SigM - Revision history

Jstuelk: /* Other original publications */

2015-05-08T13:00:23Z

‎Other original publications

Jstuelk: /* Phenotypes of a mutant */

2015-05-08T13:00:09Z

‎Phenotypes of a mutant

Jstuelk: /* References */

2014-06-13T07:04:23Z

‎References

134.76.38.147 at 13:18, 2 April 2014

2014-04-02T13:18:02Z

134.76.70.252 at 15:31, 11 November 2013

2013-11-11T15:31:56Z

Kgunka: /* Biological materials */

2013-10-28T12:05:51Z

‎Biological materials

Fabian Commichau: /* Biological materials */

2013-10-25T17:29:11Z

‎Biological materials

Kgunka: /* Biological materials */

2013-10-23T13:28:30Z

‎Biological materials

134.76.70.252 at 12:52, 16 May 2013

2013-05-16T12:52:25Z

134.76.70.252 at 09:48, 14 May 2013

2013-05-14T09:48:23Z

← Older revision		Revision as of 13:00, 8 May 2015
Line 1:		Line 1:
−	* '''Description:''' [[RNA polymerase]] ECF-type [[sigma factor]] [[SigM]] <br/><br/>	+	{{#bank: SigM}}
−	{~~\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''sigM''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yhdM ''~~
−	\|-
−	~~\|style="background:~~#~~ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background~~:~~#ABCDEF;" align="center"\| '''Product''' \|\| [[RNA polymerase]] ECF-type [[sigma factor]] [[~~SigM]]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| responsible for intrinsic resistance against beta-lactam antibiotics~~
−	\|-
−	\|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=BSU09520 sigM]
−	\|-
−	\|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=SigM SigM]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 19 kDa, 6.77~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 489 bp, 163 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yhdL]]'', ''[[yhdN]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU09520 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU09520 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU09520 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:sigM_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=sigM_1029577_1030068_-1 Expression at a glance]'''   {{PubMed\|22383849~~}~~}<br/>[[Image:sigM_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU09520]]~~
−	\|-
−	\|}

−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[transcription]]}},~~
−	~~{{SubtiWiki category\|[[sigma factors and their control]]}},~~
−	~~{{SubtiWiki category\|[[cell envelope stress proteins (controlled by SigM, V, W, X, Y)]]}},~~
−	~~{{SubtiWiki category\|[[resistance against toxins/ antibiotics]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[SigM regulon]]}}~~
−	~~=The [[SigM regulon]]=~~
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU09520
−
−	~~===Phenotypes of a mutant ===~~
−	* SigM is essential for growth and survival in nutrient broth (NB) containing 1.4 M NaCl {{PubMed\|10216858}}
−	* ''sigM'' mutants form aberrantly shaped cells, which swell and lyse spontaneously during growth in NB medium containing increased levels (0.35-0.7 M) of a wide range of different salts {{PubMed\|10216858}}
−	* increased sensitivity towards beta-lactam antibiotics {{PubMed\|22211522}}
−	* a ''[[sigM]] [[murJ]]'' double mutant is not viable (due to the lack of both lipid II flippases) {{PubMed\|25918422}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU09520&redirect=T BSU09520]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sigM-yhdLK.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13019]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' sigma-70 factor family, ECF subfamily (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−	** expression of [[CsbB]] in the absence of [[YfhO]] causes constitutive activation of [[SigM]] {{PubMed\|23632331}}
−	** shortage of available bactoprenol causes [[SigM]] activation {{PubMed\|23632331}}
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[SigM]]-[[YhdK]]-[[YhdL]] {{PubMed\|14993308}}
−	** [[SigM]]-[[RpoB]]-[[RpoC]]
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU09520&redirect=T BSU09520]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O07582 O07582]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09520]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−	* Expression of the [[SigM regulon]] in increased in ''[[ugtP]]'' mutants {{PubMed\|22362028}}
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[sigM]]-[[yhdL]]-[[yhdK]]'' {{PubMed\|9573210}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sigM_1029577_1030068_-1 sigM] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|9573210}}, [[SigM]] {{PubMed\|9573210,18179421}}
−
−	* '''Regulation:'''
−	** induced by paraquat ([[SigM]]) {{PubMed\|12775685}}
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−	** expression of [[CsbB]] in the absence of [[YfhO]] causes constitutive activation of [[SigM]] {{PubMed\|23632331}}
−	** shortage of available bactoprenol causes [[SigM]] activation {{PubMed\|23632331}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** 1A906 (''sigM''::''kan''), {{PubMed\|12207695}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A906&Search=1A906 BGSC]
−	** BP129 (''sigM::aphA3''), available in [[Fabian Commichau]]'s lab
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−	~~[[John Helmann]], Cornell University, USA [http://www.micro.cornell.edu/research/labs/helmann-lab/index.cfm Homepage]~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed>24921931 </pubmed>~~
−	~~==The [[SigM regulon]]==~~
−	~~<pubmed>18179421,17675383,17434969,</pubmed>~~
−	~~==Other original publications==~~
−	~~<pubmed>22362028 18394148,14993308,12399481,12775685,12207695,18820022,15838020,19047346,14651641,16151214 ,19465659 19745567 10216858 20057163 23103977 23632331 23070162,22211522,20817771</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 57: / Line 57: @@
 * ''sigM'' mutants form aberrantly shaped cells, which swell and lyse spontaneously during growth in NB medium containing increased levels (0.35-0.7 M) of a wide range of different salts {{PubMed|10216858}}
 * increased sensitivity towards beta-lactam antibiotics {{PubMed|22211522}}
 === Database entries ===

@@ Line 150: / Line 150: @@
 =References=
 ==The [[SigM regulon]]==
 <pubmed>18179421,17675383,17434969,</pubmed>

@@ Line 59: / Line 59: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sigM-yhdLK.html]
@@ Line 97: / Line 98: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 15: / Line 15: @@
 |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=BSU09520 sigM]
 |-
-|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/SigM SigM]
+|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=SigM SigM]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 19 kDa, 6.77

@@ Line 130: / Line 130: @@
 * '''Mutant:'''
 ** 1A906 (''sigM''::''kan''), {{PubMed|12207695}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A906&Search=1A906 BGSC]
-** BP97 (''sigM::aphA3''), available in [[Fabian Commichau]]'s lab
+** BP129 (''sigM::aphA3''), available in [[Fabian Commichau]]'s lab
 * '''Expression vector:'''

@@ Line 28: / Line 28: @@
   <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=sigM_1029577_1030068_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:sigM_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sigM_1029577_1030068_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:sigM_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU09520]]
 |-
 |}

@@ Line 23: / Line 23: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhdL]]'', ''[[yhdN]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU09520 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU09520 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU09520 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU09520 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU09520 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU09520 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:sigM_context.gif]]