Wageningen researchers have discovered that a vital plant protein originated more than 600 million years ago, long before the first plants existed. They traced its origins back to an evolutionary event in a distant unicellular ancestor, during which genetic material was reshuffled. This process gave rise to the Auxin Response Factor (ARF), a protein that continues to play a key role in the growth and development of plants and trees today. The researchers published their findings in the scientific journal Nature Communications.
Place a plant on a windowsill, and it slowly grows towards the light coming through the window. Even without eyes, the plant can "see" where the light is coming from. Underground, roots search for water and grow in its direction. This directed growth, along with many other plant growth processes, is controlled by the plant hormone auxin. The ARF protein responds to this hormone, activating or deactivating genes in the plant to regulate growth processes. Post-doctoral researcher Jorge Hernández-García investigated how such a sophisticated, coordinated system could have evolved. "At some point in evolution, plant cells must have developed a way to recognise and respond to plant hormones," he explained.
A human protein in plants
The researcher found clues to the origins of the ARF protein to the green alga Chlorokybus melkonianii, an distant cousin of the plants we find on land. His research revealed that this protein emerged from the fusion of two protein fragments: a chromatin factor and a transcription factor. Neither of these fragments originally had anything to do with the plant hormone auxin. "This fusion created an entirely new protein that took on a central role in the auxin signaling pathway," says Dolf Weijers, Professor of Biochemistry. The chromatin factor enables ARF proteins to collaborate, while the transcription factor allows the protein to bind to DNA and regulate gene activity.
Interestingly, the chromatin factor found in the crucial plant protein is not exclusive to plants. It also occurs in humans, animals, and fungi. Although biologists have studied the ARF protein for over twenty years, they had overlooked this connection until now. Therefore the post-doctoral researcher was cautious when presenting his findings to Weijers. "When you come across such an extraordinary result, your first thought is that it must be wrong. But we kept getting the same results, so it had to be correct," Hernández-García says. While the exact role of the chromatin factor in humans and animals remains unclear, it must have developed a new function within the ARF protein.
Over time, the evolution of ARF led to two classes of the protein: one that activates genes in the presence of auxin and another that suppresses genes. "This competitive interaction is essential for the fine-tuned regulation of plant growth," Hernández-García explains. The research also revealed that some features of ARF, such as its ability to bind DNA, were present from the very beginning, while others, like gene activation, developed later in evolution.
New data, ancient genes
The scientists were able to reconstruct the origins and evolution of the ARF protein thanks to newly available genomic data. "Over the past decade, it has become clear that we can better study the core traits of plants in those that have been around a bit longer in their current shape," says Weijers. He refers to mosses, ferns, and even their aquatic ancestors: unicellular green algae. These distant cousins of land plants share cellular processes and genetic material with modern plants but are easier to study. In recent years, scientists have sequenced the DNA of an increasing number of plants and their cousins, such as green algae. By studying these genomes, biologists can gain a deeper understanding of plant processes and genes. "I believe the genomic data from green algae holds many more answers to fundamental questions about plant biology," Weijers concludes.
