Plants use DNA duplication to increase their resilience 

A team of biologists has recently revealed the origins of a unique DNA duplication mechanism that grants plants additional ways to control genetic instructions. 

This discovery, led by Xuehua Zhong from the Washington University in St. Louis (WashU), holds promise for innovations in agriculture, particularly in enhancing crop resilience to environmental challenges like heat and drought. 

The research, published in the journal Science Advances, delves into DNA methylation – a biological process that plays a key role in gene regulation, directly impacting how plants respond to environmental stressors.

Complexity of plant DNA methylation

DNA methylation involves adding small chemical groups called methyl groups to DNA. This modification determines which genes are turned on or off, shaping various plant traits. 

A crucial part of this process involves silencing “jumping genes” or transposons, which are mobile DNA sequences that can disrupt normal genetic function if not controlled. In plants, this regulatory role is handled by specialized enzymes, distinct from those found in mammals.

“Mammals only have two major enzymes that add methyl groups in one DNA context, but plants actually have multiple enzymes that do that in three DNA contexts,” Zhong explained, highlighting the unique complexity of plant DNA methylation. 

“The question is – why do plants need extra methylation enzymes?” This research could pave the way for advancements in agriculture by helping scientists to tap into plant systems that naturally regulate resilience-related traits.

The role of enzymes in plant DNA

Zhong’s study focuses on two enzymes unique to plants: CMT3 and CMT2. Both enzymes are part of the chromomethylase (CMT) family, responsible for adding methyl groups to specific DNA sequences. 

CMT3 specializes in methylating so-called CHG sequences, while CMT2 targets CHH sequences. Despite their differences, these enzymes share a common ancestry, having evolved through duplication events that provided plants with extra copies of genetic information.

Evolutionary history of the enzymes 

Using the model plant Arabidopsis thaliana, also known as thale cress, Zhong’s team traced the evolutionary history of these enzymes. 

The experts discovered that CMT2 lost its ability to methylate CHG sequences due to the absence of an amino acid called arginine, a change that occurred during the enzyme’s evolution. 

“Arginine is special because it has charge. In a cell, it’s positively charged and thus can form hydrogen bonds or other chemical interactions with, for example, the negatively charged DNA,” explained co-author Jia Gwee, a graduate student at WashU.

CMT2, however, contains valine instead of arginine. Valine lacks the necessary charge to interact with CHG sequences, explaining why CMT2 no longer recognizes these DNA contexts as CMT3 does. 

To test this theory, the research team introduced arginine back into CMT2, restoring its ability to methylate both CHG and CHH sequences. 

This mutation suggests that CMT2 originally functioned as a duplicate of CMT3 – a backup enzyme with the potential to diversify its function as plant DNA complexity grew. 

“But instead of simply copying the original function, it developed something new,” Zhong noted.

Adapting to environmental stress

The study also uncovered structural features that set CMT2 apart. Notably, the enzyme has a flexible N-terminal region that influences its protein stability, a characteristic that may have helped plants adapt to various environmental conditions. 

“This is one of the ways plants evolved for genome stability and to fight environmental stresses,” Zhong explained. This structural adaptation has likely allowed plants equipped with CMT2 to thrive in diverse climates across the globe.

A significant portion of the data for this study came from the 1001 Genomes Project, which maps the genetic diversity of A. thaliana strains worldwide. 

By exploring samples from plants in the wild rather than just laboratory specimens, the researchers gained insights into how DNA methylation contributes to plants’ natural resilience.

Jumping genes and plant adaptation

The study also highlights the adaptive potential of transposons, or “jumping genes,” in plant DNA. These mobile sequences are often silenced by methylation to maintain genomic stability, but their occasional movement can aid in environmental adaptation. 

“One jump might help species deal with harsh environmental conditions,” Zhong said, explaining how these genetic shifts could help plants survive in challenging environments.

As plants navigate unpredictable climates, the diversification enabled by DNA methylation – particularly through enzymes like CMT3 and CMT2 – can provide the flexibility needed to withstand stressors like extreme temperatures and limited water availability.

Future implications for crop resilience

Understanding how CMT enzymes contribute to plant resilience opens exciting possibilities for agriculture. 

By precisely targeting the genes and methylation processes responsible for drought tolerance, heat resistance, or other resilience traits, scientists could enhance crops’ ability to thrive under changing climate conditions. 

“If we find precisely how they are regulated, then we can find a way to innovate our technology for crop improvement,” Zhong explained.

As the world faces growing agricultural challenges, insights into the DNA methylation processes that strengthen plants can provide a foundation for developing crops capable of withstanding increasingly severe environmental pressures. 

This research marks a step forward in harnessing plants’ genetic systems to create resilient agricultural ecosystems, offering a promising path to sustainable food security in the face of climate change.

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