In a landmark breakthrough that illuminates the deep evolutionary roots of terrestrial life, researchers from the University of Toronto have identified a protein pivotal to the success of land plants, shedding light on the molecular innovations that allowed green plants to conquer dry land nearly half a billion years ago. This discovery not only unravels a key step in plant evolution but also unlocks new avenues for enhancing photosynthetic efficiency and developing sustainable agricultural technologies.
At the heart of this research lies a protein known as Shikimate kinase-like 1 (SKL1). While the ancestral Shikimate kinase (SK) enzyme participates in the shikimate pathway—a critical metabolic route for producing essential aromatic amino acids—SKL1 diverged from this enzyme and acquired an indispensable new function. The protein SKL1 is exclusively found in land plants, absent from aquatic algae and other organisms, indicating it emerged alongside the first terrestrial plants roughly 500 million years ago. This timing coincides with the monumental transition of plants from aquatic to terrestrial habitats, a process that fundamentally reshaped Earth’s biosphere.
The researchers used state-of-the-art genome sequencing and CRISPR-Cas9 gene editing to dissect the role of SKL1 across diverse plant lineages. Their investigation spanned from liverworts—an ancient group of plants among the earliest colonizers of land—to the well-studied flowering plant Arabidopsis thaliana. Disrupting the SKL1 gene in liverworts led to stunted growth and pale, albino tissues indicative of defective chloroplast formation, mirroring phenotypes observed in flowering plants lacking functional SKL1. Such phenotypic parallels across distantly related plants highlight the protein’s conserved function across more than 500 million years of evolution.
Chloroplasts, the specialized organelles where photosynthesis occurs, are integral to plant energy metabolism. The formation and maintenance of chloroplasts require tightly coordinated genetic and biochemical processes, many of which remain poorly understood. SKL1’s indispensability for chloroplast biogenesis underscores its central role in the development of photosynthetically competent tissues necessary for life on land. The evolutionary novelty of SKL1 appears to hinge on its divergence from the SK enzyme; whereas SK catalyzes a metabolic step in the shikimate pathway, SKL1 has repurposed this molecular scaffold to facilitate essential steps in chloroplast assembly.
One particularly striking aspect of the study involved “rescue” experiments wherein SKL1 from liverworts was introduced into albino mutant Arabidopsis seedlings deficient in their own SKL1. This cross-species complementation restored the green pigmentation and chloroplast development in Arabidopsis, providing compelling evidence that SKL1’s function has been remarkably conserved despite vast evolutionary distances and marked differences in plant morphology.
This discovery holds profound implications not only for evolutionary biology but also for applied plant sciences. The shikimate pathway remains a primary target for many current herbicides, such as glyphosate, but these chemicals have broad-spectrum activity that raises environmental and ecological concerns. The identification of SKL1, with its unique divergence and presence only in land plants, offers a more selective molecular target. Because specific domains of SKL1 vary among plant species, future herbicides might be tailored to selectively inhibit parasitic or weed species without affecting crops or non-target flora, paving the way for more sustainable weed management strategies.
Moreover, enhancing our molecular understanding of chloroplast biogenesis via SKL1 opens exciting possibilities for crop improvement. Photosynthetic efficiency is a limiting factor for crop productivity worldwide. By manipulating SKL1 activity or expression, scientists may boost chloroplast development and function, thereby increasing photosynthetic capacity. Such advances would be pivotal in addressing food security challenges posed by a growing global population and the effects of climate change.
Understanding the evolution of SKL1 also addresses a broader scientific question: how do new protein functions evolve from existing molecular frameworks? Proteins often arise through gene duplication events followed by diversification of one copy, allowing organisms to acquire novel capabilities. SKL1 exemplifies this evolutionary principle, where duplication and neofunctionalization extended the chloroplast developmental toolkit precisely when plants first ventured onto land—a period requiring radical adaptations to light exposure, dehydration, and nutrient acquisition.
Researchers emphasize that the appearance of SKL1 aligns closely with the earliest land plant ancestors but is absent in aquatic green algae, reinforcing the notion that this protein was a critical innovation for terrestrial colonization. Its evolution likely contributed to the formation of photosynthetically active tissues capable of withstanding the challenges posed by air exposure, such as UV radiation and water scarcity.
Another dimension of interest is the demonstration of SKL1’s conserved role in liverworts, plants representing some of the earliest branches in the land plant evolutionary tree. The conservation of SKL1’s functional role across such a temporal expanse reveals remarkable evolutionary stability, implying strong selective constraints on chloroplast biogenesis mechanisms. This finding fuels further inquiries into other protein adaptations key to plant terrestrialization, enriching our comprehension of plant evolutionary biology.
The study carried out rigorous experimental approaches, combining genome editing, molecular phylogenetics, and cross-species functional assays. This multifaceted approach provides clarity regarding SKL1’s specific molecular contributions and cements its importance in chloroplast development. It also illustrates how modern molecular tools such as CRISPR enable detailed exploration of protein functions across diverse, evolutionarily informative species.
Looking forward, this research sets the stage for translational investigations aimed at engineering SKL1 or related pathways to tailor plant physiology in ways that increase resilience, productivity, and ecological compatibility. As plants remain foundational to Earth’s ecosystems and human agriculture, uncovering and harnessing such evolutionary adaptations are vital steps toward sustainable biological innovation.
In conclusion, the identification of SKL1 as an ancient, conserved regulator of chloroplast biogenesis underscores the ingenuity of evolutionary processes in equipping plants with the molecular machinery required for terrestrial life. This protein’s emergence, tracing back 500 million years, facilitated one of the most transformative chapters in Earth’s history: the greening of land. Beyond its fundamental biological significance, SKL1 now represents a promising frontier in plant science with potential applications spanning agriculture, ecology, and biotechnology.
Subject of Research: Cells
Article Title: Shikimate Kinase-Like 1 Participates in an Ancient and Conserved Role Contributing to Chloroplast Biogenesis in Land Plants
News Publication Date: July 30, 2025
Web References:
http://dx.doi.org/10.1093/molbev/msaf129
Image Credits: Thanh Nguyen
Keywords: SKL1, Shikimate kinase-like 1, chloroplast biogenesis, land plants evolution, photosynthesis, CRISPR gene editing, plant molecular evolution, herbicide targets, liverwort, Arabidopsis thaliana, gene duplication, plant terrestrialization
