WalR - Revision history

Jstuelk at 14:31, 23 July 2015

2015-07-23T14:31:37Z

Jstuelk: /* Biological materials */

2014-09-24T13:51:13Z

‎Biological materials

Jstuelk: /* The protein */

2014-09-24T13:43:21Z

‎The protein

Jstuelk: /* Other original Publications */

2014-07-03T09:23:56Z

‎Other original Publications

Jstuelk at 11:09, 13 June 2014

2014-06-13T11:09:10Z

134.76.70.252 at 10:03, 17 April 2014

2014-04-17T10:03:25Z

134.76.38.147 at 15:16, 2 April 2014

2014-04-02T15:16:52Z

Jstuelk: /* Other original Publications */

2014-02-06T15:36:19Z

‎Other original Publications

Jstuelk: /* Expression and regulation */

2014-01-15T17:22:00Z

‎Expression and regulation

Jstuelk: /* The WalR regulon */

2013-12-27T19:26:44Z

‎The WalR regulon

← Older revision		Revision as of 14:31, 23 July 2015
Line 1:		Line 1:
−	* '''Description:~~''' [[two-component systems\|two-component]] response regulator ([[transcription factors of the OmpR family\|OmpR family]]), controls cell wall metabolism <br/><br/>~~	+	{{#bank: WalR}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''walR''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yycF''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| [[two-component systems\|two-component]] response regulator ([[transcription factors of the OmpR family\|OmpR family]])~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| control of cell wall metabolism~~
−	\|-
−	\|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=BSU40410 walR]
−	\|-
−	\|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=WalR WalR]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 27 kDa, 4.876~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 705 bp, 235 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[walK]]'', ''[[trnY-Phe]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU40410 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU40410 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU40410 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yycF_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=walR_4153696_4154403_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:walR_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU40410]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[cell wall/ other]]}},~~
−	~~{{SubtiWiki category\|[[transcription factors and their control]]}},~~
−	~~{{SubtiWiki category\|[[essential genes]]}},~~
−	~~{{SubtiWiki category\|[[phosphoproteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−	~~=The [[WalR regulon]]=~~
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU40410
−
−	~~===Phenotypes of a mutant ===~~
−	* essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
−	* a constitutively active form of [[WalR]] ([[WalR]]-R204C) results in constitutive expression of the [[WalR]] regulon, and in combination with a ''[[sepF]]'' mutation to the formation of cell wall-less L-forms {{PubMed\|22122227}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU40410&redirect=T BSU40410]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yycFGHIJ-yyxA.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10001]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' [[transcription factors of the OmpR family\|OmpR family]] of two-component response regulators
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:''' phosphorylated by [[WalK]] on an Asp residue
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:''' phosphorylation likely affects DNA-binding activity
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[WalK]]-[[WalR]]
−
−	* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU40410&redirect=T BSU40410]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2D1V 2D1V] (DNA binding domain), [http://www.rcsb.org/pdb/explore.do?structureId=2ZWM 2ZWM] (receiver domain)
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P37478 P37478]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40410]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[walR]]-[[walK]]-[[yycH]]-[[yycI]]-[[walJ]]-[[htrC]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/9829949 PubMed]
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=walR_4153696_4154403_-1 walR] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−	** expressed during vegetative growth, repressed during stationary phase [http://www.ncbi.nlm.nih.gov/sites/entrez/9829949 PubMed]
−	** induced at high temperature {{PubMed\|24125693}}
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 176 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−	** pGP2633, constitutive expression in ''B. subtilis'' (based on [[pBQ200]]), available in [[Jörg Stülke]]'s lab
−	** pGP2635, expression of His-[[WalR]] in ''E. coli'' (based on [[pWH844]]), available in [[Jörg Stülke]]'s lab
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−	* [[Kevin Devine]], Dublin
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed>19019149, 18245295,18792692, 22126136, 10094672 </pubmed>~~
−	~~==The [[WalR regulon]]==~~
−	~~<pubmed>17581128,10878122,12950927, 23199363</pubmed>~~
−
−	~~==Other original Publications==~~
−	~~<pubmed>18573169,17350627,10094672,17827301,9829949,16030236,19574649, 20059685 20111065 20167622 20834167 24125693 22122227 24125693 24490131 18789936 </pubmed>~~
−	~~[[Category:Protein-coding genes]]~~

