SwrAA/1 - Revision history

Jstuelk at 08:04, 8 April 2015

2015-04-08T08:04:01Z

Jstuelk at 08:03, 8 April 2015

2015-04-08T08:03:16Z

Jstuelk at 11:32, 2 January 2015

2015-01-02T11:32:21Z

Jstuelk at 11:18, 2 January 2015

2015-01-02T11:18:12Z

Jstuelk at 15:28, 29 December 2014

2014-12-29T15:28:27Z

Jstuelk at 15:21, 29 December 2014

2014-12-29T15:21:17Z

Jstuelk at 15:14, 29 December 2014

2014-12-29T15:14:28Z

Jstuelk: /* References */

2014-12-29T15:12:51Z

‎References

Jstuelk at 14:46, 29 December 2014

2014-12-29T14:46:04Z

134.76.38.147 at 14:55, 2 April 2014

2014-04-02T14:55:02Z

← Older revision		Revision as of 08:04, 8 April 2015
Line 1:		Line 1:
−	* '''Description:~~''' modulator of [[DegU]] activity, converts [[DegU]]-P from a repressor to an activator of the [[fla~~/~~che operon]], enhances ''[[sigD]]'' transcription, controls the number of flagellar basal bodies, inactive pseudogene in strain 168 <br/><br/>~~	+	{{#bank: SwrAA/1}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''swrAA/1''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yvzD, swrAA, ifm''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| swarming motility protein~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| control of [[DegU]] activity~~
−	\|-
−	\|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=BSU35230 swrAA/1]
−	\|-
−	\|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=SwrA SwrA]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| - , -~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 336 bp, -~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[minJ]]'', ''[[swrAA/2]]''~~
−	\|-
−	~~\|style="background:#FAF8CC;" align="center"\|'''[http://subtiwiki.uni-goettingen.de/yvzD_nucleotide.txt Gene sequence (+200bp) ]'''~~
−	~~\|style="background:#FAF8CC;" align="center"\|'''[http://subtiwiki.uni-goettingen.de/yvzD_protein.txt Protein sequence]'''~~
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yvzD_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=swrAA_3621618_3621956_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:1_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU35230]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[biofilm formation]]}},~~
−	~~{{SubtiWiki category\|[[motility and chemotaxis]]}},~~
−	~~{{SubtiWiki category\|[[transcription factors and their control]]}},~~
−	~~{{SubtiWiki category\|[[pseudogenes]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[DegU regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SigD regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU35230
−
−	~~===Phenotypes of a mutant ===~~
−	* loss of swarming motility {{PubMed\|12864845}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU35230&redirect=T BSU35230]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14160]
−
−	~~=== Additional information===~~
−	* This protein is functional in undomesticated strains of ''B.subtilis'' but not in laboratory strains, such as 168, because of a frameshift mutation. Therefore laboratory strains of ''B.subtilis'' are unable to swarm.
−	* The frameshift in strain 168 is caused by a single insertion of an adenine in the codon for Tyr-12 which leads to the premature truncation of the protein in residue 13. In addition, the C-terminal section of ''swrAA'' was predicted to be an ORF (''[[yvzD]]'') by the genome project.
−	* Correction of ''[[sfp]]'', ''[[epsC]]'','' [[swrAA]]'', and ''[[degQ]]'' as well as introduction of ''rapP'' from a plasmid present in NCIB3610 results in [[biofilm formation]] in ''B. subtilis'' 168 {{PubMed\|21278284}}
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** interacts with the N-terminal domain of [[DegU]] to control the activity of [[DegU]] {{PubMed\|22496484}}
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[SwrA]]-[[DegU]]-P (N-terminal domain) {{PubMed\|24386445,22496484}}
−	** [[SwrA]]-[[SmiA]] {{PubMed\|25538299}}
−	** [[LonA]]-[[SwrA]] (degradation) {{PubMed\|25538299}}
−
−	* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU35230&redirect=T BSU35230]
−
−	* '''Structure:'''
−
−	* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O32266 O32266]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU35230]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−	* '''Operon:''' ''[[swrAA]]-[[minJ]]'' {{PubMed\|16030230}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=swrAA_3621618_3621956_-1 swrAA/1] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigD]] {{PubMed\|18567663}}, [[SigA]] {{PubMed\|18567663}}
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−	** [[DegU]]-P: transcription activation ([[SigA]] promoter) {{PubMed\|18567663}}
−
−	* '''Additional information:'''
−	** SwrA levels are 3 ... 10-fold increased on solid medium as compared to liquid medium (due to [[LonA]]/[[SmiA]]-mediated degradation of SwrA in liquid medium) {{PubMed\|25538299}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed>20735481 22092493 </pubmed>~~
−	~~==Original publications==~~
−	~~<pubmed>16091050 22773650 16357223,19389763,16030230,18567663,15066026 22496484 19389763 19749039 21278284 21602220,22329926,23190039 24386445 12864845 25538299 25843804</pubmed>~~
−	~~[[Category:Pseudogenes]]~~

