YvcL - Revision history

Fabian Commichau: /* Biological materials */

2014-12-08T14:41:10Z

‎Biological materials

Fabian Commichau: /* Biological materials */

2014-12-08T14:21:09Z

‎Biological materials

Fabian Commichau: /* Biological materials */

2014-12-08T14:20:32Z

‎Biological materials

134.76.38.147 at 14:52, 2 April 2014

2014-04-02T14:52:15Z

Jstuelk: /* Phenotypes of a mutant */

2013-12-21T18:03:46Z

‎Phenotypes of a mutant

Jstuelk at 18:00, 21 December 2013

2013-12-21T18:00:24Z

Jstuelk at 17:52, 21 December 2013

2013-12-21T17:52:18Z

Jstuelk at 17:40, 23 October 2013

2013-10-23T17:40:04Z

134.76.70.252 at 14:39, 16 May 2013

2013-05-16T14:39:51Z

134.76.70.252 at 11:21, 14 May 2013

2013-05-14T11:21:53Z

← Older revision		Revision as of 14:41, 8 December 2014
Line 1:		Line 1:
−	* '''Description:~~''' WhiA family protein, involved in Z ring assembly, putative transcription factor<br/><br/>~~	+	{{#bank: YvcL}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''yvcL''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| [[cell division]] protein~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| control of Z ring asembly~~
−	\|-
−	\|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=BSU34750 yvcL]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 36 kDa, 9.479~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 948 bp, 316 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[crh]]'', ''[[yvcK]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34750 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34750 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34750 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yvcL_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=whiA_3569573_3570523_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:yvcL_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34750]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[cell division]]}},~~
−	~~{{SubtiWiki category\|[[transcription factors and their control]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU34750
−
−	~~===Phenotypes of a mutant ===~~
−	* a ''[[yvcL]] [[zapA]]'' double mutant grows poorly, and the cells are filamentous (due to a defect in Z ring assembly) {{PubMed\|24097947}}
−	* a ''[[yvcL]] [[ezrA]]'' double mutant grows poorly, and the cells are filamentous {{PubMed\|24097947}}
−	* a ''[[yvcL]] [[minC]]-[[minD]]'' mutant grows poorly, and the cells are filamentous {{PubMed\|24097947}}
−	* a ''[[yvcL]] [[noc]]'' double mutant grows poorly, and the cells are filamentous {{PubMed\|24097947}}
−	* the defects of the ''[[yvcL]] [[zapA]]'' double mutant can be suppressed by inactivation of either ''[[gtaB]]'', ''[[pgcA]]'', or ''[[ugtP]]'' {{PubMed\|24097947}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU34750&redirect=T BSU34750]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12402]
−
−	~~=== Additional information===~~
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' WhiA family [http://www.ncbi.nlm.nih.gov/pubmed/10986251 PubMed]
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:''' suggested HTH domain at the N terminus [http://www.ncbi.nlm.nih.gov/sites/entrez/19836336 PubMed]
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−	** localizes to the nucleoid {{PubMed\|24097947}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU34750&redirect=T BSU34750]
−
−	* '''Structure:'''
−	** [http://www.rcsb.org/pdb/explore.do?structureId=3HYI 3HYI] (Crystal structure of full-length DUF199/WhiA from ''Thermotoga maritima'')
−	** [http://www.rcsb.org/pdb/explore.do?structureId=3HYJ 3HYJ] (Crystal structure of the N-terminal LAGLIDADG domain of DUF199/WhiA)
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O06975 O06975]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34750]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[yvcI]]-[[yvcJ]]-[[yvcK]]-[[yvcL]]-[[crh]]-[[yvcN]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/9237995 PubMed]
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=whiA_3569573_3570523_-1 yvcL] {{PubMed\|22383849}}
−
−	* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16272399 PubMed]
−
−	* '''Regulation:'''
−	** constitutive expression at both protein and RNA levels {{PubMed\|24097947,22383849}}
−	** very weak stimuation of expression by citrate and succinate [http://www.ncbi.nlm.nih.gov/sites/entrez/16272399 PubMed]
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:''' GP231 (''amyE::P[[rpsJ]]-lacZ, yvcL::cat'') available in [[ Jörg Stülke]]'s lab; plasmid pGP1468 was used to disrupt the gene.
−
−	* '''Expression vector:'''
−	** pGP1469 for expression in ''B. subtilis'' (in [[pGP382]], with C-terminal STREP-TAG), available in [[ Jörg Stülke]]'s lab
−	** pGP2429 (N-terminal Strep-Tag, purification from ''E. coli'' and/or ''B. subtilis'', in pDG148), for [[SPINE]], available in [[Jörg Stülke]]'s lab
−	** pGP2430 (C-terminal Strep-Tag, purification from ''E. coli'' and/or ''B. subtilis'', in pDG148), for [[SPINE]], available in [[Jörg Stülke]]'s lab
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[ Jörg Stülke]]'s and [[Boris Görke]]'s labs
−
−	* '''Antibody:''' available in [[Leendert Hamoen]]'s lab {{PubMed\|24097947}}
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−	WhiA orthologues are present in all Gram-positive bacteria and best characterized by the WhiA sporulation control factor in ''Streptomyces coelicolor''. They are thought to act as genetic regulators that have evolved from LAGLIDADG homing endonucleases (LHE).
−
−	~~=References=~~
−
−	~~<pubmed>9237995 16272399 10986251 19836336 17603302, 24097947 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 131: / Line 131: @@
 * '''Expression vector:'''
 ** pGP1469 for expression in ''B. subtilis'' (in [[pGP382]], with C-terminal STREP-TAG), available in [[ Jörg Stülke]]'s lab
-** pGP2429 (N-terminal Strep-tag, purification from ''E. coli'' and/or ''B. subtilis'', in pDG148), for [[SPINE]], available in [[Jörg Stülke]]'s lab
+** pGP2429 (N-terminal Strep-Tag, purification from ''E. coli'' and/or ''B. subtilis'', in pDG148), for [[SPINE]], available in [[Jörg Stülke]]'s lab
 * '''lacZ fusion:'''

