The Innovation Team of Agricultural Microbial Resources at the Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences (CAAS), revealed a complex interaction network between Pseudomonas syringae core effectors and plants using a systematic transcriptome study. which was published in New Phytologist entitled "The transcriptome landscape induced by Pseudomonas syringae core effectors reveals new insights into the immune network in Nicotiana benthamiana". This study provided new perspectives on global plant immunity and identified a novel signaling pathway. 

Microbe–plant interactions are highly complex: microbes secrete effectors to trigger multilayered biochemical responses, while plants in turn activate cascades of immune defenses. The model pathogen P. syringae pv. tomato (Pst) DC3000 delivers over 30 effectors into host cells via the type III secretion system (T3SS). Previous studies often focused on single effectors, but such approaches faced limitations, including artificial over expression, redundancy among effectors, and difficulty in capturing the dynamics of natural microbe–plant interactions.

In this study, researchers employed an effectorless polymutant of Pseudomonas syringae pv. tomato DC3000 DC3000D36E together with mini-Tn7 and GATEWAY expression systems to systematically analyze the transcriptomic profiles induced by 13 core effectors in Nicotiana benthamiana.

Key findings include:

The core effector repertoire collectively influenced 19% of the host transcriptome, underlying the complexity of plant–microbe interactions.

Non-pathogenic mutant strains (D36E/D36ΔfliC) triggered much broader transcriptional changes than those induced by flagellin alone, suggesting the existence of novel basal immune elicitors beyond flagellin proteins.

Comparative transcriptomics revealed not only conserved pathways jointly regulated by redundant effectors but also specific effector-mediated interaction networks.

Genetic analysis identified multiple D36E-Induced and repressed by effector (DIRE)genes, which showed broad-spectrum immune responses across different pathogen effectors. Ten DIREs were mapped to key immune components, including cell surface pattern recognition receptors (DIRE-3/-10), receptor-like cytoplasmic kinases (DIRE-1/-5), MAPK kinases (DIRE-2/-7), transcription factors (DIRE-6/-9), and downstream hydrolases (DIRE-4/-8), forming a novel conserved immune signaling pathway. 

This breakthrough provides crucial insights into potential plant immune network hubs and offers new molecular targets for crop disease resistance breeding and design.

Figure 1. Global differential gene expression in Nicotiana benthamiana induced by the core effectors.

Figure 2. Number of differentially expressed genes identified by RNA-seq in Nicotiana benthamiana after inoculation with D36E and its core effector derivatives.

Figure 3. Novel immune signaling pathways in Nicotiana benthamiana regulated by bacterial effectors.

The study was co-authored by Dr. Ma Yinan (now Assistant Research Fellow at the Institute of Biotechnology, CAAS), Ph.D. candidates Cong Shen and Li Junzhou (Associate Research Fellow), with Prof. Wei Hailei as the corresponding author. This work was supported by the State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, the National Natural Science Foundation of China, the Major Science and Technology Project of China National Tobacco Corporation, the Agricultural Science and Technology Innovation Program of the CAAS, and the BeijingInnovation Consortium of the Agriculture Research System.

This research marks an exciting new developmentfor Wei Haile's team in exploring microbe–host interaction mechanisms, following previous publications in Cell Host Microbe, 2015; Cell Reports, 2018; Molecular Plant, 2020;  Engineering, 2023; Microbiology Spectrum, 2023ab; Cell Reports, 2025.

Full article link: https://doi.org/10.1111/nph.70479