Unintelligent Design - RuBisCO Is Slowly Evolving - And Becoming Even More Embarrassing For Any Creationist Who Understands It

Photo by Kumiko SHIMIZU on Unsplash

The world’s most prolific CO₂-fixing enzyme is slowly getting better | University of Oxford

The world’s worst enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase, or RuBisCo as it is known, has featured in these blog posts several times and it described in my book, The Unintelligent Designer: Refuting the Intelligent Design Hoax as an example of the lack of intelligence in biological systems, and, as such, why it would be a major embarrassment to creationists - if they understood it.

Briefly, RuBisCo is one of the most ancient enzymes known and became an essential component of photosynthesis early on in the history of life on Earth when the first cyanobacteria evolved the ability to use the energy from sunlight to fix the carbon in atmospheric carbon dioxide (CO₂) to build the sugar glucose. Eventually, these photosynthesising cyanobacteria became incorporated into plant cells as the chloroplasts to produce the green plants at the base of most food chains. Because it is so inefficient, it quickly became probably the most abundant enzyme on Earth, making up with quantity what it lacked in quality.

But, evolution, unlike good intelligent design, is a one-way, utilitarian process in which whatever works better than preceded it will be retained and will provide the next basis for further evolution, because evolution has no mechanism to scrap a bad design and start again as any backward step will inevitably be worse, so will be quickly eliminated.

Tell me all about RuBisCo and why it's so inefficient. RuBisCo, or ribulose-1,5-bisphosphate carboxylase/oxygenase, is an enzyme crucial for the process of carbon fixation in plants, algae, and some bacteria. It catalyzes the first major step of the Calvin cycle, which is the primary pathway for carbon dioxide fixation in photosynthesis. Despite its importance, RuBisCo is often considered inefficient for several reasons:

1. Substrate specificity: RuBisCo can react with both carbon dioxide (CO₂) and oxygen (O₂). This property is known as oxygenase activity, and it results in the wasteful process of photorespiration. When RuBisCo combines with oxygen instead of carbon dioxide, it produces a molecule that cannot be used in further carbon fixation. This results in a loss of fixed carbon and energy for the plant.
2. Low catalytic efficiency: Compared to other enzymes, RuBisCo has a relatively slow catalytic rate. This means it can process only a limited number of substrate molecules per unit of time, which can limit the overall rate of carbon fixation in plants.
3. RuBisCo activation: RuBisCo requires the presence of a specific activator molecule, ribulose-1,5-bisphosphate (RuBP), to function effectively. However, the activation process is slow and inefficient, leading to a significant portion of RuBisCo molecules being inactive at any given time.
4. Photorespiration: As mentioned earlier, RuBisCo's oxygenase activity leads to the production of a compound that undergoes a series of reactions known as photorespiration. This process consumes energy and reduces the efficiency of carbon fixation by competing with the Calvin cycle.
5. Evolutionary history: RuBisCo is thought to be one of the oldest enzymes, dating back billions of years. Its structure and catalytic properties may have evolved at a time when atmospheric conditions were different, with higher carbon dioxide concentrations and lower oxygen levels. As a result, RuBisCo's efficiency in current atmospheric conditions (with relatively low CO₂ and high O₂ levels) may be compromised.

Despite its inefficiencies, RuBisCo remains essential for photosynthesis and the overall productivity of plant ecosystems. Efforts to improve its efficiency through genetic engineering and synthetic biology are ongoing, with the goal of enhancing crop yields and mitigating the effects of climate change.

How does the efficiency of RuBisCo compare to that of other enzymes in terms of reactions catalysed per second?

In terms of reactions catalyzed per second, RuBisCo typically has a lower turnover number compared to many other enzymes. Turnover number, also known as kcat, represents the number of substrate molecules converted to product per unit time by a single enzyme molecule.

For RuBisCo, its turnover number is relatively low, typically in the order of 1-10 reactions per second. This is due to its relatively slow catalytic rate compared to many other enzymes. In contrast, some enzymes can have turnover numbers in the range of hundreds to thousands of reactions per second.

The low turnover number of RuBisCo contributes to its inefficiency in carbon fixation, as it limits the rate at which carbon dioxide can be converted into organic molecules during photosynthesis. This inefficiency is one of the reasons why RuBisCo is often targeted for improvement in efforts to enhance plant productivity and address challenges such as climate change.

