Unraveling the plant cell wall integrity mechanisms in nematode feeding structures (using spatial transcriptomics)

Cyst and root-knot nematodes are destructive plant-parasites that threaten global food security by inducing permanent feeding structures in host roots. These feeding structures serve as the sole nutrient source for the nematodes. Therefore, preventing feeding structure formation is a key target for crop improvement. In this thesis, we propose a novel strategy to enhance plant immunity exploiting the plant’s own cell wall integrity (CWI) mechanism. We hypothesize that plant CWI receptors perceive the cell wall modifications required for nematode feeding structure formation and subsequently activate immune responses.

We focused on a putative CWI receptor family, the Proline-rich Extensin-like Receptor Kinases (PERKs), in the model plant Arabidopsis thaliana. We demonstrate that Arabidopsis plants overexpressing PERK13 display almost complete resistance to the cyst nematode Heterodera schachtii, while perk13 knockout plants become hyper-susceptible. Transcriptome and reporter gene expression analyses indicate that the increased susceptibility of perk13 mutants involves the upregulation of DMR6-LIKE OXYGENASE1 (DLO1), a suppressor of salicylic acid-mediated immunity. Furthermore, we show that recombinant PERK13 binds pectin in vitro, confirming its function as a CWI receptor that regulates host immunity during early H. schachtii infection.

To resolve the spatial complexity of host-parasite interactions, we introduced RNA tomography, a spatial transcriptomics technology, for use in plant tissues. By generating high-resolution spatial gene expression maps of both host and parasite simultaneously in H. schachtii-infected Arabidopsis roots, we offer novel insights into the early stages of plant-nematode interaction that would not have been possible with traditional bulk transcriptomics.

Finally, we investigated the role of Arabidopsis PERKs in infection by the root-knot nematode Meloidogyne incognita. Nine perk knockout mutants were more susceptible to the root-knot nematode than wild-type Arabidopsis plants. Of these nine, six perk knockouts displayed similar relative susceptibility to H. schachtii. Remarkably, PERK13 overexpression plants displayed increased susceptibility to M. incognita, in contrast to the near complete resistance to H. schachtii. RNA tomography revealed that PERK13 is irregularly expressed across root tissues; thus, its expression is not restricted to feeding structures or surrounding tissue. Transcriptome analysis showed that differentially expressed genes in M. incognita-infected plants overexpressing PERK13 were associated with cell wall biogenesis and restructuring, indicating that PERK13 regulates plant susceptibility through distinct cell wall modifications during feeding structure formation.

Altogether, this thesis elucidates the multifaceted role of CWI receptors during nematode infection, highlighting specific trade-offs that must be considered when engineering CWI-based nematode-resistant crops.