Difference between revisions of "Easter egg"

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* '''Description:''' [[small RNAs|small regulatory RNA]] controlling [[AhrC]] expression, peptide controlling the stability of the ''[[cggR]]-[[gapA]]'' mRNA <br/><br/>
  
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{{CategoryTree
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{| align="right" border="1" cellpadding="2"
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|Parents=
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|-
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* 1. [[Cellular processes]]
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|style="background:#ABCDEF;" align="center"|'''Gene name'''
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** 1.1. [[Cell wall and cell division]]
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|''sr1''
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|Neighbours=
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|-
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* 1.1.1. [[Cell wall synthesis]]
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykzW ''
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* 1.1.2. [[Cell shape]]
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|-
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* 1.1.3. [[Cell wall degradation/ turnover]]
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no
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* 1.1.4. [[Capsule biosynthesis and degradation]]
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|-
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* 1.1.5. [[Cell wall/ other]]
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|style="background:#ABCDEF;" align="center"| '''Product''' || [[small RNAs|small regulatory RNA]]/ regulatory peptide
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* 1.1.6. [[Cell division]]
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|-
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|Related=
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|style="background:#ABCDEF;" align="center"|'''Function''' || control of arginine metabolism and glycolysis
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none
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|-
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|}}
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 4.4 kDa, 3.89
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|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 205 bp (RNA), 120 bp (ORF), 39 aa
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|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[slp]]'', ''[[speA]]''
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|-
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/sr1_nucleotide.txt    Gene sequence        ]'''
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|style="background:#FAF8CC;" align="center"|
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|-
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|colspan="2" | '''Genetic context''' <br/> [[Image:sr1_context.gif]]
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|-
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|}
  
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== Genes in this functional category ==
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__TOC__
  
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=== Biosynthesis of peptidoglycan ===
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<br/><br/><br/>
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* [[alr]]
 
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* [[dat]]
 
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* [[ddl]]
 
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* [[gcaD]]
 
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* [[glmM]]
 
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* [[glmS]]
 
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* [[ldt]]
 
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* [[mraY]]
 
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* [[murAA]]
 
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* [[murAB]]
 
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* [[murB]]
 
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* [[murC]]
 
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* [[murD]]
 
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* [[murE]]
 
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* [[murF]]
 
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* [[murG]]
 
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* [[racE]]
 
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* [[spoVB]]
 
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* [[spoVE]]
 
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* [[yabM]]
 
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* [[yrpC]]
 
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* [[ytgP]]
 
  
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=== Biosynthesis of lipoteichoic acid ===
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* [[dgkA]]
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=The gene=
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* [[dgkB]]
 
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* [[ltaS]]
 
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* [[yfnI]]
 
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* [[yqgS]]
 
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* [[yvgJ]]
 
  
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=== Biosynthesis of teichoic acid ===  
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=== Basic information ===
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* [[dltA]]
 
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* [[dltB]]
 
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* [[dltC]]
 
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* [[dltD]]
 
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* [[dltE]]
 
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* [[ggaA]]
 
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* [[ggaB]]
 
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* [[gtaB]]
 
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* [[gtaC]]
 
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* [[mnaA]]
 
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* [[pgcA]]
 
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* [[tagA]]
 
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* [[tagB]]
 
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* [[tagC]]
 
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* [[tagD]]
 
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* [[tagE]]
 
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* [[tagF]]
 
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* [[tagG]]
 
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* [[tagH]]
 
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* [[tagO]]
 
  
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=== Biosynthesis of teichuronic acid ===
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* '''Locus tag:'''
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* [[tuaA]]
 
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* [[tuaB]]
 
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* [[tuaC]]
 
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* [[tuaD]]
 
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* [[tuaE]]
 
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* [[tuaF]]
 
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* [[tuaG]]
 
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* [[tuaH]]
 
  
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=== Penicillin-binding proteins ===  
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===Phenotypes of a mutant ===
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* [[dacA]]
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* [[dacB]]
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=== Database entries ===
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* [[dacC]]
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* [[dacF]]
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* '''DBTBS entry:''' no entry
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* [[pbpA]]
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* [[pbpB]]
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=== Additional information===
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* [[pbpC]]
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Located between the ''[[slp]]'' and ''[[speA]]'' genes.
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* [[pbpD]]
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* [[pbpE]]
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* [[pbpF]]
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* [[pbpG]]
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= Categories containing this gene/protein =
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* [[pbpH]]
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{{SubtiWiki category|[[biosynthesis/ acquisition of amino acids]]}},
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* [[pbpI]]
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{{SubtiWiki category|[[utilization of amino acids]]}},
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* [[pbpX]]
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{{SubtiWiki category|[[ncRNA]]}}
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* [[ponA]]
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=The RNA=
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* [[spoVD]]
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 +
=== Basic information/ Evolution ===
 +
 
 +
* '''Catalyzed reaction/ biological activity:''' hybridizes to ''[[ahrC]]'' mRNA and inhibits [[AhrC]] translation. [http://www.ncbi.nlm.nih.gov/sites/entrez/17020585 PubMed]
 +
 
 +
=== Extended information on the RNA===
 +
 
 +
* '''Kinetic information'''
 +
 
 +
* '''Interactions:''' Binds ''[[ahrC]]'' mRNA [http://www.ncbi.nlm.nih.gov/sites/entrez/17020585 PubMed]
 +
 