@@ Line 1: / Line 1: @@
-* '''Description:''' modulator of [[DegU]] activity,  converts [[DegU]]-P from a repressor to an activator of the ''fla/che'' operon, enhances ''[[sigD]]'' transcription, controls the number of flagellar basal bodies, inactive pseudogene in strain 168 <br/><br/>
+* '''Description:''' modulator of [[DegU]] activity,  converts [[DegU]]-P from a repressor to an activator of the [[fla/che operon]], enhances ''[[sigD]]'' transcription, controls the number of flagellar basal bodies, inactive pseudogene in strain 168 <br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 69: / Line 69: @@
 * This protein is functional in undomesticated strains of ''B.subtilis'' but not in laboratory strains, such as 168, because of a frameshift mutation. Therefore laboratory strains of ''B.subtilis'' are unable to swarm.
 * The frameshift in strain 168 is caused by a single insertion of an adenine in the codon for Tyr-12 which leads to the premature truncation of the protein in residue 13. In addition, the C-terminal section of ''swrAA'' was predicted to be an ORF (''[[yvzD]]'') by the genome project.
-* Correction of ''[[sfp]]'', ''[[epsC]]'','' [[swrAA]]'', and ''[[degQ]]'' as well as introduction of ''rapP'' from a plasmid present in NCIB3610 results in biofilm formation in ''B. subtilis'' 168 {{PubMed|21278284}}
+* Correction of ''[[sfp]]'', ''[[epsC]]'','' [[swrAA]]'', and ''[[degQ]]'' as well as introduction of ''rapP'' from a plasmid present in NCIB3610 results in [[biofilm formation]] in ''B. subtilis'' 168 {{PubMed|21278284}}
 =The protein=
@@ Line 150: / Line 150: @@
 <pubmed>20735481 22092493 </pubmed>
 ==Original publications==
-<pubmed>16091050 22773650 16357223,19389763,16030230,18567663,15066026 22496484 19389763 19749039 21278284 21602220,22329926,23190039 24386445 12864845 25538299</pubmed>
+<pubmed>16091050 22773650 16357223,19389763,16030230,18567663,15066026 22496484 19389763 19749039 21278284 21602220,22329926,23190039 24386445 12864845 25538299 25843804</pubmed>
 [[Category:Pseudogenes]]

← Older revision		Revision as of 11:32, 2 January 2015
Line 126:		Line 126:

	* '''Additional information:'''		* '''Additional information:'''
		+	** SwrA levels are 3 ... 10-fold increased on solid medium as compared to liquid medium (due to [[LonA]]/[[SmiA]]-mediated degradation of SwrA in liquid medium) {{PubMed\|25538299}}

	=Biological materials =		=Biological materials =

@@ Line 95: / Line 95: @@
 * '''[[SubtInteract|Interactions]]:'''
 ** [[SwrA]]-[[DegU]]-P (N-terminal domain) {{PubMed|24386445,22496484}}
 * '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)
@@ Line 147: / Line 149: @@
 <pubmed>20735481 22092493 </pubmed>
 ==Original publications==
-<pubmed>16091050 22773650 16357223,19389763,16030230,18567663,15066026 22496484 19389763 19749039 21278284 21602220,22329926,23190039 24386445 12864845 </pubmed>
+<pubmed>16091050 22773650 16357223,19389763,16030230,18567663,15066026 22496484 19389763 19749039 21278284 21602220,22329926,23190039 24386445 12864845 25538299</pubmed>
 [[Category:Pseudogenes]]

← Older revision		Revision as of 15:28, 29 December 2014
Line 1:		Line 1:
−	* '''Description:''' modulator of [[DegU]] activity, enhances ''[[sigD]]'' transcription, controls the number of flagellar basal bodies, inactive pseudogene in strain 168 <br/><br/>	+	* '''Description:''' modulator of [[DegU]] activity, converts [[DegU]]-P from a repressor to an activator of the ''fla/che'' operon, enhances ''[[sigD]]'' transcription, controls the number of flagellar basal bodies, inactive pseudogene in strain 168 <br/><br/>

	{\| align="right" border="1" cellpadding="2"		{\| align="right" border="1" cellpadding="2"

@@ Line 47: / Line 47: @@
 = This gene is a member of the following [[regulons]] =
+{{SubtiWiki regulon|[[DegU regulon]]}},
 =The gene=

@@ Line 1: / Line 1: @@
-* '''Description:''' control of [[DegU]] activity,  enhances ''[[sigD]]'' transcription, controls the number of flagellar basal bodies, inactive pseudogene in strain 168 <br/><br/>
+* '''Description:''' modulator of [[DegU]] activity,  enhances ''[[sigD]]'' transcription, controls the number of flagellar basal bodies, inactive pseudogene in strain 168 <br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 56: / Line 56: @@
 ===Phenotypes of a mutant ===
 === Database entries ===

@@ Line 58: / Line 58: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 96: / Line 97: @@
 === Database entries ===
 * '''Structure:'''