@@ Line 129: / Line 129: @@
 * '''Mutant:''' GP231 (''amyE::P[[rpsJ]]-lacZ, yvcL::cat'') available in [[ Jörg Stülke]]'s lab; plasmid pGP1468 was used to disrupt the gene.
-* '''Expression vector:''' pGP1469 for expression in ''B. subtilis'' (in [[pGP382]], with C-terminal STREP-TAG), available in [[ Jörg Stülke]]'s lab
+* '''Expression vector:'''
 * '''lacZ fusion:'''

@@ Line 58: / Line 58: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 94: / Line 95: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 51: / Line 51: @@
 ===Phenotypes of a mutant ===
-* a ''[[yvcL]] [[zapA]]'' double mutant grows poorly, and the cells are filamentous {{PubMed|24097947}}
+* a ''[[yvcL]] [[zapA]]'' double mutant grows poorly, and the cells are filamentous (due to a defect in Z ring assembly) {{PubMed|24097947}}
 * the defects of the ''[[yvcL]] [[zapA]]'' double mutant can be suppressed by inactivation of either ''[[gtaB]]'', ''[[pgcA]]'', or ''[[ugtP]]'' {{PubMed|24097947}}

@@ Line 52: / Line 52: @@
 ===Phenotypes of a mutant ===
 * a ''[[yvcL]] [[zapA]]'' double mutant grows poorly, and the cells are filamentous {{PubMed|24097947}}
 === Database entries ===
@@ Line 60: / Line 61: @@
 === Additional information===
@@ Line 78: / Line 77: @@
 * '''Kinetic information:'''
-* '''[[Domains]]:''' suggested HTH domain [http://www.ncbi.nlm.nih.gov/sites/entrez/19836336 PubMed]
+* '''[[Domains]]:''' suggested HTH domain at the N terminus [http://www.ncbi.nlm.nih.gov/sites/entrez/19836336 PubMed]
 * '''Modification:'''
@@ Line 89: / Line 88: @@
 * '''[[Localization]]:'''
 === Database entries ===
@@ Line 112: / Line 112: @@
 * '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16272399 PubMed]
-* '''Regulation:''' very weak stimuation of expression by citrate and succinate [http://www.ncbi.nlm.nih.gov/sites/entrez/16272399 PubMed]
+* '''Regulation:'''
 * '''Regulatory mechanism:'''
@@ Line 128: / Line 130: @@
 * '''GFP fusion:'''
-* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Boris Görke| Görke]] lab
+* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[ Jörg Stülke]]'s and [[Boris Görke]]'s labs
-* '''Antibody:'''
+* '''Antibody:''' available in [[Leendert Hamoen]]'s lab {{PubMed|24097947}}
 =Labs working on this gene/protein=

@@ Line 1: / Line 1: @@
-* '''Description:''' WhiA family protein conserved and ubiquitous among gram-positive bacteria, putative transcription factor<br/><br/>
+* '''Description:''' WhiA family protein, involved in Z ring assembly, putative transcription factor<br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 10: / Line 10: @@
 |style="background:#ABCDEF;" align="center"| '''Essential''' || no
 |-
-|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+|style="background:#ABCDEF;" align="center"| '''Product''' || [[cell division]] protein
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+|style="background:#ABCDEF;" align="center"|'''Function''' || control of Z ring asembly
 |-
 |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=BSU34750 yvcL]
@@ Line 38: / Line 38: @@
 = [[Categories]] containing this gene/protein =
 {{SubtiWiki category|[[transcription factors and their control]]}}
@@ Line 50: / Line 51: @@
 ===Phenotypes of a mutant ===
 === Database entries ===
@@ Line 76: / Line 78: @@
 * '''Kinetic information:'''
-* '''Domains:''' suggested HTH domain [http://www.ncbi.nlm.nih.gov/sites/entrez/19836336 PubMed]
+* '''[[Domains]]:''' suggested HTH domain [http://www.ncbi.nlm.nih.gov/sites/entrez/19836336 PubMed]
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 90: / Line 92: @@
 === Database entries ===
-* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=3HYI 3HYI] (Crystal structure of full-length DUF199/WhiA from ''Thermotoga maritima''), [http://www.rcsb.org/pdb/explore.do?structureId=3HYJ 3HYJ] (Crystal structure of the N-terminal LAGLIDADG domain of DUF199/WhiA)
+* '''Structure:'''
 * '''UniProt:''' [http://www.uniprot.org/uniprot/O06975 O06975]

@@ Line 35: / Line 35: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/>
@@ Line 139: / Line 135: @@
 =References=
-<pubmed>9237995 16272399 10986251 19836336 17603302, </pubmed>
+<pubmed>9237995 16272399 10986251 19836336 17603302, 24097947 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 27: / Line 27: @@
   <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=whiA_3569573_3570523_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yvcL_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=whiA_3569573_3570523_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yvcL_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34750]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[crh]]'', ''[[yvcK]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34750 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34750 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34750 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34750 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34750 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34750 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:yvcL_context.gif]]