 +
* '''Localization'''
 +
 
 +
=== Database entries ===
 +
 
 +
* '''Structure''':
 +
 
 +
=== Additional information===
 +
 
 +
Information on the structure of the RNA can be found in [http://www.ncbi.nlm.nih.gov/pubmed/17020585?ordinalpos=8&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum Heidrich ''et al''., 2006 ]
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 +
=The peptide=
 +
 
 +
=== Basic information/ Evolution ===
 +
 
 +
* '''Catalyzed reaction/ biological activity:''' the peptide controls the stability of the ''[[cggR]]-[[gapA]]'' mRNA {{PubMed|20444087}}
 +
 
 +
* '''Protein family:''' the peptide is conserved in bacilli
 +
 
 +
* '''Paralogous protein(s):'''
 +
 
 +
=== Extended information on the protein ===
 +
 
 +
* '''Kinetic information:'''
 +
 
 +
* '''Domains:'''
 +
 
 +
* '''Modification:'''
 +
 
 +
* '''Cofactor(s):'''
 +
 
 +
* '''Effectors of protein activity:'''
 +
 
 +
* '''Interactions:'''
 +
** [[GapA]]-[[YkzW]] {{PubMed|20444087}}
 +
 
 +
* '''Localization:'''
 +
 
 +
=== Database entries ===
 +
 
 +
* '''Structure:'''
 +
 
 +
* '''UniProt:''' [http://www.uniprot.org/uniprot/C0H410 C0H410]
 +
 
 +
* '''KEGG entry:'''
 +
 
 +
* '''E.C. number:'''
 +
 
 +
=== Additional information===
 +
 
 +
=Expression and regulation=
 +
 
 +
* '''Operon:''' sr1 [http://www.ncbi.nlm.nih.gov/sites/entrez/16164558 PubMed]
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* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16164558 PubMed]
 +
 
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* '''Regulation:''' Repressed in the presence of glucose by [[CcpN]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16164558 PubMed]
 +
 
 +
* '''Regulatory mechanism:''' transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16164558 PubMed]
 +
 
 +
* '''Additional information:'''
 +
 
 +
=Biological materials =
 +
 
 +
* '''Mutant:''' 168 sr1::cat, available in [[Brantl]] lab
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 +
* '''Expression vector:'''
 +
 +
* '''lacZ fusion:'''
 +
 
 +
=Labs working on this gene/protein=
 +
 
 +
[[Sabine Brantl |Sabine Brantl]], Bacterial Genetics, Friedrich-Schiller-University of Jena, Germany [http://www.uni-jena.de/AG_Bakteriengenetik_(_Doz__Dr__Sabine_Brantl_).html homepage]
 +
 
 +
=Your additional remarks=
 +
 
 +
=References=
 +
 
 +
<pubmed>16164558 17020585 17576690, 20444087 </pubmed>
 +
 
 +
[[Category:Protein-coding genes]]

Revision as of 14:21, 30 November 2010

Gene name sr1
Synonyms ykzW
Essential no
Product small regulatory RNA/ regulatory peptide
Function control of arginine metabolism and glycolysis
MW, pI 4.4 kDa, 3.89
Gene length, protein length 205 bp (RNA), 120 bp (ORF), 39 aa
Immediate neighbours slp, speA
Gene sequence
Genetic context
Sr1 context.gif





The gene

Basic information

  • Locus tag:

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry

Additional information

Located between the slp and speA genes.


Categories containing this gene/protein

biosynthesis/ acquisition of amino acids, utilization of amino acids, ncRNA

The RNA

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: hybridizes to ahrC mRNA and inhibits AhrC translation. PubMed

Extended information on the RNA

  • Kinetic information
  • Localization

Database entries

  • Structure:

Additional information

Information on the structure of the RNA can be found in Heidrich et al., 2006

The peptide

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: the peptide controls the stability of the cggR-gapA mRNA PubMed
  • Protein family: the peptide is conserved in bacilli
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • Structure:
  • KEGG entry:
  • E.C. number:

Additional information

Expression and regulation

  • Regulation: Repressed in the presence of glucose by CcpN PubMed
  • Regulatory mechanism: transcription repression PubMed
  • Additional information:

Biological materials

  • Mutant: 168 sr1::cat, available in Brantl lab
  • Expression vector:
  • lacZ fusion:

Labs working on this gene/protein

Sabine Brantl, Bacterial Genetics, Friedrich-Schiller-University of Jena, Germany homepage

Your additional remarks

References

Matthias Gimpel, Nadja Heidrich, Ulrike Mäder, Hans Krügel, Sabine Brantl
A dual-function sRNA from B. subtilis: SR1 acts as a peptide encoding mRNA on the gapA operon.
Mol Microbiol: 2010, 76(4);990-1009
[PubMed:20444087] [WorldCat.org] [DOI] (I p)

Nadja Heidrich, Isabella Moll, Sabine Brantl
In vitro analysis of the interaction between the small RNA SR1 and its primary target ahrC mRNA.
Nucleic Acids Res: 2007, 35(13);4331-46
[PubMed:17576690] [WorldCat.org] [DOI] (I p)

Nadja Heidrich, Alberto Chinali, Ulf Gerth, Sabine Brantl
The small untranslated RNA SR1 from the Bacillus subtilis genome is involved in the regulation of arginine catabolism.
Mol Microbiol: 2006, 62(2);520-36
[PubMed:17020585] [WorldCat.org] [DOI] (P p)

Andreas Licht, Sven Preis, Sabine Brantl
Implication of CcpN in the regulation of a novel untranslated RNA (SR1) in Bacillus subtilis.
Mol Microbiol: 2005, 58(1);189-206
[PubMed:16164558] [WorldCat.org] [DOI] (P p)

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