TnrA - Revision history

Jstuelk: /* The TnrA regulon */

2015-03-13T15:37:22Z

‎The TnrA regulon

Jstuelk: /* Labs working on this gene/protein */

2015-03-05T12:37:03Z

‎Labs working on this gene/protein

Jstuelk: /* Database entries */

2015-02-19T09:22:26Z

‎Database entries

Jstuelk at 09:18, 19 February 2015

2015-02-19T09:18:20Z

Jstuelk: /* Other original publications */

2014-09-19T12:25:45Z

‎Other original publications

Jstuelk at 13:18, 22 June 2014

2014-06-22T13:18:44Z

134.76.38.147 at 13:31, 2 April 2014

2014-04-02T13:31:52Z

134.76.70.252 at 10:36, 7 January 2014

2014-01-07T10:36:58Z

134.76.70.252 at 16:06, 11 November 2013

2013-11-11T16:06:21Z

Jstuelk: /* Other original publications */

2013-07-03T09:21:20Z

‎Other original publications

← Older revision		Revision as of 15:37, 13 March 2015
Line 1:		Line 1:
−	* '''Description:~~''' transcriptional pleiotropic regulator ([[MerR family]]) involved in global nitrogen regulation <br/><br/>~~	+	{{#bank: TnrA}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''tnrA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''scgR ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| transcription activator/ repressor ([[MerR family]])~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\|regulation of nitrogen assimilation~~
−	\|-
−	\|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=BSU13310 tnrA]
−	\|-
−	\|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=TnrA TnrA]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Metabolic function and regulation of this protein in [[SubtiPathways\|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=tnrA tnrA]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 12 kDa, 10.235~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 330 bp, 110 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[mgtE]]'', ''[[ykzB]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU13310 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU13310 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU13310 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:tnrA_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=tnrA_1397411_1397743_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:tnrA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU13310]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[biosynthesis/ acquisition of amino acids]]}}, [[glutamate metabolism]],~~
−	~~{{SubtiWiki category\|[[transcription factors and their control]]}},~~
−	~~{{SubtiWiki category\|[[regulators of core metabolism]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[GlnR regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[TnrA regulon]]}}~~
−	~~=The [[TnrA regulon]]=~~
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU13310
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU13310&redirect=T BSU13310]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/tnrA.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11805]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' [[MerR family]]
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−	** K(D) value for the binding site in the ''tnrA'' promoter region: 55 nM {{PubMed\|16547045}}
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:''' feedback-inhibited [[GlnA]] prevents [[TnrA]] from DNA binding
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[TnrA]]-[[NrgB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17001076 PubMed]
−	** [[TnrA]]-[[GlnA]], this interaction results in loss of [[TnrA]] DNA-binding activity as well as in inhibition of [[GlnA]] {{PubMed\|23535029,11719184}}
−
−	* '''[[Localization]]:''' membrane-associated via [[NrgA]]-[[NrgB]] under conditions of poor nitrogen supply {{PubMed\|21435182}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU13310&redirect=T BSU13310]
−
−	* '''Structure:'''
−	** [http://pdb.org/pdb/search/structidSearch.do?structureId=4r22 4R22] (the TnrA-DNA complex) {{PubMed\|25691471}}
−	** [http://pdb.org/pdb/search/structidSearch.do?structureId=4s0r 4S0R] (the [[TnrA]]-[[GlnA]] complex) {{PubMed\|25691471}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/Q45666 Q45666]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13310]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''tnrA'' (according to [http://dbtbs.hgc.jp/COG/prom/tnrA.html DBTBS])
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tnrA_1397411_1397743_-1 tnrA] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−	** expression is autocativated (TnrA) and repressed by [[GlnR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16547045 PubMed]
−	** expressed in the absence of good nitrogen sources (glutamine or ammonium) ([[TnrA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10671441,16547045 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [[TnrA]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/10671441,16547045 PubMed]
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:''' GP252 (in frame deletion), available in the [[Stülke]] lab
−	** 1A851 ( ''tnrA''::''erm''), {{PubMed\|8799114}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A851&Search=1A851 BGSC]
−	** 1A851 ( ''tnrA''::''erm''), {{PubMed\|8799114}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A851&Search=1A851 BGSC]
−
−	* '''Expression vector:'''
−	** for expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP171 available in [[Stülke]] lab
−	** pGP229 (N-terminal Strep-tag, for [[SPINE]], expression in ''B. subtilis'', in [[pGP380]]), available in [[Stülke]] lab
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:''' available in the [[Karl Forchhammer]] lab
−
−	~~=Labs working on this gene/protein=~~
−	* [[Susan Fisher]], Boston, USA [http://www.bumc.bu.edu/microbiology/research/susan-h-fisher-phd/ homepage]
−	* [[Maria Schumacher]], Durham, NC, USA [http://www.dukeschumacherlab.com/index.html homepage]
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed>22625175 10231480 18086213</pubmed>~~
−
−	~~==The [[TnrA regulon]]==~~
−	~~<pubmed>12823818,</pubmed>~~
−	~~==Control of TnrA activity by the [[trigger enzymes\|trigger enzyme]] [[GlnA]]==~~
−	~~<pubmed>11719184, 12139611, 17085574 19233925, 16885465, </pubmed>~~
−	~~==Other original publications==~~
−	<pubmed>12374841,15547269,9287005, 12950915,10671441,16547045,16547045 ,8799114, 15150225, 11029411,17001076,15547269, 2573733, 8636055, 16493705, 6141156 18667567 21435182 23535029 23808168 25157083 25691471</pubmed>
−	~~[[Category:Protein-coding genes]]~~

