Rosa Rubicondior: Refuting Creationism - The Evolution of Complexity

Stomata on a leaf surface.

How plants evolved a molecular switch to cope with heat

Creationists routinely portray complex biochemical pathways as systems that must have been designed as complete working units. Remove one component, they argue, and the system ceases to function; therefore, by the presuppositional false dichotomy that characterises creationism, all the components must have been assembled simultaneously by an intelligent designer.

Evolution does not work by assembling entirely new systems from nothing, however. It modifies what is already present. Existing proteins acquire new interactions, mutations alter their stability or activity, and old signalling pathways are recruited for additional purposes. A comparatively small change can connect existing components and produce a new, environmentally responsive function.

An elegant example has now been described by Shao-Li Yang and colleagues from VIB, Ghent University, KU Leuven and collaborating institutions. Their study, published in Nature Plants, identifies a molecular pathway that helps Arabidopsis thaliana cool its leaves during heat stress. It also shows how evolution produced the regulatory switch by altering the electrical charge at a particular position in an existing protein.

Plants cannot escape into the shade when conditions become dangerously hot. One of their principal cooling mechanisms is transpiration: stomata—microscopic pores in the leaf surface—open, allowing water to evaporate and remove heat. This resembles sweating in animals, although excessive stomatal opening also risks dehydration. Plants must therefore regulate the process rather than simply leave their stomata permanently open.

The newly discovered pathway centres on UBP24, a protein belonging to a family of enzymes known as deubiquitylases. Ubiquitin molecules attached to a protein can help to determine its location, activity or destruction; deubiquitylases remove those molecular tags. Under high-temperature conditions, B4 RAF kinases activate another kinase, OPEN STOMATA 1, or OST1. OST1 then attaches a phosphate group to the amino acid serine at position 360 in UBP24.

That phosphate group introduces a negative electrical charge which stabilises UBP24. The stabilised enzyme removes ubiquitin from AHA1, a proton pump in the guard-cell plasma membrane, helping to prevent its internalisation and degradation. With AHA1 retained at the membrane, the machinery that opens the stomata remains active, allowing greater evaporation and cooling.

The researchers tested the importance of the single amino-acid position experimentally. A version of UBP24 in which serine 360 was replaced with alanine, which cannot be phosphorylated, failed to restore heat-induced stomatal opening in plants lacking functional UBP24. Replacing it with negatively charged aspartic acid, which mimics the charge produced by phosphorylation, restored the response. The important feature was therefore not some mysterious vital essence but a chemically explicable change in molecular charge.

The evolutionary comparison was equally revealing. UBP24-related proteins occur throughout the green-plant lineage, while OST1-like kinases can be traced back to streptophyte algae. The phosphorylatable site at position 360 appears to have arisen later, broadly coinciding with the evolution of actively controlled, water-driven stomatal opening in vascular plants. Evolution did not need to invent all the components together: an amino-acid substitution made an existing protein responsive to an existing kinase, connecting older molecular machinery to a new physiological role.

Yeast illustrates another way in which evolution can exploit the same chemical principle. In the corresponding position of the yeast protein Ubp3, the genome specifies glutamic acid—an amino acid carrying a permanent negative charge. Removing that charge reduced the protein’s stability and impaired yeast growth. Plants evolved a switchable charge, supplied by reversible phosphorylation, whereas yeast retained a fixed negatively charged amino acid. Different evolutionary histories arrived at variations on the same useful piece of chemistry.

Nothing in this process required foresight, a plan or the simultaneous creation of a complete pathway. Mutations produced variations in protein sequence; some altered charge, stability and interactions; and natural selection retained combinations that improved survival under particular conditions. What now looks like an integrated molecular cooling system is precisely what evolutionary theory predicts: old components modified, co-opted and connected by a succession of small, heritable changes.

How Evolution Turned Molecular Charge into a Switch. Proteins are not simply static building blocks. Their shape, stability, location and interactions can change when cells attach or remove small chemical groups. One of the most important of these modifications is phosphorylation, in which an enzyme attaches a phosphate group to a particular amino acid in a protein.

A phosphate group introduces negative electrical charge. This can alter the way different parts of the protein interact, change its three-dimensional shape or affect how readily other molecules bind to it. Because another enzyme can remove the phosphate, phosphorylation provides cells with a reversible molecular switch.

In Arabidopsis thaliana, heat activates B4 RAF kinases, which activate the kinase OST1. OST1 then phosphorylates the amino acid serine at position 360 in UBP24. The resulting negative charge stabilises UBP24 and allows more of it to remain available for use.

UBP24 is a deubiquitylase: an enzyme that removes ubiquitin from other proteins. One of its targets is AHA1, a proton pump in the guard-cell membrane. Ubiquitylation can encourage AHA1 to be removed from the membrane and degraded. By removing ubiquitin, stabilised UBP24 helps to retain AHA1 at the membrane, where it contributes to stomatal opening and evaporative cooling.

