Rubisco “Highly Tuned” for Fixing Atmospheric Carbon

Rubisco sounds like a brand of cracker or something, but it’s actually an air cleaner your life depends on.  It’s an enzyme that fixes atmospheric carbon for use by photosynthetic microbes and plants.  In doing so, it sweeps the planet of excess carbon dioxide – the greenhouse gas implicated in discussions of global warming – making it a politically important molecule as well the most economically important enzyme on earth.  Rubisco is the most common enzyme in the world, too; every person on earth benefits from his or her own 12 to 25 pounds of these molecular machines, which process 15% of the total pool of atmospheric carbon per year.  For a long time, biochemists thought this enzyme was slow and inefficient.  That view is changing.  Rubisco now appears to be perfectly optimized for its job.

Rubisco’s cute name is a handy anagram for the clumsier appellation ribulose bisphosphate carboxylase.  Tcherkez et al. first broke the paradigmatic logjam about this enzyme’s purported inefficiency with an article in PNAS,¹ titled, “Despite slow catalysis and confused substrate specificity, all ribulose bisphosphate carboxylases may be nearly perfectly optimized.”  Howard Griffiths commented this week in Nature² about this paper and the new findings about its optimization.  Though his article referred to evolution seven times, and only mentioned design twice, the latter word seemed the most valuable player.

There are four classes of Rubisco, some more efficient at fixing carbon than others.  Its reputation as a slow enzyme (2-8 catalytic events per second) may be unfair.  Carbon dioxide in gaseous form has to compete for access to the active site against the much more abundant and lighter oxygen.  Griffiths shows what a difficult job this molecule has to perform; no wonder it leaks somewhat.  But, as he explains, even the leaks are accommodated:

It is curious that Rubisco should fix CO2 at all, as there is 25 times more O2 than CO2 in solution at 25°C, and a 500-fold difference between them in gaseous form.  Yet only 25% of reactions are oxygenase events at this temperature, and carbon intermediates ‘lost’ to the carbon fixation reactions by oxygenase action are metabolized and partly recovered by the so-called photorespiratory pathway.  Catalysis begins with activation of Rubisco by the enzyme Rubisco activase, when first CO2 and then a magnesium ion bind to the active site.  The substrate, ribulose bisphosphate, then reacts with these to form an enediol intermediate, which engages with either another CO2 or an O2 molecule, either of which must diffuse down a solvent channel to reach the active site.

This is a harder job than designing a funnel that will pass only tennis balls, when there are 500 times more ping-pong balls trying to get through.  Not only is Rubisco good at getting the best mileage from a sloppy process, it may actually turn the inefficiency to advantage.  Griffiths started by claiming, “evolution has made the best of a bad job,” but ended by saying that the enzyme’s reputation as “intransigent and inefficient” is a lie.  Why?  It now appears that “Rubisco is well adapted to substrate availability in contrasting habitats.”  This means its inefficiency is really disguised adaptability.

Experimenters thought they could “improve” on Rubisco by mutating it.  They found that their slight alterations to the reactivity of the enediol intermediate drastically favored the less-desirable oxygenase reaction.  This only served to underscore the contortions the molecule must undergo to optimize the carboxylase reaction:

Such observations provided the key to the idea that in the active site the enediol must be contorted to allow CO2 to attack more readily despite the availability of O2 molecules.  The more the enediol mimics the carboxylate end-product, Tcherkez et al. conclude, the more difficult it is for the enzyme to free the intermediate from the active site when the reaction is completed.  When the specificity factor and selectivity for CO2 are high, the impact on associated kinetic properties is greatest: kcat [i.e., the rate of enzyme catalytic events per second] becomes slower.
So, rather than being inefficient, Rubisco has become highly tuned to match substrate availability.

Another finding about the inner workings of Rubisco bears on dating methods and climate models.  Scientists have known that Rubisco favors the lighter, faster-moving carbon isotope ¹²C over ¹³C.  By measuring the ratio of these stable isotopes in organic deposits, paleoclimatologists have inferred global carbon dioxide abundances and temperatures (knowing that Rubisco processes the isotopes differently).  That assumption may be dubious:

Several other correlates are also explained by this relationship.  For instance, Rubisco discriminates more against ¹³C than against ¹²C, the two naturally occurring stable isotopes in CO2.  But when the specificity factor is high, the ¹³C reaction intermediate binds more tightly, and so carbon isotope discrimination is higher (that is, less ¹³C is incorporated); in consequence, the carbon-isotope signals used to reconstruct past climates should perhaps now be re-examined.  In contrast, higher ambient temperatures (30-40 °C) reduce the stability of the enediol, and Rubisco oxygenase activity and photorespiration rate increase.

