Merge children of Sucrose Catabolic Process?

[gocentral]

I'd like to suggest that some (maybe all) of the children of sucrose catabolic process be merged.

GO:0005987 sucrose catabolic process has three children: >>GO:0019575 sucrose catabolic process, using beta-fructofuranosidase [7 gene products] >>GO:0019574 sucrose catabolic process, using glucoside 3-dehydrogenase [0 gene products] >>GO:0010131 sucrose catabolic process, using invertase or sucrose synthase [6 gene products]

GO:0019575 and GO:0010131 should definitely be merged because "invertase" is the common name for "beta-fructofuranosidase". See http://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec.

I'm also not sure why we have three separate BP for the three separate reactions that can potentially breakdown sucrose. Aren't these equivalent to Molecular functions? GO:0004564 beta-fructofuranosidase activity GO:0016157 sucrose synthase activity GO:0033757 glucoside 3-dehydrogenase activity

Would it be better to merge them all back into the parent?

P.S. And, of course, once this is straightened out, I'll have a "regulation of" term to request.

-Dianna

Reported by: diannafisk

Original Ticket: geneontology/ontology-requests/8627

[gocentral]

Hi Dianna,

Looking at MetaCyc and doing a bit of reading, I think it's worth capturing some of the different routes of sucrose breakdown (esp for regulation terms) but agree that the current phrasing isn't the best. So howabout:

1. sucrose catabolic process via 3'-ketosucrose. (rename existing GO:0019574) (synonym: sucrose catabolic process using glucoside 3-dehydrogenase)

2. sucrose catabolic process to glucose and fructose (going via 3.2.1.48 or 3.2.1.26) (synonym: sucrose hydrolysis) (rename existing GO:0019575)

3. sucrose catabolic process via fructose and UDP-glucose ; GO:NEW (going via 2.4.1.13, sucrose synthase) (obsolete GO:0010131, and suggest new term or GO:0019575 as replacements).

Part of the issue is whether 'sucrose catabolism' ends with E.g. glucose and fructose. Or whether further metabolism of glucose and fructose still counts as sucrose catabolism. The MetaCyc pathways go beyond the initial synthase/invertase/dehydrogenase step.

Becky

Original comment by: rebeccafoulger

[gocentral]

• assigned_to: nobody --> rfoulger

Original comment by: rebeccafoulger

[gocentral]

Hi Becky,

This would certainly fix my original issue (that there were essentially two terms that included invertase).

For yeast, at least, I certainly wouldn't consider glucose metabolism or fructose metabolism to be part of sucrose metabolism. Those processes are their own biologically significant branches of metabolism that occur whether or not sucrose is the original source. The enzymes involved in glucose and fructose are also regulated independently of invertase.

Were you thinking that maybe Sucrose catabolism would have "has_part" relationships with glucose catabolism (6007) and fructose catabolism (19317)?

Would you need to do the same for all other disaccharides (e.g. melibiose metabolism, which produces glucose and galactose)?

I guess it can be pretty arbitrary to decide when one process begins and one ends. Do we have any GO standards for this?

Thanks!

-Dianna

Original comment by: diannafisk

[gocentral]

Hi Dianna and Becky,

I have been looking at the MetaCyc pathways for these sucrose metabolism terms and the other sucrose pathways they have - see http://metacyc.org/META/NEW-IMAGE?object=SUCROSE-DEG.

As I think you've probably guessed, defining an endpoint for these pathways is a bit arbitrary; MetaCyc have the endpoints as where other pathways take over (e.g. various flavours of glycolysis), but if you look at KEGG's pathways, they just have a big map of all the reactions and interconversions: http://www.genome.jp/kegg-bin/show\_pathway?ec00500+C00089. MetaCyc also have overlap between their pathways. Reactome represents things yet another way: http://www.reactome.org/entitylevelview/PathwayBrowser.html\#DB=gk\_current&FOCUS\_SPECIES\_ID=48887&FOCUS\_PATHWAY\_ID=71387&ID=188980&VID=2802197

I think that if we want to represent pathways, we will have to be specific about the pathway products (and possibly intermediates, too) in the term name, and clarify in the definition. These terms based on enzyme names aren't all that useful as (1) several enzymes can often catalyse the same reaction, and (2) there are often several names for the same enzyme, so we end up in the situation that we have here for invertase / sucr. synthase / beta-fructofur...ase. As to what constitutes a pathway, I would advocate representing what is canonical and what is useful.

Original comment by: girlwithglasses

[gocentral]

I'll do the following next week:

1. OBSOLETE GO:0010131 sucrose catabolic process, using invertase or sucrose synthase Reason 1: It talks about 2 separate reactions. Reason 2: invertase is the same as 'beta-fructofuranosidase' (3.2.1.26).

2. Rename GO:0019574 FROM: sucrose catabolic process, using glucoside 3-dehydrogenase The chemical reactions and pathways resulting in the breakdown of sucrose, catalyzed by the enzyme glucoside 3-dehydrogenase (EC:1.1.99.13). MetaCyc:SUCROSEUTIL2-PWY TO: sucrose catabolic process via 3'-ketosucrose The chemical reactions and pathways resulting in the breakdown of sucrose, which proceeds via the conversion of sucrose to 3'-ketosucrose. 3'-ketosucrose is hydrolyzed to 3-ketoglucose and fructose. The 3-ketoglucose can then be converted the glucose. exact synonym: sucrose catabolic process, using glucoside 3-dehydrogenase exact synonym: sucrose catabolic process to D-glucose MetaCyc:SUCROSEUTIL2-PWY

3. OBSOLETE: GO:0019575 sucrose catabolic process, using beta-fructofuranosidase MetaCyc:SUCUTIL-PWY (NB: The MetaCyc pathway doesn't quite fit with the definition, since there's several routes of sucrose degradation that use 3.2.1.26).

4. Create new term to match SUCUTIL-PWY: sucrose catabolic process to fructose-6-phosphate and glucose-6-phosphate ; GO:0019575 The chemical reactions and pathways resulting in the breakdown of sucrose, which proceeds by phosphorylation of sucrose to form sucrose-6-phosphate. The subsequent actions of a hydrolase and a fructokinase then generate fructose-6-phosphate and glucose-6-phosphate. MetaCyc:SUCUTIL-PWY

NB: Haven't created a term to replace GO:0010131, because it's covered by individual enzyme reactions (3.2.1.26 and 2.4.1.13).

Becky

Original comment by: rebeccafoulger

[gocentral]

OBSOLETED: GO:0010131 sucrose catabolic process, using invertase or sucrose synthase OBSOLETED: GO:0019575 sucrose catabolic process, using beta-fructofuranosidase

Created new term: sucrose catabolic process to fructose-6-phosphate and glucose-6-phosphate ; GO:0036008

Thanks, Becky

Original comment by: rebeccafoulger

[gocentral]

• status: open --> closed-accepted

Original comment by: rebeccafoulger