Biologists have delved into the mechanisms of DNA methylation in plants, which could lead to the development of crops that are more resilient to changes in the environment, such as extreme heat or drought.
Researchers at Washington University in St. Louis have identified the source of a fascinating duplication that enables plants to have various methods to ignore DNA instructions. This discovery could allow scientists to harness existing plant mechanisms to enhance traits that improve resilience to environmental challenges like heat and drought.
The research, spearheaded by Xuehua Zhong, a professor of biology within the Arts & Sciences department, was published on November 6 in Science Advances.
Zhong’s latest work examines DNA methylation, a natural biological occurrence in cells where small chemical units known as methyl groups attach to DNA. This process regulates gene expression, impacting how organisms react to environmental factors.
A key function of this process includes silencing certain sections of DNA that relocate within an organism’s genome. These mobile genetic elements, known as transposons or jumping genes, can cause harm if not properly managed. While enzymes oversee this process, mammals and plants have evolved distinct enzymes to facilitate methylation.
“Mammals have only two primary enzymes that add methyl groups in a single DNA context, whereas plants possess several enzymes that operate across three different DNA contexts,” stated Zhong, who serves as the Dean’s Distinguished Professorial Scholar and directs the plant and microbial biosciences program at WashU. “This is the core of our study. The question we’re exploring is why plants require these additional methylation enzymes.”
Zhong’s findings may lead to innovative advancements in agriculture by boosting crop resilience. “Specific genes or their combinations enhance certain traits,” explained Zhong. “If we can pinpoint how they are regulated, we can innovate technological approaches for improving crops.”
Evolving Different Functions
The current research focuses on two enzymes unique to plants: CMT3 and CMT2. Both are tasked with adding methyl groups to DNA; however, CMT3 is specialized for CHG sequences, while CMT2 targets CHH sequences. Despite their differing roles, they belong to the same chromomethylase (CMT) family, which evolved through duplication events resulting in additional genetic information for plants.
By investigating the common plant model Arabidopsis thaliana, or thale cress, Zhong and her team analyzed how these duplicated enzymes developed distinct functions over time. They found that during evolution, CMT2 lost the capability to methylate CHG sequences due to the absence of a crucial amino acid known as arginine.
“Arginine is unique because it carries a charge,” explained Jia Gwee, a graduate biology student and co-first author of the study. “In a cellular environment, it holds a positive charge, allowing it to form hydrogen bonds or engage in chemical interactions with negatively charged DNA.”
In contrast, CMT2 incorporates valine, an uncharged amino acid. “Valine cannot recognize the CHG context as CMT3 does, which likely accounts for the differences between the two enzymes,” Gwee noted, who has received the Dean’s Award for Graduate Research Excellence in Arts & Sciences.
To validate this evolutionary change, Zhong’s lab introduced a mutation that replaced valine with arginine in CMT2. As they anticipated, this alteration enabled CMT2 to perform both CHG and CHH methylation. This indicates that CMT2 was initially a duplicate of CMT3, serving as a backup as the complexity of DNA increased. “Instead of merely replicating the original function, it evolved to fulfill a new role,” Zhong clarified.
The study also revealed insights into the unique structure of CMT2. The enzyme contains a long, flexible N-terminal region that influences its protein stability. “This is one method plants adapted to ensure genome stability and contend with environmental pressures,” Zhong remarked. Such a feature might explain why CMT2 evolved in plants that endure varied conditions worldwide.
A significant portion of the data for this research was sourced from the 1001 Genomes Project, which seeks to uncover whole-genome sequence variations across different A. thaliana strains globally.
“We’re extending our research beyond controlled laboratory settings,” Zhong said. “We are exploring all wild accessions of plants with this broader data set.” She believes that part of the success of A. thaliana in thriving under environmental stress can be attributed to the diversification that occurs during methylation, which includes the activity of jumping transposons. “A single jump could enable a species to better cope with harsh environmental conditions.”
