Plant Cells Unleash Their Inner Warriors When Battling Disease

Recent studies from scientists at the Salk Institute uncover how plant cells adapt roles to safeguard themselves against pathogens. Upon encountering a threat, the cells shift into a specialized immune mode and temporarily transform into PRimary IMmunE Responder (PRIMER) cells — a newly identified cell category that serves as a center to launch the immune response. The researchers also identified that PRIMER cells are encircled by another cell category referred to as bystander cells, which appear to be vital for disseminating the immune response across the plant.

The results, published in Nature on January 8, 2025, draw researchers nearer to grasping the plant immune system — an increasingly crucial undertaking amid the escalating challenges of antimicrobial resistance and climate change, which both amplify the spread of infectious diseases.

“In nature, plants are constantly under assault and require a robust immune system,” states Professor Joseph Ecker, senior author of the research, Salk International Council Chair in Genetics, and Howard Hughes Medical Institute investigator. “Yet plants lack mobile, specialized immune cells like we do — they have to devise a completely different system wherein every cell can react to immune threats without neglecting their other responsibilities. Up until now, we weren’t quite certain how plants were managing to do this.”

Plants face a myriad of pathogens, such as bacteria that infiltrate through leaf surface pores or fungi that invade plant “skin” cells directly. Given that plant cells are fixed in place, when they confront any of these pathogens, they become solely accountable for responding and notifying nearby cells. Another fascinating consequence of the immobile cell nature is the possibility that different pathogens can enter a plant at distinct locations and at various times, resulting in multiple immune response phases occurring concurrently throughout the plant.

With variables like timing, location, response state, and more all influencing the situation, an infected plant is a complex entity to analyze. To address this, the Salk team employed two advanced cell profiling methodologies known as time-resolved single-cell multiomics and spatial transcriptomics. By integrating the two, the group could capture the plant immune response in each cell with unprecedented spatiotemporal accuracy.

“Uncovering these rare PRIMER cells and their adjacent bystander cells is a significant insight into how plant cells communicate to withstand the numerous external threats they face on a daily basis,” comments first author Tatsuya Nobori, a former postdoctoral researcher in Ecker’s lab and current group leader at The Sainsbury Laboratory in the United Kingdom.

The team introduced bacterial pathogens to the leaves of Arabidopsis thaliana — a flowering weed in the mustard family widely used as a research model. They subsequently assessed the plant’s reaction to comprehensively identify each cell’s condition upon infection. Through this analysis, they identified a new immune response state, termed PRIMER, that appeared in cells at specific immune hotspots. The PRIMER cells exhibited a novel transcription factor — a type of protein that governs gene expression — named GT-3a, likely serving as an important upstream alarm for alerting other cells to an active plant immune response.

Moreover, the cells surrounding these PRIMER cells proved to be equally critical. Referred to as “bystander cells,” the cells adjacent to PRIMER cells were active in regulating genes that facilitate long-distance cell-to-cell communication. The researchers intend to clarify this relationship in subsequent studies, but for now, they suspect that the interactions between PRIMER and bystander cells are crucial for propagating the immune response throughout the leaf.

This novel spatiotemporal, cell-specific understanding of the plant immune response has already been made available as a reference database for researchers globally. As pathogens continue to evolve and spread amid climate-related environmental changes and increasing antibiotic resistance, the database serves as an essential springboard for ensuring a future filled with thriving plants and crops.

“There is a great deal of interest and demand for detailed cell atlases these days, so we are thrilled to create a new one that is publicly accessible for other researchers to utilize,” states Ecker. “Our atlas could lead to numerous new discoveries about how individual plant cells respond to environmental stressors, which will be vital for developing more climate-resilient crops.”

Other contributors include Joseph Nery of Salk; Alexander Monell of Salk and UC San Diego; Travis Lee of Salk and Howard Hughes Medical Institute; Yuka Sakata, Shoma Shirahama, and Akira Mine of University of Kyoto in Japan.

The research was supported by the Howard Hughes Medical Institute and the Human Frontiers Science Program.