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Is the RubisCO enzyme an ineffective leftover of evolution?

Or is it a design element?

Published: 25 January 2020 (GMT+10)
Figure 7 of Tcherkez, 2016.reaction-pathway
Figure 1. Reaction pathway of RubisCO when either carbon dioxide or oxygen is added. E: RubisCO enzyme. PGA: 3-phospho-D-glycerate, P-glycolate: phosphoglycolate

One of our readers, J.D. from the U.S., asked us a question about the efficiency of the RubisCO enzyme, which takes part in plant respiration:

Hello! So, a certain person I interact with claims that RubisCO, an enzyme in the body, is ‘proof’ that evolution is true, because of its rather poor efficiency and its tendency to accidentally use oxygen instead of carbon dioxide. He says this shows that evolution has selected what works, instead of a well-designed system. Of course, this is patent nonsense; all the other irrefutable evidences show that this argument is fallacious somewhere. I was only able to find one paragraph on the subject in your website, and it did not satisfactorily answer the question: how is he incorrect, and why did God make the enzyme so seemingly poorly?

CMI-US’s Dr Matthew Cserhati responds:

For those readers who don’t know what the question is about, we are talking about the RubisCO enzyme1 (Ribulose-1,5-bisphosphate carboxylase/oxygenase), which plays an important initial step in the Calvin cycle. This is a process whereby plants generate sugar from carbon dioxide (CO2) and water (H2O) by using energy in the form of ATP, the well-known energy molecule which is produced during photosynthesis. The usual substrates2 of RubisCO are the sugar molecule ribulose-1,5-bisphosphate (RuBP) with five carbon atoms and carbon dioxide (upper half of figure 1). Its products are two molecules of 3-phospho-D-glycerate (PGA), with three carbon atoms each. PGA is later transformed into different types of sugars such as glucose which have six carbon atoms.

Some evolutionists point out that RubisCO works extremely slowly, incorporating only three molecules of carbon dioxide per second, compared to other enzymes, which can incorporate up to 10,000 molecules of their own substrates per second. The evolutionary argument is that RubisCO is very slow, therefore God would surely not have created such an inefficient enzyme. Rather, evolutionists claim that the enzyme evolved over millions of years, and natural selection simply chose that version of the enzyme which just so happened to work. In other words, if it isn’t broken, don’t fix it. According to evolutionary logic, that variant of RubisCO happened to be selected which just so happened to be this slow.

RubisCO is allegedly one of the earliest enzymes to have evolved on earth. According to evolutionary theory, this enzyme first appeared billions of years ago, when the earth’s atmosphere was anoxic.3 Therefore, RubisCO is allegedly incapable of effectively coping with oxygen, because it supposedly first appeared in nature before there was any oxygen in the atmosphere.

Are these arguments valid? Could God have done better? Is RubisCO just a marginally effective enzyme, barely able to get the job done? Is it merely just a leftover of millions of years of chance modifications?

Is RubisCO really that ineffective?

We cannot claim to know the mind of God when He designed living things, or proteins in those living things, for that matter. Let’s look at a few things which show that RubisCO is more efficient than we may think, and why evolution does not provide a sound argument for its existence.

Oxygen is present in much larger quantities in the atmosphere than carbon dioxide. The partial pressure4 of oxygen is 700 times that of carbon dioxide. Because the two substrate molecules are somewhat similar, it is also hard to discriminate between oxygen and carbon dioxide. This means that RubisCO simply cannot avoid reacting with oxygen at times.

But is the way RubisCO reacts with oxygen merely a random interaction? As a matter of fact, oxygen is also a substrate of RubisCO. This is simply a case of something called “enzyme promiscuity”, which means that an enzyme can react with more than one substrate. This is quite common among enzymes. This is something like how certain guns can use multiple types of ammunition, or how some cars can use multiple types of fuel. There are several enzymes involved in processes inside the cell such as signal transduction, gene regulation, steroid biochemistry, immunity and detoxification processes, which have more than one substrate. For example, a whole class of enzymes called kinases is made up of proteins which only recognize amino acid motifs (which are only parts of proteins) as opposed to entire proteins.5

When too much oxygen is produced from photosynthesis, plants switch from using carbon dioxide to a process called “photorespiration”, where they use excess oxygen as a substrate instead of carbon dioxide (bottom part of figure 1).6,7 This reaction is less efficient and produces only one molecule of PGA and one phosphoglycolate8 instead of two molecules of PGA and also uses up one energy molecule (ATP).

advancedaquarist.comPAR
Figure 2. PAR = photosynthetically active radiation. The relationship between photosynthesis, oxygen production, light levels, and RubisCO activity on a clear sunny day in Hawaii. Plants are active during the morning and evening hours when they are capable enough of handling lower levels of light. During this time RubisCO is active. However, at noontime, when light levels are much higher, and photosynthesis is very active, this produces excess oxygen, which plants must funnel off through photorespiration.

