Rapid DNA repair prevents harmful genetic intrusion in plants

Inside every plant cell, an ancient struggle plays out. It is not dramatic like a predator-prey chase, but it is essential for life. DNA from chloroplasts – once free-living bacteria – still tries to sneak into the plant’s nuclear genome. Sometimes this sneaking helps evolution, but often it is dangerous.

Plants need ways to stop this intrusion. A new study from the Max Planck Institute of Molecular Plant Physiology explores this battle. It shows how rapid DNA repair guards the plant’s genome from being overwhelmed by foreign sequences.

Led by Dr. Enrique Gonzalez-Duran and Professor Dr. Ralph Bock, the research shines a light on a quiet but powerful line of defense.

The team studied tobacco plants. They wanted to understand how breaks in nuclear DNA might open the door for unwanted genetic visitors. The results go far beyond botany, suggesting universal mechanisms that may apply to animals and humans too.

How DNA invades plants

Plants evolved from ancestors that once swallowed bacteria. Over time, those bacteria became chloroplasts and mitochondria. Some of their genes jumped to the host’s nuclear DNA. This process, called endosymbiotic gene transfer (EGT), has shaped eukaryotic evolution for billions of years.

Even today, EGT continues. Most organellar DNA transfers fail or get degraded, but sometimes they succeed. A piece of chloroplast DNA slips into the nucleus, settles in, and even becomes active.

This can help the plant adapt, but it can also damage the host’s genome. If the insertion disrupts a vital gene or rearranges chromosomes, it can cause long-lasting harm. The researchers wanted to know how plants prevent this from happening too often.

Breaks in DNA invite invasion

The key lies in DNA double-strand breaks (DSBs). These are serious injuries in the genome. If not repaired quickly, they become open doors for foreign DNA.

Normally, the cell repairs the breaks using fast-acting pathways like non-homologous end joining (NHEJ) and polymerase-theta-mediated end joining (TMEJ).

To explore their role, the team disabled these two repair systems in tobacco plants. The plants still grew, though some developed slowly. But under the surface, big changes were unfolding.

Without these repair pathways, DSBs lingered longer. That gave chloroplast DNA more time to enter and integrate into the nuclear genome. When the researchers tracked more than 650,000 seedlings, they saw a dramatic increase in EGT events, up to 20 times more in some cases.

“The magnitude of the effect suggests that rapid DNA repair is essential for plants to maintain long-term genome stability,” said Dr. Enrique Gonzalez-Duran.

Repairs stop gene invasion

The researchers developed a clever screening system. They inserted a gene into chloroplasts that only conferred resistance to kanamycin when transferred to the nucleus. Using this setup, they could detect when EGT had occurred by seeing which plants survived the antibiotic.

The team found that EGT does not just happen during plant regeneration. It occurs in real time, over weeks and months. Tobacco leaves continued to produce new gene transfer events throughout a 120-day experiment. The longer the DSBs remained unrepaired, the more EGT happened.

Unrepaired breaks give chloroplast DNA a chance to settle in. In normal cells, fast repair seals the break before foreign DNA can sneak in. In mutant cells, delays allow invasion.

Foreign DNA changes future generations

To see whether these gene transfers affected offspring, the team bred the mutant plants. They looked at how kanamycin resistance was passed down. In many cases, it followed expected patterns. But some lines showed fewer resistant seedlings than expected.

This mismatch pointed to instability. Some of the inserted genes did not last into the next generation. In a surprising twist, the researchers found that mutations in one repair pathway, NHEJ, actually made the transferred DNA more stable once it entered the nucleus.

Even more striking was what happened in the male reproductive cells. When mutant plants served as pollen donors, the number of EGT events in offspring exploded. Certain mutants, like polqΔHel-4, showed a 20-fold increase in gene transfers during pollen formation.

“These DNA repair pathways are conserved in animals and fungi,” noted Professor Dr. Ralph Bock. “Our findings could explain similar genome instability mechanisms in other organisms, including humans.”

Mutant plants for genetic research

The researchers also built a set of genetically modified tobacco plants with defects in NHEJ, TMEJ, or both.

The mutants help study DNA integration, editing, and stress response. Some showed surprising results – unlike in Arabidopsis, POLQ loss in tobacco didn’t stop regeneration.

This reveals how repair systems may differ across species. Bleomycin tests confirmed the mutants had weaker DNA repair.

Fast repair helps keeps DNA safe

Plants with faulty repair systems allowed foreign DNA to integrate at high rates. If left unchecked, these insertions could interrupt genes and cause chaos. Over time, this would reshape the genome in ways that could harm the plant’s survival.

“Our discovery provides fundamental insights into genome protection and the risks of gene transfer,” said Gonzalez-Duran. “It reveals how crucial fast DNA repair is, not just to fix damage, but also to defend the integrity of the genome itself.”

The researchers conclude that plants rely on rapid repair not because it is perfect, but because it limits the damage foreign DNA can cause. Even if the repair introduces small errors, it is still better than letting organellar DNA flood the nucleus.

Though done in tobacco, the findings apply broadly. Animals and fungi share similar DNA repair systems. In humans, faulty repair can let mitochondrial DNA disrupt the genome, even triggering cancer. Studying plants shows how fast repair helps maintain stability across life.

The study is published in the journal Nature Plants.

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