Difference between revisions of "Nfo"
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|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 | ||
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqfT]]'', ''[[cshB]]'' | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqfT]]'', ''[[cshB]]'' | ||
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− | | | + | |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] |
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|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]'''   {{PubMed|22383849}}<br/>[[Image:nfo_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU25130]] | ||
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|} | |} | ||
__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 = | ||
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===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] | ||
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=== Additional information=== | === Additional information=== | ||
− | + | * Nfo is functionally redundant with [[ExoA]] | |
− | |||
− | |||
− | |||
=The protein= | =The protein= | ||
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* '''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:''' | ||
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* '''Operon:''' ''[[nfo]]-[[yqfU]]'' {{PubMed|12486072}} | * '''Operon:''' ''[[nfo]]-[[yqfU]]'' {{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:''' | ||
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* '''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:''' | ||
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=References= | =References= | ||
− | <pubmed>18203828,16237020,12949090, 19930460,12486072, 21441501 </pubmed> | + | ==Reviews== |
+ | <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 This image was kindly provided by SubtiList
| |
Expression at a glance PubMed |
Contents
Categories containing this gene/protein
DNA repair/ recombination, sporulation proteins
This gene is a member of the following regulons
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
- BsubCyc: BSU25130
- 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
- BsubCyc: BSU25130
- Structure:
- UniProt: P54476
- KEGG entry: [3]
- E.C. number:
Additional information
Expression and regulation
- 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
- Mutant:
- available in Mario Pedraza-Reyes' lab
- GP899 (nfo::kan) and GP1502 (nfo::cat), 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