Review annotations to glucuronoside metabolic/biosynthetic/catabolic/ process

[raymond91125]

Dear all,

The proposal has been made to obsolete
GO:0019389 glucuronoside metabolic process
GO:0019390 glucuronoside biosynthetic process
GO:0019391 glucuronoside catabolic process

see geneontology/go-ontology#28506. The biosynthetic and catabolic processes are MF's. Thus the metabolic process is unnecessary.

Experimental annotations that need to be reviewed are here:
https://docs.google.com/spreadsheets/d/1E5TBXr3jK1m5UcSqnzHMFXVXUvqDYf6GaMFeymN-7g4/edit?gid=0#gid=0

Impacted groups:
RGD 1
BHF-UCL 1
EcoCyc 1
MGI 1

** Group contacts: https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv

Mappings that need to be reviewed:
None.

Thanks.

[RLovering]

UCL done

[slaulederkind]

RGD finished

[amandamackie]

I've deleted the annotation in EcoCyc but enteric bacteria can use D-glucuronosides as a carbon source so we require a catabolic process GO term. Is there a suggested replacement term for GO:0019391 glucuronoside catabolic process?

[pgaudet]

Hi @amandamackie

Do you have a paper describing this? just so we can add a reference. If the process exists we'll keep the term. Right now it looked liked just a post-translational modification.

Thanks, Pascale

[raymond91125]

Perhaps this MetaCyc https://biocyc.org/pathway?orgid=META&id=GLUCUROCAT-PWY is relevant.

[pgaudet]

This looks like a real pathway - right @rozaru ?
maybe we should un-obsolete the term (sorry!) and describe the pathway more precisely- we can include start and end with the description in MetaCyc. And please add the MetaCyc xref.

Thanks, Pascale

[LiNiMGI]

MGI done.

[raymond91125]

@amandamackie Is this term sufficient? GO:0042840 D-glucuronate catabolic process

[amandamackie]

GO:0042840 D-glucuronate catabolic process is not sufficient for EcoCyc. We require a glucuronide catabolic process term that can be assigned to the transporters and enzymes that import and cleave glucuronides to glucuronate.

[raymond91125]

@amandamackie I'd like to clarify two specific points if you would.

1. I don't think catabolic processes usually include transporter functions. @pgaudet Isn't that true?

2. The definitions of these two terms are nearly identical but the starting chemicals.
   GO:0019391 "The chemical reactions and pathways resulting in the breakdown of glucuronosides, compound composed of a hydroxy compound linked to a glucuronate residue."
   GO:0042840 "The chemical reactions and pathways resulting in the breakdown of D-glucuronate, the D-enantiomer of glucuronate." MetaCyc:GLUCUROCAT-PWY starts with Beta-D-Glucuronides although it is being XREFed as a narrow match by GO:0042840.

[raymond91125]

PMID:28389557 points to many different glucuronides (glucuronosides). But the first step seems to always involve β-Glucuronidase.

[amandamackie]

Based on this I would not need a glucuronide catabolic process term for transporters but still require it for glucuronidase?
I see now there is a glucuronoside transport term (GO:0015779) that I could use.

[pgaudet]

Hi @amandamackie
This sounds perfect, thanks!

[pgaudet]

@raymond91125

We need to change GO:0015779 glucuronoside transport to GO:0015779 glucuronoside transmembrane transport

Thanks, Pascale

[raymond91125]

@raymond91125

We need to change GO:0015779 glucuronoside transport to GO:0015779 glucuronoside transmembrane transport

Thanks, Pascale

Doesn't then GO:0015779 become essentially the same as GO:0015164 glucuronoside transmembrane transporter activity?
There is systemic circulation involved. PMID:28266877