Research in the Parker group

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 reactions to competing environmental stresses such as drought or nutrition shortage. We interrogate mainly plant-microbe interactions and stress network architecture in the model species Arabidopsis thaliana. This provides a molecular genetic framework for constructing pathways and a reference point for comparative studies with other species. Ultimately, our aim is to identify 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 structural determinations to computational phylogenetics and analysis of evolutionary covariation. The following projects are currently running in the lab:

1. Decision-making and execution of plant NLR immunity (Xinhua Sun, Joram Dongus, Dmitry Lapin). 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 the rapid transcriptional reprogramming of defences as one important resistance output, and regulated cell death (RCD) as a second immunity branch. Further 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.  Variation in biotic stress networks between plant lineages (Dmitry Lapin, Joel Fernandes, Oliver Johandrees). Using the known stress pathway functions and properties in Arabidopsis we are investigating how the 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 defence signalling module and pathway usage between plant species.

3. Structural analysis of immunity components (Huanhuan Sun). 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 the 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 (Anthony Piro, Charles Uhlmann).  In this project, we’re exploiting genetic material in Arabidopsis to explore how plants discriminate between beneficial 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. Here we are examining the extent of natural variation in A. thaliana defence pathway homeostasis in response to two different ambient temperatures (20^oC and 16^oC) – essentially a genotype x environment (G x E) experiment within the normal range of this species. The analysis has uncovered extensive 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 increased pathogen resistance. We’re using GWAS and QTL studies 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 want 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 (Paul Runge).  Together with Rubén Alcázar (University of Barcelona) and Eric Kemen (Uni Tübingen), we’re characterizing natural Arabidopsis thaliana populations in and around the town of Gorzów 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 these 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 these areas, please contact Jane Parker (parker@mpipz.mpg.de) with a CV and a short description of your scientific interests.

Recent Publications

Dongus JA, Bhandari D, Patel M, Archer L, Dijkgraaf L, Deslandes L, Shah J, Parker JE. 2019. Arabidopsis PAD4 lipase-like domain is sufficient for resistance to green peach aphid. Mol Plant Microbe Interact. 2019 Nov 8. doi: 10.1094/MPMI-08-19-0245-R. [Epub ahead of print]

Lapin D, Kovacova V, Sun X, Dongus J, Bhandari DD, von Born P, Bautor J, Guarneri N, Stuttmann J, Beyer A, Parker JE. 2019. A coevolved EDS1-SAG101-NRG1 module mediates cell death signaling by TIR-domain immune receptors. Plant Cell. Oct;31(10):2430-2455. doi: 10.1105/tpc.19.00118. Epub 2019 Jul 16.

Voss M, Toelzer C, Bhandari DD, Parker JE, Niefkind K. 2019. Arabidopsis immunity regulator EDS1 in a PAD4/SAG101-unbound form is a monomer with an inherently inactive conformation. J Struct Biol. 2019 Sep 21:107390. doi: 10.1016/j.jsb.2019.09.007.

Deremetz A, Le Roux C, Idir Y, Brousse C, Agorio A, Gy I, Parker JE and Bouché N. 2019. Antagonistic actions of FPA and IBM2 regulate transcript processing from genes containing heterochromatin. Plant Physiol. 180: 392-403.

Bhandari DD, Lapin, D, Kracher B, von Born P, Bautor J, Niefind K, Parker JE. 2019. An EDS1 heterodimer signalling surface enforces timely reprogamming of immunity genes in Arabidopsis. Nature Comms 10: Article 722.