How a genetic division helped plants conquer polluted soils

Phytochelatin synthases (PCS) produce phytochelatins, tiny cysteine-rich peptides that bind and neutralize toxic metal ions such as cadmium and arsenic. These molecules act as the plant’s natural detoxification system, sequestering harmful elements in vacuoles to prevent cellular damage.

Although previous studies have explored individual PCS genes in model plants like Arabidopsis thaliana (AtPCS1, AtPCS2), the broader picture of how PCS genes diversified during plant evolution has remained unclear.

Without understanding this evolutionary history, it has been difficult to explain why plants vary so widely in their metal tolerance. Based on these challenges, researchers sought to uncover how gene duplication and functional divergence shaped the evolution of PCS in plant genomes.

A research team from the Fondazione Edmund Mach and the University of Pisa has traced the evolutionary origin of the metal detoxification mechanism of plants.

Their findings, published in Horticultural researchreveal that a long-neglected duplication of PCS genes occurred early in the evolution of flowering plants.

By combining genome-wide phylogenetic reconstruction with laboratory and plant-level experiments, the researchers discovered how this duplication, split into D1 and D2 lineages, allowed plants to fine-tune their biochemical defense against heavy metal stress.

The study analyzed more than 130 complete plant genomes to map the evolutionary journey of PCS genes. The researchers discovered an ancient duplication, dubbed “D duplication,” that emerged during the first diversification of eudicots and has been preserved ever since. This event divided the PCS genes into two families: D1 and D2.

To explore their functions, the team isolated MdPCS1/MdPCS2 from apple and MtPCS1/MtPCS2 from barrel medic and introduced them into Arabidopsis thaliana mutants lacking native PCS activity. Laboratory analyzes revealed that D2-type PCS enzymes were significantly more active than their D1 counterparts, demonstrating an increased ability to synthesize phytochelatins and bind cadmium and arsenic.

In living plants, D2 genes conferred stronger growth recovery and higher tolerance to metal stress, while D1 genes maintained a general thiol balance and moderate detoxification capacity. Sequence analysis identified two key amino acid residues likely responsible for their functional divergence.

The results suggest that the two types of genes were retained because their complementary roles ensured efficient detoxification – a remarkable example of an evolutionary fine-tuning that continues to protect modern crops.

“Our results reveal how evolution has refined a vital survival mechanism,” said Dr. Claudio Varotto, the study’s corresponding author.

“The two copies of the PCS gene have coexisted for over a hundred million years because they complement each other: D1 provides stability, while D2 provides energy. This dual system gives plants the flexibility to adapt to a range of metal-related challenges. It is a perfect illustration of how ancient genetic innovation continues to shape plant resilience today.”

This discovery not only deepens our understanding of plant evolution, but also opens new avenues for sustainable agriculture. By targeting PCS gene expression or transferring D2-type PCS activity into susceptible crops, breeders could create varieties that thrive in contaminated soil while reducing heavy metal accumulation in edible parts.

Such genetic knowledge could also improve phytoremediation strategies, in which plants are used to clean up polluted environments.

As the world faces increasing soil contamination, understanding how plants have evolved to tolerate toxic metals offers both scientific inspiration and practical tools for a safer agricultural future.