Difference between revisions of "FapR"

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* '''Description:''' write here <br/><br/>
+
* '''Description:''' repressor of fatty acid synthetic genes <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' ||  
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|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional repressor
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
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|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of fatty acid biosynthesis
 +
|-
 +
|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=BSU15880 fapR]
 +
|-
 +
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=FapR FapR]
 +
|-
 +
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=fapR fapR]'''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 5.393   
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 5.393   
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 564 bp, 188 aa  
 
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 564 bp, 188 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' ||  
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[recG]]'', ''[[plsX]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ylpC_nucleotide.txt    Gene sequence     (+200bp)  ]'''
+
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU15880 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU15880 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU15880 DNA_with_flanks]
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ylpC_protein.txt Protein sequence]'''
 
 
|-
 
|-
 
|colspan="2" | '''Genetic context''' <br/> [[Image:ylpC_context.gif]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:ylpC_context.gif]]
 +
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 +
|-
 +
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=fapR_1661967_1662533_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:fapR_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU15880]]
 
|-
 
|-
 
|}
 
|}
  
 
__TOC__
 
__TOC__
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/>
  
−
<br/><br/>
+
= [[Categories]] containing this gene/protein =
 +
{{SubtiWiki category|[[biosynthesis of lipids]]}},
 +
{{SubtiWiki category|[[transcription factors and their control]]}}
  
 +
= This gene is a member of the following [[regulons]] =
 +
{{SubtiWiki regulon|[[ComA regulon]]}},
 +
{{SubtiWiki regulon|[[FapR regulon]]}}
 +
=The [[FapR regulon]]=
 
=The gene=
 
=The gene=
  
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:'''
+
* '''Locus tag:''' BSU15880
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU15880&redirect=T BSU15880]
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ylpC.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fapR-plsX-fabDG.html]
  
 
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13400]
 
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13400]
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=The protein=
 
=The protein=
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' FapR regulates the expression of at least 10 genes (the ''fap'' regulon). It autoregulates its own expression. Malonyl-CoA, a precursor of fatty acid biosynthesis, binds to FapR changing its conformation to a non-DNA binding state. Hence, conditions that cause malonyl-CoA accumulation, like fatty acid biosynthesis inhibition, derepress the ''fap'' regulon.
  
−
* '''Protein family:'''
+
* '''Protein family:''' fapR family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:'''
+
* '''Effectors of protein activity:''' malonyl-CoA and malonyl-[[AcpA|ACP]] act as the molecular inducer of the FapR regulon {{PubMed|20201588}}
  
−
* '''Interactions:'''
+
* '''[[SubtInteract|Interactions]]:'''  
 +
** malonyl-[[AcpA|ACP]]-[[FapR]] {{PubMed|20201588}}
  
−
* '''Localization:'''
+
* '''[[Localization]]:'''
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU15880&redirect=T BSU15880]
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2F3X 2F3X] (complex with effector),  [http://www.rcsb.org/pdb/explore.do?structureId=2F41 2F41]
  
−
* '''Swiss prot entry:'''
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/O34835 O34835]
  
−
* '''KEGG entry:'''
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU15880]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
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* '''Operon:'''  
+
* '''Operon:''' ''[[fapR]]-[[plsX]]-[[fabD]]-[[fabG]]-[[acpA]]'' {{PubMed|12737802,19850612}}
 +
 
 +
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=fapR_1661967_1662533_1 fapR] {{PubMed|22383849}}
  
−
* '''Sigma factor:'''  
+
* '''Sigma factor:''' [[SigA]] {{PubMed|16932747}}
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
 +
** repressed in the absence of malonyl-CoA or malonyl-[[AcpA|ACP]] ([[FapR]]) {{PubMed|20201588}}
 +
** expressed at high cell density ([[ComA]]) {{PubMed|16091051}}
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
 +
** [[ComA]]: transcription activation ([[ComA]]) {{PubMed|16091051}}
 +
** [[FapR]]: transcription repression {{PubMed|12737802}}
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
 +
** number of protein molecules per cell (minimal medium with glucose and ammonium): 85 {{PubMed|24696501}}
 +
** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 490 {{PubMed|21395229}}
 +
** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 412 {{PubMed|21395229}}
 +
** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 729 {{PubMed|21395229}}
  
 
=Biological materials =
 
=Biological materials =
−
 
 
* '''Mutant:'''
 
* '''Mutant:'''
  
Line 117: Line 146:
  
