SigD - Revision history

Jstuelk: /* Original publications */

2015-08-10T09:01:09Z

‎Original publications

Jstuelk: /* Original publications */

2015-07-15T10:37:18Z

‎Original publications

Jstuelk: /* Biological materials */

2015-07-03T14:47:28Z

‎Biological materials

Atkovacs at 13:16, 2 July 2015

2015-07-02T13:16:38Z

Jstuelk: /* Expression and regulation */

2015-02-12T14:18:37Z

‎Expression and regulation

Jstuelk at 15:52, 29 December 2014

2014-12-29T15:52:11Z

Jstuelk: /* Reviews */

2014-09-25T08:19:33Z

‎Reviews

Jstuelk at 09:12, 11 August 2014

2014-08-11T09:12:43Z

134.76.38.147 at 13:44, 2 April 2014

2014-04-02T13:44:57Z

Jstuelk at 19:51, 4 December 2013

2013-12-04T19:51:41Z

← Older revision		Revision as of 09:01, 10 August 2015
Line 1:		Line 1:
−	* '''Description:~~''' [[RNA polymerase]] [[sigma factor]]~~ SigD ~~<br/><br/>~~	+	{{#bank: SigD}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''sigD''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''flaB ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| [[RNA polymerase]] [[sigma factor]] SigD~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| regulation of flagella, motility, chemotaxis and autolysis~~
−	\|-
−	\|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=BSU16470 sigD]
−	\|-
−	\|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=SigD SigD]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 29 kDa, 5.167~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 762 bp, 254 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[cheD]]'', ''[[swrB]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16470 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16470 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16470 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:sigD_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=sigD_1716493_1717257_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:sigD_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16470]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[transcription]]}},~~
−	~~{{SubtiWiki category\|[[sigma factors and their control]]}},~~
−	~~{{SubtiWiki category\|[[motility and chemotaxis]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CodY regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[DegU regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SigD regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[Spo0A regulon]]}}~~
−
−	~~=The [[SigD regulon]]=~~
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU16470
−
−	~~===Phenotypes of a mutant ===~~
−	* Inactivation of ''[[alsR]]'', ''[[sigD]]'' and ''[[sigW]]'' increases competitive fitness of ''Bacillus subtilis'' under non-sporulating conditions {{PubMed\|22344650}}
−	* mucoid phenotype due to the overproduction of poly-gamma-glutamate (because of the loss of ''[[motA]]-[[motB]]'' expression) {{PubMed\|24296669}}
−	* not essential for pellicle biofilm formation, but mutant is outcompeted by the wild-type strain when competed during pellicle formation {{PubMed\|26122431}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16470&redirect=T BSU16470]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fla-che.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10751]
−
−	~~=== Additional information===~~
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' sigma-70 factor family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:''' interaction with [[FlgM]] inhibits SigD activity {{PubMed\|10207036}}
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[SigD]]-[[FlgM]] {{PubMed\|10207036}}, [[SigD]]-([[RpoB]]-[[RpoC]])
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16470&redirect=T BSU16470]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P10726 P10726]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16470]
−
−	* '''E.C. number:'''
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−	* '''Operon:''' part of the [[fla-che operon]]
−	** ''[[flgB]]-[[flgC]]-[[fliE]]-[[fliF]]-[[fliG]]-[[fliH]]-[[fliI]]-[[fliJ]]-[[ylxF]]-[[fliK]]-[[flgD]]-[[flgE]]-[[fliL]]-[[fliM]]-[[fliY]]-[[cheY]]-[[fliZ]]-[[fliP]]-[[fliQ]]-[[fliR]]-[[flhB]]-[[flhA]]-[[flhF]]-[[flhG]]-[[cheB]]-[[cheA]]-[[cheW]]-[[cheC]]-[[cheD]]-[[sigD]]-[[swrB]]'' {{PubMed\|9657996,8157612,15175317}}
−	** ''[[ylxF]]-[[fliK]]-[[flgD]]-[[flgE]]-[[fliL]]-[[fliM]]-[[fliY]]-[[cheY]]-[[fliZ]]-[[fliP]]-[[fliQ]]-[[fliR]]-[[flhB]]-[[flhA]]-[[flhF]]-[[flhG]]-[[cheB]]-[[cheA]]-[[cheW]]-[[cheC]]-[[cheD]]-[[sigD]]-[[swrB]]'' {{PubMed\|20233303}}
−	** ''[[sigD]]-[[swrB]]'' {{PubMed\|9335309}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sigD_1716493_1717257_1 sigD] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−	** ''[[flgB]]'': [[SigA]] {{PubMed\|9657996}}, [[SigD]] {{PubMed\|9657996}}
−	** ''[[ylxF]]'': [[SigD]] {{PubMed\|20233303}}
−	** ''[[sigD]]'': [[SigA]] {{PubMed\|9335309}}
−
−	* '''Regulation:''' see [[fla-che operon]]
−
−	* '''Regulatory mechanism:''' see [[fla-che operon]]
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** 1A716 ( ''sigD''::''cat''), {{PubMed\|2832368}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A716&Search=1A716 BGSC]
−	** DS6420 (marker-less in NCIB3610) {{PubMed\|22329926}}
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
−
−	* '''FLAG-tag construct:''' GP948 (ermC, based on [[pGP1087]]), available in the [[Stülke]] lab
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed> 20233302 25251856 </pubmed>~~
−
−	~~==The [[SigD regulon]]==~~
−	~~<pubmed>15033535,2111808,</pubmed>~~
−
−	~~==Original publications==~~
−	<pubmed> 26122431,22344650 22329926,21097624,22956758 21856853 8955328,7708689,9648743, 8169223,9096206,15175317, 2498284,16357223, 3127378, 26170408 9144176,18820022,7602586,2832368,8195064,11987133,,14651647, 9335309 9657996,8157612,15175317 10809682 8932324 20233303 17850253 10207036 16428420 24296669 25099370 24386445</pubmed>
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 160: / Line 160: @@
 ==Original publications==
-<pubmed> 26122431,22344650 22329926,21097624,22956758 21856853  8955328,7708689,9648743, 8169223,9096206,15175317, 2498284,16357223, 3127378, 9144176,18820022,7602586,2832368,8195064,11987133,,14651647, 9335309 9657996,8157612,15175317 10809682 8932324 20233303 17850253 10207036 16428420 24296669 25099370 24386445</pubmed>
+<pubmed> 26122431,22344650 22329926,21097624,22956758 21856853  8955328,7708689,9648743, 8169223,9096206,15175317, 2498284,16357223, 3127378, 26170408 9144176,18820022,7602586,2832368,8195064,11987133,,14651647, 9335309 9657996,8157612,15175317 10809682 8932324 20233303 17850253 10207036 16428420 24296669 25099370 24386445</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 135: / Line 135: @@
 ** 1A716 ( ''sigD''::''cat''), {{PubMed|2832368}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A716&Search=1A716 BGSC]
 ** DS6420 (marker-less  in NCIB3610) {{PubMed|22329926}}
 * '''Expression vector:'''

