Lipoxygenase activity

[gocentral]

Hi, the GO term GO:0016165 lipoxygenase activity might require some review. In the literature lipoxygenase activity includes the oxygenation of different substrates (arachidonate/linoleate) and some of their derivatives into product with different regio- and stereo-specificities. Therefore, it is misleading to assign that term to a specific reaction involving linoleate and the production of (9Z,11E)-(13S)-13-hydroperoxyoctadeca-9,11-dienoate. Thanks for your help.

Reported by: lbreuza

Original Ticket: geneontology/ontology-requests/10241

[gocentral]

• labels: Other term-related request --> Other term-related request, enzymes
• assigned_to: Paola Roncaglia

Original comment by: paolaroncaglia

[gocentral]

Dear Lionel,

Thanks for your comments. Indeed, the enzyme entry corresponding to 1.13.11.12 (that GO:0016165 maps to) has been modified several times lately, see http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/13/11/12.html The reaction described in the enzyme entry is the same listed in the definition of GO:0016165, but the name is different: GO:0016165 should be renamed 'linoleate 13S-lipoxygenase activity', with the original name (lipoxygenase activity) kept as a broad synonym. Other specific instances of lipoxygenase activities have corresponding enzyme entries (see http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/13/11/), but there is no generic grouping enzyme entry for 'lipoxygenase'. The enzyme parent term of EC1/13/11/12 corresponds to the single parent of GO:0016165. As for current manual annotations to GO:0016165, there are 20 (for 11 proteins), and I'm afraid that some of them may describe a different reaction than the one in GO:0016165. I will ask curators to check and let me know if their annotations may still sit well under 'linoleate 13S-lipoxygenase activity'. If not, they may be moved to other 'lipoxygenase' terms in GO (there are several), or I could create new terms if needed. Once this is done, I can safely rename GO:0016165 as 'linoleate 13S-lipoxygenase activity'.

For reference, the annotation breakdown per database is: Gramene 2 PINC 2 TAIR 10 UniProtKB 6

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

Hi Paola,

I'll look at the TAIR annotations.

Tanya

Original comment by: tberardini

[gocentral]

Thanks Tanya. Paola

Original comment by: paolaroncaglia

[gocentral]

Hi Paola,

I've checked the UniProt annotations; P38418 LOX2 Q9LNR3 LOX3 Q9FNX8 LOX4 Q9CAG3 LOX6 would all be OK under linoleate 13S-lipoxygenase activity

Q06327 LOX1 Q9LUW0 LOX5 will need a new GO term 'linoleate 9S-lipoxygenase activity' EC 1.13.11.58 (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/13/11/58.html)

I updated the two PINC annotations to a different lipoxygenase term.

For Gramene annotations contact Pankaj Jaiswal (jaiswalp@science.oregonstate.edu)

Thanks, Rachael.

Original comment by: rachhuntley

[gocentral]

Hi Rachael, thanks.

Here's the term you need:

[Term] id: GO:1990136 name: linoleate 9S-lipoxygenase activity namespace: molecular_function def: "Catalysis of the reaction: linoleate + O2 = (9S,10E,12Z)-9-hydroperoxy-10,12-octadecadienoate." [EC:1.13.11.58, GOC:rph, RHEA:30294] synonym: "9-lipoxygenase activity" RELATED [] synonym: "9S-lipoxygenase activity" RELATED [] synonym: "linoleate 9-lipoxygenase activity" RELATED [] synonym: "linoleate:oxygen 9S-oxidoreductase activity" EXACT [] is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen

I've just emailed Pankaj. Cheers, Paola

Original comment by: paolaroncaglia

[gocentral]

Thanks, all done. Rachael.

Original comment by: rachhuntley

[gocentral]

(1) Switched one annotation to another term. (2) Removed three annotations.

(3) http://www.jbc.org/content/286/17/15205 "...AtLOX1 and AtLOX5 exhibiting 9-LOX activity and AtLOX2, AtLOX3, AtLOX4, and AtLOX6 showing predominantly 13-LOX activity."

Annotated LOX1 and LOX5 to GO:1990136.

(4) Need new term/s. PMID:10455113, http://lu:8080/pubsearch/pdfs/1257.pdf (Internal TAIR link)

For AT3G01420: Substrate: linoleic acid Products: 8(Z),11(Z),14(Z)-Heptadecatrienal 2(R)-Hydroxy-9(Z),12(Z),15(Z)-octadecatrienoic acid 8(Z),11(Z),14(Z)-Heptadecatrienoic acid

Original comment by: tberardini

[gocentral]

Hi Tanya,

I can't find entries in Rhea or the Enzyme Nomenclature for the reactions above (PMID:10455113). I can't even find ChEBI IDs for the products. Therefore I wouldn't know what exact names we should use for the new GO term(s). I have filed a request to Rhea (https://sourceforge.net/p/rhea-ebi/reaction-requests-updates/38/), hopefully they can help. If not, I'd suggest moving the annotation for AT3G01420 to the generic parent term GO:0016702 ! oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen

I've also not yet heard back from Gramene.

I'll hold onto renaming GO:0016165 as 'linoleate 13S-lipoxygenase activity' for a little longer. Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

Paola: Could you please move the current annotation(s?) for AT3G01420 to GO:0016702?

I moved the annotation.

Original comment by: tberardini

[gocentral]

Emailed Pankaj again today.

Original comment by: paolaroncaglia

[gocentral]

Emailed Pankaj again today (as I need some clarifications on his previous reply before I can proceed).

Original comment by: paolaroncaglia

[gocentral]

Renamed GO:0016165 as 'linoleate 13S-lipoxygenase activity'.

Setting this ticket to 'pending' waiting for the RHEA ticket to be looked at (https://sourceforge.net/p/rhea-ebi/reaction-requests-updates/38/).

Original comment by: paolaroncaglia

[gocentral]

• status: open --> pending-accepted

Original comment by: paolaroncaglia

[gocentral]

Copying from https://sourceforge.net/p/rhea-ebi/reaction-requests-updates/38/:

[me] Could I please have Rhea entries to annotate the following reactions as seen in PMID:10455113 (http://www.ncbi.nlm.nih.gov/pubmed/?term=10455113): Substrate: linoleic acid Products: 8(Z),11(Z),14(Z)-Heptadecatrienal 2(R)-Hydroxy-9(Z),12(Z),15(Z)-octadecatrienoic acid 8(Z),11(Z),14(Z)-Heptadecatrienoic acid These would be needed to create GO terms to represent the corresponding enzymatic activities.

[Lucila] I've created a Rhea reaction to describe the enzymatic activity for PIOX (α-dioxygenase): Rhea:16332 α-linolenate +O2 <=> 2R-hydroperoxy-α-linolenate The products you mention in your request are not due to the specific activity of this enzyme. They are produced from 2R-hydroperoxy-α-linolenate, either spontaneously or by other enzymes present in the cell lysate (PMID:10455113, PMID:12432929, PMID:16137659).

TAIR annotations are ok anyway, as they were moved to the parent term...

Original comment by: paolaroncaglia

[gocentral]

• status: pending-accepted --> closed-accepted

Original comment by: paolaroncaglia