The molecular machine behind the carbon footprint

Photo credit: Kumiko SHIMIZU, via Unsplash.

I explained why, if nature is designed, it can present optimal green energy solutions. (See here and here.) Now I’ll 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 sophisticated molecular machine called rubisco. Although one of a kind, rubisco has received a lot of hate over the years for being “slow”. Many enzymes process a thousand molecules per second, but rubisco can only process three per second. For this reason, it has been described as “slow” and “notoriously inefficient”. (Bathellier et al. 2018) The justification for these pejorative adjectives does not exist in my opinion because, after careful study for fifty years, no one has been able to improve it. (Bathellier et al. 2018) I would like to suggest (Bathellier et al. 2018) that its slowness could be due to the complexity of the chemical reaction. If either function of the rubisco was abandoned, its mechanism could be improved in some respects. However, there would almost certainly be tradeoffs. So I’m not suggesting that rubisco can’t be optimized for a different purpose, as optimality is always intrinsically linked to function. But I predict that in the long term it will be recognized for its optimality, given the global constraints of the ecosystem.

Forget what you heard Rubisco is pretty cool

What rubisco actually does is complicated. Rubisco grabs a CO2 molecule (mostly) and attaches it to a sugar chain. (Bathellier et al. 2018) Rubisco then takes the extended carbon chain and cuts it, producing two identical phosphoglycerate molecules. (PDB-101 Molecule of the Month) Making identical molecules is advantageous because only one set of enzymes is then required for the rest of the way. In addition, phosphoglycerate is a molecule very familiar to the cell. Most of the molecules will be reintroduced into the carbon fixation cycle, but some of them will also be siphoned off to produce sugars. Every bite of food you have taken is directly or indirectly the result of this amazing enzyme.

Just another side reaction of promiscuity?

I said rubisco gets CO2 most of the time because every now and then he catches O2 instead of. We have thus arrived at the paradox where O2 rivals rubisco’s CO2 binding site and has been said to “initiate an unnecessary photorespiratory pathway leading to loss of bound carbon”. (Satagopan and Spreitzer 2008) I’d like to throw a crazy idea that this could be a possible regulatory feature designed to balance carbon and oxygen in the atmosphere, slowing rubisco if oxygen is already plentiful and CO2 is rare. (Galmes et al. 2014) Others gave better technical explanations, suggesting that oxygen binding is probably the result of a compromise between chemical and metabolic constraints:

It is possible that the chemical stress imposed by the CO2 inertia 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 study of Rubisco from diatoms, which possess carbon concentrating mechanisms, strongly suggests that when the pressure on Kc (Michaelis apparent constant for CO2) is relieved (that is, when the CO2 is not limiting), there is an alternative evolutionary pathway towards a better specificity by suppressing the activity of the oxygenase, without altering the activity of the carboxylase. Therefore, it is very likely that the oxygenase activity is the result of a compromise: the structure of the active site adapts to allow maximum torsion and positioning of the enolate for CO.2 responsiveness (at the level CO2 mole fraction) even if O2 can also react; alternatively, the active site of the enzyme can adjust its structure (including Mg2 + coordination) to greatly decrease the likelihood of the enolate forming a triplet and then reacting with O2, but CO2 responsiveness also decreases. In kinetic terms, the manipulation of oxygenase activity via the geometry of the enolate affects the oxygenation and carboxylation transition states themselves and therefore can be anticipated to change the energy barrier of CO.2 and oh2 addition (and therefore specificity) as well as the 12C / 13C isotopic effect associated with CO2 more, as observed experimentally.

Bathellier et al. 2018

Either way, rubisco is nothing less than an incredible design, validated by its abundance in the ecosystem, the inability of engineers to improve it dramatically after more than fifty years of study, and its ability to extract the CO2 out of the atmosphere, balancing the atmosphere. (Bathellier et al. 2018)

Coincidences of Darwinism?

As I said, plants are icons of sustainability. They create essential products for other living organisms while using waste – every environmental engineer’s dream design. Are these conceptions at the ecosystem level mere coincidences of Darwinism? Can ecosystem constraints be taken into account without forethought?

These are important questions to consider. Another key question is: is it possible that, because we called the rubisco “sengoureux”, we missed the wisdom of its design? Perhaps we are wrongly prioritizing efficiency over sustainability. Would this have happened if we had had more respect for nature’s intelligent design for clean, green energy?


  • Bathellier, Camille, Guillaume Tcherkez, George H. Lorimer and Graham D. Farquhar. 2018. “Rubisco isn’t really that bad.” Plant, Cell & Environment.
  • Blankenship, Robert E., David M. Tiede, James Barber, Gary W. Brudvig, Graham Fleming, Maria Ghirardi, MR Gunner, et al. 2011. “Compare photosynthetic and photovoltaic efficiencies and recognize the potential for improvement. ” Science 332 (6031): 805-9.
  • Cestellos-Blanco, Stefano, Hao Zhang, Ji Min Kim, Yue-Xiao Shen and Peidong Yang. 2020. “Photosynthetic Semiconductor Biohybrids for Solar Biocatalysis.” Natural catalysis 3 (3): 245-55.
  • Galmés, J., M. To. Conesa, A. Díaz-Espejo, A. Mir, JA Perdomo, U. Niinemets, and J. Flexas. 2014. “Catalytic properties of Rubisco optimized for current and future climatic conditions. ” Plant science: an international journal of experimental plant biology 226 (September): 61-70.
  • Satagopan, Sriram, and Robert J. Spreitzer. 2008. “Plant-like substitutions in the large subunit carboxyl terminus of Chlamydomonas Rubisco increase CO2/O2 Specificity.” BMC Plant Biology 8 (July): 85.

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