April 2026

To prevent frequent outbreak of diseases, plants have acquired a complex and multi-layered immune system. Cell surface immune receptors recognize conserved pathogen-associated molecular patterns (PAMPs) and initiate basal defences, known as PAMP-triggered immunity (PTI), while intracellular receptors activate effector-triggered immunity (ETI). Over the past years, this view has evolved toward a model of mutual potentiation, where PTI and ETI reinforce each other to generate robust defence. Yet one fundamental question has remained unresolved: how are these immune responses coordinated across the highly heterogeneous cellular landscape of a leaf?

Our study (you can find it now on the biorxiv server: https://www.biorxiv.org/content/10.64898/2026.04.06.716646v1)  led by our amazing postdoc Shanshuo Zhu provides a compelling answer by positioning autophagy, not simply as a degradation pathway, but as a spatial organizer of immunity across cell types. Our findings try to decipher the long-standing controversial role of autophagy as a pro- or anti-immunity factor: autophagy partitions immune responses between cell-types, aligning defence outputs with cellular context.

Resolving a long-standing paradox

Autophagy has been implicated in contrasting roles during plant-microbe interactions, promoting susceptibility in some contexts while enhancing resistance in others or restricting cell death. This ambiguity has persisted for over a decade, largely because most studies treated the leaf as a homogeneous tissue. Advances in single-cell RNA sequencing have opened new avenues to resolve cell-type-specific responses, an essential step for understanding Pseudomonas infections that enter through stomata and establish within the mesophyll.

By combining single-cell transcriptomics with cell-type-specific complementation approaches, we reveal that this paradox dissolves when spatial context is considered. Autophagy exerts distinct, even opposing functions in different cell-types, likely explaining conflicting observations in the literature.

Guard cells: facilitating pathogen entry

At the leaf surface, guard cells form the first line of defence by closing stomata to prevent bacterial invasion. Intriguingly, our study shows that autophagy actively promotes early stomatal re-opening during infection, thereby facilitating pathogen entry.

Mechanistically, this process is linked to the vacuolar recycling of the ABA receptor PYL4. By targeting PYL4 for degradation, autophagy dampens ABA signalling, which would otherwise maintain stomatal closure. In autophagy-deficient plants, elevated ABA signalling prevents re-opening, restricting bacterial entry.

This finding reframes autophagy as a pathway that pathogens may exploit early during infection – not by directly suppressing immunity, but by modulating physiological gatekeeping at the tissue interface.

Mesophyll: restraining and enabling immunity

Once bacteria bypass the stomatal barrier, the battleground shifts to the mesophyll. Here, autophagy plays a fundamentally different role. We initially hypothesized a mesophyll-specific role, as autophagy-deficient mutants exhibited severe phenotypes, such as chlorosis and tissue collapse upon syringe infiltration, likely originating from mesophyll cells.

Our scRNAseq analysis revealed that loss of autophagy leads to a pre-activated immune state, characterized by elevated expression of key regulators such as the EDS1–PAD4–ADR1 node. At first glance, this might suggest enhanced resistance, possibly also explaining the severe phenotype after infection. However, our investigation reveals a striking uncoupling: despite elevated immune signalling, canonical PTI outputs, such as ROS production and transcriptional responses, are impaired.

This disconnect leads to a central conceptual advance:
immune activation alone is not sufficient for effective defence.

Instead, autophagy appears to maintain the functional integrity and spatial organization of immune signalling networks, ensuring that activation translates into execution. Without it, signalling becomes misregulated, amplified yet ineffective.

We are currently trying to deliver the final evidence that this is indeed driven by the cell-type specific role of autophagy.

A spatial model of immune coordination

Taken together, our work supports a model in which autophagy orchestrates immunity across different cell-types:

• Guard cells: autophagy promotes pathogen entry by enabling stomatal re-opening
• Mesophyll cells: autophagy constrains and organizes immune signalling to ensure effective defence response

This dual role transforms autophagy into a spatial coordinator, aligning immune strategies with tissue-specific demands.

Implications for PTI-ETI potentiation

The findings also offer a fresh perspective on PTI-ETI interplay. The impaired PTI outputs observed in autophagy mutants provide a plausible explanation for previously reported defects in ETI-associated responses, including EDS1-dependent hypersensitive cell death. Here, we are also looking into final experiments to validate a cell-type specific role for autophagy in this process.

Our current working model suggests that autophagy may be required but for maintaining the conditions under which PTI and ETI can effectively potentiate each other. EDS1 may play a central role in it, since it has been shown to be an autophagy target, being essential to constrain immune signalling (Clavel et al., 2024).

Beyond degradation: toward proteostasis-driven immunity

In summary, our study reinforces an emerging view of proteostasis pathways as central regulators of immunity explaining why pathogens love to hijack it – see also our recent review article “Every step you take: How pathogens hijack host proteostasis“.

Our findings raise several intriguing questions:

• How is autophagy itself spatially regulated during infection?
• Do pathogens actively manipulate autophagy in a cell-type-specific manner?
• Would this explain contrasting functions of effectors from the same pathogen inhibiting or activcating autophagy?
• Can spatial control of proteostasis be engineered to enhance crop resistance?

By integrating single-cell resolution with genetics and cell biology, we established a unifying framework:

Plant immunity is not only multilayered but also spatially partitioned-a concept recognized for decades—and autophagy emerges as a key organizer of this architecture.