← Older revision		Revision as of 13:51, 24 September 2014
Line 129:		Line 129:

	* '''Expression vector:'''		* '''Expression vector:'''
		+	** pGP2633, constitutive expression in ''B. subtilis'' (based on [[pBQ200]]), available in [[Jörg Stülke]]'s lab
		+	** pGP2635, expression of His-[[WalR]] in ''E. coli'' (based on [[pWH844]]), available in [[Jörg Stülke]]'s lab

	* '''lacZ fusion:'''		* '''lacZ fusion:'''

← Older revision		Revision as of 13:43, 24 September 2014
Line 76:		Line 76:

	* '''Paralogous protein(s):'''		* '''Paralogous protein(s):'''
−

	=== Extended information on the protein ===		=== Extended information on the protein ===

@@ Line 151: / Line 151: @@
 ==Other original Publications==
-<pubmed>18573169,17350627,10094672,17827301,9829949,16030236,19574649, 20059685 20111065 20167622 20834167 24125693 22122227 24125693 24490131 </pubmed>
+<pubmed>18573169,17350627,10094672,17827301,9829949,16030236,19574649, 20059685 20111065 20167622 20834167 24125693 22122227 24125693 24490131 18789936 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 1: / Line 1: @@
-* '''Description:''' [[two-component systems|two-component]] response regulator, controls cell wall metabolism <br/><br/>
+* '''Description:''' [[two-component systems|two-component]] response regulator ([[transcription factors of the OmpR family|OmpR family]]), controls cell wall metabolism <br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 10: / Line 10: @@
 |style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 |-
-|style="background:#ABCDEF;" align="center"| '''Product''' || [[two-component systems|two-component]] response regulator
+|style="background:#ABCDEF;" align="center"| '''Product''' || [[two-component systems|two-component]] response regulator ([[transcription factors of the OmpR family|OmpR family]])
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' || control of cell wall metabolism
@@ Line 73: / Line 73: @@
 * '''Catalyzed reaction/ biological activity:'''
-* '''Protein family:''' OmpR family of two-component transcription regulators
+* '''Protein family:''' [[transcription factors of the OmpR family|OmpR family]] of two-component response regulators
 * '''Paralogous protein(s):'''

← Older revision		Revision as of 10:03, 17 April 2014
Line 123:		Line 123:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 176 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 59: / Line 59: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yycFGHIJ-yyxA.html]
@@ Line 95: / Line 96: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2D1V 2D1V] (DNA binding domain), [http://www.rcsb.org/pdb/explore.do?structureId=2ZWM 2ZWM] (receiver domain)

@@ Line 108: / Line 108: @@
 =Expression and regulation=
-* '''Operon:''' ''[[walR]]-[[walK]]-[[yycH]]-[[yycI]]-[[walJ]]-[[yyxA]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/9829949 PubMed]
+* '''Operon:''' ''[[walR]]-[[walK]]-[[yycH]]-[[yycI]]-[[walJ]]-[[htrC]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/9829949 PubMed]
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=walR_4153696_4154403_-1 walR] {{PubMed|22383849}}

@@ Line 145: / Line 145: @@
 <pubmed>19019149, 18245295,18792692, 22126136, 10094672 </pubmed>
 ==The [[WalR regulon]]==
-<pubmed>17581128,10878122,12950927, </pubmed>
+<pubmed>17581128,10878122,12950927, 23199363</pubmed>
 ==Other original Publications==
 <pubmed>18573169,17350627,10094672,17827301,9829949,16030236,19574649, 20059685 20111065 20167622 20834167 24125693 22122227 24125693</pubmed>
 [[Category:Protein-coding genes]]