@@ Line 60: / Line 60: @@
 * Inactivation of ''[[alsR]]'', ''[[sigD]]'' and ''[[sigW]]'' increases competitive fitness of ''Bacillus subtilis'' under non-sporulating conditions {{PubMed|22344650}}
 * mucoid phenotype due to the overproduction of poly-gamma-glutamate (because of the loss of ''[[motA]]-[[motB]]'' expression) {{PubMed|24296669}}
 === Database entries ===
@@ Line 133: / Line 134: @@
 * '''Mutant:'''
 ** 1A716 ( ''sigD''::''cat''), {{PubMed|2832368}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A716&Search=1A716 BGSC]
 * '''Expression vector:'''
@@ Line 158: / Line 162: @@
 ==Original publications==
-<pubmed> 22344650 22329926,21097624,22956758 21856853  8955328,7708689,9648743, 8169223,9096206,15175317, 2498284,16357223, 3127378, 9144176,18820022,7602586,2832368,8195064,11987133,,14651647, 9335309 9657996,8157612,15175317 10809682 8932324 20233303 17850253 10207036 16428420 24296669 25099370 24386445</pubmed>
+<pubmed> 26122431,22344650 22329926,21097624,22956758 21856853  8955328,7708689,9648743, 8169223,9096206,15175317, 2498284,16357223, 3127378, 9144176,18820022,7602586,2832368,8195064,11987133,,14651647, 9335309 9657996,8157612,15175317 10809682 8932324 20233303 17850253 10207036 16428420 24296669 25099370 24386445</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 111: / Line 111: @@
 =Expression and regulation=
-* '''Operon:'''
+* '''Operon:''' part of the [[fla-che operon]]
 ** ''[[flgB]]-[[flgC]]-[[fliE]]-[[fliF]]-[[fliG]]-[[fliH]]-[[fliI]]-[[fliJ]]-[[ylxF]]-[[fliK]]-[[flgD]]-[[flgE]]-[[fliL]]-[[fliM]]-[[fliY]]-[[cheY]]-[[fliZ]]-[[fliP]]-[[fliQ]]-[[fliR]]-[[flhB]]-[[flhA]]-[[flhF]]-[[flhG]]-[[cheB]]-[[cheA]]-[[cheW]]-[[cheC]]-[[cheD]]-[[sigD]]-[[swrB]]'' {{PubMed|9657996,8157612,15175317}}
 ** ''[[ylxF]]-[[fliK]]-[[flgD]]-[[flgE]]-[[fliL]]-[[fliM]]-[[fliY]]-[[cheY]]-[[fliZ]]-[[fliP]]-[[fliQ]]-[[fliR]]-[[flhB]]-[[flhA]]-[[flhF]]-[[flhG]]-[[cheB]]-[[cheA]]-[[cheW]]-[[cheC]]-[[cheD]]-[[sigD]]-[[swrB]]'' {{PubMed|20233303}}
@@ Line 123: / Line 123: @@
 ** ''[[sigD]]'': [[SigA]] {{PubMed|9335309}}
-* '''Regulation:'''
+* '''Regulation:''' see [[fla-che operon]]
-* '''Regulatory mechanism:'''
+* '''Regulatory mechanism:''' see [[fla-che operon]]
 * '''Additional information:'''

