Mfd - Revision history

Jstuelk: /* References */

2015-07-24T11:05:17Z

‎References

Jstuelk: /* Reviews */

2015-07-24T11:04:42Z

‎Reviews

Jstuelk: /* Original publications */

2015-06-11T08:41:29Z

‎Original publications

Jstuelk at 07:20, 3 March 2015

2015-03-03T07:20:08Z

Jstuelk: /* Original publications */

2014-10-27T13:40:43Z

‎Original publications

Fabian Commichau: /* Biological materials */

2014-10-07T13:35:19Z

‎Biological materials

134.76.70.252 at 09:52, 17 April 2014

2014-04-17T09:52:41Z

134.76.38.147 at 12:46, 2 April 2014

2014-04-02T12:46:49Z

Jstuelk: /* Expression and regulation */

2014-03-08T16:44:29Z

‎Expression and regulation

Jstuelk at 16:43, 8 March 2014

2014-03-08T16:43:56Z

← Older revision		Revision as of 11:05, 24 July 2015
Line 1:		Line 1:
−	* '''Description:''' [[transcription]]-repair coupling factor, eliminates genetic damage from transcriptionally active genes during [[sporulation]], required for increased mutagenesis of lagging strand genes <br/><br/>	+	{{#bank: Mfd}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''mfd''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| [[transcription]]-repair coupling factor~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| promotes strand-specific DNA repair by displacing~~
−	~~[[RNA polymerase]] stalled at a nucleotide lesion and directing~~
−
−	~~the (A)BC excinuclease to the RNA damage site~~
−	\|-
−	\|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=BSU00550 mfd]
−	\|-
−	\|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=Mfd Mfd]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 133 kDa, 5.367~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 3531 bp, 1177 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[fin]]'', ''[[spoVT]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00550 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00550 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00550 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:mfd_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=mfd_60430_63963_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:mfd_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00550]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[DNA repair/ recombination]]}},~~
−	~~{{SubtiWiki category\|[[transcription]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU00550
−
−	~~===Phenotypes of a mutant ===~~
−	* in an ''mfd'' knock-out, the cell's ability to accumulate adaptive mutations in stationary phase is depressed. [http://www.pubmed.com/16950921 PubMed]
−	* increased UV-induced mutagenesis via [[PolY1]]/ [[PolY2]]-mediated translesion synthesis {{PubMed\|24118570}}
−	* the mutation suppresses the mucoid phenotype of ''[[motA]]'' or ''[[motB]]'' mutants {{PubMed\|24296669}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00550&redirect=T BSU00550]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10118]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** promotes strand-specific DNA repair by displacing [[RNA polymerase]] stalled at a nucleotide lesion and directing the (A)BC excinuclease to the RNA damage site
−	** is required for roadblock transcription repression by transcription factors with binding sites downstream of the promoter (as for [[CcpA]] {{PubMed\|9535092}} and [[CodY]] {{PubMed\|21699902}})
−	** required for the processing of genetic damage during [[sporulation]] {{PubMed\|24118570}}
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):''' [[RecG]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[Mfd]] interacts with the [[RNA polymerase]] {{PubMed\|21710567}}
−	** [[Mfd]]-[[UvrA]] {{PubMed\|16464004}}
−	** [[Mfd]]-[[RpoB]] {{PubMed\|20702425}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00550&redirect=T BSU00550]
−
−	* '''Structure:'''
−	** [http://www.proteopedia.org/wiki/index.php/2eyq 2EYQ] (Mfd from ''E. coli'') {{PubMed\|16469698}}
−	** [http://www.pdb.org/pdb/explore/explore.do?structureId=3MLQ 3MLQ] (RNA polymerase interacting domain of ''Thermus thermophilus'' [[Mfd]] with the ''Thermus aquaticus'' [[RpoB]] beta1 domain) {{PubMed\|20702425}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P37474 P37474]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00550]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:'''
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mfd_60430_63963_1 mfd] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−	** expressed throughout growth and [[sporulation]], during [[sporulation]] both in the mother cell and the forespore {{PubMed\|24118570}}
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 103 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 611 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−	* '''Mutant:''' GP1167 (del ermC), available in [[Jörg Stülke]]'s lab
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:''' GP1510 (spc, based on [[pGP1870]], [[pGP1389]]-derivative ), available in [[Jörg Stülke]]'s lab
−
−	* '''YFP fusion:''' GP1511 (spc, based on [[pGP1871]], [[pGP1389]]-derivative ), available in [[Jörg Stülke]]'s lab
−
−	* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Fabian Commichau]]'s lab
−
−	* '''Antibody:'''
−
−	* '''Strep-tag construct:''' GP890 (spc, based on [[pGP1389]]), available in the [[Stülke]] lab
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed>17239578 15063847 17917874 8811173 7968917 15720542 16464004 19023283 22201950 22749141 22933559 26132790</pubmed>~~
−
−	~~== Original publications ==~~
−	~~<pubmed>8594198,20435731 ,104170,16950921,9535092, 16469698 21699902 22178973 22248542 22960746 21710567,20702425 24296669 21145481 24118570 25326311 25961799 25713353</pubmed>~~
−	~~[[Category:Protein-coding genes]]~~

