Joined: May 2002
Nuts. I had a larger post on RUBISCO inefficiency and whether it is necessary or due to historical constraints, but then lost it. But here is the t.o. post:
A google search
One example of the "constraints" view:
Nature 409, 1083 - 1091 (2001)
The habitat and nature of early life
E. G. NISBET* AND N. H. SLEEP
Nature google archived
Is Rubisco a 'qwerty' enzyme?
Where CO2 is in excess, as in the air, Rubisco87 preferentially selects 12C. For 3.5 Gyr, this isotopic signature in organic carbon, and the reciprocal signature in inorganic carbonate, has recorded Rubisco's role in oxygenic photosynthesis as the main link between atmospheric and biomass carbon32. But Rubisco itself may long predate oxygenic photosynthesis, as many non-photosynthetic microaerobic and aerobic bacteria use it. Unlike the many enzymes whose efficiency has been so honed by the aeons as to approach 100% (for example, catalase), Rubisco works either as carboxylase or oxygenase in photosynthesis and photorespiration88. This apparent 'inefficiency', capable of undoing the work of the photosynthetic process, is paradoxical, yet fundamental to the function of the carbon cycle in the biosphere. Without it, the amount of CO2 in the air would probably be much lower.
It is possible that Rubisco is not subject to evolutionary pressures because it has a monopoly. The qwerty keyboard, which is the main present link between humanity and the silicon chip, may be a parallel: legend is that qwerty was designed to slow typists' fingers so that the arms of early mechanical typewriters would not jam. It is among the worst, not the best, of layouts, and only minor evolution occurred (English has Y where German has Z). Perhaps the same applies to Rubisco: if so, genetic engineering to improve Rubisco might lead to a productivity runaway that removes all atmospheric CO2.
However, I think that the "life has pushed CO2 concentration down almost as low as enzymes can push it" might be a better explanation, despite the common mention of the historical constraints explanation in textbooks and webpages:
|Code Sample |
|firstname.lastname@example.org (Laurence A. Moran) wrote in message news:<email@example.com>...|
> You might be interested in something from one of my textbooks ...
> "Since extensive searches of Rubisco mutants have not uncovered
> a mutant enzyme that catalyzes only the carboxylation of ribulose-
> 1,5-bis phosphate, photorespiration may be physiologically
> essential or chemically unavoidable."
> In other words, your experiment has already been tried with mutants of
> rubisco. It doesn't seem possible to have the carboxylation reaction
> without the "reverse" oxygenation reaction (what you call "poisoning").
> I suspect that's because the chemical mechanism is a bit sloppy and can't
> distinguish between oxygen and carbon dioxide. (Carbon dioxide and oxygen
> compete for the same active site in the enzyme.)
> It may be possible to engineer a completely different protein that doesn't
> catalyze photorespiration but why bother? You may have noticed that plants
> are doing quite nicely without our help. :-)
Yeah, I wonder about this example. Two points indicate that getting a
"better" rubisco might not be possible:
1) O2 looks like this: O=O
CO2 looks like this: O=C=O
...they are quite similar, nonpolar, and very small, which might
indicate that discrimination is intrinsically difficult.
2) I think (IIRC) that the "confusion" depends much upon the relative
concentrations of the two molecules. Currently O2 is something like
21% of the atm, but CO2 is down at 300-something ppm (but rising fast,
thanks to cars and stuff). So concentration-wise O2 is much much more
common. If you have something like 5% CO2 (something which I've heard
was at least possible back in dino times), competition is much less of
an issue (IIRC).
It is likely that rubisco originated under high-CO2, low-O2
conditions; but it may be that it has adapted as far as possible to
current conditions and it's simply as good as a protein can get in
On the other hand, if someone designs a better rubisco then I'm wrong
and then it is a great anti-ID example.
(Although a better rubisco might suck enough CO2 out of the air to
sink us even further into ice ages than we already are (geologically
speaking). Does Canada really deserve to be buried under a vertical
mile of ice just because they beat us at hockey on Sunday?)