But, according to a new study by three biologists in the Department of Biology, Oxford University, RuBisCo is not stuck in an evolutionary rut, unable to change without becoming even worse at all. It has been evolving, albeit almost imperceptibly slowly over time at least in the angiosperms, as a rate of about 1 nucleotide substitution every 900,000 years on average, compared to say, the SARS-CoV-2 virus that causes COVID-19, which has evolved at about 1 nucleotide substitution every two weeks! This amounts to one amino acid substitution every 2.7 million years

Incredibly slow though this rate of evolution of RuBisCo is (and that slow rate can be added to the list of reasons it is so inefficient) this is not good news for creationists. It means that not only have they to explain why their putative intelligent designer created such an inefficient enzyme in the first place but why it is now correcting its mistake so slowly. A super-intelligent, omniscient designer would not have made a mistake in the first place and would not now be correcting that mistake at a snail's pace.

The Oxford scientists who made this discovery have published their work, open access, in the journal PNAS and describe it in a news item from the University of Oxford:

New research led by the University of Oxford has found that rubisco – the enzyme that fuels all life on Earth – is not stuck in an evolutionary rut after all. The largest analysis of rubisco ever has found that it is improving all the time – just very, very slowly. These insights could potentially open up new routes to strengthen food security. The results have been published today in Proceedings of the National Academy of Sciences [PNAS].

The most abundant enzyme on Earth, rubisco, has been providing the energy which fuels life on our planet for the last three billion years. While rubisco fixes billions of tons of CO₂ each year, the enzyme is notoriously inefficient. This has created a biological paradox that has puzzled researchers for decades. Why is the enzyme that has been fuelling life for over 3 billion years not much better at doing its job? Many plant scientists have debated whether the enzyme is stuck in an 'evolutionary rut', making it impossible for it to get any better.

But new research from the University of Oxford has revealed that rubisco is continually improving, but that this improvement is occurring at a glacial pace.

Our research demonstrates for the first time that evolution is consistently improving rubisco and that further improvement of the enzyme is possible. Importantly, this insight provides renewed optimism for efforts to engineer the enzyme to help feed the world.

Jacques Bouvier, lead author
Department of Biology,
University of Oxford, Oxford, UK.

The researchers analysed rubisco gene sequences from across a wide range of photosynthetic organisms and quantified the rate of rubisco evolution for the first time. They found that its sequence has altered in minute increments of just one DNA base change every 900,000 years – a stark contrast from the COVID-19 genome, for example, which is evolving one base change every two weeks. This puts rubisco in the 1% of slowest evolving genes on Earth.

Despite this slow rate of change, the researchers found that the enzyme is harnessing this evolution to get better at fixing CO₂. The authors also found that this slowly improving CO₂ fixation is resulting in improvements to photosynthesis; plants are evolving to get better at turning CO₂ into sugar, but the rate of improvement is so slow that it appears frozen.

For decades scientists have aspired to engineer an improved rubisco to boost growth and yields of crop plants. But despite much effort, success has been limited, and many have wondered whether rubisco is already optimised, making these attempts futile. However, the insights from this study offer renewed hope. In particular, unravelling the mystery of what is holding back rubisco’s rate of evolution may uncover new ways of enhancing crop yields.

Because rubisco assimilates the sugars which fuel life on Earth, improving this enzyme is one of the most promising avenues to help combat food insecurity. There has been heated debate as to whether there is scope to improve the enzyme; our new research provides a clear answer to this question. If evolution can improve rubisco, so can we!

Jacques Bouvier.

We have shown that rubisco is not frozen in time but is instead continually evolving to get better. We now need to understand the factors that are holding rubisco back to enable us to realise its true potential.

Professor Steven Kelly, senior author
Department of Biology
University of Oxford, Oxford, UK

This new insight offers encouragement to efforts which aim to increase yields in food, fibre, and fuel crops by targeting rubisco engineering. Improving rubisco could be key to supporting the food needs of a growing global population.

Significance

Rubisco is the most abundant enzyme on Earth and is the source of almost all biological carbon. Here we uncover the trajectory of rubisco adaptive evolution in plants. We reveal that rubisco has experienced continuous directional selection toward higher carbon dioxide/oxygen specificity, carboxylase turnover, and carboxylation efficiency. Moreover, we find that this directional selection toward improved catalytic efficiency has resulted in a corresponding improvement in leaf-level CO₂ assimilation. Together, these findings have significant implications for our understanding of the past, present, and future of rubisco evolution.

Abstract

Rubisco is the primary entry point for carbon into the biosphere. However, rubisco is widely regarded as inefficient leading many to question whether the enzyme can adapt to become a better catalyst. Through a phylogenetic investigation of the molecular and kinetic evolution of Form I rubisco we uncover the evolutionary trajectory of rubisco kinetic evolution in angiosperms. We show that rbcL is among the 1% of slowest-evolving genes and enzymes on Earth, accumulating one nucleotide substitution every 0.9 My and one amino acid mutation every 7.2 My. Despite this, rubisco catalysis has been continually evolving toward improved CO₂/O₂ specificity, carboxylase turnover, and carboxylation efficiency. Consistent with this kinetic adaptation, increased rubisco evolution has led to a concomitant improvement in leaf-level CO₂ assimilation. Thus, rubisco has been slowly but continually evolving toward improved catalytic efficiency and CO₂ assimilation in plants.

Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) converts atmospheric CO₂ into the sugars that fuel the majority of life on Earth. The enzyme evolved ~3 billion years ago when the atmosphere contained high levels of CO₂ (≥10,000% present atmospheric levels) and comparatively little O₂ (≤0.1% present atmospheric levels) (Fig. 1) (1–7). Since emergence, the enzyme has helped guide the atmosphere on a trajectory of increasing O₂ and declining CO₂ (1, 8) such that current concentrations of CO₂ (0.04%) and O₂ (20.95%) are inverted compared to when the enzyme first evolved (Fig. 1).

Fig. 1.

The evolutionary history of rubisco in the context of atmospheric CO₂ (%) and O₂ (%) following divergence from the ancestral rubisco-like protein (RLP). Important branch points in the phylogeny at which rubisco diverged into different evolutionary lineages are indicated by gray vertical bars. To provide additional context, the time-period at which the First and Second Great Oxidation events occurred along this evolutionary trajectory are also labeled and referenced as gray vertical bars. Graphics of atmospheric CO₂ and O₂ levels were adapted from the TimeTree resource [http://www.timetree.org; (9)].

Although all extant rubisco are descended from a single ancestral rubisco-like protein (10–12), the enzyme is found in a variety of compositional forms across the tree of life (Fig. 1) (13, 14). The simplest manifestations are the Form II and Form III variants found in protists, archaea, and some bacteria which are composed of a dimer, or dimers, of the ~50 kDa rubisco large subunit (RbcL) (14–17). In contrast, Form I rubisco is a hexadecamer comprised of four RbcL dimers organized in an antiparallel core capped at either end by the ~15 kDa rubisco small subunit (RbcS) (14, 18). Of these three Forms, only Form I and II have been recruited for oxygenic photosynthesis (17), with Form I being responsible for the vast majority of global CO₂ assimilation (17, 19).

Within Form I rubisco the active site is located in RbcL (16, 20, 21). As a result, interspecific differences in Form I kinetics are primarily attributable to sequence variation in RbcL (22–33). Despite not playing a direct role in catalysis, RbcS influences the function of rubisco (34, 35) and its incorporation in the holoenzyme enables its higher kinetic efficiency (36). Specifically, RbcS enhances the stability and assembly of the holoenzyme complex (21, 37–42), improves the efficiency of CO₂ binding (43), and is thought to act as a reservoir for CO₂ accumulation (44). Accordingly, rubisco function is altered when RbcS is mutated (45–47), or when chimeric holoenzymes are created in vivo (48–52) and in vitro (53–58). Moreover, there is increasing recognition of the importance of both environment (59) and organ-specific (60, 61) differences in plant RbcS isoform expression on holoenzyme catalysis. However, even though RbcS influences holoenzyme function, sequence variation in RbcL remains the primary determinant of variation in kinetics (22–33).

Although there is kinetic variability between rubisco orthologs, the enzyme is considered to be an inefficient catalyst. For example, the maximum substrate-saturated turnover rate of Form I rubisco (<12 s⁻¹) (62) is slower than average (63). In addition, rubisco catalyzes a reaction with O₂ (64–66) that is competitive with CO₂ and results in the loss of fixed carbon via photorespiration (67–69). As a consequence, rubisco appears poorly suited to the current O₂-rich/CO₂-poor atmosphere (Fig. 1). Moreover, it appears that instead of improving enzyme function, multiple lineages have evolved alternative strategies to overcome rubisco’s shortcomings. For example, higher rates of CO₂ assimilation are often achieved either by synthesizing large quantities of rubisco [~50% of soluble protein in plants (70) and some microbes (71, 72)], or by operating CO₂-concentrating mechanisms (73–75). As a result, many have questioned whether the enzyme is already perfectly adapted and whether further kinetic improvements are possible (16, 65, 69, 76–80). Obtaining answers to these questions would shed light on the “rubisco paradox”—helping to explain why this enzyme of such paramount importance appears poorly adapted for its role.

