possible endonuclease obsoletions?

[gocentral]

endonuclease G activity GO:0019000 endonuclease VIII activity GO:0008845 .....gene products ?

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/1175":https://sourceforge.net/p/geneontology/ontology-requests/1175

[gocentral]

• assigned_to: nobody --> girlwithglasses

Original comment by: girlwithglasses

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Logged In: YES user_id=473796

Hi Val, I believe you're right - both of these are gene products. A bit more about each:

Endonuclease VIII: According to PMID:12713806, it has a number of activities including: recognizes thymine glycol, dihydrothymine, beta- ureidoisobutyric acid and urea residues functions both as a DNA glycosylase and as a lyase on sites of base loss (AP sites) recognize 5-hydroxycytosine, 5-hydroxyuracil and uracil glycol and acts via beta,delta-elimination producing a 3' phosphate at the site of the strand break possesses a 5' phosphodiesterase activity that can remove a 5' deoxyribose generated by treatment of an AP site with an AP endonuclease. *binds asymmetrically to damaged DNA 3' to the abasic site and primarily on the damage-containing strand.

Endonuclease G: "a mitochondrion-specific nuclease that translocates tothe nucleus during apoptosis. Once released from mitochondria, endoG cleaves chromatin DNA into nucleosomal fragments independently of caspases. Therefore, endoG represents acaspase-independent apoptotic pathway initiated from the mitochondria." oligonucleosomal DNA fragmentation EndoG catalyzes both high molecular weight DNA cleavage and oligonucleosomal DNA breakdown in a sequential fashion. EndoG cooperates with exonuclease and DNaseI to facilitate DNA processing PMID:12941691

DSB also arise in replicating DNA as a result of cleavage of viral a sequences by endonuclease G PMID:12928502

Endonuclease G (endoG) accounts for a large part of this mitochondrial nuclease activity. It is essentially a nonspecific nuclease for all nucleic acid species including double-stranded DNA, single-stranded DNA, single-stranded RNA, and RNADNA duplexes EndoG has recently been reported to be an apoptotic nuclease PMID:12444964

I'll formulate comments and alternative terms for these two and then obsolete them.

Original comment by: girlwithglasses

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Logged In: YES user_id=473796

To be obsoleted: endonuclease VIII activity ; GO:0008845 This term was made obsolete because it represents a gene product. To update annotations, consider the molecular function terms 'DNA glycosylase activity ; GO:0019104', 'DNA lyase activity ; GO:0003906', 'pyrimidine-specific oxidized base lesion DNA N-glycosylase activity ; GO:0000703', 'phosphoric diester hydrolase activity ; GO:0008081', 'endonuclease activity ; GO:0004519' and 'damaged DNA binding ; GO:0003684'.

endonuclease G activity ; GO:0019000 This term was made obsolete because it represents a gene product. To update annotations, consider the molecular function terms 'endodeoxyribonuclease activity ; GO:0004520' and 'endoribonuclease activity ; GO:0004521'.

If there are no problems with this, I'll obsolete those terms on Monday (Oct 27th).

Original comment by: girlwithglasses

[gocentral]

• priority: 5 --> 9

Original comment by: girlwithglasses

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Logged In: YES user_id=451873

Done.

Original comment by: jl242

[gocentral]

• milestone: --> 224410
• labels: --> Other term-related request
• status: open --> closed-fixed

Original comment by: jl242

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• priority: 9 --> 5

Original comment by: mah11

[gocentral]

• milestone: 224410 --> PomBase

Original comment by: mah11