A pathogen lncRNA secreted into rice sequesters a host miRNA for virulence | Nature

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Subjects

- Infectious diseases

- Long non-coding RNAs

- Microbe

- miRNAs

Abstract

Plants and animals respond to pathogens through pattern recognition receptor and Nod-like receptor proteins1. Pathogens commonly use protein effectors to suppress host immunity for successful infection2. However, the existence of non-protein effector classes remains comparatively understudied. Here we report an RNA–RNA recognition mechanism governing pathogen–host interaction, mediated by a regulatory RNA-encoding DNA sequence that separately generates two complementary regulatory RNAs. Specifically, a long non-coding RNA transcribed from this DNA region in the fungal pathogen Magnaporthe oryzae translocates into host rice cells and sequesters a complementary microRNA (miRNA), derived from a distinct host DNA region, thereby subverting host immunity. In turn, this rice-derived miRNA promotes disease resistance by repressing the expression of PKR1, a gene that encodes a negative regulator of host immunity. Sequestration of the host miRNA by the fungal long non-coding RNA releases PKR1 expression to facilitate fungal infection. We discovered that this regulatory RNA-encoding DNA sequence is probably widely present across diverse life species, mediating interactions between pathogens and their plant hosts. Collectively, our findings provide an approach for effective disease control using miRNAs derived from this important DNA region.

Main

Host–pathogen interactions represent fundamental processes in nature1,3. Plants rely on innate immunity through cell-surface pattern recognition receptors and intracellular Nod-like receptors to detect pathogen cues1,4, whereas animals combine similar innate pathways with adaptive immunity5. Most known immune regulators are protein-coding genes2, some of which are highly conserved across species6,7.

Pathogens secrete protein effectors to suppress host immunity. Previous studies revealed that microRNAs (miRNAs) and small RNAs act as cross-kingdom regulators of infection8,9,10. However, whether DNA regions encoding other non-protein-coding RNAs contribute to host–pathogen recognition and disease outcome remains unclear. Most eukaryotic genomic DNA does not encode proteins and is often called genetic ‘dark matter’, with poorly understood functions11,12,13. Conserved protein-coding DNA regions, such as transcription factors HOX14,15 and SOX16,17, are well studied, but conserved DNA regions that code for long non-coding RNAs (lncRNAs) are rarely investigated.

Although some conserved and species-specific non-protein-coding sequences are implicated in virulence or host immunity18,19,20, none have been reported to participate directly in pathogen–host recognition or to act as transported pathogenic effectors. Here we demonstrate that the devastating pathogenic fungus Magnaporthe oryzae delivers lncRNA into rice (Oryza sativa) cells to bind to a host miRNA, thereby facilitating infection.

Fungal lnc117761 regulates pathogenicity

To investigate potential roles for lncRNAs in the interaction between microorganisms and hosts during eukaryotic disease progression, we studied the rice blast disease caused by the pathogenic fungus M. oryzae as a bio-interaction model to identify fungal pathogenesis-associated lncRNAs. For this purpose, we searched for lncRNAs with expression that is correlated with infection of rice by the M. oryzae Guy11 strain. We collected RNA samples from four different stages of the M. oryzae life cycle: mycelium, conidiophore, appressorium and infection hypha (colonization). RNA sequencing (RNA-seq) analysis identified many lncRNAs that are highly expressed at the appressorium and invasive hypha stage (Fig. 1a). lnc117761 (1,589 nucleotides (nt)) exhibited the highest expression among the detected lncRNAs (Fig. 1b and Supplementary Table 1). Deletion mutant Δlnc117761 had severely reduced pathogenicity compared with the wild-type strain Guy11 (Fig. 1c–e and Extended Data Fig. 1a–f). lnc117761 is conserved in 150 different M. oryzae strains with only minor variations, including three single-nucleotide polymorphisms or two insertions–deletions in the 5′ sequences of some strains (Supplementary Table 2).

Fig. 1: Fungal lnc117761 is required for M. oryzae pathogenicity and capable of pairing with rice miR5827.The alternative text for this image may have been generated using AI.Full size image

a, Circos plot for lncRNAs differentially expressed at four developmental stages of Guy11 (vegetative mycelia (VEG), conidia (CON), appressoria (APP) and invasive hyphae (COL)), with the top 10 highlighted on the basis of RNA-seq data. Chr., chromosome. b, Expression levels of lnc117761 in Guy11 normalized to MoTUBULIN. CM, complete medium; MM, minimal medium. c–e, Infected rice leaves in punch inoculation assay. The leaves were photographed 5 days after inoculation (c), and blast lesion lengths (d) were measured. Fungal biomass (e) was measured by qPCR of MoPOT2. f, Infectio