Term label update for "fermentation"

[ddooley]

• Guidelines
  Currently the GO term "fermentation" definition focuses on anaerobic fermentation. The FoodOn ontology needs both aerobic and anaerobic fermentation terms, so we'd like to see these terms disambiguated.

BTW, we see the GO (non-planned process) "fermentation" term favours casting the objective of fermentation as an energy producing process, but our interest is in defining a subclass "food fermentation" which handles food processing objectives.

• GO term ID and label for which you request a definition update
  http://purl.obolibrary.org/obo/GO_0006113 "fermentation"

• New proposed definition (genus-differentia pattern, plus additional information if needed)
  We'd like the label changed to "anaerobic fermentation".
  We don't see the need to change the GO definition for fermentation unless a more general parent "fermentation" class is introduced.

Our FoodOn curators have been crafting a more general "fermentation" definition, though it may still require description of output compounds:
"Fermentation is a metabolic process which transforms organic substances by various living microorganisms and the enzymes they produce."

Note, CHMO "fermentation mentions bioreactor specifically, and a planned process, so we will be recommending that CHML change its label to "bioreactor fermentation".

• Reference(s)
  FoodOn issue Fermented foods FoodOntology/foodon#320
  https://pmc.ncbi.nlm.nih.gov/articles/PMC10991178/ (anaerobic / microaerobic and aerobic bacteria referenced).
  https://en.wikipedia.org/wiki/Aerobic_fermentation
  https://www.sciencedirect.com/science/article/abs/pii/B0122270703005705

• Additional information

[cmungall]

Interesting!

Let me try and unpack this a bit. First, let's examine the proposal from a GO perspective. As I understand, you want to relabel the existing fermentation term because of the phenomena of aerobic fermentation. Classic examples of aerobic fermentation are either pathological (cancer/Warburg) or industrial, so it's not surprising we don't see this represented in GO annotations (or in MetaCyc or KEGG). However, as I understand, it is present in natural strains of S cer and S pombe ("Crabtree effect")(although perhaps it is only typically activated in industrial contexts?). I would be curious to see what curators in these organisms say (@edwong57 @ValWood).

As far as coordinating with other ontologies, I have some recommendations here and urge you to be careful, but let's first sort out what is in scope for GO first.

[ValWood]

Fermantation is very little studied in fission yeast. Although I have heard that pombe exhibits crabtree effect, I haven't seen any papers describing it. @PCarme @Antonialock do you have any input here about aerobic vs anaerobic fermentation ?

[PCarme]

I don't personally know much about the topic in S. pombe, but one researcher from my previous team works on carbon metabolism. I could ask him if he knows of any sources on crabtree effect in S. pombe

[ValWood]

We could change the primary name of
http://purl.obolibrary.org/obo/GO_0006113 "fermentation"
to anaerobic fermentation to match the definition

but we would not want to change the definition to cover non-evolved gene-specific processes. Food fermentation is out of scope for GO.

[ValWood]

I could ask him if he knows of any sources on crabtree effect in S. pombe

that would be useful to know...

[Antonialock]

Pombe and cerevisiae are both capable of fermenting in the presence of oxygen. I don't know what the current thinking in the field is but from memory it at least used to be thought of as a competition strategy (when food is abundant, rapidly eat all the simple energy and produce alcohol, to starve and poison other organisms). This I suppose contrasts to some bacteria that switch strategy (fermentation/respiration) depending on whether oxygen is present.

do we need to specify if it occurs anaerobically or aerobically as part of the def?

The def of aerobic respiration states "The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor. "

so the fermentation def could be updated to something like "The enzymatic release of energy from compounds which requires a molecule other than oxygen as the terminal electron acceptor. "

[Antonialock]

I assume the fermentation process itself is the same in yeast, regardless of whether it happens in the presence/absence of oxygen (same gene products/pathway).

I therefore do not think we need different terms for aerobic fermentation and anaerobic fermentation.

[deustp01]

Classic examples of aerobic fermentation are either pathological (cancer/Warburg) or industrial, so it's not surprising we don't see this represented in GO annotations (or in MetaCyc or KEGG). However, as I understand, it is present in natural strains of S cer and S pombe

And also, if PMID: 19748317 is right, in trypanosomes. Here's a long quote (Box 1 of that review) that aims to distinguish types of energy metabolism that may be generally helpful.

A) Aerobic energy metabolism is defined as the complete oxidation of substrates to carbon dioxide and water. The majority of ATP in aerobic energy metabolism is produced via the mitochondrial respiratory chain and oxidative phosphorylation. Oxygen acts as the final electron acceptor to re-oxidise the reduced coenzyme NADH.
B) Fermentation is defined as the degradation of substrates via processes that produce their own oxidants to balance production and re-oxidation of reduced coenzyme NADH. The fermentation of glucose to lactate is a well known example of such a process. In some cases fermentation is linked to an electron transport chain and oxidative phosphorylation (not shown in this figure). However, in that case the final electron acceptor is not oxygen, but for instance endogenously produced fumarate.
C) Aerobic fermentation is the term often used to describe the form of metabolism that is used by all trypanosomatids. In this process the substrates used in energy metabolism are not completely oxidised, but instead fermentation products such as acetate and succinate are excreted. However, in this case the electron transport chain uses oxygen as final electron acceptor. Depending on the composition of the electron-transport chain this process of oxidation of NADH can be accompanied by oxidative phosphorylation. It is remarkable that trypanosomatids on the one hand produce fermentation products under all conditions studied so far, but on the other hand need oxygen as final electron acceptor for optimal functioning and cannot really depend on true fermentative processes.

My nonexpert guess looking at these definitions is that this is yet another pathway / process boundary issue. Draw the boundaries narrowly and there is only one kind of fermentation with no meaningful sub-differentia. Draw it a bit more broadly, to include fates of the immediate product of the core fermentation process and an aerobic / anaerobic distinction may become meaningful.