Resistance pathway dynamics in plant immunity

Research in the Parker lab

We study how plants activate and control their innate immune responses. The regulation of immunity pathways is crucial for combating diseases caused by pathogens, accommodating neutral or beneficial microbes, and prioritizing responses to competing environmental stresses such as drought or nutrition shortage. We interrogate plant-microbe interactions and stress network architecture mainly in the model species Arabidopsis thaliana. This provides a molecular genetic framework for constructing pathways and a reference point for comparative studies with other plant species. Ultimately, our aim is to identify the key players and processes in cells and tissues that enable plants to respond effectively to microbes in the environment. We use approaches ranging from genetics, RNA-seq, ChIP-seq, LC-MS/MS mass-spectrometry, live-cell imaging/FRET-FLIM and protein biochemistry/structure analysis to computational phylogenomics and evolutionary covariation studies.

Current Projects in the lab are:

1. Decision-making and execution of plant NLR immunity. While NLR activation mechanisms are now quite well understood, there are major gaps in our knowledge of how activated NLRs mobilize anti-microbial defences. Using Arabidopsis, we are characterizing some key processes and protein complexes that link NLRs to rapid transcriptional reprogramming of defences, as one important resistance output, and regulated cell death (RCD) as another immunity branch. The study involves a functional dissection of the transcriptional and cell death machineries in ETI, and concerted roles of signalling NLRs with non-NLR signal transducers (the EDS1 family of nucleocytoplasmic proteins) in controlling leaf cell and tissue immune responses.

2.  Biotic stress network architecture across seed plant lineages. Using the known stress pathway functions and properties in Arabidopsis we are investigating how defence networks operate in unrelated plant species such as the solanaceous model, Nicotiana benthamiana (tobacco), and monocot crops, barley and rice. This analysis is starting to reveal interesting levels of variation in the usage of defence signalling modules and pathways between plant clades.

3. Immunity protein complex biochemistry and structure-guided functions. To gain a molecular (atomic-level) understanding of immunity pathway functions and dynamics we’re expressing recombinant protein versions of key NLR activation and signalling components, working towards a structural determination of immunity modules by crystallography and cryo-EM. These experiments, done in collaboration with Jijie Chai’s group at MPIPZ/Uni. Cologne, should provide crucial molecular insights to how plants regulate and execute immune responses. 

4. Impact of immunity pathways on root accommodation of a fungal endophyte.  Here, we’re exploiting genetic material in Arabidopsis to investigate how plants discriminate between beneficial, neutral and harmful (pathogenic) microbes in the soil. In a collaboration with the group of Alga Zuccaro (Uni. Cologne), we’re examining a root accommodation programme between Arabidopsis and fungal endophyte strains, which the host is normally able to contain and benefit from in terms of resilience to biotic and abiotic stresses. We’re testing the effects of different immunity/biotic stress mutants and nutrient conditions on plant-endophyte colonization outcomes. This will allow us to identify which environmental cues and parameters are key to plant accommodation vs. defence decisions.  

5. Within-species genetic variation in immunity responses to temperature. We are examining the extent of natural variation in A. thaliana defence pathway homeostasis in response to two different ambient temperatures (20oC and 16oC) - essentially a genotype x environment (G x E) experiment within the normal range of this species. The analysis has uncovered considerable variation in temperature-conditioned accumulation of the stress hormone SA. Our results suggest genetic plasticity in the regulation of defence outputs and potential benefits of high SA levels in terms of pathogen resistance. We’re using GWAS to identify candidate genes underlying SA x temp trait variation and investigating whether differences in SA pathway homeostasis can be explained at the level of molecular cross-talk within the plant stress hormone network. We also aim to test how robust the differential G x E interactions are under field conditions.

6. Analysis of NLR maintenance in a wild A. thaliana population. Together with Rubén Alcázar (University of Barcelona) and Eric Kemen (Uni Tübingen), we’ve been sampling and characterizing natural Arabidopsis thaliana populations in and around the town of Gorzów (Gw) in Poland. In these populations, a complex locus of eight NLR (DM2) genes has been maintained at moderate frequency. We’re measuring the distribution of DM2 and other NLR genes in the populations and isolating pathogens from the field. Also, individual plants at different Gorzów sites are being sampled over multiple years for leaf-associated microbes. Computational network analysis of the leaf microbiota combined with plant-microbe reconstitution assays in genetically defined Gw individuals should allow us to relate plant genotype with microbial community structure and ask whether NLR composition contributes to the structuring of microbial populations beyond determining local pathogen resistance.

 If you’re interested in joining the group to pursue research in any of these areas, please contact with a CV and a short description of your scientific interests.



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