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The Molecular Machine Behind Carbon Balance

Emily Reeves
Photo credit: Kumiko SHIMIZU, via Unsplash.

I have been explaining why, if nature is designed, it may exhibit optimal green energy solutions. (See here and here.) Now I will offer an illustration.

The action of removing carbon from the atmosphere and turning it into a sugar molecule is made possible in plants by a very fancy molecular machine called rubisco. Despite being one of a kind, rubisco has received a lot of hate through the years for being “slow.” Many enzymes process a thousand molecules per second, but rubisco can only process three per second. Because of this, it has been called “sluggish” and “notoriously inefficient.” (Bathellier et al. 2018) Justification for these derogatory adjectives does not exist in my personal opinion because, after extensive study for fifty years, no one has been able to make it better. (Bathellier et al. 2018) I’d like to suggest (Bathellier et al. 2018) that its slowness might be due to the complexity of the chemical reaction. If one or another function of rubisco were ditched, its mechanism might be able to be enhanced in certain respects. However, there would almost certainly be trade-offs. So I am not suggesting that rubisco cannot be optimized for a different purpose as optimality is always intrinsically tied to function. But I predict that in time it will be recognized for its optimality, given the overall constraints of the ecosystem.

Forget What You’ve Heard, Rubisco’s Pretty Cool

What rubisco actually does is complicated. Rubisco grabs a CO2 molecule (most of the time) and attaches it to a sugar chain. (Bathellier et al. 2018) Rubisco then takes the lengthened carbon chain and clips it, thus producing two identical phosphoglycerate molecules. (PDB-101 Molecule of the Month) Making identical molecules is advantageous because then only a single set of enzymes is required for the remainder of the pathway. Additionally, phosphoglycerate is a highly familiar molecule to the cell. Most of the molecules will be fed back into the carbon fixation cycle, but some of them will also be siphoned off to produce sugars. Every bite of food you have ever taken is directly or indirectly the result of this amazing enzyme.

Just Another Promiscuous Side Reaction?

I said that rubisco grabs CO2 most of the time because occasionally it grabs O2 instead. Thus we have come to the paradox where O2 competes with rubisco’s CO2 binding site and this has been said to “initiate a wasteful photorespiratory pathway leading to the loss of fixed carbon.” (Satagopan and Spreitzer 2008) I’d like to throw a wild idea out there that this may be a possible regulatory feature designed to balance carbon and oxygen in the atmosphere, slowing rubisco down if oxygen is already plentiful and CO is scarce. (Galmés et al. 2014) Others have given better technical explanations, suggesting that the binding of oxygen is likely the result of a compromise between chemical and metabolic constraints:

It is possible that the chemical constraint imposed by CO2 inertness or scarcity (especially in a low CO2 context) is such that the observed specificity represents the best compromise allowing carboxylation at a physiologically acceptable rate. In fact, a recent catalytic survey of Rubisco from diatoms, which possess carbon concentrating mechanisms, strongly suggests that when the pressure on Kc (apparent Michaelis constant for CO2) is relieved (i.e., when CO2 is not limiting), there is an alternative evolutionary path to a better specificity by suppressing oxygenase activity, without impairing carboxylase activity. Therefore, it is very likely that the oxygenase activity is the result of a trade-off: the active site structure adapts to allow maximal enolate twisting and positioning for CO2 reactivity (at the prevailing CO2 mole fraction) even though O2 can also react; alternatively, the enzyme active site can tune its structure (including Mg2+ coordination) to decrease dramatically the probability of the enolate forming a triplet and then reacting with O2, but CO2 reactivity also decreases. In kinetic terms, manipulating oxygenase activity via the geometry of the enolate affects the transition states of oxygenation and carboxylation themselves and consequently can be anticipated to change the energy barrier of CO2 and O2 addition (and thus specificity) as well as the 12C/13C isotope effect associated with CO2 addition, as observed experimentally. 

Bathellier et al. 2018

Regardless, rubisco is nothing short of an incredible design, as validated by its abundance in the ecosystem, engineers’ inability to drastically improve it after fifty+ years of study, and its ability to pull CO2 out of the atmosphere, balancing the atmosphere. (Bathellier et al. 2018) 

Coincidences of Darwinism? 

As I’ve indicated, plants are icons of sustainability. They create critical products for other living organisms while utilizing waste products — every environmental engineer’s dream design. Are these ecosystem-level designs mere coincidences of Darwinism? Can consideration of ecosystem constraints really occur without foresight? 

These are important questions to consider. Another key question is: Is it possible that because we’ve been calling rubisco “sluggish” we have missed the wisdom of its design? Perhaps we incorrectly prioritize efficiency over sustainability. Would this have occurred if we had more respect for the intelligent design in nature for clean, green energy?

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