DNA methylation is a crucial biological process that plays a significant role in regulating gene activity within living cells. This process involves adding small chemical groups, called methyl groups, to DNA, which helps control which genes are active and which are not. This regulation affects a wide range of traits, including how organisms respond to their environments.
A key aspect of DNA methylation is the silencing of certain segments of DNA that move within the genome, known as transposons or “jumping genes.” If not controlled, these genes can cause damage to the organism’s DNA.
While this process is regulated by enzymes, mammals and plants use different sets of enzymes to add methyl groups to their DNA. According to Professor Xuehua Zhong, a researcher at Washington University in St. Louis, mammals rely on just two major enzymes for DNA methylation in one specific context. In contrast, plants have developed multiple enzymes that can operate in three distinct DNA contexts.
“Mammals only have two enzymes that add methyl groups in one DNA context, but plants have multiple enzymes that function in three contexts,” said Professor Zhong. “The key question is why plants need these extra enzymes.”
The study focuses on two plant-specific enzymes, CMT3 and CMT2, both of which add methyl groups to DNA. CMT3 targets CHG sequences, while CMT2 acts on CHH sequences. Despite their differences in function, both enzymes belong to the same chromomethylase (CMT) family, which evolved through duplication events, providing plants with additional genetic resources.
To explore how these enzymes evolved, Professor Zhong and her team studied the model plant Arabidopsis thaliana. They discovered that over time, CMT2 lost its ability to methylate CHG sequences due to the absence of an important amino acid, arginine.
“Arginine is special because it has a positive charge, which allows it to form chemical bonds with negatively charged DNA,” explained Jia Gwee, a graduate student at Washington University. “In contrast, CMT2 has valine, an amino acid without charge, which prevents it from recognizing the CHG context, unlike CMT3.”
To test this theory, the researchers introduced a mutation to restore arginine to CMT2. As expected, the modified enzyme was able to methylate both CHG and CHH sequences, suggesting that CMT2 was originally a duplicate of CMT3. Initially, CMT2 likely functioned as a backup enzyme to help manage the increasing complexity of DNA. However, over time, it evolved a new function.
“This research reveals that CMT2 was not just a copy of CMT3,” said Professor Zhong. “It developed its own unique function over time.”
The study also provided insights into CMT2’s unique structure. The enzyme features a long, flexible N-terminal, which plays a crucial role in stabilizing the protein. According to Professor Zhong, this flexibility may be one reason plants have evolved to maintain genomic stability and respond to environmental stress.
“This feature is likely why CMT2 evolved in plants that thrive in a wide variety of conditions across the globe,” she said.
The findings offer valuable insights into how plants have adapted their genetic machinery to maintain stability and thrive in diverse environments, paving the way for future research on crop improvement.
Related topics: