Scientists have developed a comprehensive resource detailing the behavior of plant cells during immune reactions, revealing a new and rare cell type known as the Primary IMmunE Responder (PRIMER), which serves as a central hub for coordinating defensive strategies in plants. This accessible database sheds light on plant immune responses, which is increasingly vital in the era of climate change and rising antimicrobial resistance.
Human bodies utilize a diverse array of immune cells that move between organs, dealing with everything from minor injuries to major illnesses. In contrast, plants must rely on their individual cells to handle their own immune responses due to their immobile nature. Each plant cell has the dual responsibility of managing its immunity while also performing essential functions, such as photosynthesis for energy and growth. However, the mechanisms that allow these multitasking cells to detect threats, communicate them, and mount an effective defense have remained largely unknown.
Recent research conducted by scientists at the Salk Institute has revealed how plant cells adapt their roles to defend against pathogens. When faced with a potential threat, these cells adopt a distinct immune state and transform into PRimary IMmunE Responder (PRIMER) cells. This newly identified cell population acts as a central hub to initiate the immune response. Furthermore, the researchers found that PRIMER cells are accompanied by neighboring cells termed bystander cells, which appear to play a crucial role in spreading the immune response throughout the plant.
The study, published in Nature on January 8, 2025, enhances our understanding of the plant immune system. This knowledge is becoming ever more relevant as antimicrobial resistance and climate change pose increasing challenges that facilitate the spread of infectious diseases.
“Plants are constantly under attack and need an effective immune system to survive,” explains Professor Joseph Ecker, the study’s senior author and a notable figure in genetics research. “Unlike animals, plants lack mobile, specialized immune cells, which forces them to create an entirely different defense mechanism whereby each cell must react to immune threats while fulfilling their other roles. Until now, the details of this process have been somewhat unclear.”
Plants encounter myriad pathogens, including bacteria that infiltrate through leaf pores and fungi that breach plant cell surfaces. When these pathogens are recognized, the stationary plant cells must independently address the threat and signal their nearby neighbors. The fixed position of plant cells also means that various pathogens might invade different areas at different times, leading to multiple phases of immune responses occurring simultaneously across the plant.
Given the complexity influenced by factors such as timing, location, and response state, understanding an infected plant is no small feat. To address this complexity, the Salk team employed two advanced cell profiling methods: time-resolved single-cell multiomics and spatial transcriptomics. By combining these techniques, they successfully captured the plant immune response at an unprecedented level of detail.
“The identification of these rare PRIMER cells and their neighboring bystander cells provides significant insights into how plant cells communicate to endure the various external challenges they face daily,” says Tatsuya Nobori, the first author of the study and a leading researcher at The Sainsbury Laboratory in the UK.
To explore these dynamics, the team introduced bacterial pathogens to the leaves of Arabidopsis thaliana, a flowering plant in the mustard family frequently used in research. They extensively analyzed the plant’s immune response to pinpoint the specific state of each cell following infection. Through this, they identified the novel immune state, dubbed PRIMER, which formed in cells located at distinct immune hotspots. The PRIMER cells exhibited a new transcription factor known as GT-3a, a protein essential for regulating gene activity, indicating its potential role as an early warning signal for other cells within the plant’s immune network.
The neighboring cells surrounding the PRIMER cells are equally significant. Known as “bystander cells,” these adjacent cells were found to express genes that facilitate long-distance communication between cells. Future studies will aim to clarify the interplay between PRIMER and bystander cells, but early indications suggest that their interactions are vital for disseminating the immune response across the leaf.
This innovative and detailed perspective on the plant immune response is now available as a reference database for researchers globally. As pathogens evolve and spread in conjunction with climate-related environmental shifts and increasing antibiotic resistance, this database serves as a crucial foundation for ensuring the future health of plants and crops.
“There is a growing interest in comprehensive cell atlases in the scientific community, and we are thrilled to contribute a publicly accessible one for researchers to utilize,” Ecker adds. “Our atlas has the potential to lead to numerous new insights regarding how individual plant cells react to environmental stressors, which is essential for developing more resilient crops in the face of climate challenges.”
Other contributors to this research include Joseph Nery, Alexander Monell, Travis Lee of Salk, and Yuka Sakata, Shoma Shirahama, and Akira Mine from the University of Kyoto in Japan.
This research was supported by the Howard Hughes Medical Institute and the Human Frontiers Science Program.