The initial hypothesis that attempted to explain the above rubisco paradox proposed that rubisco is constrained by catalytic trade-offs that limit the enzyme’s adaptation. This theory was pioneered by two studies (81, 82) which found antagonistic correlations between rubisco kinetic traits and proposed that these trade-offs were caused by constraints on its catalytic mechanism. However, recent evidence has questioned this hypothesis as the sole mechanism to explain the rubisco paradox. Specifically, analysis of larger species sets have revealed that kinetic trait correlations are not strong (83–85). In addition, phylogenetic signal in rubisco kinetics causes kinetic trait correlations to be overestimated unless phylogenetic comparative methods are employed (22, 23). Thus, when larger datasets are analyzed with phylogenetic methods, the strength of catalytic trade-offs are substantially reduced (22, 23). Instead, phylogenetic constraints have had a larger impact on limiting enzyme adaptation compared to catalytic trade-offs (22, 23). These recent findings motivate a revaluation of the rubisco paradox, and an investigation of whether rubisco is evolving for improved catalysis and CO₂ assimilation in plants.

Here, we address these issues through a phylogenetic interrogation of the molecular and kinetic evolution of the Form I holoenzyme. We reveal that RbcL has evolved at a slower rate than >98% of all other gene/protein sequences across the tree of life. Through simultaneous evaluation of molecular and kinetic evolution of rubisco during the radiation of C₃ angiosperms, we reveal that the enzyme has been continually evolving toward improved CO₂/O₂ specificity, carboxylase turnover rate, and carboxylation efficiency. Furthermore, we demonstrate that enhanced rubisco evolution is associated with increased rates of CO₂ assimilation and higher photosynthetic nitrogen-use efficiencies. Thus, rubisco is not perfectly adapted, but is slowly evolving toward improved catalytic efficiency and CO₂ assimilation.

There is a great deal for creationists to devise strategies for ignoring here:

Firstly, there is the embarrassment of RuBisCo itself which provides such compelling evidence for a mindless utilitarian evolutionary process which is predicted to produce suboptimal, near-enough-is-good-enough processes that then become fixed in the phylogenic tree, and against any involvement of intelligence, let alone omniscient, omnipotent intelligence, in the design, because such designs would be perfect examples of maximal efficiency combined with minimal complexity.

Secondly, there is the evidence that, slow though it is, RuBisCo has changed over time to gradually improved efficiency, albeit more slowly than 98% of other examples of evolving biological systems and many orders of magnitude more slowly than, for example, viruses. At first sight this might not appear to be a problem for creationism, except that changing to become more efficient means the original was sub-optimal as are the current versions, which are still evolving. An intelligent designer, even if it had realised its original design was less than perfect, would have produced a new, improved version is a single step, not at the painfully slow rate of 1 nucleotide substitution per 900,000 years.

Lastly, there is the evidence from this paper that the scientists have no doubt that the changes are an evolutionary change, and that the reason for RuBisCo's legendary inefficiency was due to a mindless evolutionary process, and that RuBisCo is an evolved and evolving enzyme, with no hint that supernatural intervention was involved at any point.

From being a major embarrassment for those creationists who understand it, RuBisCo has just become an even bigger embarrassment for creationism.

---

The Unintelligent Designer: Refuting The Intelligent Design Hoax

ID is not a problem for science; rather science is a problem for ID. This book shows why. It exposes the fallacy of Intelligent Design by showing that, when examined in detail, biological systems are anything but intelligently designed. They show no signs of a plan and are quite ludicrously complex for whatever can be described as a purpose. The Intelligent Design movement relies on almost total ignorance of biological science and seemingly limitless credulity in its target marks. Its only real appeal appears to be to those who find science too difficult or too much trouble to learn yet want their opinions to be regarded as at least as important as those of scientists and experts in their fields.

Available in Hardcover, Paperback or ebook for Kindle

The Malevolent Designer: Why Nature's God is Not Good

This book presents the reader with multiple examples of why, even if we accept Creationism's putative intelligent designer, any such entity can only be regarded as malevolent, designing ever-more ingenious ways to make life difficult for living things, including humans, for no other reason than the sheer pleasure of doing so. This putative creator has also given other creatures much better things like immune systems, eyesight and ability to regenerate limbs that it could have given to all its creation, including humans, but chose not to. This book will leave creationists with the dilemma of explaining why evolution by natural selection is the only plausible explanation for so many nasty little parasites that doesn't leave their creator looking like an ingenious, sadistic, misanthropic, malevolence finding ever more ways to increase pain and suffering in the world, and not the omnibenevolent, maximally good god that Creationists of all Abrahamic religions believe created everything. As with a previous book by this author, "The Unintelligent Designer: Refuting the Intelligent Design Hoax", this book comprehensively refutes any notion of intelligent design by anything resembling a loving, intelligent and maximally good god. Such evil could not exist in a universe created by such a god. Evil exists, therefore a maximally good, all-knowing, all-loving god does not.

Illustrated by Catherine Webber-Hounslow.

Available in Hardcover, Paperback or ebook for Kindle

Advertisement

Thank you for sharing!

Tweet Link