EpsC - Revision history

Jstuelk at 08:33, 10 October 2014

2014-10-10T08:33:56Z

Jstuelk at 08:12, 10 October 2014

2014-10-10T08:12:11Z

134.76.38.147 at 14:50, 2 April 2014

2014-04-02T14:50:07Z

134.76.70.252 at 11:43, 7 January 2014

2014-01-07T11:43:40Z

Jstuelk at 15:24, 24 May 2013

2013-05-24T15:24:47Z

134.76.70.252 at 14:38, 16 May 2013

2013-05-16T14:38:15Z

134.76.70.252 at 11:20, 14 May 2013

2013-05-14T11:20:19Z

134.76.70.252 at 13:54, 13 May 2013

2013-05-13T13:54:58Z

Jstuelk at 11:37, 27 March 2013

2013-03-27T11:37:18Z

JGerwig at 14:35, 30 August 2012

2012-08-30T14:35:54Z

← Older revision		Revision as of 08:33, 10 October 2014
Line 1:		Line 1:
−	* '''Description:~~''' UDP-sugar epimerase, required for extracellular polysaccharide synthesis, this gene is inactive in ''B. subtilis'' 168 <br/><br/>~~	+	{{#bank: EpsC}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''epsC''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yveM ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| unknown~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| [[biofilm formation]]~~
−	\|-
−	\|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=BSU34350 epsC]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Regulation of this protein in [[SubtiPathways\|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=epsC epsC]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 66 kDa, 8.775~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1794 bp, 598 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[epsD]]'', ''[[epsB]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34350 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34350 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34350 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yveM_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=epsC_3526407_3528203_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:epsC_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34350]]
−	\|-
−	\|}
−
−	~~__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\|[[membrane proteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[AbrB regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[EAR riboswitch]]}},~~
−	~~{{SubtiWiki regulon\|[[RemA regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SinR regulon]]}}~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU34350
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU34350&redirect=T BSU34350]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/eps.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11861]
−
−	~~=== Additional information===~~
−	* 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:'''
−
−	* '''Protein family:''' polysaccharide synthase family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):''' SpsM ([[YodU]], [[YpqP]])
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:''' cell membrane (according to Swiss-Prot)
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU34350&redirect=T BSU34350]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P71052 P71052]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34350]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−	* '''Operon:''' ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]'' {{PubMed\|15661000}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=epsC_3526407_3528203_-1 epsC] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|15661000}}
−
−	* '''Regulation:'''
−	** repressed by [[SinR]] {{PubMed\|15661000}}
−
−	* '''Regulatory mechanism:'''
−	** [[SinR]]: transcription anti-activation (prevents binding of [[RemA]]) {{PubMed\|23646920}}
−	** [[RemA]]: transcription activation {{PubMed\|23646920}}
−	** [[AbrB]]: transcription repression {{PubMed\|20817675}}
−
−	* '''Additional information:'''
−	** induction by sequestration of [[SinR]] by [[SinI]] or [[SlrA]] {{PubMed\|15661000,19788541}}
−	** the [[EAR riboswitch]] (eps-associated [[RNA switch]]) located between'' [[epsB]]'' and ''[[epsC]]'' mediates processive antitermination and allows expression of the long eps operon {{PubMed\|20374491}}
−	** the ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]'' operon is not expressed in a ''[[ymdB]]'' mutant {{PubMed\|21856853}}
−	** the amount of the mRNA is substantially decreased upon depletion of [[Rny\|RNase Y]] (this is likely due to the increased stability of the ''[[sinR]]'' mRNA) {{PubMed\|21815947}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed> 20384681 20735481 </pubmed>~~
−	~~==Original publications==~~
−	~~===The EAR [[RNA switch]]===~~
−	~~<pubmed>20374491 20230605 </pubmed>~~
−	~~===Regulation of the ''eps'' operon===~~
−	~~<pubmed>15661000,16430695,18047568,18647168 20817675 21856853 21815947 23646920</pubmed>~~
−	~~===Other original publications===~~
−	~~<pubmed> 21278284 </pubmed>~~
−	~~[[Category:Protein-coding genes]]~~

@@ Line 1: / Line 1: @@
-* '''Description:''' putative UDP-sugar epimerase, may be involved in extracellular polysaccharide synthesis, this gene is inactive in ''B. subtilis'' 168  <br/><br/>
+* '''Description:''' UDP-sugar epimerase, required for extracellular polysaccharide synthesis, this gene is inactive in ''B. subtilis'' 168  <br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 77: / Line 77: @@
 * '''Protein family:''' polysaccharide synthase family (according to Swiss-Prot)
-* '''Paralogous protein(s):'''
+* '''Paralogous protein(s):''' SpsM ([[YodU]], [[YpqP]])
 === Extended information on the protein ===

@@ Line 59: / Line 59: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/eps.html]
@@ Line 95: / Line 96: @@
 === Database entries ===
 * '''Structure:'''

@@ 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=BSU34350 epsC]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm]'''
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=epsC epsC]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 66 kDa, 8.775

@@ Line 46: / Line 46: @@
 {{SubtiWiki regulon|[[AbrB regulon]]}},
 {{SubtiWiki regulon|[[EAR riboswitch]]}},
 {{SubtiWiki regulon|[[SinR regulon]]}}
 =The gene=
@@ Line 115: / Line 117: @@
 * '''Regulatory mechanism:'''
-** [[SinR]]: transcription repression {{PubMed|15661000}}
+** [[SinR]]: transcription anti-activation (prevents binding of [[RemA]]) {{PubMed|23646920}}
 ** [[AbrB]]: transcription repression {{PubMed|20817675}}
@@ Line 151: / Line 154: @@
 <pubmed>20374491 20230605 </pubmed>
 ===Regulation of the ''eps'' operon===
-<pubmed>15661000,16430695,18047568,18647168 20817675 21856853 21815947</pubmed>
+<pubmed>15661000,16430695,18047568,18647168 20817675 21856853 21815947 23646920</pubmed>
 ===Other original publications===
 <pubmed> 21278284 </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=epsC_3526407_3528203_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:epsC_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=epsC_3526407_3528203_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:epsC_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34350]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[epsD]]'', ''[[epsB]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34350 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34350 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34350 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34350 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34350 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34350 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:yveM_context.gif]]

@@ Line 37: / Line 37: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 113: / Line 109: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=epsC_3526407_3528203_-1 epsC] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] {{PubMed|15661000}}
+* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|15661000}}
 * '''Regulation:'''
@@ Line 155: / Line 151: @@
 <pubmed>20374491 20230605 </pubmed>
 ===Regulation of the ''eps'' operon===
-'''Additional publications:'''  {{PubMed|20817675}}
+<pubmed>15661000,16430695,18047568,18647168 20817675 21856853 21815947</pubmed>
 ===Other original publications===
 <pubmed> 21278284 </pubmed>
 [[Category:Protein-coding genes]]

← Older revision		Revision as of 14:35, 30 August 2012
Line 1:		Line 1:
−	* '''Description:''' putative UDP-sugar epimerase, involved in extracellular polysaccharide synthesis, this gene is inactive in ''B. subtilis'' 168 <br/><br/>	+	* '''Description:''' putative UDP-sugar epimerase, may be involved in extracellular polysaccharide synthesis, this gene is inactive in ''B. subtilis'' 168 <br/><br/>

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