Difference between revisions of "PolY1"

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* '''Description:''' translesion synthesis (TLS-) DNA polymerase Y1 <br/><br/>
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* '''Description:''' translesion synthesis (TLS-) DNA polymerase Y1, important for stationary phase mutagenesis, promotes efficient [[replisome]] progression through lagging-strand genes, thereby reducing potentially detrimental breaks and single-stranded DNA at these loci <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
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|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || generation of mutations in stationary phase
 
|style="background:#ABCDEF;" align="center"|'''Function''' || generation of mutations in stationary phase
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|-
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|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=BSU23870 polY1]
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|-
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|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=PolY1 PolY1]
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|-
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|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=polY1 polY1]'''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 9.953   
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 9.953   
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1242 bp, 414 aa  
 
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1242 bp, 414 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gndA]]'', ''[[yqzJ]]''
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gndA]]'', ''[[mifM]]''
 
|-
 
|-
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|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14319&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
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|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU23870 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU23870 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU23870 DNA_with_flanks]
 
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|-
 
|-
 
|-
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|colspan="2" | '''Genetic context''' <br/> [[Image:yqjH_context.gif]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:yqjH_context.gif]]
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
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|-
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|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=polYA_2482269_2483513_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:polY1_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU23870]]
 
|-
 
|-
 
|}
 
|}
  
 
__TOC__
 
__TOC__
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<br/><br/><br/><br/>
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<br/><br/><br/><br/>
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<br/><br/><br/><br/>
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<br/><br/>
 +
 +
= [[Categories]] containing this gene/protein =
 +
{{SubtiWiki category|[[DNA repair/ recombination]]}}
 +
 +
= This gene is a member of the following [[regulons]] =
  
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<br/><br/><br/><br/>
 
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
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* '''Coordinates:'''
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* '''Locus tag:''' BSU23870
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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reduced UV-induced mutagenesis {{PubMed|12644484}}
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU23870&redirect=T BSU23870]
  
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqjHI.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqjHI.html]
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
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* '''Catalyzed reaction/ biological activity:'''  
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* '''Catalyzed reaction/ biological activity:''' Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1) (according to Swiss-Prot)
  
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* '''Protein family:'''
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* '''Protein family:''' DNA polymerase type-Y family (according to Swiss-Prot)
  
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* '''Paralogous protein(s):'''
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* '''Paralogous protein(s):''' [[PolY2]], [[UvrX]], [[YozK]]-[[YobH]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
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* '''Interactions:'''
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* '''[[SubtInteract|Interactions]]:'''
 +
** [[PolY1]]-[[DnaN]] (required for untargeted mutagenesis) {{PubMed|15469515}}
 +
** [[PolA]]-[[PolY1]]-[[DnaN]] {{PubMed|16045613}}
  
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* '''Localization:'''
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* '''[[Localization]]:''' cytoplasm (homogeneous)
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU23870&redirect=T BSU23870]
  
 
* '''Structure:'''
 
* '''Structure:'''
  
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* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P54545 P54545]
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* '''UniProt:''' [http://www.uniprot.org/uniprot/P54545 P54545]
  
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* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU23870]
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* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU23870]
  
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* '''E.C. number:'''
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* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.7.7 2.7.7.7]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
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* '''Operon:'''  
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* '''Operon:''' ''[[polY1]]-[[gndA]]'' (according to [http://dbtbs.hgc.jp/COG/prom/yqjHI.html DBTBS])
  
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* '''[[Sigma factor]]:'''  
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* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=polYA_2482269_2483513_-1 polY1] {{PubMed|22383849}}
  
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* '''Regulation:'''  
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* '''Sigma factor:'''
 +
 
 +
* '''Regulation:''' constitutively expressed {{PubMed|15469515}}
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
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* '''Additional information:'''  
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* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
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== Reviews ==
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# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
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<pubmed> 22933559 </pubmed>
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== Original publications ==
 +
<pubmed> 12644484 15469515 16045613 19924481 23686288 25713353</pubmed>
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[[Category:Protein-coding genes]]