@@ Line 147: / Line 147: @@
 =Labs working on this gene/protein=
+* [[Susan Fisher]], Boston, USA [http://www.bumc.bu.edu/microbiology/research/susan-h-fisher-phd/ homepage]
-[[Susan Fisher]], Boston, USA [http://www.bumc.bu.edu/microbiology/research/susan-h-fisher-phd/ homepage]
+* [[Maria Schumacher]], Durham, NC, USA [http://www.dukeschumacherlab.com/index.html homepage]
 =Your additional remarks=

@@ Line 101: / Line 101: @@
 * '''Structure:'''
 ** [http://pdb.org/pdb/search/structidSearch.do?structureId=4r22 4R22] (the TnrA-DNA complex) {{PubMed|25691471}}
 * '''UniProt:''' [http://www.uniprot.org/uniprot/Q45666 Q45666]

@@ Line 100: / Line 100: @@
 * '''Structure:'''
 * '''UniProt:''' [http://www.uniprot.org/uniprot/Q45666 Q45666]
@@ Line 159: / Line 160: @@
 <pubmed>11719184, 12139611, 17085574 19233925, 16885465, </pubmed>
 ==Other original publications==
-<pubmed>12374841,15547269,9287005, 12950915,10671441,16547045,16547045 ,8799114, 15150225, 11029411,17001076,15547269, 2573733, 8636055, 16493705, 6141156 18667567 21435182 23535029 23808168 25157083 </pubmed>
+<pubmed>12374841,15547269,9287005, 12950915,10671441,16547045,16547045 ,8799114, 15150225, 11029411,17001076,15547269, 2573733, 8636055, 16493705, 6141156 18667567 21435182 23535029 23808168 25157083 25691471</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 159: / Line 159: @@
 <pubmed>11719184, 12139611, 17085574 19233925, 16885465, </pubmed>
 ==Other original publications==
-<pubmed>12374841,15547269,9287005, 12950915,10671441,16547045,16547045 ,8799114, 15150225, 11029411,17001076,15547269, 2573733, 8636055, 16493705, 6141156 18667567 21435182 23535029 23808168 </pubmed>
+<pubmed>12374841,15547269,9287005, 12950915,10671441,16547045,16547045 ,8799114, 15150225, 11029411,17001076,15547269, 2573733, 8636055, 16493705, 6141156 18667567 21435182 23535029 23808168 25157083 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 1: / Line 1: @@
-* '''Description:''' transcriptional pleiotropic regulator invoved in global nitrogen regulation <br/><br/>
+* '''Description:''' transcriptional pleiotropic regulator ([[MerR family]])  involved in global nitrogen regulation <br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 10: / Line 10: @@
 |style="background:#ABCDEF;" align="center"| '''Essential''' || no
 |-
-|style="background:#ABCDEF;" align="center"| '''Product''' || transcription activator/ repressor
+|style="background:#ABCDEF;" align="center"| '''Product''' || transcription activator/ repressor ([[MerR family]])
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' ||regulation of nitrogen assimilation
@@ Line 73: / Line 73: @@
 * '''Catalyzed reaction/ biological activity:'''
-* '''Protein family:'''
+* '''Protein family:''' [[MerR family]]
 * '''Paralogous protein(s):'''

@@ Line 59: / Line 59: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/tnrA.html]
@@ Line 96: / Line 97: @@
 === 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=TnrA TnrA]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/fatty_acid_synthesis.html Lipid synthesis], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)], [http://subtiwiki.uni-goettingen.de/pathways/ile_val_leu.html Ile, Leu, Val], <br/>[http://subtiwiki.uni-goettingen.de/pathways/glutamate.html Ammonium/ glutamate], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/pathways/cellwall.html Cell wall], <br/>[http://subtiwiki.uni-goettingen.de/pathways/CoA_synthesis.html Coenzyme A], [http://subtiwiki.uni-goettingen.de/pathways/phosphorelay.html Phosphorelay], [http://subtiwiki.uni-goettingen.de/pathways/other_nitrogen_sources/index.html Alternative nitrogen sources]'''
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=tnrA tnrA]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 12 kDa, 10.235

@@ 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=BSU13310 tnrA]
 |-
-|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/TnrA TnrA]
+|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=TnrA TnrA]
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/fatty_acid_synthesis.html Lipid synthesis], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)], [http://subtiwiki.uni-goettingen.de/pathways/ile_val_leu.html Ile, Leu, Val], <br/>[http://subtiwiki.uni-goettingen.de/pathways/glutamate.html Ammonium/ glutamate], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/pathways/cellwall.html Cell wall], <br/>[http://subtiwiki.uni-goettingen.de/pathways/CoA_synthesis.html Coenzyme A], [http://subtiwiki.uni-goettingen.de/pathways/phosphorelay.html Phosphorelay], [http://subtiwiki.uni-goettingen.de/pathways/other_nitrogen_sources/index.html Alternative nitrogen sources]'''