NTRs: Kinetoplast DNA and Kinetoplast DNA replication

[Achchuthan]

Term 1: Accession: GO:xxxxxx Name: kinetoplast DNA Ontology: cellular_component Synonyms: kinetoplast dna network, kDNA Definition: The circular DNA molecules of kinetoplast that are topologically interlocked to form a single network. It consists of maxicircles present in a few dozen copies, and minicircles present in thousands of copies. Maxicircles encode typical mitochondrial gene products such as rRNAs and subunits of respiratory chain complexes and minicircles encode guide RNAs (gRNAs). is_a: GO:0000262 ! mitochondrial chromosome [BFO:0000050 relation] BFO:0000050: GO:0020023 ! kinetoplast Taxonomic restriction: NCBITaxon:5653 ## Kinetoplastea Source: PMID:8045928, PMID:8561456, PMID:12455998, PMID:15967722, PMID:17462016, GOC:ach

Term 2: Accession: GO:xxxxxx Name: kinetoplast DNA replication Ontology: biological_process Synonyms: kDNA replication, replication of kinetoplast DNA, kinetoplast DNA synthesis Definition: The process of doubling of the number of maxicircles and minicircles and distribution of the progeny into two daughter networks, which are identical to the parent kinetoplast DNA network. is_a: GO:0006264 ! mitochondrial DNA replication [BFO:0000066 relation] BFO:0000066: GO:0020023 ! kinetoplast Taxonomic restriction: NCBITaxon:5653 ## Kinetoplastea Source: PMID:8045928, PMID:8561456, PMID:12455998, PMID:15967722, PMID:17462016, GOC:ach

[pgaudet]

+[Term] +id: GO:0140909 +name: kinetoplast DNA replication +namespace: biological_process +namespace: The process of doubling of the number of maxicircles and minicircles and distribution of the progeny into two daughter networks, which are identical to the parent kinetoplast DNA network. {xref="PMID:8561456", xref="PMID:17462016", xref="PMID:15967722", xref="PMID:8045928", xref="GOC:ach", xref="PMID:12455998"} +synonym: "kDNA replication" EXACT [] +synonym: "kinetoplast DNA synthesis" EXACT [] +synonym: "replication of kinetoplast DNA" EXACT [] +intersection_of: GO:0006260 ! DNA replication +intersection_of: occurs_in GO:0020023 ! kinetoplast +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/24001 xsd:anyURI +created_by: pg +creation_date: 2022-09-16T12:15:31Z +

[pgaudet]

Hi @Achchuthan ,

I created 'kinetoplast DNA replication', but I am not clear how 'kinetoplast DNA' would be different from 'kinetoplast' - in GO kinetoplast is defined as "A sub-structure within the large single mitochondrion of kinetoplastid parasites and which is closely associated with the flagellar pocket and basal body of the flagellum." but in wikipedia they have "A kinetoplast is a network of circular DNA (called kDNA) inside a large mitochondrion that contains many copies of the mitochondrial genome" if the wikipedia definition is right, then the kinetoplast is the same as kinetoplast DNA, isn't it?

I can update the definiton of kinetoplast if needed.

Thanks, Pascale

[Achchuthan]

Hi @pgaudet,

Sorry, somehow I missed your responses to this issue. I think the Wikipedia definition is misleading and I would stick with the current GO definition for kinetoplast, which I think describes kinetoplast better.

Kinetoplast is a specialized region of the single mitochondrion of kinetoplastid species, which harbours the kinetoplast DNA, whereas kDNA is composed of thousands of circular molecules (maxi-circles and mini-circles) topologically interlocked to form a single network (PMID:30018700).

Hope this makes sense? Please let me know, if you have any other questions.

Thanks & best wishes, Achchuthan

[Achchuthan]

Hi @pgaudet,

Just a reminder regarding my response to your question, in case you missed the response in the issue.

Thanks, Ach

[pgaudet]

Thanks for the reminder!

For kinetoplast DNA - this seems outside the scope of GO; we create terms to annotate gene products, not genes (or DNA). What genes were you planning to annotate with this term? That could help finding a suitable replacement/reformulation.

Thanks, Pascale

[Achchuthan]

Thanks @pgaudet for your reply and clarification. I didn't have any particular gene products to be annotated with "Kinetoplast DNA". I only required the term for "Kinetoplast DNA replication", which you have already provided me. When I worked on this term, I requested "Kinetoplastid DNA" as well as there are terms for other organellar genomes such as "Mitochondrial chromosome"

No worries, if this is outside the scope of GO. I think we can close this issue.

Thanks & best wishes, Ach

[pgaudet]

Great, thanks !