrB) PubMed
  • Regulatory mechanism:
  • Additional information:
    • the mRNA is very stable (half-life > 15 min) PubMed
    • the yydF portion of the mRNA belongs to the most stable mRNAs in B. subtilis PubMed
    • the amount of the mRNA is substantially decreased upon depletion of RNase Y PubMed

Biological materials

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

Labs working on this gene/protein

Your additional remarks

References

Reviews

Susanne Gebhard
ABC transporters of antimicrobial peptides in Firmicutes bacteria - phylogeny, function and regulation.
Mol Microbiol: 2012, 86(6);1295-317
[PubMed:23106164] [WorldCat.org] [DOI] (I p)

Original publications

Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Herzberg C, Stülke J  
RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y. 
Mol Microbiol. 2011 81(6): 1459-1473. 
PubMed:21815947

Bronwyn G Butcher, Yi-Pin Lin, John D Helmann
The yydFGHIJ operon of Bacillus subtilis encodes a peptide that induces the LiaRS two-component system.
J Bacteriol: 2007, 189(23);8616-25
[PubMed:17921301] [WorldCat.org] [DOI] (I p)

G Hambraeus, C von Wachenfeldt, L Hederstedt
Genome-wide survey of mRNA half-lives in Bacillus subtilis identifies extremely stable mRNAs.
Mol Genet Genomics: 2003, 269(5);706-14
[PubMed:12884008] [WorldCat.org] [DOI] (P p)