Figure 2 depicts the relationship between photosynthesis, light levels, oxygen, and RubisCO activity. We should note that when light levels are the highest (around noontime), the more active the photosynthetic apparatus is, thereby producing more oxygen and energy. But oxygen is a poisonous substance, because it damages organic molecules. The rate of photosynthesis at this time of day is so high that plants cannot keep up with either detoxifying the excess oxygen or making use of the energy to produce sugars.9 This is known as photo-oxidative stress. This is like a factory assembly line which is moving so fast that the factory workers are incapable of stacking away all of the created products. Therefore, the photosynthetic apparatus shuts down around noontime so as not to produce too much toxic oxygen. If light levels could be held constant, then there would be no problem coming from excess oxygen production. For this reason, agriculturalists grow plants in greenhouses, where the light level is held at a fixed level all throughout the day for maximum productivity.

RubisCO is not a random evolutionary leftover, rather it is a built-in safety mechanism, designed to protect the plant from toxic excess oxygen. Photosynthesis is decoupled at the highest levels of activity to prevent oxygen poisoning. The skeptic in question in the email simply doesn’t know his biochemistry well enough!

Enzyme kinetics show that RubisCO is quite efficient

Besides the use of RubisCO in photorespiration, let’s look at arguments from enzyme kinetics, which further prove that this enzyme is not an inefficient evolutionary leftover.

frequency-plot
Figure 3. Frequency plot of 66,472 kcat parameter values for known enzymes taken from the BRENDA database. The x-axis corresponds to the log10 value of kcat. The boundaries for the catalytic range of RubisCO can be seen in green.

Compared to other enzymes, RubisCO is not particularly slow, given the fact that it has to contend with a high concentration of oxygen in its environment. An enzyme’s speed is measured by the parameter kcat, otherwise known as the turnover number, which is equal to the number of reactions an enzyme can handle per second.

Several enzymes are dubbed “perfect catalysts” because they have a high turnover of up to 106 reactions per second. Such enzymes include carbonic anhydrase (CA), superoxide dismutase (SOD), and triose phosphate isomerase (TPI).

These examples are more the exception and not the rule among enzymes. The value of this parameter for the RubisCO enzyme is 1–10 s-1 (between 1 and 10 reactions per second). The turnover number for 60% of the enzymes in the BRENDA (The Comprehensive Enzyme Information System) database10 is between 1–100 s-1 (1 and 100 per second) (see figure 3).11

Another parameter which characterizes enzyme kinetics is the so-called Michaelis constant (Km), which describes the concentration of the substrate at which the enzyme reaction happens at half of its maximum speed. The lower this concentration, the faster the enzyme can process its substrate. According to data from the BRENDA database, the median Km value for enzymes is 130 μM.12 Compared to other molecules, the Km value of carbon dioxide is less than 10 μM for most variants of the RubisCO enzyme. In this respect RubisCO is actually a rather efficient enzyme!

Conclusion

The presence of RubisCO in so many species speaks against its evolutionary origin. Evolution means change, not stasis. If this enzyme stayed the same over millions of years, it resists change, and not vice-versa.13 RubisCO is found everywhere in nature, from cyanobacteria (a group of photosynthetic bacteria) to algae and higher plants.14 It is also the most abundant protein in the world and makes up 25–30% of the protein mass of leaves. If evolution is true, then one of two things is true. Either RubisCO would have had vast amounts of time to be streamlined and made more efficient. Or, during this time RubisCO should have been eliminated by natural selection. The fact that it still exists yet didn’t become more ‘efficient’ (according to evolutionists) speaks against evolution.

Based on these evidences, the argument that RubisCO is a slow and leaky enzyme, and therefore a case of bad design does not hold up under scrutiny. Many enzymes are promiscuous, a well-known fact of biochemistry. In fact, as opposed to a random evolutionary leftover, the promiscuity of RubisCO is an intentional design element to protect plants from toxic excess oxygen produced during photosynthesis. RubisCO is also not that slow compared to thousands of other enzymes. This enzyme does its work rather efficiently in building up sugars from its substrates. God designed the RubisCO enzyme to get its job done, and it does so effectively.

