Proposal to create the GO term “Hydrogen Biosynthetic
Process” and its child terms
Jane’s opinion is that “Hydrogen is generally thought of as a byproduct, so we don't want to add a grouping
term for H2 production/biosynthesis, because it would cover so many reactions and you are just interested
in a subset of these. We think the best way is to put most of these terms under 'fermentation'”:
suggested arrangement:
fermentation ; GO:0006113
--[isa]fermentative hydrogen production ; GO:NEW (or carbohydrate fermentation)
----[isa]xylose fermentation ; GO:NEW (related synonym: hydrogen production from xylose
------[isa]xylose catabolic process to x (if we know what x is)
fermentative hydrogen production
The fermentative conversion of organic substances to hydrogen.
synonym: H2-producing fermentation
Wikipedia: Fermentative_hydrogen_production
MENGO team members agree with the suggestion of this term and provide the figure and references below
to support it.
However, we also are of the opinion that besides fermentatiove hydrogen production, hydrogen can also be
produced via biophotolysis thus the proposed term “Hydrogen biosynthetic process via biophotolysis.
Biophotolysis: The action of light on biological systems that results in dissociation
of water into molecular hydrogen and oxygen, H2O --- H2 + 1⁄2 O2 (in
cyanobacteria and microalgae).
We also believe that two child terms are needed under “fermentative hydrogen
biosynthetic process” viz: hydrogen biosynthetic process via PFOR pathway and
hydrogen biosynthetic process via PFL pathway. See Reference and figure below
There are several reasons why hydrogen production should not be considered as a byproduct and
thus justify the creation of the term “Hydrogen biosynthetic process” which will form an umbrella
under which the above terms will fall.
Rationale for creating the term “Hydrogen biosynthetic process”.
Hydrogen biosynthetic process is one of the fundamental processes in nature. Some
of the machineries involved in this process (hydrogenases, electron transfer
proteins and cofactors) are used in some of the most ancient respiratory processes
that developed on Earth >3 billion years ago. In contrast, processes such as
fermentation are more recent inventions. Hydrogen biosynthetic process has been
leveraged by living cells for various physiological processes with two main goals:
disposal of excess reducing equivalents (or regeneration of oxidized electron
carriers), which results in the emission of hydrogen (as seen in fermentation);
cycling where hydrogen produced by one metabolic system is consumed by another
within the same cell. The first process, allows the development of microbial
communities where excess electrons or reducing equivalents from one organism
allow the growth of their neighbors.
Thus, Hydrogen biosynthetic process should be a higher level GO term.
[Note: To the bioenergy community hydrogen is often a main product and not a byproduct.]
In effect the “Hydrogen biosynthetic process” hierarchy should be structured as such:
Hydrogen biosynthetic process
---Fermentative hydrogen biosynthetic process
-------Hydrogen biosynthetic process via PFOR pathway
-------Hydrogen biosynthetic process via PFL pathway
---Hydrogen biosynthetic process via nitrogenase
---Hydrogen biosynthetic process via biophotolysis
References
PMID:20395274
Attached paper (hy5)
PMID:20692761