AI predicts cross-kingdom interactions at the plant-pathogen interface
This is one of the funded projects for our 2025 Undergraduate vacation bursary, click here to return to the list of 15 projects.
| This project is going to be… | Experimental (lab/field based) |
| Institute | The University of Oxford |
| Project supervisor | Dr. Jie Huang |
| Title of Project | AI predicts cross-kingdom interactions at the plant-pathogen interface |
| Date of Project Commencement | 21 July 2025 |
| Duration (weeks) | 6 |
| Brief Description of Project | Artificial intelligence has reached a significant milestone with the development of AlphaFold, a revolutionary protein-structure prediction technology that has greatly enhanced our ability to model molecular interactions in biology. Our laboratory leverages the latest AlphaFold-Multimer platform to predict putative apoplastic protein complexes that may play key roles in plant immunity.Recently, I employed this approach to uncover novel interactions between defense-related hydrolase enzymes from tomato and secreted effector proteins from major tomato pathogens (Homma and Huang et al., 2023). The AI-predicted cross-kingdom protein complexes were subsequently validated through a suite of biochemical techniques, including activity-based protein profiling (ABPP) and co-immunoprecipitation (Co-IP). Building on the success of this strategy, we have expanded our application of AlphaFold-Multimer to investigate additional plant-pathogen systems. Most recently, we have generated a comprehensive dataset of candidate apoplastic protein interactions between the model plant Nicotiana benthamiana and three bacterial pathogen Pseudomonas syringae. This project aims to experimentally validate these predicted interactions using molecular cloning, agroinfiltration, recombinant protein expression and purification, as well as biochemical assays such as ABPP and Co-IP.The student undertaking this project will gain hands-on experience at the forefront of plant pathology research, acquiring essential laboratory skills while developing a deeper understanding of plant immunity and the power of AI-driven predictions in biology. Beyond the laboratory, the student will have the opportunity to engage with the broader research community through participation in lab meetings, journal clubs, and collaborative discussions. Additionally, this project offers the invaluable experience of working within the world-class research environment of the University of Oxford, renowned for its excellence in education and groundbreaking scientific contributions. I will serve as the primary day-to-day supervisor for this project. I am a postdoctoral researcher in the Plant Chemetics Laboratory, led by Prof. Renier van der Hoorn at the University of Oxford. I have extensive experience in mentoring student research projects, with two of my supervised students having been awarded the BSPP Undergraduate Prize.This proposal is submitted with the full support of Prof. Renier van der Hoorn, ensuring that the project will be hosted within the Plant Chemetics Laboratory. The student will also have the opportunity to engage with the broader research group through participation in lab meetings, journal clubs, and collaborative discussions. Recommended reading for the project1. AlphaFold-Multimer predicts cross-kingdom interactions at the plant-pathogen interface 2. Activity-based proteomics uncovers suppressed hydrolases and a neo-functionalised antibacterial enzyme at the plant–pathogen interface3. The Increasing Impact of Activity-Based Protein Profiling in Plant Science |