@@ Line 156: / Line 156: @@
 =References=
 ==Reviews==
-<pubmed>17239578 15063847 17917874 8811173 7968917 15720542 16464004 19023283 22201950 22749141 22933559 </pubmed>
+<pubmed>17239578 15063847 17917874 8811173 7968917 15720542 16464004 19023283 22201950 22749141 22933559 26132790</pubmed>
 == Original publications ==
 <pubmed>8594198,20435731 ,104170,16950921,9535092, 16469698 21699902 22178973 22248542 22960746 21710567,20702425 24296669 21145481 24118570 25326311 25961799 25713353</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 158: / Line 158: @@
 <pubmed>17239578 15063847 17917874 8811173 7968917 15720542 16464004 19023283 22201950 22749141 22933559 </pubmed>
 == Original publications ==
-<pubmed>8594198,20435731 ,104170,16950921,9535092, 16469698 21699902 22178973 22248542 22960746 21710567,20702425 24296669 21145481 24118570 25326311 25713353</pubmed>
+<pubmed>8594198,20435731 ,104170,16950921,9535092, 16469698 21699902 22178973 22248542 22960746 21710567,20702425 24296669 21145481 24118570 25326311 25961799 25713353</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 1: / Line 1: @@
-* '''Description:''' [[transcription]]-repair coupling factor, eliminates genetic damage from transcriptionally active genes during [[sporulation]] <br/><br/>
+* '''Description:''' [[transcription]]-repair coupling factor, eliminates genetic damage from transcriptionally active genes during [[sporulation]], required for increased mutagenesis of lagging strand genes <br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 158: / Line 158: @@
 <pubmed>17239578 15063847 17917874 8811173 7968917 15720542 16464004 19023283 22201950 22749141 22933559 </pubmed>
 == Original publications ==
-<pubmed>8594198,20435731 ,104170,16950921,9535092, 16469698 21699902 22178973 22248542 22960746 21710567,20702425 24296669 21145481 24118570 25326311 </pubmed>
+<pubmed>8594198,20435731 ,104170,16950921,9535092, 16469698 21699902 22178973 22248542 22960746 21710567,20702425 24296669 21145481 24118570 25326311 25713353</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 158: / Line 158: @@
 <pubmed>17239578 15063847 17917874 8811173 7968917 15720542 16464004 19023283 22201950 22749141 22933559 </pubmed>
 == Original publications ==
-<pubmed>8594198,20435731 ,104170,16950921,9535092, 16469698 21699902 22178973 22248542 22960746 21710567,20702425 24296669 21145481 24118570 </pubmed>
+<pubmed>8594198,20435731 ,104170,16950921,9535092, 16469698 21699902 22178973 22248542 22960746 21710567,20702425 24296669 21145481 24118570 25326311 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 144: / Line 144: @@
 * '''YFP fusion:''' GP1511 (spc, based on [[pGP1871]], [[pGP1389]]-derivative ), available in [[Jörg Stülke]]'s lab
-* '''two-hybrid system:'''
+* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Fabian Commichau]]'s lab
 * '''Antibody:'''

← Older revision		Revision as of 09:52, 17 April 2014
Line 130:		Line 130:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 103 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 611 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 61: / Line 61: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 101: / Line 102: @@
 === Database entries ===
 * '''Structure:'''

← Older revision		Revision as of 16:44, 8 March 2014
Line 128:		Line 128:

	* '''Additional information:'''		* '''Additional information:'''
−	** expressed throughout growth and [[sporulation]], during [[sporulation]] expressed both in the forespore and the mother cell {{PubMed\|24118570}}

	=Biological materials =		=Biological materials =

@@ Line 75: / Line 75: @@
 ** promotes strand-specific DNA repair by displacing [[RNA polymerase]] stalled at a nucleotide lesion and directing the (A)BC excinuclease to the RNA damage site
 ** is required for roadblock transcription repression by transcription factors with binding sites downstream of the promoter (as for [[CcpA]] {{PubMed|9535092}} and [[CodY]] {{PubMed|21699902}})
 * '''Protein family:'''
@@ Line 122: / Line 123: @@
 * '''Regulation:'''
 * '''Regulatory mechanism:'''
@@ Line 153: / Line 155: @@
 <pubmed>17239578 15063847 17917874 8811173 7968917 15720542 16464004 19023283 22201950 22749141 22933559 </pubmed>
 == Original publications ==
-<pubmed>8594198,20435731 ,104170,16950921,9535092, 16469698 21699902 22178973 22248542 22960746 24118570 21710567,20702425 24296669 21145481 24118570 </pubmed>
+<pubmed>8594198,20435731 ,104170,16950921,9535092, 16469698 21699902 22178973 22248542 22960746 21710567,20702425 24296669 21145481 24118570 </pubmed>
 [[Category:Protein-coding genes]]