 
=References=
 
=References=
 +
==Reviews==
 +
<pubmed>17919287,</pubmed>
 +
==The [[FapR regulon]]==
 +
<pubmed>12737802, </pubmed>
 +
==Other original publications==
 +
'''Additional publications:''' {{PubMed|23102226}}
 +
<pubmed>18941141, 18820022, 18384517, 16932747,19850612 16091051 20201588 </pubmed>
  
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
[[Category:Protein-coding genes]]

Latest revision as of 14:19, 17 April 2014

  • Description: repressor of fatty acid synthetic genes

Gene name fapR
Synonyms ylpC
Essential no
Product transcriptional repressor
Function regulation of fatty acid biosynthesis
Gene expression levels in SubtiExpress: fapR
Interactions involving this protein in SubtInteract: FapR
Metabolic function and regulation of this protein in SubtiPathways:
fapR
MW, pI 21 kDa, 5.393
Gene length, protein length 564 bp, 188 aa
Immediate neighbours recG, plsX
Sequences Protein DNA DNA_with_flanks
Genetic context
YlpC context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
FapR expression.png















Categories containing this gene/protein

biosynthesis of lipids, transcription factors and their control

This gene is a member of the following regulons

ComA regulon, FapR regulon

The FapR regulon

The gene

Basic information

  • Locus tag: BSU15880

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: FapR regulates the expression of at least 10 genes (the fap regulon). It autoregulates its own expression. Malonyl-CoA, a precursor of fatty acid biosynthesis, binds to FapR changing its conformation to a non-DNA binding state. Hence, conditions that cause malonyl-CoA accumulation, like fatty acid biosynthesis inhibition, derepress the fap regulon.
  • Protein family: fapR family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity: malonyl-CoA and malonyl-ACP act as the molecular inducer of the FapR regulon PubMed

Database entries

  • Structure: 2F3X (complex with effector), 2F41
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation:
  • Additional information:
    • number of protein molecules per cell (minimal medium with glucose and ammonium): 85 PubMed
    • number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 490 PubMed
    • number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 412 PubMed
    • number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 729 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

Yasutaro Fujita, Hiroshi Matsuoka, Kazutake Hirooka
Regulation of fatty acid metabolism in bacteria.
Mol Microbiol: 2007, 66(4);829-39
[PubMed:17919287] [WorldCat.org] [DOI] (P p)

The FapR regulon

Other original publications

Additional publications: PubMed

Mariano A Martinez, María-Eugenia Zaballa, Francis Schaeffer, Marco Bellinzoni, Daniela Albanesi, Gustavo E Schujman, Alejandro J Vila, Pedro M Alzari, Diego de Mendoza
A novel role of malonyl-ACP in lipid homeostasis.
Biochemistry: 2010, 49(14);3161-7
[PubMed:20201588] [WorldCat.org] [DOI] (I p)

Mariano A Martinez, Diego de Mendoza, Gustavo E Schujman
Transcriptional and functional characterization of the gene encoding acyl carrier protein in Bacillus subtilis.
Microbiology (Reading): 2010, 156(Pt 2);484-495
[PubMed:19850612] [WorldCat.org] [DOI] (I p)

Yong-Mei Zhang, Charles O Rock
Transcriptional regulation in bacterial membrane lipid synthesis.
J Lipid Res: 2009, 50 Suppl(Suppl);S115-9
[PubMed:18941141] [WorldCat.org] [DOI] (P p)

Letal I Salzberg, John D Helmann
Phenotypic and transcriptomic characterization of Bacillus subtilis mutants with grossly altered membrane composition.
J Bacteriol: 2008, 190(23);7797-807
[PubMed:18820022] [WorldCat.org] [DOI] (I p)

Gustavo E Schujman, Silvia Altabe, Diego de Mendoza
A malonyl-CoA-dependent switch in the bacterial response to a dysfunction of lipid metabolism.
Mol Microbiol: 2008, 68(4);987-96
[PubMed:18384517] [WorldCat.org] [DOI] (I p)

Gustavo E Schujman, Marcelo Guerin, Alejandro Buschiazzo, Francis Schaeffer, Leticia I Llarrull, Georgina Reh, Alejandro J Vila, Pedro M Alzari, Diego de Mendoza
Structural basis of lipid biosynthesis regulation in Gram-positive bacteria.
EMBO J: 2006, 25(17);4074-83
[PubMed:16932747] [WorldCat.org] [DOI] (P p)

Natalia Comella, Alan D Grossman
Conservation of genes and processes controlled by the quorum response in bacteria: characterization of genes controlled by the quorum-sensing transcription factor ComA in Bacillus subtilis.
Mol Microbiol: 2005, 57(4);1159-74
[PubMed:16091051] [WorldCat.org] [DOI] (P p)

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