@@ Line 46: / Line 46: @@
 = This gene is a member of the following [[regulons]] =
 {{SubtiWiki regulon|[[CodY regulon]]}},
 {{SubtiWiki regulon|[[SigD regulon]]}},
 {{SubtiWiki regulon|[[Spo0A regulon]]}}
@@ Line 129: / Line 130: @@
 ** [[CodY]]: transcription repression {{PubMed|12730172}}
 ** [[DegU]] (non-phosphorylated): transcription activation {{PubMed|17850253}}
 * '''Additional information:'''
@@ Line 161: / Line 164: @@
 ==Original publications==
-<pubmed> 22344650 22329926,21097624,22956758 21856853  8955328,7708689,9648743, 8169223,9096206,15175317, 2498284,16357223, 3127378, 9144176,18820022,7602586,2832368,8195064,11987133,,14651647, 9335309 9657996,8157612,15175317 10809682 8932324 20233303 17850253 10207036 16428420 24296669 25099370 </pubmed>
+<pubmed> 22344650 22329926,21097624,22956758 21856853  8955328,7708689,9648743, 8169223,9096206,15175317, 2498284,16357223, 3127378, 9144176,18820022,7602586,2832368,8195064,11987133,,14651647, 9335309 9657996,8157612,15175317 10809682 8932324 20233303 17850253 10207036 16428420 24296669 25099370 24386445</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 155: / Line 155: @@
 =References=
 ==Reviews==
-<pubmed> 20233302 </pubmed>
+<pubmed> 20233302 25251856 </pubmed>
 ==The [[SigD regulon]]==

@@ Line 61: / Line 61: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fla-che.html]
@@ Line 97: / Line 98: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 58: / Line 58: @@
 ===Phenotypes of a mutant ===
 * Inactivation of ''[[alsR]]'', ''[[sigD]]'' and ''[[sigW]]'' increases competitive fitness of ''Bacillus subtilis'' under non-sporulating conditions {{PubMed|22344650}}
 === Database entries ===
@@ Line 158: / Line 159: @@
 ==Original publications==
-<pubmed> 22344650 22329926,21097624,22956758 21856853  8955328,7708689,9648743, 8169223,9096206,15175317, 2498284,16357223, 3127378, 9144176,18820022,7602586,2832368,8195064,11987133,,14651647, 9335309 9657996,8157612,15175317 10809682 8932324 20233303 17850253 10207036 16428420 </pubmed>
+<pubmed> 22344650 22329926,21097624,22956758 21856853  8955328,7708689,9648743, 8169223,9096206,15175317, 2498284,16357223, 3127378, 9144176,18820022,7602586,2832368,8195064,11987133,,14651647, 9335309 9657996,8157612,15175317 10809682 8932324 20233303 17850253 10207036 16428420 24296669</pubmed>
 [[Category:Protein-coding genes]]