Uncovering the secrets of methylation in plants

Flowers of the Arabidopsis thaliana plant model. Credit: Conor Gearin/The Whitehead Institute

Growth is a complex process for multicellular organisms – including plants. In the days or weeks it takes to go from seed to plant to full plant, plants express hundreds of genes in different places and at different times.

In order to perform this gene symphony, plants rely in part on an elegant regulatory method called DNA methylation. By adding or removing small molecules called methyl groups to a strand of DNA, a plant can silence or activate different regions of its genetic code without changing the underlying sequence.

In a new paper from the lab of Whitehead Institute member Mary Gehring’s lab, researchers led by Ben Williams, a former postdoc in Gehring’s lab (now an assistant professor at the University of California, Berkeley) deconstruct the role of the proteins that govern this genetic control system, revealing how Enzymes that regulate methylation can influence basic decisions by plants such as when to produce flowers. “We are starting to see that there is actually a much broader role for demethylation.” [in plant development] than we thought,” Gering said.

In the typical plant Arabidopsis thaliana, methylation is regulated in part by enzymes encoded by a family of four genes called DEMETER genes. The protein products of these genes are responsible for the demethylation, or removal of methyl groups from DNA, allowing different parts of the strand to be expressed. “You have these enzymes that can go in and completely change the way DNA is read in different cells, which I find very interesting,” Williams said.

But deciphering the role of each DEMETER gene has been difficult in the past, because one member of this gene family in particular, called DME, is necessary for seed growth. Hit the DME, and the seed is aborted. “We had to design a synthetic gene to work around that,” Williams said. “We had to make plants that would rescue reproductive failure, but then remain mutated for the rest of the life cycle.”

The researchers achieved this by placing the DME gene under the control of a genetic component called a promoter that allowed it to be expressed in a cell that was only present in the plant while the seed was growing. Once the plant crosses the critical point where DME was needed for development, the gene will not be expressed, allowing the plant to grow as a knockdown of DME. “It was an exciting thing, I finally got the knockout,” Gering said.

Now, for the first time, researchers can create plants with any set of genes of the DEMETER family that have been knocked out, and then compare them to try to understand what the enzymes produced by each of the four genes do.

As expected, plants lacking any of the dimethyl demethylases ended up with regions of their genomes with too many methyl groups (this is called hypermethylation). These regions often overlapped, indicating that the four DEMETER genes share the responsibility for the demethylation of specific regions of the genome.

“When one of these enzymes goes missing, the others are surprisingly good at knowing they need to step up and do the job instead,” Williams said. “So the system has flexibility built into it, which makes sense if it’s going to be involved in making important decisions like when to make flowers. You want there to be multiple levels of responsibility, right? It’s like an organization, you don’t, I don’t want to place all the responsibility on you.” One person – you want a few people who can take on that responsibility.”

Williams hypothesizes that while DEMETER enzymes can interfere with each other when needed, each is specialized for DNA demethylation in certain types of plant tissues. “If you look at the protein sequences, you will find that they are really similar,” he said. “What is different about them is that they are expressed in different types of cells.”

A conclusive result of the study was reached when the researchers knocked out all four genes in the DEMETER family at the same time. “All flowering plants have this really important decision about when to make flowers,” Williams said. “For plants in the wild, that decision usually depends on temperature and the pollinators. What we found really strange is that these mutants immediately blossomed. It’s as if they put no effort into the decision. They made a few leaves, then blooms, and flower “.

When the researchers delved deeper, they saw that one region of the genome in particular that controls flowering time is under very careful and persistent regulation by methylation and demethylation of enzymes. “We don’t really know why they’re doing that,” he said. “But when you eliminate the demethylases, that gene becomes methylated, and then it is turned off. That sends plants into a spontaneous flowering state.”

In the future, the researchers plan to investigate other findings associated with the quadruple knockout of the DEMETER genes. “When we removed all four enzymes, it resulted in a lot of interesting phenotypes and tons of things to study,” Williams said. “We’ve learned by doing this that with DEMETER, like many gene families, we’ve had to kick all the players out to see the importance of what they’re doing.”

Gehring will continue research at the Whitehead Institute. Williams recently started his own lab at the University of California, Berkeley. “I feel very fortunate that this project has given me two or three different approaches that I can take in my new lab,” Williams said. “It opened a lot of doors, which is very rewarding.”

An epigenetic variant reveals how gene regulation is inherited and maintained

more information:
Ben B Williams et al., Somatic DNA demethylation generates tissue-specific methylation states and affects flowering time, Plant Cell (2021). DOI: 10.1093/plcell/koab319

Submitted by the Whitehead Institute for Biomedical Research

the quote: Uncovering the mysteries of methylation in plants (2022, January 12) Retrieved January 16, 2022 from https://phys.org/news/2022-01-uncovering-mysteries-methylation.html

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