EpsE - Revision history

Jstuelk: /* References */

2014-09-25T08:19:53Z

‎References

Jstuelk at 10:30, 5 August 2014

2014-08-05T10:30:44Z

Jstuelk: /* Reviews */

2014-07-07T08:15:48Z

‎Reviews

134.76.38.147 at 14:49, 2 April 2014

2014-04-02T14:49:55Z

134.76.70.252 at 11:43, 7 January 2014

2014-01-07T11:43:30Z

134.76.70.252 at 14:21, 18 November 2013

2013-11-18T14:21:43Z

Jstuelk at 15:25, 24 May 2013

2013-05-24T15:25:06Z

134.76.70.252 at 14:38, 16 May 2013

2013-05-16T14:38:05Z

134.76.70.252 at 11:20, 14 May 2013

2013-05-14T11:20:08Z

134.76.70.252 at 13:54, 13 May 2013

2013-05-13T13:54:47Z

← Older revision		Revision as of 08:19, 25 September 2014
Line 1:		Line 1:
−	* '''Description:~~''' inhibitor of motility and glycosyltransferase required for EPS biosynthesis <br/><br/>~~	+	{{#bank: EpsE}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''epsE''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yveO ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| glycosyltransferase, inhibitor of motility~~
−	\|-
−	~~\|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=BSU34330 epsE]
−	\|-
−	\|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=EpsE EpsE]
−	\|-
−	\|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=epsE epsE]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 32 kDa, 9.804~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 834 bp, 278 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[epsF]]'', ''[[epsD]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34330 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34330 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34330 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yveO_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=epsE_3524417_3525253_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:epsE_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34330]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[motility and chemotaxis]]}},~~
−	~~{{SubtiWiki category\|[[biofilm formation]]}},~~
−	~~{{SubtiWiki category\|[[membrane proteins]]}},~~
−	~~{{SubtiWiki category\|[[phosphoproteins]]}}~~
−
−	~~= 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:''' BSU34330
−
−	~~===Phenotypes of a mutant ===~~
−	** smooth colonies on MsGG medium, no [[biofilm formation]] {{PubMed\|22113911}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU34330&redirect=T BSU34330]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/eps.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11863]
−
−	~~=== Additional information===~~
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** arrests flagellar rotation in a manner similar to that of a clutch, by disengaging motor force-generating elements in cells embedded in the biofilm matrix, separates the cytoplasmic [[FliG]] motor from the [[MotA]]-[[MotB]] stator {{PubMed\|18566286}}
−	** biosynthesis of extracellular polysaccharides {{PubMed\|21170308}}
−
−	* '''Protein family:''' glycosyltransferase 2 family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:''' phosphorylated by [[EpsB]] on a Tyr residue {{PubMed\|25085422}}
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[EpsE]]-[[FliG]] {{PubMed\|18566286}}
−
−	* '''[[Localization]]:''' cell membrane, forms spots at flagellar basal bodies {{PubMed\|18566286}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU34330&redirect=T BSU34330]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P71054 P71054]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34330]
−
−	* '''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=epsE_3524417_3525253_-1 epsE] {{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=~~
−
−	* [[Daniel Kearns]], Indiana University, Bloomington, USA, [http://www.bio.indiana.edu/facultyresearch/faculty/Kearns.html homepage]
−	* [[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]
−
−	~~=Your additional remarks=~~
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed>20735481 24988880 </pubmed>~~
−
−	~~==Original publications==~~
−	~~===The EAR [[RNA switch]]===~~
−	~~<pubmed>20374491 20230605 </pubmed>~~
−	~~===Other original publications===~~
−	~~<pubmed>22113911 15661000,16430695,18047568, 18566286 18647168 21170308 20817675 21856853 21815947 23646920 25085422</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 46: / Line 46: @@
 {{SubtiWiki category|[[motility and chemotaxis]]}},
 {{SubtiWiki category|[[biofilm formation]]}},
-{{SubtiWiki category|[[membrane proteins]]}}
+{{SubtiWiki category|[[membrane proteins]]}},
 = This gene is a member of the following [[regulons]] =
@@ Line 91: / Line 92: @@
 * '''Domains:'''
-* '''Modification:'''
+* '''Modification:''' phosphorylated by [[EpsB]] on a Tyr residue {{PubMed|25085422}}
 * '''Cofactor(s):'''
@@ Line 164: / Line 165: @@
 <pubmed>20374491 20230605 </pubmed>
 ===Other original publications===
-<pubmed>22113911 15661000,16430695,18047568, 18566286 18647168 21170308 20817675 21856853 21815947 23646920</pubmed>
+<pubmed>22113911 15661000,16430695,18047568, 18566286 18647168 21170308 20817675 21856853 21815947 23646920 25085422</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 158: / Line 158: @@
 =References=
 ==Reviews==
-<pubmed>20735481 </pubmed>
+<pubmed>20735481 24988880 </pubmed>
 ==Original publications==
 ===The EAR [[RNA switch]]===

@@ Line 64: / Line 64: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/eps.html]
@@ Line 102: / Line 103: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 18: / Line 18: @@
 |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=EpsE EpsE]
 |-
-|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=epsE epsE]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 32 kDa, 9.804

@@ 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=BSU34330 epsE]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/EpsE EpsE]
+|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=EpsE EpsE]
 |-
 |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]'''

@@ Line 51: / Line 51: @@
 {{SubtiWiki regulon|[[AbrB regulon]]}},
 {{SubtiWiki regulon|[[EAR riboswitch]]}},
 {{SubtiWiki regulon|[[SinR regulon]]}}
@@ Line 123: / Line 124: @@
 * '''Regulatory mechanism:'''
-** [[SinR]]: transcription repression {{PubMed|15661000}}
+** [[SinR]]: transcription anti-activation (prevents binding of [[RemA]]) {{PubMed|23646920}}
 ** [[AbrB]]: transcription repression {{PubMed|20817675}}
@@ Line 159: / Line 161: @@
 <pubmed>20374491 20230605 </pubmed>
 ===Other original publications===
-<pubmed>22113911 15661000,16430695,18047568, 18566286 18647168 21170308 20817675 21856853 21815947</pubmed>
+<pubmed>22113911 15661000,16430695,18047568, 18566286 18647168 21170308 20817675 21856853 21815947 23646920</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 33: / Line 33: @@
   <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=epsE_3524417_3525253_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:epsE_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=epsE_3524417_3525253_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:epsE_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34330]]
 |-
 |}

@@ Line 26: / Line 26: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[epsF]]'', ''[[epsD]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34330 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34330 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34330 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34330 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34330 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34330 DNA_with_flanks]
 |-
 |-