Salk Institute reveals how YAF9B protects plant DNA repair

Sunlight powers plant growth, but it can also cause damage. The very rays that fuel development continually break DNA inside plant cells.

Plants cannot escape these conditions as animals can. Instead, they must repair the harm exactly where they are rooted.

Research from the Salk Institute has found that plants possess a dedicated repair protein designed for this task.

Sunlight: vital yet harmful

Plants face continual environmental pressure. Sunlight, radiation, drought and nutrient-poor soil can each disrupt the genetic instructions their cells depend upon.

To remain healthy, plants use repair mechanisms that monitor DNA around the clock. However, precisely how these repairs are controlled, particularly in tissues that produce new growth, has remained difficult to establish.

“Plants are unique because the same thing that gives them the ability to grow – sunlight – is constantly damaging their DNA,” said Julie Law, a professor at the Salk Institute.

“The question is, how do they cope with that level of DNA damage?”

Damage concealed by dense packing

Repairing DNA is complicated by the way it is packaged.

Within every cell, DNA is tightly wound around proteins known as histones. These structures are then compressed into a dense substance called chromatin.

This compact arrangement keeps the genome orderly, but it can also hide damaged sites. A repair system cannot mend a break it is unable to access.

“In order to repair damaged DNA, you first need to detect the damage and then recruit the proteins required to unwind the chromatin and repair the DNA,” Law said.

A DNA repair protein evolved by plants

To make this dense packaging accessible, plants use supporting proteins that serve as first responders. They relax chromatin, direct repair machinery towards the break and help ensure the process remains on course.

A key group of these proteins is known as YAF9. It is an ancient family found across many forms of life, although plants have adapted it in their own way.

“The YAF9 family of proteins is found in yeast, animals, and plants,” said Neeraja Vegesna, a former graduate student researcher in Law’s lab.

“But plants evolved a second version, YAF9B, that is specifically activated after DNA damage occurs.”

Plants therefore use two forms. YAF9A operates throughout the plant as a broad repair assistant, whereas YAF9B is a specialist primarily activated when damage occurs.

When the DNA repair response begins

The researchers examined both genes by exposing seedlings to DNA-breaking radiation. YAF9A remained active regardless of the conditions.

YAF9B behaved in another way. It was inactive under normal conditions but rapidly switched on once DNA began to break.

This reaction is controlled by a regulatory switch called SOG1. After damage, SOG1 binds to a short signal within the YAF9B gene and activates it. When the team disrupted that signal, the response failed completely.

The protein also responded selectively to particular forms of damage. Treatments that broke both DNA strands activated it, while cold, salt, heat and most other stresses had little effect.

Stem cells receive added protection

YAF9B was not activated throughout the entire plant. Its activity was highest at the shoot tip and root tips, which contain large numbers of stem cells.

These stem cells generate every new root, shoot and leaf. Any error within them can be passed into everything the plant subsequently produces.

“These stem cells are what generate the rest of the plant,” said Law.

“The hypothesis is that the plant produces this factor to help protect those cells and give them a better chance of carrying out highly accurate DNA repair.”

Rapid repair compared with accurate repair

Plants have more than one method for repairing a broken DNA strand. The faster option, called non-homologous end joining, simply reconnects the separated ends.

Its speed comes at a cost. Although the repair generally holds, it may create errors or small mutations.

The slower method, homology-directed repair, reconstructs the damaged region by using an undamaged copy as a template. It requires longer, but preserves the original genetic code.

Both YAF9A and YAF9B proved important to this more precise pathway.

Plants with YAF9 mutations recover poorly

To investigate this, the team created plants lacking one or both YAF9 genes. In a general assessment of plant health, only those without both genes had difficulties, indicating that the proteins can compensate for one another.

A more targeted experiment revealed greater complexity. When researchers focused solely on the accurate repair pathway, removing either gene individually greatly reduced repair, showing that the two proteins are not merely interchangeable.

They also associate with different partners in the cell. YAF9A works alongside two established repair complexes, while YAF9B connects with only one, creating a specialised form intended for emergency conditions.

This is the first evidence connecting that complex with break repair in plants.

“Accurate DNA repair is essential for maintaining genome stability, but it depends on many proteins working together within chromatin,” said Law.

“What’s exciting about this study is that we identified YAF9B as a DNA damage-responsive chromatin reader that helps cells carry out high-fidelity DNA repair, revealing a novel innovation used by plants to protect their genomes.”

Better crops may result

The findings also have practical implications. Gene-editing technologies such as CRISPR often depend on the rapid, error-prone repair pathway in plants, limiting the precision with which scientists can insert replacement genes.

Learning how plants favour the more accurate pathway could help address this limitation. The team now aims to establish how the proteins divide their responsibilities during repair.

“Our next goal is to understand how these chromatin effectors coordinate different stages of DNA repair and how exactly YAF9B promotes accurate and effective DNA repair,” said Law.

“If we can understand how plants promote high-fidelity repair, we may eventually be able to improve genome editing technologies in plants,” Law added.