similar functions requiring new term

gocentral commented 18 years ago

Hi Amelia,

I wanted to run this by you before creating anything at TAIR. We have an enzyme CCD1 which has been annotated with GO:0045549 (9-cis-epoxycarotenoid dioxygenase activity). Although the term name is correct for the function of this gene, the definition is not. GO:0045549 refers specifically to the formation of xanthoxin and C-25 apocarotenoids in abscisic acid biosynthesis. Gene CCD1, however, encodes an enzyme which also has 9-cis-epoxycarotenoid dioxygenase activity but the product are different (See PMID 11316814). I don't know of a generic name to classify the products to write the definition and am therefore seeking your advice. Should GO:0045549 be renamed to reflect its definition (ie something like: 9-cis-epoxycarotenoid dioxygenase activity, xanthoxin-producing; and the new term 9-cis-epoxycarotenoid dioxygenase activity, non-xanthoxin-producing? I find it a bit lame but it'd do the trick I suppose.

Let me know what you think

Christophe

Reported by: c_tissier

Original Ticket: "geneontology/ontology-requests/3361":https://sourceforge.net/p/geneontology/ontology-requests/3361

gocentral commented 18 years ago

assigned_to: nobody --> girlwithglasses

Original comment by: c_tissier

gocentral commented 18 years ago

Logged In: YES user_id=473796

Hello Christophe,

I've just had a look at the article you mentioned and that from which the original definition came. From that original article, it seems that GO:0045549 was intended to encompass two reactions, and we could create new child terms for them instead. These reactions involve cleavage at the C11-C12 bond, so this could be specified in the term names and definitions.

9-cis-epoxycarotenoid 11,12-dioxygenase activity ; GO:0045549 def: "Catalysis of the reaction: 9-cis-epoxycarotenoid + O2 = xanthoxin + C25 apocarotenoid. This reaction is the oxidative cleavage of the C11-C12 bond in 9-cis-epoxy-carotenoids (e.g. neoxanthin and violaxanthin) to form xanthoxin and a C-25 apocarotenoid."

The new child terms: 9'-cis-neoxanthin 11,12-dioxygenase activity ; GO:00new01 Catalysis of the reaction: 9'-cis-neoxanthin + O2 = xanthoxin + C25-allenic- apo-aldehyde. MetaCyc:RXN-698 (KEGG:R06952)

9-cis-violaxanthin 11,12-dioxygenase activity ; GO:00new02 Catalysis of the reaction: 9-cis-violaxanthin + 02 = xanthoxin + C25-epoxy- apo-aldehyde. (KEGG:R06953)

The reactions in the other paper are all cleavage at C9-C10, and they involve a variety of different carotenoids, not just the epoxy carotenoids that GO: 0045549 mentions. Therefore it might be best to have something like this:

carotenoid dioxygenase activity [i] 9-cis-epoxycarotenoid 11,12-dioxygenase activity ; GO:0045549 ---[i] 9-cis-violaxanthin 11,12-dioxygenase activity ; GO:00new02 ---[i] 9-cis-zeaxanthin 11,12-dioxygenase activity ; GO:00new01 [i] carotenoid 9,10-dioxygenase activity ; GO:00new03 ---[i] 9-cis-epoxycarotenoid 9,10-dioxygenase activity ; GO:00new04

with defs:

carotenoid 9,10-dioxygenase activity ; GO:00new03 Catalysis of the reaction: C40 carotenoid + O2 = C27 apocarotenoid + C13 terpenoid.

9-cis-epoxycarotenoid 9,10-dioxygenase activity ; GO:00new04 Catalysis of the reaction: 9-cis-epoxycarotenoid + O2 = C27 apocarotenal + C13 cyclohexone.

There are also some reactions that produce two C13 terpenoids and a C14 dialdehyde. I think that this would have to be two separate reactions, i.e.

carotenoid + O2 = C27 apocarotenoid + C13 terpenoid

then

apocarotenoid + O2 = C14 dialdehyde + C13 terpenoid

... because where the carotenoid is one of the 9-cis-epoxycarotenoids, the second reaction doesn't occur. A term representing the two reactions could be added to the process ontology, e.g.

carotenoid catabolism to C14 dialdehyde by carotenoid dioxygenase The chemical reactions resulting in the breakdown of carotenoids, mediated by a carotenoid dioxygenase enzyme. A carotenoid undergoes oxidative cleavage at the C9-C10 bond to form a C13 terpenoid and a C27 apocarotenoid. This apocarotenoid then undergoes a further C9-C10 cleavage, forming a second C13 terpenoid and a C14 dialdehyde.

Terms can be added for each of those reactions if you want to be specific...

Hope that is helpful and not just long-winded and confusing!

Cheers, Amelia.

Original comment by: girlwithglasses

gocentral commented 18 years ago

Logged In: YES user_id=1320989

Hi Amelia,

thanks for looking into this. after reading it a few times, it now all makes sense :)

First I agree with you that we should create two GO child terms one each for neoxanthin and violaxanthin:[i] 9-cis-epoxycarotenoid 11,12-dioxygenase activity ; GO:0045549 ---[i] 9-cis-violaxanthin 11,12-dioxygenase activity ; GO:00new01 ---[i] 9-cis-zeaxanthin 11,12-dioxygenase activity ; GO:00new02

for now we don't have any example of that (11,12-dioxygenase activity of a compound that's not an epoxycarotenoid!) but in the future we may have to create:

carotenoid dioxygenase activity [i] carotenoid 11,12-dioxygenase activity ; as well.

One thing that is rather confusing, I think, and probably deserves to be explained in the definition, is that a cis-epoxycarotenoid can have both a 9-cis and a 9'-trans. What characterizes this enzyme is its ability to cleave 9,10 both in cis and trans (more efficiently it seems). Those activities should be the parent terms:

---[i] 9-cis-carotenoid 9,10-dioxygenase activity ; ---[i] 9-trans-carotenoid 9,10-dioxygenase activity ;

so we'd end up with something like:

[i] carotenoid 9,10-dioxygenase activity ; ---[i] 9-cis-carotenoid 9,10-dioxygenase activity ; ------[i] 9-cis-epoxycarotenoid 9,10-dioxygenase activity ; ---------[i] C27 apocarotenoid 9,10-dioxygenase activity (9-cis-violaxanthin 9,10-dioxygenase was not shown to occur) ; ---------[i] 9-cis-neoxanthin 9,10-dioxygenase activity ; ---[i] 9-trans-carotenoid 9,10-dioxygenase activity ; ------[i] 9-trans-C40 carotenoids 9,10-dioxygenase activity (I am not sure that the epoxy-concept is relevent as the enzyme cleaves non-epoxy sites... I leave it to you); ---------[i] 9-cis-violaxanthin 9,10-dioxygenase activity (cleavage 9') ; ---------[i] 9-cis-neoxanthin 9,10-dioxygenase activity (cleavage 9') ; ---------[i] trans-violaxanthin 9,10-dioxygenase activity ; ------[i] 9-trans-C27 apocarotenoid 9,10-dioxygenase activity; ---------[i] 5,6-epoxy-3-hydroxy-9-apo-β-caroten-12'-al 9,10-dioxygenase activity;

anyways... you get the jist!

etc...

Chris

Original comment by: c_tissier

gocentral commented 17 years ago

assigned_to: girlwithglasses --> nobody

Original comment by: mah11

gocentral commented 16 years ago

assigned_to: nobody --> tairtb

Original comment by: mah11