Small DNA tweak protects plants from devastating crop disease

Farmers lose billions of dollars each year to diseases that clog a plant’s veins and leave entire fields limp. New work from UC, Davis shows that a carefully edited immune sensor can help crops recognize some of the bacteria behind those losses – a threat that’s growing as the climate warms.

The discovery builds on decades of study into how plants notice invaders and trigger internal alarms. It also highlights a fast moving molecular arms race, because microbes constantly tweak the proteins on their surface to slip past detection.

Rebuilding crop disease defenses

A team led by Gitta Coaker, a plant disease expert at UC Davis, found that natural versions of a plant sensor called FLS2 can detect one piece of a bacterial protein – but often miss similar ones.

By studying FLS2 genes from different plant species, they identified specific building blocks – or amino acids – that affect how well the sensor recognizes threats.

When they changed just 13 of these in a crop-friendly version, the sensor regained its ability to detect bacteria it had previously overlooked.

“We were able to resurrect a defeated receptor – one where the pathogen has won – and enable the plant to have a chance to resist infection in a much more targeted and precise way,” said Coaker.

She sees the strategy as a template for updating other sensors that guard against diverse pests.

Sensor targets bacterial tail

Many plants use FLS2 to detect a small piece of a bacterial tail protein called flagellin. This 22-amino-acid piece, known as flg22, triggers the plant’s immune system.

When FLS2 recognizes flg22, it sets off a strong defense response, flooding plant cells with calcium and reactive oxygen to fight off the bacteria.

But if bacteria make small changes to the end of flg22, the sensor may not detect them. That allows the bacteria to spread through the plant’s water-carrying tissue. The result is bacterial wilt – a fast-moving disease that can wipe out tomato or potato plants almost overnight.

AI guides plant edits

To predict which edits would matter most, the team turned to AlphaFold, an AI model that guesses protein shapes to near-atomic detail. The software flagged residues on FLS2’s concave surface that should touch the tricky flg22 variants.

Those predictions steered the lab work, trimming months of trial and error from the project. Matching computer output with greenhouse assays confirmed that the redesigned receptor could sense multiple strains at nanomolar peptide doses.

Importantly, the new sensor left normal growth untouched, a key point for breeders wary of yield penalties. The study shows that AI can make molecular tinkering far less of a guessing game.

Reprogramming crop disease defense

Plants cannot produce antibodies on demand, so boosting pattern recognition is their safest bet. Replacing a handful of residues acts like a firmware update, expanding what the cell sees without rewriting the entire gene.

In one test, tomato leaves expressing the edited receptor produced a reactive oxygen burst 20 times stronger than controls when exposed to Ralstonia peptides. Disease symptoms dropped sharply in subsequent challenge assays.

“This approach could be a path toward broad-spectrum resistance that doesn’t rely on chemical sprays,” said Coaker. She added that farmers need options that fit current management budgets.

Blocking bacteria at the root

Ralstonia solanacearum is one of the world’s most damaging crop diseases, capable of infecting over 200 plant species. It causes wilt and brown rot, leading to more than $1 billion in global losses each year.

Once inside, the bacteria clog water vessels, blocking sprays and antibiotics from reaching the infection. The best defense is early detection at the root, where the plant’s immune system can still recognize the invader.

To help crops do that, scientists are using CRISPR to make tiny edits – just a few genetic “spelling changes” – in immune receptor genes. These edits don’t add any foreign DNA and are treated like traditional breeding in countries such as the U.S.

By combining these enhanced receptors with other resistance genes, plant breeders may slow the rise of new, harder-to-stop bacterial strains. This could reduce the need for fungicides and antibiotics, which would also help protect soil and water.

Small-scale farmers, especially in warm regions where tomatoes, peppers, and eggplants are dietary staples, could benefit the most. Healthier crops mean more reliable income and better food security for their communities.

Future of plant immunity

Coaker’s group is now training machine learning models to rank other receptors for editability.

Early simulations suggest that tweaking as few as eight residues can widen perception for several unrelated microbial patterns.

If that holds up, crop scientists could one day scan whole pathogen genomes in silico and pre-test receptor updates before a disease outbreak ever starts.

The study is published in the journal Nature Plants.

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