#11744 ntr/tpv tRNA-guanine transglycosylation

[Valerie Wood]

There is a similar issue to
ontology-requests/11743/ for queuosine

I captured this as "GO:1990397 queuosine salvage" which is how it is described in the paper.
and although this seems to fit

GO:1990397 queuosine salvage
Any process which produces queuosine from derivatives of it, without de novo synthesis.

it isn't really salvage in the way that it is represented in the GO graph. Here, GO:1990397 queuosine salvage is a descendent of queuosine biosynthesis but the queuosine isn't 'salvaged' endogenously by fission yeast. it is acquired from a dietary source. So an annotation to "queuosine biosynthesis" is incorrect.

I think to annotate this paper I needed instead a process term
tRNA-guanine transglycosylation instead?
defined as
the insertion of queuine into target tRNAs by the replacement of a genetically encoded guanine
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2802272/

The existing term arrangement around
queuosine salvage
and
queuosine biosynthesis looks dodgy (in particular the parentage to tRNA modification)

[Harold J. Drabkin]

Q modification in trna:
In some organisms Q is swapped into the TRNA molecule. In others, it starts by modifying a G residue.

[Valerie Wood]

So here it seems we need:

queuosine biosynthesis (with taxon restrictions limiting it to the organsims which synthesise it).

and

tRNA-guanine transglycosylation
for organims which only utilize the dietary queuosine to modify tRNA's

The reaction is
tRNA guanine + queuine = tRNA queuine + guanine.
so it seems that its guanine that is salvaged?

from
PMID: 24911101 abstract
Queuosine (Q) is a modification found at the wobble position of tRNAs with GUN anticodons. Although Q is present in most eukaryotes and bacteria, only bacteria can synthesize Q de novo. Eukaryotes acquire queuine (q), the free base of Q, from diet and/or microflora, making q an important but under-recognized micronutrient for plants, animals, and fungi.

[Tanya Berardini]

Harold, do you agree with Val's suggestion?

[Harold J. Drabkin]

So I"m wondering if this is maybe a problem with the concept of salvage.
In these instances, the Q is coming from diet or bacteria (assume somehow transported of bacterially excreted Q through gut).
Does the term "salvage" imply re-use in the same cell (maybe yes in most cases). That is, Q derived from tRNA turnover? I suppose it could occur.

[Valerie Wood]

Harold: So I"m wondering if this is maybe a problem with the concept of salvage.

I agree. In this context it isn't really "salvage', but that was not clear to me when I used/requested the term. I think usually when we use the term salvage we mean "obtained from an endogenous degradative pathway" not from a dietary source?

I think there are a number of issues here.

1. Def of salvage should be refined? This is a bigger issue (new ticket), or rolled into 2?

2. Salvage should not be a descendent of biosynthesis?
   See
   https://sourceforge.net/p/geneontology/ontology-requests/11728/

3. I originally requested the term GO:1990397 queuosine salvage
   https://sourceforge.net/p/geneontology/ontology-requests/10926/
   Might be better to obsolete ?

It is defined incorrectly to describe
tRNA-guanine transglycosylation

I think it would be less confusing all round to start with a new term

"tRNA-guanine transglycosylation"
correctly defined.

Too many problems to unpick.....

1. GO:0008616 queuosine biosynthetic process
   should not be a descendent of tRNA modification
   unless all queuosine biosynthesis is part of tRNA modification

[Valerie Wood]

NB queuosine salvage only has 2 annotatins both from pombe.
You could redefine/rename/change parents as "tRNA-guanine transglycosylation"

Whichever is easiest.