References and notes

  1. An enzyme is a protein which performs a function within the cell, e.g. it transforms one type of molecule into another type. Return to text.
  2. An enzyme’s substrate is the molecule that it reacts with, its reaction partner. Return to text.
  3. Anoxic means that there is no oxygen in the environment. Return to text.
  4. The pressure exerted by one gas in a mixture of gases (e.g. oxygen in air) if it occupied a space by itself, without the other component gases. Return to text.
  5. Atkins, W.M., Biological messiness vs. biological genius: Mechanistic aspects and roles of protein promiscuity. J Steroid Biochem Mol Biol. 151:3–11, 2015; DOI:10.1016/j.jsbmb.2014.09.010. Return to text.
  6. Tcherkez, G., The mechanism of Rubisco-catalysed oxygenation, Plant, Cell & Environment 39(5):983–97, 2016; DOI:10.1111/pce.12629. Return to text.
  7. Parry, M.A., et al., Manipulation of Rubisco: the amount, activity, function and regulation, Journal of Experimental Botany 54(386):1321–33, 2003; DOI:10.1093/jxb/erg141. Return to text.
  8. This is a two-carbon acid with a phosphate group. Return to text.
  9. Matsubara, S., Schneider, T., and Maurino, V.G., Dissecting Long-Term Adjustments of Photoprotective and Photo-Oxidative Stress Acclimation Occurring in Dynamic Light Environments, Frontiers of Plant Science 7:1690, 2016; DOI: 10.3389/fpls.2016.01690. Return to text.
  10. Jeske, L., et al. BRENDA in 2019: a European ELIXIR core data resource. Nucleic Acids Res. 47(D1):D542-D549, 2019; DOI:10.1093/nar/gky1048. Return to text.
  11. Bathellier, C., et al., Rubisco isn’t really so bad, Plant, Cell & Environment 41(4):705–716, 2018. Return to text.
  12. Here μM stands for micromole, that is, one millionth of a mole (designated by the Greek letter μ). A mole is a quantity which corresponds to 6.022 x 1023 molecules. Return to text.
  13. Cserhati, M., Creation aspects of conserved noncoding sequences, J Creation 21(2):101–108, 2007. Return to text.
  14. Ślesak, I., et al., RubisCO Early Oxygenase Activity: A Kinetic and Evolutionary Perspective. Bioessays 39(11), 2017; DOI:10.1002/bies.201700071. Return to text.

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Readers’ comments

Alf F.
What a pleasure it is for us laymen to have quality Bible-believing scientists over at CMI. Please increase your specialist staff wherever possible, and keep up the great standards and life-saving work. I cannot always afford to subscribe for the year, but I can share links and articles like this which educate with such clarity, and despite the unfavourable exchange rate from South Africa I shall certainly be making a donation this time round. It is a small price, considering that the Theory of Evolution is the biggest single cause of unbelief and apostasy on earth today.
Doug L.
This is a good case in point of the type of arguments we have to deal with. Suppose knowledge of these details of RubisCO were not yet known and you are a student in a university classroom. You couldn't give a good answer like Dr. Cserhati did. What does a Christian do in that case? This is a general shortcoming, IMO, in Christian education both in our Sunday Schools and in our Christian schools. There are countless arguments like this from evolutionists. The one thing they have in common is that they're based on incomplete knowledge, unjustified assumptions, and an anti-Christian spin or viewpoint. But the unjustified assumptions and the spin are put out there as if they were so "obvious" that they don't need to be justified. I'd really like to see some kind of curriculum for high school level kids to prepare them for what they'll face in a university. It should focus on questions on these which we CAN answer and on questions like these which we CANNOT answer, at least at this time. We can't answer every argument the world will throw at our kids. They've had 150 years of building up this mountain of arguments. But if we firmly educate our kids on questions like these then they'll realize that they don't have to be able to answer everything and their faith won't be shaken when someone challenges them with these questions.This should be a critical aspect of Christian education.
Joel E.
What a great read, thank you! One of the main arguments is that the plant compensates for rubisCO's slow speed by making more of it. But if rubisCO has typical speed for an enzyme, why aren't the other "slow" enzymes produced in large amounts? Why wouldn't the amount of the enzyme produced be correlated with its relative speed?
Matthew Cserhati
Hello Joel,
No, RubisCO has a typical speed for an enzyme. The reason it is present in such great quantities is because of the important role it plays in photosynthesis. "Slow" enzymes might not be produced in greater quantities because they might not play such an important role in the cell.
Paul C.
Because Rubisco works slowly, plants produce an abundance of the enzyme. This is to the advantage of all plant-eating species including humans. Not only does it make plants a better source of proteins for our diet, but the rubisco has also been found to effectively enhance our immune systems, helping us to avoid getting sick as often. See Nishi, 2011, Biosci, Biotechnol, Biochem. So, it seems that God knew what he was doing in making rubisco slow and putting lots of it in plants. It's really a gift to humanity.
Nicholas K.
Quite a detailed, technical read, but l found the Conclusion gave a very good argument which can be used in Creation apologistics; ie. If there were vast amounts of time (required in evolution) then something supposedly 'inefficient' would be streamlined and made more 'efficient'; or else it would be eliminated by natural selection. This is a very good point that can be used to refute supposed 'poor' design arguments/proof for random evolution.
Mike T.
When I read about the incredible complexity and intricate interconnectedness and interdependence of ... molecules! Operating as apparently self-motivated machines, performing with such amazing efficiency and proficiency - not just one or two components, but multiple components - and enzymes! Where did they come from, and what happened before they arrived on the cellular scene?! - I fall down before the Creator who thought this and planned this and spoke it into existence - and it worked! And I thank Him for opening my blinded eyes to see and believe.

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