Those considerations aside, Griffiths is most interested in two things: how this enzyme evolved, and whether we can improve on it.  If we can raise its carboxylation efficiency, we might be able to increase crop yields.  So far, genetic engineers have not succeeded.³

As for the evolution of Rubisco, he mentions three oddball cases but fails to explain exactly how they became optimized for their particular circumstances – only that they are optimized.  Yet their abilities seem rather remarkable.  For instance, though the “least efficient” forms of Rubisco reside in microbes living in anaerobic sediments, where oxygen competition is not a problem, “One bacterium can express all three catalytically active forms (I, II and III), and switches between them depending on environmental conditions.”  In another real-world case, “some higher plants and photosynthetic microorganisms have developed mechanisms to suppress oxygenase activity: CO2-concentrating mechanisms are induced either biophysically or biochemically.”  In another example, “Rubisco has not been characterized in the so-called CAM plants, which use a form of photosynthesis (crassulacean acid metabolism) adapted for arid conditions.”  These plants, including cacti and several unrelated species scattered throughout the plant kingdom, have other mechanisms for dealing with their extreme environments.  In every mention of evolution, therefore, Griffiths assumed it rather than explaining it: viz., “The systematic evolution of enzyme kinetic properties seems to have occurred in Rubisco from different organisms, suggesting that Rubisco is well adapted to substrate availability in contrasting habitats.”

So, can we improve on it?  If so, given all the praise for what evolution accomplished, Griffiths seems oblivious to the implications of his own concluding sentence:

Other research avenues include manipulating the various components of Rubisco and cell-specific targeting of chimaeric Rubiscos.  Potential pitfalls here are that the modified Rubisco would not only have to be incorporated and assembled by crop plants, but any improved performance would have to be retained by the plants.  Finally, one suggestion is that we should engineer plants that can express two types of Rubisco – each with kinetic properties to take advantage of the degree of shading within a crop canopy.  Such rational design would not only offer practical opportunities for the future, but also finally give the lie to the idea that Rubisco is intransigent and inefficient.

What, students, is a synonym for “rational design”?

¹Tcherkez et al., “Despite slow catalysis and confused substrate specificity, all ribulose bisphosphate carboxylases may be nearly perfectly optimized,” Proceedings of the National Academy of Sciences USA, published online before print April 26, 2006, 10.1073/pnas.0600605103 PNAS | May 9, 2006 | vol. 103 | no. 19 | 7246-7251.
²Howard Griffiths, “Plant biology: Designs on Rubisco,” Nature 441, 940-941 (22 June 2006) | doi:10.1038/441940a; Published online 21 June 2006.
³If and when they do, the benefit would be tuned for humans and their livestock, not necessarily for the ecology or atmosphere.

Folks, here you have it again.  What Griffiths meant as a paper praising evolution is really a paper demonstrating intelligent design.  We dare any evolutionist to explain how this “highly-tuned” enzyme, with the optimized contortions of its intermediates and its “highly conserved” (i.e., unevolved) active site, arose by an unguided process, especially how a lowly bacterium – the simplest of organisms – evolved three forms of it and can switch between them depending on environmental conditions!  And don’t say it evolved because evolution is a fact.

Here again, also, we see how further research is giving “the lie to the idea” that something in nature “is intransigent and inefficient.”  Evolutionists love to showcase examples of inefficiency in nature, to give the impression that any God or designer would not do such a bungled job.  The only bungling is in the theories of evolutionists who look at optimized, rational design in the face and can’t see a rational designer.  Human rational design applied to improving on nature’s engineering marvels does not support evolution, it supports intelligent design.  If human intelligence is required to copy or modify a design, one cannot say that the original design “emerged” by an unguided, purposeless, material process.  Why is that such a hard concept for the Darwinists to grasp?  Why can’t they see the illogic of their position?  As usual, they merely assume evolution can perform any engineering job necessary, even designing nanomachinery that exceeds our human capabilities.

Notice the snippet about climate models in this story, also.  It goes to show that assumptions about the unobservable past, like foundations under a house of cards, can shift under new research.  Though Griffiths was not specific about the degree of alteration climate models might suffer, this is a point to remember whenever popular science reports glibly claim things like “218.24267 gazillion years ago, the atmosphere went through a period of global warming followed by a snowball earth.”

You may never have heard about this indispensable enzyme that helps keep you breathing and gives you salad to eat (and, indirectly, meat from plant-eating animals).  Astrobiologists had better pay attention.  Mars and Venus have lots of carbon dioxide, but no Rubisco.  Earth has just enough CO2 to help moderate the atmospheric temperature, but not too much to cause a catastrophic greenhouse effect; that balance is maintained in part by this highly-tuned enzyme.  Our ability to read and write and think these thoughts owes to the convergence of numerous improbable factors, including our planet’s optimal distance from the sun, a global magnetic field, a planetary mass that retains the right ingredients but lets others escape, a transparent atmosphere, a star that produces radiation with just the right energy range for molecular reactions, and optimally engineered molecular machines in plants that can harvest that energy.  As a result, our lungs have air, our bodies have food, and our eyes have beauty and variety to enjoy.  If this looks like intelligent design, and if that has philosophical or religious implications, so be it.  Thank God for Rubisco.