TapA - Revision history

Jstuelk: /* Reviews */

2015-04-26T15:36:39Z

‎Reviews

Jstuelk: /* Original publications */

2015-04-22T08:47:21Z

‎Original publications

134.76.38.147 at 14:12, 2 April 2014

2014-04-02T14:12:30Z

Jstuelk at 17:23, 6 February 2014

2014-02-06T17:23:09Z

JGerwig: /* Biological materials */

2014-01-27T16:57:04Z

‎Biological materials

JGerwig: /* Biological materials */

2014-01-27T16:56:29Z

‎Biological materials

134.76.70.252 at 11:12, 7 January 2014

2014-01-07T11:12:22Z

134.76.70.252 at 14:18, 18 November 2013

2013-11-18T14:18:36Z

Atkovacs: /* Expression and regulation */

2013-11-08T15:37:11Z

‎Expression and regulation

Jstuelk at 15:19, 24 May 2013

2013-05-24T15:19:29Z

← Older revision		Revision as of 15:36, 26 April 2015
Line 1:		Line 1:
−	* '''Description:~~''' required for the anchoring of the [[TasA]] amyloid fibers to the cell and for the initiation of fiber polymerization, minor fiber component~~	+	{{#bank: TapA}}
−	~~<br/><br/>~~

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''tapA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yqhD, yqxM ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| [[TasA]] anchoring/assembly protein~~
−	\|-
−	~~\|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=BSU24640 tapA]
−	\|-
−	\|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=TapA TapA]
−	\|-
−	\|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=tapA tapA]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 28 kDa, 6.677~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 759 bp, 253 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[sipW]]'', ''[[yqzG]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24640 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24640 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24640 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yqxM_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=yqxM_2554486_2555247_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:tapA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24640]]
−	\|-
−	\|}
−
−	~~__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\|[[RemA regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SinR regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU24640
−
−	~~===Phenotypes of a mutant ===~~
−	* no biofilm formation {{PubMed\|24488317}}
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24640&redirect=T BSU24640]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqxM-sipW-tasA.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11076]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[TapA]]-[[TasA]] {{PubMed\|24488317}}
−	** [[SipW]]-[[TapA]] {{PubMed\|10559173}}
−
−	* '''[[Localization]]:'''
−	** attached to the cell surface (on the outside of the cell), associated with peptidoglycan {{PubMed\|21477127}}
−	** secretion requires [[SipW]] {{PubMed\|10559173}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24640&redirect=T BSU24640]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P40949 P40949]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24640]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[tapA]]-[[sipW]]-[[tasA]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yqxM_2554486_2555247_-1 tapA] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]
−
−	* '''Regulation:'''
−	** repressed by [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]
−	** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10464223,17720793 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10464223,17720793 PubMed]
−	** [[SinR]]: transcription repression {{PubMed\|16430695}}
−	** [[RemA]]: transcription activation {{PubMed\|23646920}}
−	** [[LutR]]: transcription activation {{PubMed\|24196425}}
−
−	* '''Additional information:'''
−	** induction by sequestration of [[SinR]] by [[SinI]] or [[SlrA]] {{PubMed\|15661000,19788541}} or by SlrR {{PubMed\|20351052}}
−	** the ''[[tapA]]-[[sipW]]-[[tasA]]'' 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:''' pGP1926 (in [[pAC6]]), available in [[Stülke]] lab
−
−	* '''GFP fusion:'''
−
−	* '''YFP fusion:''' GP1537 lacA::p(tapA-yfp ermC), available in [[Stülke]] lab
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed> 21488983 </pubmed>~~
−	~~==Original publications==~~
−	~~<pubmed>18430133,18047568,18647168, 20351052,16430695,10464223,17720793, 19605685 20431016 10559173 21477127 21856853 21815947 23646920 24488317 25894589</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 161: / Line 161: @@
 <pubmed> 21488983 </pubmed>
 ==Original publications==
-<pubmed>18430133,18047568,18647168, 20351052,16430695,10464223,17720793, 19605685 20431016 10559173 21477127 21856853 21815947 23646920 24488317</pubmed>
+<pubmed>18430133,18047568,18647168, 20351052,16430695,10464223,17720793, 19605685 20431016 10559173 21477127 21856853 21815947 23646920 24488317 25894589</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 60: / Line 60: @@
 * no biofilm formation {{PubMed|24488317}}
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqxM-sipW-tasA.html]
@@ Line 101: / Line 102: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 58: / Line 58: @@
 ===Phenotypes of a mutant ===
-The mutants are able to form a biofilm in the presence of D-amino acids {{PubMed|20431016}}
+* no biofilm formation {{PubMed|24488317}}
 === Database entries ===
@@ Line 91: / Line 90: @@
 * '''Cofactor(s):'''
-* '''Effectors of protein activity:''' D-amino acids lead to disappearance of TapA from the cell wall {{PubMed|21477127}}
+* '''Effectors of protein activity:'''
 * '''[[SubtInteract|Interactions]]:'''
-** [[TapA]]-[[TasA]] {{PubMed|21477127}}
+** [[TapA]]-[[TasA]] {{PubMed|24488317}}
 ** [[SipW]]-[[TapA]] {{PubMed|10559173}}
@@ Line 160: / Line 159: @@
 <pubmed> 21488983 </pubmed>
 ==Original publications==
-<pubmed>18430133,18047568,18647168, 20351052,16430695,10464223,17720793, 19605685 20431016 10559173 21477127 21856853 21815947 23646920</pubmed>
+<pubmed>18430133,18047568,18647168, 20351052,16430695,10464223,17720793, 19605685 20431016 10559173 21477127 21856853 21815947 23646920 24488317</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 146: / Line 146: @@
 * '''GFP fusion:'''
-* '''YFP fusion:''' GP1537 lacA::p(tapA-yfp ermC)
+* '''YFP fusion:''' GP1537 lacA::p(tapA-yfp ermC), available in [[Stülke]] lab
 * '''two-hybrid system:'''

