proposed obsoletion "reactive oxygen species biosynthetic process" branch

[ValWood]

What do we mean by GO:0010730 negative regulation of hydrogen peroxide biosynthetic process

Definition (GO:0010730 GONUTS page) Any process that decreases the rate, frequency or extent of hydrogen peroxide biosynthesis. The chemical reactions and pathways resulting in the formation of hydrogen peroxide (H2O2), a potentially harmful byproduct of aerobic cellular respiration which can cause damage to DNA.

The annotations are for things like

" We conclude that cytochrome c loss during ischaemia, caused by outer membrane permeabilization, is a major determinant of H₂O₂ production by mitochondria under pathophysiological conditions. We further suggest that in hypoxia, production of H₂O₂ to activate signalling pathways may be also mediated by decreased oxidized cytochrome c and less superoxide scavenging."

seems to be increased production of free radicals -- H202 biosynthesis seem to be an odd way to curate these observations?

7 EXP

[deustp01]

Piling on, in the part of the metabolic world I know about, hydrogen peroxide is only ever a chemically unavoidable toxic byproduct of metabolic processes, and mechanisms exist to break it down rapidly. Pathological processes can interfere with these breakdown processes. Not much scope, if any, for normal biosynthesis or regulation of it as GO biological processes.

But plants and archaea may be different.

[ValWood]

Thanks @deustp01

"reactive oxygen species biosynthetic process" and its descendants including regulation has 142 EXP annotations (109 metazoan, 33 plant, 1 fungi)

Unless any evidence of biosynthesis I suggest we obsolete the branch?

For some context, one of our community used this term for a phenotype which increases H202 (and for the ones I looked at this seems to always be the case). It is difficult to explain why this is not an appropriate GO annotation if the terms exist in GO.

Some pathogens may increase ROS production, I think I have come across that, but not by biosynthesis (and this would be in the pathogen-host interaction branch anyways)

[pgaudet]

For some species - at least plants- this seems relevant? See https://www.uniprot.org/uniprotkb/Q5G234/entry

Catalyzes the oxidation of various aldopyranoses and disaccharides on carbon-2 to the corresponding 2-keto sugars concomitant with the reduction of O2 to H2O2. Plays an important role in lignin degradation of wood rot fungi by supplying the essential cosubstrate H2O2 for the ligninolytic peroxidases, lignin peroxidase and manganese-dependent peroxidase

There are some RHEA reactions: https://www.rhea-db.org/rhea/?query=chebi:16240

Maybe a taxon constraint would be more appropriate ?

[ValWood]

OK! I still think maybe we could lose the grouping term "reactive oxygen species biosynthetic process"?

[pgaudet]

possibly!