CggR - Revision history

Jstuelk at 14:21, 19 August 2014

2014-08-19T14:21:33Z

134.76.38.147 at 14:47, 2 April 2014

2014-04-02T14:47:42Z

134.76.70.252 at 11:41, 7 January 2014

2014-01-07T11:41:47Z

Jstuelk at 15:25, 13 July 2013

2013-07-13T15:25:07Z

134.76.70.252 at 14:36, 16 May 2013

2013-05-16T14:36:16Z

134.76.70.252 at 11:18, 14 May 2013

2013-05-14T11:18:11Z

134.76.70.252 at 13:52, 13 May 2013

2013-05-13T13:52:50Z

Jstuelk at 09:51, 3 January 2013

2013-01-03T09:51:41Z

134.76.70.252 at 16:03, 7 August 2012

2012-08-07T16:03:44Z

134.76.70.252 at 09:24, 23 April 2012

2012-04-23T09:24:59Z

← Older revision		Revision as of 14:21, 19 August 2014
Line 1:		Line 1:
−	* '''Description:~~''' repressor of the glycolytic ''[[gapA]]'' operon, [[DeoR family]]<br/><br/>~~	+	{{#bank: CggR}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''cggR''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yvbQ ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| central glycolytic genes regulator~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| transcriptional regulator~~
−	\|-
−	\|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=BSU33950 cggR]
−	\|-
−	\|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=cggR cggR]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 37,2 kDa,5.68~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1020 bp, 340 amino acids~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[gapA]]'', ''[[araE]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU33950 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU33950 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU33950 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:cggR_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=cggR_3482752_3483774_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:cggR_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU33950]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[carbon core metabolism]]}},~~
−	~~{{SubtiWiki category\|[[transcription factors and their control]]}},~~
−	~~{{SubtiWiki category\|[[regulators of core metabolism]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CggR regulon]]}}~~
−	~~=The [[CggR regulon]]:=~~
−	* ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpi]]-[[pgm]]-[[eno]]''
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU33950
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU33950&redirect=T BSU33950]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14085]
−
−	~~=== Additional information===~~
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' transcription repression of the glycolytic ''[[gapA]]'' operon
−
−	* '''Protein family:''' sorC transcriptional regulatory family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−	** DNA binding domain (H-T-H motif) (37–56)
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:''' fructose 1.6-bisphosphate [http://www.ncbi.nlm.nih.gov/sites/entrez/12622823 PubMed] and dihydroxyacetone phosphate, glucose-6-phosphate and fructose-6-phosphate [http://www.ncbi.nlm.nih.gov/sites/entrez/18554327 PubMed] act as inducer and result in release of CggR from the DNA
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** active as dimer (according to {{PubMed\|20408793}})
−
−	* '''[[Localization]]:''' cytoplasma {{PubMed\|20572937}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU33950&redirect=T BSU33950]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2OKG 2OKG] ( effector binding domain), [http://www.rcsb.org/pdb/explore.do?structureId=3BXH 3BXH] (in complex with fructose-6-phosphate), complex with Fructose-6-Phosphate [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=65242 NCBI], effector binding domain [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=44226 NCBI]
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O32253 O32253]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33950]
−
−	~~=== Additional information===~~
−
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:'''
−	** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpi]]-[[pgm]]-[[eno]]'' {{PubMed\|11489127}}
−	** ''[[cggR]]-[[gapA]]'' {{PubMed\|11489127}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=cggR_3482752_3483774_-1 cggR] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|11489127}}
−
−	* '''Regulation:'''
−	** expression activated by glucose (77-fold) ([[CggR]]) {{PubMed\|12850135,12622823}}
−
−	* '''Regulatory mechanism:'''
−	** ''[[cggR]]'': transcription repression {{PubMed\|11489127}}
−
−	* '''Database entries:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html DBTBS]
−
−	* '''Additional information:'''
−	** The primary mRNAs of the operon are highly unstable. The primary mRNA is subject to processing at the very end of the ''[[cggR]]'' open reading frame. This results in stable mature ''[[gapA]]'' and ''[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' mRNAs. {{PubMed\|11489127}} The processing event requires the [[Rny\|RNase Y]] {{PubMed\|19193632}}.
−	** The intracellular concentration of CggR is about 230 nM (according to {{PubMed\|20408793}}).
−	** The accumulation of the ''[[cggR]]-[[gapA]]'' mRNA is strongly dependent on the presence of the [[YkzW]] peptide, due to stabilization of the mRNA {{PubMed\|20444087}}.
−	** the mRNA is substantially stabilized upon depletion of [[Rny\|RNase Y]] {{PubMed\|21815947}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** GP311 (in frame deletion), available in [[Jörg Stülke]]'s lab
−	** SM-NB7 (cggR-spc), available in [[Anne Galinier]]'s and [[Boris Görke]]'s labs
−
−	* '''Expression vector:''' pGP705 (N-terminal His-tag, in [[pWH844]]), available in [[Jörg Stülke]]'s lab
−
−	* '''lacZ fusion:''' pGP504 (in [[pAC7]]), pGP509 (in [[pAC6]]), available in [[Jörg Stülke]]'s lab
−
−	* '''GFP fusion:'''
−
−	* '''Antibody:''' available in [[Jörg Stülke]]'s lab
−
−	~~=Labs working on this gene/protein=~~
−
−	~~[[Stephane Aymerich \|Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed> 20408793 </pubmed>~~
−
−	~~==Original Publications==~~
−
−	~~<pubmed>20462860 22190493 23280112 21815947 19193632,12850135, 12622823,18186488,10799476,11489127, 12123463,12634343, 18052209 , 17293407 20361740 20444087 18554327,</pubmed>~~
−	~~[[Category:Protein-coding genes]]~~

