Cross-Kingdom RNA Interference in Plant Pathogen Interactions

Cross-kingdom RNA interference encompasses the bidirectional transfer of RNA molecules between plants and their pathogens, enabling one organism to modulate gene expression in another. Fungal and oomycete pathogens deploy small RNAs to suppress host immunity by hijacking the plant’s RNA-induced silencing machinery, while plants counterattack by exporting small RNAs or even messenger RNAs that silence virulence genes in the invader. These RNAs travel via extracellular vesicles or through direct uptake pathways, and their activity depends on conserved components such as Dicer-like enzymes and Argonaute proteins. Advances in delivery methods—ranging from transgenic expression of double-stranded RNAs (host-induced gene silencing) to exogenous application of RNA sprays (spray-induced gene silencing)—have demonstrated practical potential for sustainable disease control. Mechanistic studies of vesicle biogenesis, endocytic uptake and systemic transport are rapidly elucidating how distinct kingdoms exploit shared silencing pathways, offering new strategies to protect global crop production.

Research from Nature Portfolio

Recent studies have demonstrated that fungal pathogens secrete small RNAs via extracellular vesicles that are taken up by plant cells through clathrin-mediated endocytosis, with key vesicle markers coordinating this process and host endocytic components enabling gene suppression. Foundational work has also shown that foliar applications of long double-stranded RNAs can be taken up by pathogens via a plant-mediated pathway, processed by fungal silencing machinery and transported systemically, offering proof of concept for RNA-based disease control strategies in diverse crop–pathogen systems.

Cross-Kingdom RNA Interference in Plant Pathogen Interactions publication trend

The graph below shows the total number of articles in cross-kingdom rna interference in plant pathogen interactions across all publications each year (not limited to Nature Index journals).

Technical terms

Cross-kingdom RNA interference: Gene-silencing interactions in which small RNAs produced by one organism modulate gene expression in another organism from a different biological kingdom.

Small RNAs (sRNAs): Short non-coding RNA molecules, such as siRNAs and microRNAs, that guide sequence-specific silencing of target genes.

Extracellular vesicles (EVs): Lipid-bound particles released by cells that transport diverse biomolecules, including RNA, between organisms.

Host-induced gene silencing (HIGS): A strategy in which plants express double-stranded RNAs to trigger RNA interference in invading pathogens.

Spray-induced gene silencing (SIGS): Topical application of RNA molecules to plants to induce RNAi-mediated control of pathogens upon uptake.

Argonaute proteins: Core components of the RNA-induced silencing complex that bind small RNAs and mediate target recognition and cleavage.

Clathrin-mediated endocytosis (CME): A cellular uptake mechanism involving clathrin-coated vesicles that internalises extracellular materials, including RNA-loaded vesicles.

References

1. Fungal small RNAs ride in extracellular vesicles to enter plant cells through clathrin-mediated endocytosis. Nature Communications (2023).
2. Plant mRNAs move into a fungal pathogen via extracellular vesicles to reduce infection. Cell Host & Microbe (2023).
3. An RNAi-Based Control of Fusarium graminearum Infections Through Spraying of Long dsRNAs Involves a Plant Passage and Is Controlled by the Fungal Silencing Machinery. PLOS Pathogens (2016).
4. Spray‐induced gene silencing for disease control is dependent on the efficiency of pathogen RNA uptake. Plant Biotechnology Journal (2021).
5. Oomycete small RNAs bind to the plant RNA-induced silencing complex for virulence. eLife (2020).
6. Small RNAs and extracellular vesicles: New mechanisms of cross-species communication and innovative tools for disease control. PLOS Pathogens (2019).
7. Trans-kingdom Cross-Talk: Small RNAs on the Move. PLOS Genetics (2014).