> But is this true of chemoautotrophs? I realize that, for example,
> Nitrosomonas and Nitrobacter need relatively high E0 levels, so that 1/10
> of the oxygen level would not be enough for them, but 1/5 would be - and
> _their_ niche really hasn't changed that much. Similarly for some of the
> methanogens, which don't even need (in fact can't tolerate) high oxygen
> levels. Obviously we would expect considerable substituting at non-active
> sites, and some increase in overall efficiency, but perhaps not all that
> much - AFAIK hemoglobin is remarkably similar at the active site
> throughout the vertebrates, despite many millions of years of divergent
> evolution.
>
> Yours,
>
> Bill Morse

This is a really interesting point, and I can think of supporting examples
of enzymes who are very sensitive to oxygen but whose active sites haven't
changed on the timescale of billions of years.  Nitrogenase (mentioned
earlier) is one good example that has stayed relatively unchanged at the
protein level but is now apparently exquisitely regulated by aerobic
organisms, e.g. cyanobacteria that only use nitrogenase at night, when they
aren't doing oxygenic photosynthesis (how cool is that?!).

But then there's always the argument that a good portion of what we're
seeing isn't really that 'ancient' (e.g. pre-oxygen).  So for example the
ammonia oxidizing pathway in chemoautotrophs such as Nitrosomonas absolutely
requires oxygen around that you mentioned.  But the best studied examples of
these organisms do have alternative growth pathways available, e.g.
Nitrosomonas species that can grow in the total absence of oxygen by
oxidizing pyruvate and using nitrite as a terminal electron acceptor and
proton pump.  While the enzymes for anaerobic growth, such as pyruvate
dehydrogense, are widely and deeply distributed across the tree of life and
are arguably ancient, ammonia oxidation enzymes are typically restricted to
a particular class or sub-class of related organisms.  This suggests that
this is a pathway that probably didn't evolve until after the atmosphere
became oxidizing, maybe consistent with what you know of the oxygen
requirements of these guys?

Methanogens are another neat example I don't know much about and would like
to hear your ideas.  How much simpler can it get than to run biochemistry on
H2 and CO2?  But contrarily, aren't there a lot of ideas floating around
that methanogens are really a fairly late-emerging group of organisms, and
so the LUCA probably wasn't doing methanogenesis?
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