@@ Line 58: / Line 58: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]
@@ Line 96: / Line 97: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2OKG 2OKG] ( effector binding domain),  [http://www.rcsb.org/pdb/explore.do?structureId=3BXH 3BXH] (in complex with fructose-6-phosphate),  complex with Fructose-6-Phosphate [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=65242 NCBI], effector binding domain [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=44226 NCBI]

@@ Line 16: / Line 16: @@
 |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=BSU33950 cggR]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
+|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=cggR cggR]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 37,2 kDa,5.68

@@ Line 114: / Line 114: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=cggR_3482752_3483774_-1 cggR] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] {{PubMed|11489127}}
+* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|11489127}}
 * '''Regulation:'''
@@ Line 133: / Line 133: @@
 * '''Mutant:'''
-** GP311 (in frame deletion), available in [[Stülke]] lab
+** GP311 (in frame deletion), available in [[Jörg Stülke]]'s lab
 ** SM-NB7 (cggR-spc), available in [[Anne Galinier]]'s and [[Boris Görke]]'s labs
-* '''Expression vector:''' pGP705 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
+* '''Expression vector:''' pGP705 (N-terminal His-tag, in [[pWH844]]), available in [[Jörg Stülke]]'s lab
-* '''lacZ fusion:''' pGP504 (in [[pAC7]]), pGP509 (in [[pAC6]]), available in [[Stülke]] lab
+* '''lacZ fusion:''' pGP504 (in [[pAC7]]), pGP509 (in [[pAC6]]), available in [[Jörg Stülke]]'s lab
 * '''GFP fusion:'''
-* '''Antibody:''' available in [[Stülke]] lab
+* '''Antibody:''' available in [[Jörg Stülke]]'s lab
 =Labs working on this gene/protein=
@@ Line 155: / Line 155: @@
 ==Original Publications==
-'''Additional publications:''' {{PubMed|20462860}}
-<pubmed> 22190493 23280112 </pubmed>
+<pubmed>20462860 22190493 23280112 21815947 19193632,12850135, 12622823,18186488,10799476,11489127, 12123463,12634343, 18052209 , 17293407 20361740 20444087 18554327,</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 29: / Line 29: @@
   <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=cggR_3482752_3483774_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:cggR_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=cggR_3482752_3483774_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:cggR_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU33950]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gapA]]'', ''[[araE]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU33950 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU33950 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU33950 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU33950 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU33950 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU33950 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:cggR_context.gif]]

@@ Line 37: / Line 37: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
@@ Line 160: / Line 156: @@
 ==Original Publications==
 '''Additional publications:''' {{PubMed|20462860}}
-<pubmed> 22190493 </pubmed>
+<pubmed> 22190493 23280112 </pubmed>
   <big>''Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Herzberg C, Stülke J''  </big>
   <big>'''RNA processing in ''Bacillus subtilis'': identification of targets of the essential RNase Y.''' </big>

@@ Line 13: / Line 13: @@
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' || transcriptional regulator
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''