Should GO:0016174 NAD(P)H oxidase exist?

[ValWood]

I am looking at a paper describing a plant NADH(P) oxidase, and Im trying to figure what its activity is (A fungal gene directly regulators the activity of the gene product)

there are 2 slightly different reactions

GO:0016174    NAD(P)H oxidase activity Catalysis of the reaction: NAD(P)H + H+ + O2 = NAD(P)+ + hydrogen peroxide.

GO:0016175 superoxide-generating NADPH oxidase activity Catalysis of the reaction: NAD(P)H + O2 = NAD(P)H + O2-. PMID:10806195

I assumed the reaction catalysed was GO:0016175 superoxide-generating NADPH oxidase activity

but all arabidopsis are annotated to GO:0016174

form the paper intro Generation of a burst of reactive oxygen species (ROS) catalyzed by NADPH oxidase (Nox) is an important defense mechanism for both mammals and plants against invading microbes (Doke, 1983; Reeves et al., 2002; Lambeth, 2004; Torres and Dangl, 2005). In phagocytes, activation of the membrane-associated NADPH oxidase (gp91phox/NOX2) to produce ROS in response to microbial or inflammation signals involves cytosolic recruitment of a heterotrimeric phagocyte oxidase complex (phox) together with the small GTP binding protein Rac2 (Diebold and Bokoch, 2001; Lambeth, 2004). The discovery of new functional members of the Nox family has led to the recognition that ROS production is a ubiquitous eukaryotic signaling system to control various dif- ferentiation processes, including cell proliferation, apoptosis, and hormone responses in animals (Suh et al., 1999; Lambeth et al., 2000; Lardy et al., 2005), programmed cell death and root hair growth in plants (Foreman et al., 2003; Carol et al., 2005), and sexual development and spore germination in filamentous fungi (Lara-Ortiz et al., 2003; Malagnac et al., 2004; Aguirre et al., 2005).

then I found this in another paper:

NADPH oxidase enzymes belong to a family of transmembrane proteins able to transport electrons across a membrane -usually the plasma membrane- from a cytosolic electron donor to oxygen -the extracellular acceptor- thus catalyzing the generation of O•− 2 (Lambeth, 2004). However, the lifespan of superoxide molecules, which are rapidly dismutated to H2O2 either spontaneously or through the action of apoplastic superoxide dismutases (SOD), is extremely short (Bowler et al., 1994). NADPH oxidase (NOX) activity was first described in mammal phagocytic cells and consists of two plasma membrane proteins, gp91phox and p22phox (phox for phagocyte oxidase). This protein complex is regulated by its interaction with other cytosolic proteins (p47phox, p67phox, p40phox, and Rac2) producing the active form (Cross and Segal, 2004; Lambeth, 2004). Although these mammalian protein complexes are the most studied NOXs, these enzymes have also been characterized in other animals, fungi, and plants. NADPH oxidase enzymes share a basic structure consisting of six transmembrane domains, two heme-binding sites and a long cytoplasmic C-terminal which includes FAD and NADPH binding sites (Bedard et al., 2007).

so it seems that the reaction catalysed is

GO:0016175 superoxide-generating NADPH oxidase activity Catalysis of the reaction: NAD(P)H + O2 = NAD(P)H + O2-.

Should GO:0016174 exist? I can't find an EC number or a ref.

[mah11]

Should GO:0016174 exist? I can't find an EC number or a ref.

I can't help with the plant annotations or the bigger existential question, but GO:0016174 has EC:1.6.3.1 as an xref.

There are separate RHEA entries for the NADH and NADPH reactions - RHEA:11264 & RHEA:11260 - but it looks like neither is xref'd to any GO term.

[deustp01]

there are 2 slightly different reactions

GO:0016174 NAD(P)H oxidase activity Catalysis of the reaction: NAD(P)H + H+ + O2 = NAD(P)+ + hydrogen peroxide.

GO:0016175 superoxide-generating NADPH oxidase activity Catalysis of the reaction: NAD(P)H + O2 = NAD(P)H + O2-. PMID:10806195

and also

However, the lifespan of superoxide molecules, which are rapidly dismutated to H2O2 either spontaneously or through the action of apoplastic superoxide dismutases (SOD), is extremely short

Putting these two pieces together, and also noting limited knowledge of the relevant chemistry, I wonder if the two GO terms in fact represent two views of the identical molecular function, one that defines the reaction in terms of the immediate product of the reaction enabled by the oxidase activity and the other in terms of the first relatively stable product of that reaction.

