Identifying PRIMER Cells and their Role in Defense Signaling

A diverse population of immune cells that move from one organ to another and react to anything from cuts to colds to cancer is how human bodies protect themselves. However, this luxury is not available to plants.

Plant cells are immobile, so in addition to their many other duties, such as converting sunlight into energy or using that energy to grow, each cell must also manage its immunity. It is still unclear how these multitasking cells manage to identify threats, convey those threats, and react appropriately.

Scientists from the Salk Institute have discovered a new way for plant cells to switch roles to defend themselves from infections. The cells temporarily transform into PRimary IMmunE Responder (PRIMER) cells, a new cell population that serves as a hub to start the immune response, when a threat is encountered.

Additionally, the researchers found that PRIMER cells are encircled by a different cell population known as bystander cells, which they believe is crucial for spreading the immune response throughout the plant.

The research was published in the journal Nature. It advances knowledge of the plant immune system, a task that is becoming more and more crucial in light of the growing risks of antimicrobial resistance and climate change, both of which accelerate the spread of infectious diseases.

In nature, plants are constantly being attacked and require a well-functioning immune system. But plants do not have mobile, specialized immune cells like we do they must come up with an entirely different system where every cell can respond to immune attacks without sacrificing their other duties. Until now, we were not quite sure how plants were accomplishing this.”

Joseph Ecker, Professor and Study Senior Author, Salk Institute

Ecker is a Salk International Council Chair in Genetics and Howard Hughes Medical Institute investigator.

Numerous pathogens are encountered by plants, such as fungi that directly infiltrate plant “skin” cells or bacteria that enter through pores on the leaf surface. Since plant cells are immobile, they are solely in charge of reacting to and warning neighboring cells when they come into contact with any of these pathogens.

Immobile cells also have the intriguing side effect of allowing various pathogens to enter a plant at different times and places, which causes different immune response stages to occur concurrently throughout the plant.

An infected plant is a complex organism to comprehend because of the many variables at play, including timing, location, response state, and more. The Salk team used two advanced cell profiling methods, time-resolved single-cell multiomics and spatial transcriptomics, to address this.

By combining the two, the team achieved previously unheard-of spatiotemporal resolution in capturing the plant immune response in each cell.

Discovering these rare PRIMER cells and their surrounding bystander cells is a huge insight into how plant cells communicate to survive the many external threats they face day-to-day.”

Tatsuya Nobori, Study First Author and Former Postdoctoral Researcher, Salk Institute

Nobori is the current group leader at The Sainsbury Laboratory in the United Kingdom.

The group exposed the leaves of Arabidopsis thaliana, a flowering weed in the mustard family that is frequently used as a model in studies, to bacterial pathogens. After that, they examined the plant's reaction to fully determine the condition of every cell after infection.

By doing this, they found that cells at particular immune hotspots developed a novel immune response state that they named PRIMER. GT-3a, a novel transcription factor a class of protein that controls gene expression, was expressed by the PRIMER cells. This protein is probably a crucial upstream alarm for warning other cells of an active plant immune response.

Furthermore, the cells that surrounded these PRIMER cells turned out to be just as significant. The cells that were right next to PRIMER cells were known as “bystander cells” because they were expressing genes that allow for long-distance cell-to-cell communication.

For the time being, the researchers believe that the interactions between PRIMER and bystander cells are crucial to spreading the immune response throughout the leaf, but they intend to clarify this relationship in subsequent studies.

Researchers from all over the world can already access this new spatiotemporal, cell-specific understanding of the plant immune response as a reference database. The database provides a crucial starting point for maintaining a future full of robust plants and crops as pathogens continue to develop and spread in the face of environmental changes brought on by climate change and an increase in antibiotic resistance.

There is a lot of interest and demand for detailed cell atlases these days, so we are excited to create a new one that is publicly available for other researchers to use. Our atlas could lead to many new discoveries about how individual plant cells respond to environmental stressors, which will be crucial for creating more climate-resilient crops.”

Joseph Ecker, Professor and Study Senior Author, Salk Institute