← Older revision		Revision as of 16:56, 27 January 2014
Line 145:		Line 145:

	* '''GFP fusion:'''		* '''GFP fusion:'''
		+
		+	* '''YFP fusion:''' GP1537 lacA::p(tapA-yfp ermC)

	* '''two-hybrid system:'''		* '''two-hybrid system:'''

@@ Line 19: / Line 19: @@
 |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=TapA TapA]
 |-
-|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], [http://subtiwiki.uni-goettingen.de/wiki/index.php/Protein_secretion Protein secretion]'''
+|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=tapA tapA]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 6.677

@@ Line 17: / Line 17: @@
 |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=BSU24640 tapA]
 |-
-|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/TapA TapA]
+|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=TapA TapA]
 |-
 |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], [http://subtiwiki.uni-goettingen.de/wiki/index.php/Protein_secretion Protein secretion]'''

@@ Line 129: / Line 129: @@
 ** [[SinR]]: transcription repression {{PubMed|16430695}}
 ** [[RemA]]: transcription activation {{PubMed|23646920}}
 * '''Additional information:'''

@@ Line 40: / Line 40: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 52: / Line 48: @@
 = This gene is a member of the following [[regulons]] =
 {{SubtiWiki regulon|[[AbrB regulon]]}},
 {{SubtiWiki regulon|[[SinR regulon]]}}
@@ Line 122: / Line 119: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yqxM_2554486_2555247_-1 tapA] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]
+* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]
 * '''Regulation:'''
@@ Line 131: / Line 128: @@
 ** [[AbrB]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10464223,17720793 PubMed]
 ** [[SinR]]: transcription repression {{PubMed|16430695}}
 * '''Additional information:'''
@@ Line 159: / Line 157: @@
 <pubmed> 21488983 </pubmed>
 ==Original publications==
- <big>''Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, Herzberg C, Hübner S, Stülke J''  </big>
+<pubmed>18430133,18047568,18647168, 20351052,16430695,10464223,17720793, 19605685 20431016 10559173 21477127 21856853 21815947 23646920</pubmed>
 [[Category:Protein-coding genes]]