In a biological process context, it looks from the citations here like the immediate product has important functions despite its instability. Also there are GO molecular function terms for superoxide dismutase activity that could be used together with the GO:0016175 function to annotate the generation of H2O2 via superoxide when that's needed. So perhaps GO:0016174 is less fine-grained than is needed for good annotation?

[ValWood]

I wondered if this was the case. So you think GO:0016175 rather than GO:0016174? The H2O2 is the defense signalling molecule so in that case it might make more sense to use GO:0016174 NAD(P)H oxidase activity. Does the reactive oxygen species do anything other than cause damage?

Most plant annotation use GO:0016174 but most human and mouse use uses the sulphoxide term:

https://www.ebi.ac.uk/QuickGO/annotations?goUsage=descendants&goUsageRelationships=is_a,part_of,occurs_in&goId=GO:0016175&taxonId=9606&taxonUsage=descendants

Also for the regulator human https://www.uniprot.org/uniprot/P19878

[hdrabkin]

RHEA:11260 : H(+) + NADPH + O2 = H2O2 + NADP(+) Yes the term is real. GO:0016174 NAD(P)H oxidase activity Catalysis of the reaction: NAD(P)H + H+ + O2 = NAD(P)+ + hydrogen peroxide (H2O2)

[hdrabkin]

EC 1.6.3.1 PMID: 10401672 PMID: 10601291 PMID: 11822874 (refs are from the RHEA entry; I will update GO:0016174

[hdrabkin]

The EC was there already in the term info.

[hdrabkin]

Update done. I assume I can close this.

[ValWood]

so even though EC's exist, this is definitely not the case?

"two views of the identical molecular function, one that defines the reaction in terms of the immediate product of the reaction enabled by the oxidase activity and the other in terms of the first relatively stable product of that reaction."

if not, I'm not sure how to figure out which one I am annotating, and the common parent is

GO:0050664 oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor which is n't very satisfactory?

So in that case, if these 2 term definitely exist to describe different reactions, would it be possible to have a parent grouping term?

[ValWood]

Actually GO:0050664 oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor is OK.

or make the term name of GO:0050664 oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor

NADPH oxidase

currently broad for NADPH oxidase | broad for GO:0016174 NAD(P)H oxidase activity

[hdrabkin]

Forgot to mention that I also added the EC name as an exact synonym NAD(P)H oxidase (H(2)O(2)-forming) I could change to make THAT the name of 664, to make it more explicit, since the other term has 'superoxide' forming. I would not want to make a grouping term that I would feel the the need to make do not annotate since one makes superoxide and the other does not.

[hdrabkin]

OK; changed the name to bring it more in line with it's sib. That should make it very clear

[hdrabkin]

on nuts forgot to add 'activity' I'll get this right yet.

[ValWood]

OK thanks! I'll figure it out ;)

[hdrabkin]

Also noticed sib term does not have a RHEA; requesting [help #180802] in the subject line of all future correspondence to RHEA about this issue.

[ValWood]

Hi Harold, any news on this one?

Thanks Val

[hdrabkin]

Note if I didn't mention this before, consider GO:0016174 as a grouping term because its NAD(P). However, RHEA ids can either be NAD, OR NADP, not both. Only to be used IF one doesn't know; presumably, a paper would have an assay (?). If the enzyme in question CAN use both, it doesn't do it at the same time; hence the two reactions RHEA:63180 NADPH + 2 O2 = H+ + NADP+ + 2 superoxide RHEA:63184 NADH + 2 O2 = H+ + NAD+ + 2 superoxide But not Public yet (will be on June release; so then can add and close this ticket.

[hdrabkin]

Rheas are now public. Made children of GO:0016175 +id: GO:0106291 +name: superoxide-generating NADH oxidase activity.

+id: GO:0106292 +name: superoxide-generating NADPH oxidase activity

[hdrabkin]

Made children for GO:0016174 with RHEA references.; removed rhea from GO:0016174

+id: GO:0106293 +name: NADH oxidase H202-forming activity

+id: GO:0106294 +name: NADPH oxidase H202-forming activity

Since RHEA has supplied the defs, I will defer to them that these are valid terms and close the ticket.