Rnc - Revision history

Jstuelk: /* Reviews */

2015-04-26T15:08:43Z

‎Reviews

Jstuelk: /* Reviews */

2015-04-26T14:47:57Z

‎Reviews

Jstuelk: /* Reviews */

2015-03-08T16:29:05Z

‎Reviews

Jstuelk: /* Original publications */

2015-02-04T12:58:29Z

‎Original publications

Jstuelk: /* Basic information/ Evolution */

2015-02-04T12:58:01Z

‎Basic information/ Evolution

134.76.70.252 at 09:34, 17 April 2014

2014-04-17T09:34:30Z

134.76.70.252 at 11:46, 8 April 2014

2014-04-08T11:46:36Z

134.76.38.147 at 13:42, 2 April 2014

2014-04-02T13:42:25Z

134.76.70.252 at 13:20, 16 May 2013

2013-05-16T13:20:18Z

134.76.70.252 at 10:12, 14 May 2013

2013-05-14T10:12:41Z

← Older revision		Revision as of 15:08, 26 April 2015
Line 1:		Line 1:
−	* '''Description:~~''' [[RNase]] III; required for the degradation of sense/antisense transcripts in Gram positive, low GC bacteria<br/><br/>~~	+	{{#bank: Rnc}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''rnc''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''rncS ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| yes~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| endoribonuclease III~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| cleaves both 5'- and 3'-sites <br/>of the small cytoplasmic RNA precursor (''[[scr]]'')~~
−	\|-
−	\|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=BSU15930 rnc]
−	\|-
−	\|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=Rnc Rnc]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 28 kDa, 8.076~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 747 bp, 249 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[acpA]]'', ''[[smc]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU15930 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU15930 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU15930 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:rnc_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=rnc_1665710_1666459_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:rnc_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU15930]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[Rnases]]}},~~
−	~~{{SubtiWiki category\|[[translation]]}},~~
−	~~{{SubtiWiki category\|[[protein secretion]]}},~~
−	~~{{SubtiWiki category\|[[essential genes]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[stringent response]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU15930
−
−	~~===Phenotypes of a mutant ===~~
−	* essential {{PubMed\|23300471,12682299,11123676}}
−	* the ''[[rnc]]'' gene can be deleted in strains cured of the [[Skin element]] and [[SPß prophage]] (or upon deletion of the toxin genes ''[[txpA]]'' and ''[[yonT]]'') {{PubMed\|23300471}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU15930&redirect=T BSU15930]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rnc-smc-ftsY.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11537]
−
−	~~=== Additional information===~~
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** Endonucleolytic cleavage of double-stranded RNA to 5'-phosphomonoester (according to Swiss-Prot)
−	** cleaves both 5'- and 3'-sites of the small cytoplasmic RNA precursor (''[[scr]]'')
−	** degradation of ''[[txpA]]'' mRNA-[[RatA]] RNA duplex (encoded on the [[Skin element]]) {{PubMed\|23300471}}
−	** degradation of ''[[yonT]]'' mRNA-''[[as-yonT]]'' RNA duplex (encoded on the [[SP-beta prophage]]) {{PubMed\|23300471}}
−	** degradation of the ''[[roxS]]''-''[[ppnKB]]'' and ''[[roxS]]-[[sucC]]'' RNA duplexes {{PubMed\|25643072}}
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU15930&redirect=T BSU15930]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P51833 P51833]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU15930]
−
−	* '''E.C. number:''' 3.1.26.3
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[rnc]]-[[smc]]-[[ftsY]]'' {{PubMed\|11021934}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rnc_1665710_1666459_1 rnc] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|11021934}}
−
−	* '''Regulation:'''
−	** [[RelA]] dependent downregulation (Class I) during stringent response {{PubMed\|11948165}}
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 314 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 605 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−	[[David Bechhofer]], Mount Sinai School, New York, USA [http://www.mountsinai.org/Research/Centers%20Laboratories%20and%20Programs/Bechhofer%20Laboratory?citype=Physician&ciid=Bechhofer%20David%20H%201255565 Homepage]
−
−	~~[[Ciaran Condon]], IBPC, Paris, France [http://www.ibpc.fr/UPR9073/condon/index_en.html Homepage]~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed> 17194582 16179796 8936814 16855311 23300472 25292357 25808661</pubmed>~~
−
−	~~==Original publications==~~
−	~~<pubmed>9393702 11123676 7527387 9677377 17576666, 11021934 6409421 22123973 22412379 25643072 23300471</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 152: / Line 152: @@
 =References=
 ==Reviews==
-<pubmed> 17194582 16179796 8936814 16855311 23300472 25292357</pubmed>
+<pubmed> 17194582 16179796 8936814 16855311 23300472 25292357 25808661</pubmed>
 ==Original publications==

@@ Line 152: / Line 152: @@
 =References=
 ==Reviews==
-<pubmed> 17194582 16179796 8936814 16855311 23300472 </pubmed>
+<pubmed> 17194582 16179796 8936814 16855311 23300472 25292357</pubmed>
 ==Original publications==

@@ Line 155: / Line 155: @@
 ==Original publications==
- <big>''Durand S, Gilet L, Condon C''  </big>
+<pubmed>9393702 11123676 7527387 9677377 17576666, 11021934 6409421 22123973 22412379 25643072 23300471</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 77: / Line 77: @@
 ** degradation of ''[[txpA]]'' mRNA-[[RatA]] RNA duplex (encoded on the [[Skin element]]) {{PubMed|23300471}}
 ** degradation of ''[[yonT]]'' mRNA-''[[as-yonT]]'' RNA duplex (encoded on the [[SP-beta prophage]]) {{PubMed|23300471}}
 * '''Protein family:'''

← Older revision		Revision as of 09:34, 17 April 2014
Line 125:		Line 125:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 314 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 605 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ 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=BSU15930 rnc]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/wiki/index.php/Protein_secretion Protein secretion]'''
+|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=Rnc Rnc]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 8.076

@@ Line 59: / Line 59: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rnc-smc-ftsY.html]
@@ Line 98: / Line 99: @@
 === Database entries ===
 * '''Structure:'''

@@ 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=rnc_1665710_1666459_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:rnc_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rnc_1665710_1666459_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:rnc_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU15930]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[acpA]]'', ''[[smc]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU15930 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU15930 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU15930 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU15930 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU15930 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU15930 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:rnc_context.gif]]