EpsN - Revision history

134.76.38.147 at 14:49, 2 April 2014

2014-04-02T14:49:00Z

134.76.70.252 at 11:42, 7 January 2014

2014-01-07T11:42:45Z

Jstuelk at 15:47, 24 May 2013

2013-05-24T15:47:16Z

134.76.70.252 at 14:37, 16 May 2013

2013-05-16T14:37:25Z

134.76.70.252 at 11:19, 14 May 2013

2013-05-14T11:19:20Z

134.76.70.252 at 13:53, 13 May 2013

2013-05-13T13:53:58Z

Jstuelk at 11:46, 27 March 2013

2013-03-27T11:46:32Z

134.76.70.252 at 16:08, 7 August 2012

2012-08-07T16:08:29Z

134.76.70.252 at 09:35, 23 April 2012

2012-04-23T09:35:06Z

134.76.70.252 at 06:54, 17 April 2012

2012-04-17T06:54:11Z

← Older revision		Revision as of 14:49, 2 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' extracellular polysaccharide synthesis <br/><br/>~~	+	{{#bank: EpsN}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''epsN''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yvfE ''~~
−	\|-
−	~~\|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=BSU34230 epsN]
−	\|-
−	\|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=epsN epsN]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 42 kDa, 5.843~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1164 bp, 388 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[epsO]]'', ''[[epsM]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34230 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34230 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34230 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yvfE_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=epsN_3515062_3516228_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:epsN_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34230]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[biofilm formation]]}}~~
−
−	~~= 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:''' BSU34230
−
−	~~===Phenotypes of a mutant ===~~
−	** smooth colonies on MsGG medium, no [[biofilm formation]] {{PubMed\|22113911}}
−
−	~~=== Database entries ===~~
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/eps.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11873]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' degT/dnrJ/eryC1 family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/Q795J3 Q795J3]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34230]
−
−	* '''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=epsN_3515062_3516228_-1 epsN] {{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 ''[[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}}
−	** 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}}
−
−	~~=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>20735481 </pubmed>~~
−	~~==Original publications==~~
−	~~===The EAR [[RNA switch]]===~~
−	~~<pubmed>20374491 20230605 </pubmed>~~
−	~~===Other original publications===~~
−	~~<pubmed>22113911 15661000,16430695,18047568,18647168 20720312 20817675 21856853 21815947 23646920</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ 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=BSU34230 epsN]
 |-
-|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=epsN epsN]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 42 kDa, 5.843

@@ Line 45: / Line 45: @@
 {{SubtiWiki regulon|[[AbrB regulon]]}},
 {{SubtiWiki regulon|[[EAR riboswitch]]}},
 {{SubtiWiki regulon|[[SinR regulon]]}}
@@ Line 116: / 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 152: / Line 154: @@
 <pubmed>20374491 20230605 </pubmed>
 ===Other original publications===
-<pubmed>22113911 15661000,16430695,18047568,18647168 20720312 20817675 21856853 21815947</pubmed>
+<pubmed>22113911 15661000,16430695,18047568,18647168 20720312 20817675 21856853 21815947 23646920</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=epsN_3515062_3516228_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:epsN_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=epsN_3515062_3516228_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:epsN_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34230]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[epsO]]'', ''[[epsM]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34230 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34230 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34230 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34230 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34230 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34230 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:yvfE_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 114: / Line 110: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=epsN_3515062_3516228_-1 epsN] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] {{PubMed|15661000}}
+* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|15661000}}
 * '''Regulation:'''
@@ Line 156: / Line 152: @@
 <pubmed>20374491 20230605 </pubmed>
 ===Other original publications===
-'''Additional publications:''' {{PubMed|20817675}}
+<pubmed>22113911 15661000,16430695,18047568,18647168 20720312 20817675 21856853 21815947</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 13: / Line 13: @@
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' || [[biofilm formation]]
 |-
 |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]'''