"To understand the plant immune receptor protein complex, I generated two transgenic lines. One contains a pair of over-accumulating Resistance (R) proteins without causing autoimmunity. It leads to a genetic validation of interactive relationships of a paired R proteins (1). It also showed paired R proteins require a balanced expression to achieve a fine-tuned function. Another line contains an additional inducible pathogenic protein, recognized by the corresponding R proteins. This line is currently used by me and two PhD students, who are co-supervised by me and Prof Jonathan Jones. One student Bruno has used this line to generate a genome-wide gene profile to further understand what genes are induced by the effector-triggered immunity (ETI). I have used the biochemical approach in this line to investigate the components within the active R protein complex. In addition, I thought why not take the advantage of this line using genetics? I designed a forward genetic screen and generated a mutagenesis population of M2. This work has been successfully progressed by an international rotation PhD program, in which another student Joanna has taken over as the main part of her PhD project. Currently, we have isolated 50 M3 mutant plants showing good phenotypes that we can progress further. This work together with Bruno’s started with my Obj. 1, and I will be the co-corresponding author in both cases.
For Obj. 2 and 3, because the technology has been improved for the chromatin profile, I decided to change the method to a cost-effective method, ATAC-seq. To increase the sequencing resolution, I have also developed a sequence capture method for focused studies on genes of interests, such as genes activated by ETI. The results along with the method will be submitted for publication soon. In addition, I have learned how to perform large-scale data analysis and how to apply statistics. I have developed a user-friendly software together with my colleague from the bioinformatics team (2). This data analysis pipeline can be applied to any quantitative analysis of capture-seq data.
My proposed work has covered many perspectives of plant immunity, including plant and microbe interactions in relation to available resources, such as nutrients and water in the plant (3); and programmed cell death, which is known as apoptosis or necrosis in mammals (4). Regarding those topics in relation to ETI and their downstream gene activations, I was invited to write two commentaries to provide insights and perspectives towards the future research directions.
Excitingly, when I was studying how plant transcription factors perceive signals from the R proteins, and how they activate defense genes, I isolated a mutant that can compromise partially ETI but can enhance the R protein activated cell death. This has uncoupled bacterial resistance from cell death. Based on this and other unpublished results, I applied and won a 3-year BBSRC future leader fellowship grant. The main question I am trying to address is: what sits in the ‘black box’ between the activation of R proteins and the rapid expression changes of the downstream defense genes? Answers will lead us to a holistic understanding of plant immunity, which in turn will enable the search for effective and sustainable solutions to plant diseases, especially to economically important crops. Winning another 3-year grant enables me to continue to work on the important objectives I have initiated during my MSCA, leads me to become a future leader in my research field, and more importantly, will enable me to get closer to the real solutions of these big questions.
Reference
(1) SU Huh#, V Cevik#, P Ding* et al. (2017) PLoS Pathogens
(2) P Ding#£, JDG Jones£. (2017) Developmental Cell
(3) RK Shrestha#, P Ding#, et al. (2018) GigaScience
(4) P Ding#£, H Guo, JDG Jones£. (2018) Cell Research
(#first author, *second author, £corresponding author)"