Latest revision as of 07:18, 3 March 2015

  • Description: translesion synthesis (TLS-) DNA polymerase Y1, important for stationary phase mutagenesis, promotes efficient replisome progression through lagging-strand genes, thereby reducing potentially detrimental breaks and single-stranded DNA at these loci

Gene name polY1
Synonyms yqjH
Essential no
Product translesion synthesis (TLS-) DNA polymerase Y1
Function generation of mutations in stationary phase
Gene expression levels in SubtiExpress: polY1
Interactions involving this protein in SubtInteract: PolY1
Metabolic function and regulation of this protein in SubtiPathways:
polY1
MW, pI 46 kDa, 9.953
Gene length, protein length 1242 bp, 414 aa
Immediate neighbours gndA, mifM
Sequences Protein DNA DNA_with_flanks
Genetic context
YqjH context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
PolY1 expression.png















Categories containing this gene/protein

DNA repair/ recombination

This gene is a member of the following regulons

The gene

Basic information

  • Locus tag: BSU23870

Phenotypes of a mutant

reduced UV-induced mutagenesis PubMed

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1) (according to Swiss-Prot)
  • Protein family: DNA polymerase type-Y family (according to Swiss-Prot)

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Sigma factor:
  • Regulation: constitutively expressed PubMed
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant: GP1111 (spc), available in Stülke lab
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

Reviews

Justin S Lenhart, Jeremy W Schroeder, Brian W Walsh, Lyle A Simmons
DNA repair and genome maintenance in Bacillus subtilis.
Microbiol Mol Biol Rev: 2012, 76(3);530-64
[PubMed:22933559] [WorldCat.org] [DOI] (I p)

Original publications

Samuel Million-Weaver, Ariana N Samadpour, Daniela A Moreno-Habel, Patrick Nugent, Mitchell J Brittnacher, Eli Weiss, Hillary S Hayden, Samuel I Miller, Ivan Liachko, Houra Merrikh
An underlying mechanism for the increased mutagenesis of lagging-strand genes in Bacillus subtilis.
Proc Natl Acad Sci U S A: 2015, 112(10);E1096-105
[PubMed:25713353] [WorldCat.org] [DOI] (I p)

Richard T Pomerantz, Isabel Kurth, Myron F Goodman, Mike E O'Donnell
Preferential D-loop extension by a translesion DNA polymerase underlies error-prone recombination.
Nat Struct Mol Biol: 2013, 20(6);748-55
[PubMed:23686288] [WorldCat.org] [DOI] (I p)

Andrea M Rivas-Castillo, Ronald E Yasbin, E Robleto, Wayne L Nicholson, Mario Pedraza-Reyes
Role of the Y-family DNA polymerases YqjH and YqjW in protecting sporulating Bacillus subtilis cells from DNA damage.
Curr Microbiol: 2010, 60(4);263-7
[PubMed:19924481] [WorldCat.org] [DOI] (I p)

Stéphane Duigou, S Dusko Ehrlich, Philippe Noirot, Marie-Françoise Noirot-Gros
DNA polymerase I acts in translesion synthesis mediated by the Y-polymerases in Bacillus subtilis.
Mol Microbiol: 2005, 57(3);678-90
[PubMed:16045613] [WorldCat.org] [DOI] (P p)

Stéphane Duigou, S Dusko Ehrlich, Philippe Noirot, Marie-Françoise Noirot-Gros
Distinctive genetic features exhibited by the Y-family DNA polymerases in Bacillus subtilis.
Mol Microbiol: 2004, 54(2);439-51
[PubMed:15469515] [WorldCat.org] [DOI] (P p)

Huang-Mo Sung, Gabriel Yeamans, Christian A Ross, Ronald E Yasbin
Roles of YqjH and YqjW, homologs of the Escherichia coli UmuC/DinB or Y superfamily of DNA polymerases, in stationary-phase mutagenesis and UV-induced mutagenesis of Bacillus subtilis.
J Bacteriol: 2003, 185(7);2153-60
[PubMed:12644484] [WorldCat.org] [DOI] (P p)

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