GO: 8425 ubiquinone biosynthesis methyltransferase activity

[gocentral]

Hello,

The undefined term GO: 8425 'ubiquinone biosynthesis methyltransferase activity' sounds a bit funny.

I think it's supposed to represent '
2-hexaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity'- see SGD COQ5, and all other annotations are genes related to COQ5.

However COQ5 is very similar to E. coli Ubi5 which has '2-octaprenyl-6-methoxy-1,4-benzoquinone methylase activity'.

In PMID: 9083049 they say that "that the length of the isoprene tail does not play a crucial role in substrate recognition, since normal substrates for this C-methylation contain eight and six isoprene units, in E. coli and S. cerevisiae, respectively"

I dont know how to represent the activity, maybe just '2-prenyl-6-methoxy-1,4-benzoquinone methyltransferase activity'? or '2-(n)prenyl-6-methoxy-1,4-benzoquinone methyltransferase activity'? Maybe someone with stronger biochemistry background can comment...

This activity is SAM-dependent so it should probably get the parent :GO:8757 S-adenosylmethionine-dependent methyltransferase activity.

Thanks

Pascale

Reported by: pgaudet

Original Ticket: "geneontology/ontology-requests/2367":https://sourceforge.net/p/geneontology/ontology-requests/2367

[gocentral]

Logged In: YES user_id=803460

Maybe this term should be merged with its parent, "quinone cofactor methyltransferase activity"?

In any case, this term also need the GO:8757 S-adenosylmethionine-dependent methyltransferase activit parent.

Pascale

Original comment by: pgaudet

[gocentral]

Logged In: YES user_id=451873

(from Kirill)

IMHO I think one should not create over-generous categories like '2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity' unless there is a sufficient number of activities like

2-hexaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity 2-octaprenyl-6-methoxy-1,4-benzoquinone methylase activity

Both of these look fine. However, they have to be distinguished as the pathways of ubiquinone biosynthesis in yeast and E. coli are similar but not identical. If there is an experimental confirmation that some enzyme exhibits both activities, then it could be annotated with both.

> Maybe this term should be merged with its parent, "quinone cofactor > methyltransferase activity"?

No, that one looks very broad to me. "quinone cofactor methyltransferase activity" probably should also include such activities as 2-heptaprenyl-1,4-naphthoquinone methyltransferase (see PubMed:9139683)

> In any case, this term also need the GO:8757 > S-adenosylmethionine-dependent methyltransferase activit parent.

Yes I agree

Kirill

Original comment by: jl242

[gocentral]

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Thanks Jane and Kirill,

Is the conclusion to change the term "GO: 8425 ubiquinone biosynthesis methyltransferase activity" to "2-hexaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity"?

Pascale

Original comment by: pgaudet

[gocentral]

Logged In: YES user_id=451873

(from Kirill)

IMHO I think one should not create over-generous categories like '2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity' unless there is a sufficient number of activities like

2-hexaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity 2-octaprenyl-6-methoxy-1,4-benzoquinone methylase activity

Both of these look fine. However, they have to be distinguished as the pathways of ubiquinone biosynthesis in yeast and E. coli are similar but not identical. If there is an experimental confirmation that some enzyme exhibits both activities, then it could be annotated with both.

> Maybe this term should be merged with its parent, "quinone cofactor > methyltransferase activity"?

No, that one looks very broad to me. "quinone cofactor methyltransferase activity" probably should also include such activities as 2-heptaprenyl-1,4-naphthoquinone methyltransferase (see PubMed:9139683)

> In any case, this term also need the GO:8757 > S-adenosylmethionine-dependent methyltransferase activit parent.

Yes I agree

Kirill

Original comment by: jl242

[gocentral]

Logged In: YES user_id=451873

I think Kirill's suggesting that 'ubiquinone biosynthesis methyltransferase activity ; GO:0008425' should be changed to '2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity', with the two children '2-hexaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity' and '2-octaprenyl-6-methoxy-1,4-benzoquinone methylase activity' (and given that extra parentage). But I'd better check that!

Original comment by: jl242

[gocentral]

• labels: --> Other term-related request
• milestone: --> TermGenie
• assigned_to: nobody --> jl242

Original comment by: jl242

[gocentral]

Logged In: YES user_id=451873

Kirill says yes, so I'll go ahead and make the changes...

Original comment by: jl242

[gocentral]

Logged In: YES user_id=451873

Changed the name of 'ubiquinone biosynthesis methyltransferase activity ; GO:0008425' -> '2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity'. Added two new child terms:

2-hexaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity ; GO:0043334 2-octaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity ; GO:0043333

Original comment by: jl242

[gocentral]

• status: open --> closed-accepted

Original comment by: jl242