Difference between revisions of "Nfo"

From SubtiWiki
Jump to: navigation, search
(→‎References)
 
(20 intermediate revisions by 5 users not shown)
Line 13: Line 13:
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || repair of oxidative DNA damage in spores
 
|style="background:#ABCDEF;" align="center"|'''Function''' || repair of oxidative DNA damage in spores
 +
|-
 +
|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=BSU25130 nfo]
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 32 kDa, 5.371   
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 32 kDa, 5.371   
Line 20: Line 22:
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqfT]]'', ''[[cshB]]''
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqfT]]'', ''[[cshB]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14443&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU25130 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU25130 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU25130 DNA_with_flanks]
 
|-
 
|-
 
|-
 
|-
Line 26: Line 28:
 
|colspan="2" | '''Genetic context''' <br/> [[Image:yqfS_context.gif]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:yqfS_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>
 +
|-
 +
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=nfo_2593281_2594174_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:nfo_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU25130]]
 
|-
 
|-
 
|}
 
|}
  
 
__TOC__
 
__TOC__
−
 
 
<br/><br/><br/><br/>
 
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/>
  
 
= [[Categories]] containing this gene/protein =
 
= [[Categories]] containing this gene/protein =
Line 47: Line 53:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
* an ''[[exoA]] [[nfo]]'' double mutant is impaired in germination and spore outgrowth due to the accumulation of DNA lesions, this can be rescued by inactivation of ''[[disA]]'' {{PubMed|24244006}}
 +
* an ''[[exoA]] [[nfo]]'' double mutant is sensitive to radiation {{PubMed|24123749}}
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU25130&redirect=T BSU25130]
  
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqfSU.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqfSU.html]
Line 55: Line 64:
  
 
=== Additional information===
 
=== Additional information===
−
 
+
* Nfo is functionally redundant with [[ExoA]]
−
 
 
−
 
 
−
 
 
 
=The protein=
 
=The protein=
  
Line 81: Line 87:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''[[SubtInteract|Interactions]]:'''
  
−
* '''Localization:'''
+
* '''[[Localization]]:'''
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU25130&redirect=T BSU25130]
  
 
* '''Structure:'''
 
* '''Structure:'''
Line 100: Line 107:
 
* '''Operon:''' ''[[nfo]]-[[yqfU]]'' {{PubMed|12486072}}  
 
* '''Operon:''' ''[[nfo]]-[[yqfU]]'' {{PubMed|12486072}}  
  
−
* '''[[Sigma factor]]:''' [[SigG]] {{PubMed|12486072}}
+
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=nfo_2593281_2594174_-1 nfo] {{PubMed|22383849}}
 +
 
 +
* '''Sigma factor:''' [[SigG]] {{PubMed|12486072}}
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 109: Line 118:
 
* '''Additional information:'''  
 
* '''Additional information:'''  
 
The gene ''[[yqfT]]'' is located between ''[[nfo]]'' and ''[[yqfU]]'', but is transcribed in the opposite direction.
 
The gene ''[[yqfT]]'' is located between ''[[nfo]]'' and ''[[yqfU]]'', but is transcribed in the opposite direction.
 +
** number of protein molecules per cell (minimal medium with glucose and ammonium): 262 {{PubMed|24696501}}
 +
** number of protein molecules per cell (complex medium with amino acids, without glucose): 659 {{PubMed|24696501}}
 +
** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 612 {{PubMed|21395229}}
 +
** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 355 {{PubMed|21395229}}
 +
** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 628 {{PubMed|21395229}}
  
 
=Biological materials =
 
=Biological materials =
−
 
+
* '''Mutant:'''  
−
* '''Mutant:''' available in [[Mario Pedraza-Reyes]]' lab
+
** available in [[Mario Pedraza-Reyes]]' lab
 +
** GP899 (''nfo''::''kan'') and GP1502 (''nfo''::''cat''), available in [[Stülke]] lab  
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 129: Line 144:
  
 
=References=
 
=References=
−
'''Additional publications:''' {{PubMed|21441501}}
+
==Reviews==
−
<pubmed>18203828,16237020,12949090, 19930460,12486072, </pubmed>
+
<pubmed> 22933559 </pubmed>
 +
== Original publications ==
 +
<pubmed>24244006,18203828,16237020,12949090, 19930460,12486072, 21441501 24123749 24123749 24914186 </pubmed>
  
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Latest revision as of 08:02, 11 June 2014

  • Description: type IV apurinic/apyrimidinic endonuclease

Gene name nfo
Synonyms yqfS
Essential no
Product type IV apurinic/apyrimidinic endonuclease
Function repair of oxidative DNA damage in spores
Gene expression levels in SubtiExpress: nfo
MW, pI 32 kDa, 5.371
Gene length, protein length 891 bp, 297 aa
Immediate neighbours yqfT, cshB
Sequences Protein DNA DNA_with_flanks
Genetic context
YqfS context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
Nfo expression.png















Categories containing this gene/protein

DNA repair/ recombination, sporulation proteins

This gene is a member of the following regulons

SigG regulon

The gene

Basic information

  • Locus tag: BSU25130

Phenotypes of a mutant

  • an exoA nfo double mutant is impaired in germination and spore outgrowth due to the accumulation of DNA lesions, this can be rescued by inactivation of disA PubMed
  • an exoA nfo double mutant is sensitive to radiation PubMed

Database entries

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

Additional information

  • Nfo is functionally redundant with ExoA

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Endonucleolytic cleavage to 5'-phosphooligonucleotide end-products (according to Swiss-Prot)
  • Protein family: AP endonuclease 2 family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • Structure:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation:
    • expressed late during sporulation in the forespore (SigG) PubMed
  • Regulatory mechanism:
  • Additional information:

The gene yqfT is located between nfo and yqfU, but is transcribed in the opposite direction.

    • number of protein molecules per cell (minimal medium with glucose and ammonium): 262 PubMed
    • number of protein molecules per cell (complex medium with amino acids, without glucose): 659 PubMed
    • number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 612 PubMed
    • number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 355 PubMed
    • number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 628 PubMed

Biological materials

  • 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

Retrieved from "https://subtiwiki.uni-goettingen.de/wiki//index.php?title=Nfo&oldid=205717"