One position, two ways of supplying charge

Serine normally carries no electrical charge, but it can be phosphorylated. It therefore provides a switchable negative charge that can be added or removed according to conditions.

Aspartic acid and glutamic acid, by contrast, ordinarily carry a negative charge under cellular conditions. If either occupies the corresponding position, the protein has a more permanent, genetically encoded negative charge and does not require phosphorylation there.

The researchers exploited this distinction experimentally. Replacing UBP24’s serine with alanine—which cannot be phosphorylated—prevented the protein from restoring normal heat-induced stomatal opening. Replacing it with negatively charged aspartic acid produced a phosphomimetic form that restored the response.

A related yeast protein, Ubp3, naturally contains glutamic acid at the corresponding position. When the researchers replaced it with uncharged alanine, the protein became less stable and yeast growth was impaired. Plants and yeast therefore use variations of the same chemical principle: protein function regulated by negative charge.

This illustrates how small evolutionary changes can have significant biological consequences. Mutations that replace one amino acid, create or remove a phosphorylation site, or alter the recognition sequence used by a kinase can change when and how an existing protein functions. In vascular plants, a phosphorylatable site connected existing proteins to an environmentally responsive pathway. No entirely new biochemical system had to appear at once; evolution modified and reconnected components that were already present.

Glossary

Kinase

An enzyme that transfers a phosphate group, usually from ATP, to another molecule such as a protein.

Phosphorylation

The attachment of a phosphate group to a molecule. In proteins, this can change electrical charge, shape, stability, activity or interactions with other proteins.

Phosphosite

A particular amino-acid position in a protein at which phosphorylation can occur. Serine, threonine and tyrosine are common phosphosites.

Ubiquitin

A small protein that can be attached to another protein. Depending on how it is attached, ubiquitin can affect that protein’s activity, location, internalisation or degradation.

Ubiquitylation

The cellular process by which one or more ubiquitin molecules are attached to a protein.

Deubiquitylation

The removal of ubiquitin from a protein by an enzyme known as a deubiquitylase. UBP24 is one such enzyme.

Phosphomimetic

An experimentally introduced amino-acid substitution—usually aspartic or glutamic acid—that imitates some effects of phosphorylation by supplying a negative charge. It approximates rather than reproduces every property of an attached phosphate group.

Based on: Yang et al., “Evolutionary tuning of the molecular charge state of UBP24 shapes responses to high temperature”, Nature Plants (2026); and the VIB research release.

The research paper in Nature Plants was accompanied by the a VIB press release:

How plants evolved a molecular switch to cope with heat
Ghent, 26 August – As climate change drives more frequent and intense heat waves, plants face growing challenges to survive and remain productive. Researchers at VIB, Ghent University, KU Leuven, and their international collaborators have now uncovered an evolutionary innovation that helps plants cope with high temperatures. Published in Nature Plants, the study uncovers a molecular mechanism that helps plants stay cool under heat stress and could help researchers identify new ways to strengthen crop resilience.
In short:

Researchers led by Prof. Ive De Smet (VIB-UGent) discovered a molecular mechanism that helps plants stay cool during heat stress by keeping their natural cooling system active.
The study, published in Nature Plants, identifies the protein UBP24 as a key regulator that helps leaf pores (stomata) remain open, allowing plants to cool themselves through evaporation.
The mechanism appears to be an evolutionary innovation that emerged alongside actively controlled stomata, helping plants better adapt to rising temperatures.
The findings provide new insights into plant heat resilience and could support future efforts to develop crops better equipped for climate change and more frequent heat waves.

Keeping cool when temperatures rise

Unlike animals, plants cannot move to a cooler location when temperatures soar. Instead, they rely on built-in mechanisms to avoid overheating.

One of the most important cooling mechanisms involves tiny pores on the leaf surface called stomata. When temperatures increase, these pores can open, allowing water to evaporate and cool the leaf, much like how sweating cools the human body. Scientists have long known that stomata help plants cope with heat, but many of the underlying molecular processes remained poorly understood.

Led by Prof. Ive De Smet (VIB-UGent Center for Plant Systems Biology), the researchers – including the teams of Prof. Kevin Verstrepen (VIB-KU Leuven Center for Microbiology) and Prof. Kris Gevaert (VIB-UGent Center for Medical Biotechnology) - discovered a previously unknown pathway that helps stomata open during heat stress. Central to this mechanism is a protein called UBP24. High temperatures trigger a modification that stabilizes UBP24. This change stabilizes other proteins that keep stomata open and maintain the plant’s natural cooling system.

Towards more resilient crops

Understanding how plants respond to heat is becoming increasingly important as temperatures continue to rise worldwide. The newly discovered mechanism helps explain how plants keep their leaves cool under hot conditions. While the research is fundamental in nature, it provides new insight into the biological processes that support heat resilience in plants and could eventually inform efforts to develop more climate-resilient crops.

As heat waves become more frequent and intense, understanding how plants naturally cope with high temperatures is more important than ever. By uncovering one of the mechanisms plants use to regulate their cooling system, we gain new insights into the biological processes that help plants remain resilient under heat stress.

Professor Ive De Smet, senior author.
.Department of Plant Biotechnology and Bioinformatics
Ghent University
Ghent, Belgium.

An evolutionary innovation

By comparing UBP24 across dozens of plant species, the researchers discovered that a molecular switch enabling the protein to respond to heat appeared in vascular plants around the same time that actively controlled stomatal opening and closing evolved. This seemingly small change gave plants a new way to fine-tune their response to heat.

Surprisingly, the story extends beyond plants. The team found that a related protein in yeast relies on a similar principle to function under heat stress, despite hundreds of millions of years of evolutionary distance between the two organisms.

Finding similar solutions in organisms as different as plants and yeast was particularly exciting. It suggests that this is a remarkably ancient and effective way for cells to deal with heat.

Shao-Li Yang, first author.
.Department of Plant Biotechnology and Bioinformatics
Ghent University
Ghent, Belgium.

As climate change increases the frequency and intensity of heat waves, understanding how plants naturally cope with high temperatures is becoming ever more important. By uncovering a molecular switch that helps plants regulate their cooling system, the researchers reveal one of the ways plants have adapted to life in a changing environment. These insights not only deepen our understanding of plant evolution but may also guide future efforts to develop crops that are better prepared for a warming world.

Publication:
Yang, SL., Liu, H., Xu, X. et al. Evolutionary tuning of the molecular charge state of UBP24 shapes responses to high temperature.
Nat. Plants (2026). https://doi.org/10.1038/s41477-026-02345-1

Abstract
Protein evolution is shaped by sequence variation that modulates protein properties—for example, through the gain or loss of post-translational modifications. Among these, reversible phosphorylation alters a protein’s overall electrical charge and enables organisms to dynamically respond to environmental fluctuations. In plants, the hydro-active opening of stomata, microscopic pores that regulate gas exchange and leaf temperature, is governed by phosphorylation-dependent signalling. Here we identify a mechanism involving the deubiquitylase UBIQUITIN-SPECIFIC PROTEASE 24 (UBP24) that promotes stomatal opening in Arabidopsis thaliana under heat. UBP24 is phosphorylated at serine 360 by the kinase OPEN STOMATA 1, which is activated by B4 RAF kinases in response to heat stress. This phosphorylation stabilizes UBP24, enabling the deubiquitylation of a plasma membrane H⁺-ATPase to promote stomatal opening. This reveals a heat-responsive signalling pathway that evolved in vascular plants to regulate stomatal function. Strikingly, a similar evolutionary feature exists in Saccharomyces cerevisiae, where the UBP24 homologue Ubp3 requires a constitutively negatively charged residue at the homologous site to support growth after heat shock. Our findings uncover a conserved molecular mechanism in which negative charge, via phosphorylation or acidic residues, modulates deubiquitylase function, supporting adaptive thermal responses in plants and yeast and highlighting how charge-based regulation promotes cellular resilience under stress.

Yang, SL., Liu, H., Xu, X. et al. Evolutionary tuning of the molecular charge state of UBP24 shapes responses to high temperature.
Nat. Plants (2026). https://doi.org/10.1038/s41477-026-02345-1

© 2026 Springer Nature Ltd.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

This research does more than identify another mechanism by which plants survive high temperatures. It reveals something of the evolutionary history of that mechanism. The proteins involved did not appear together as parts of a newly designed cooling system. They already existed, performing other functions, before mutations altered their interactions and connected them to the regulation of stomata.

A phosphorylatable amino acid at one position in UBP24 allowed an existing kinase to change the protein’s electrical charge. That change stabilised UBP24, which protected an existing proton pump and helped existing guard cells to open existing stomata. What looks superficially like an irreducibly complex system is instead a chain of older components progressively modified and recruited into a new regulatory pathway.

The comparison with yeast reinforces the point. Evolution has exploited the same elementary chemical property in different ways: a permanent negative charge supplied by an acidic amino acid in yeast and a reversible charge supplied by phosphorylation in vascular plants. Natural selection neither understood the chemistry nor anticipated the outcome. It merely preserved heritable variations that improved survival and reproduction under the conditions in which their carriers lived.

Evolutionary theory was not an optional interpretation added after the experiments. It guided the comparison of proteins across species, explained why corresponding amino-acid positions were examined and allowed the researchers to reconstruct how the regulatory system changed through time. It also provides the framework within which these findings might eventually help scientists to develop crops better able to withstand increasingly frequent heatwaves.

Once again, the evidence reveals no sudden act of creation and no foresightful engineer assembling a complete system. It reveals inherited molecular machinery, mutation, co-option and selection—evolution working with whatever history had made available, one small change at a time.

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