Plant Extracellular Vesicles Contain Diverse Small RNA Species and Are Enriched in 10- to 17-Nucleotide “Tiny” RNAs

Abstract

Small RNAs (sRNAs) that are 21 to 24 nucleotides (nt) in length are found in most eukaryotic organisms and regulate numerous biological functions, including transposon silencing, development, reproduction, and stress responses, typically via control of the stability and/or translation of target mRNAs. Major classes of sRNAs in plants include microRNAs (miRNAs) and small interfering RNAs (siRNAs); sRNAs are known to travel as a silencing signal from cell to cell, root to shoot, and even between host and pathogen. In mammals, sRNAs are transported inside extracellular vesicles (EVs), which are mobile membrane-bound compartments that participate in intercellular communication. In addition to sRNAs, EVs carry proteins, lipids, metabolites, and potentially other types of nucleic acids. Here we report that Arabidopsis (Arabidopsis thaliana) EVs also contain diverse species of sRNA. We found that specific miRNAs and siRNAs are preferentially loaded into plant EVs. We also report a previously overlooked class of "tiny RNAs" (10 to 17 nt) that are highly enriched in EVs. This RNA category of unknown function has a broad and very diverse genome origin and might correspond to degradation products.

Abundant expression of maternal siRNAs is a conserved feature of seed development

“…To determine whether siren loci are specific to B. rapa, or are present in more diverse species, we utilized public data from A. thaliana and rice (Autran et al, 2011;Baldrich et al, 2019;Huang et al, 2019;Kirkbride et al, 2019;Rodrigues et al, 2013). Using these datasets we identified 16,422 small RNA loci in A. thaliana and 122,661 loci in rice.…”

The Multiple Facets of Plant–Fungal Interactions Revealed Through Plant and Fungal Secretomics

“…EVs were isolated from apoplastic fluids of Arabidopsis leaves (Baldrich et al, 2019) and analysed for sRNAs. Arabidopsis EVs contain a high number of sRNAs whose sises, classes and identities vary, including miRNAs, siRNAs, as well as so-called tinyRNAs (tyRNAs, 10-17 nt-long) of unknown function and originating from mRNA, rRNA and miRNA precursors.…”

“…Arabidopsis EVs contain a high number of sRNAs whose sises, classes and identities vary, including miRNAs, siRNAs, as well as so-called tinyRNAs (tyRNAs, 10-17 nt-long) of unknown function and originating from mRNA, rRNA and miRNA precursors. Conversely, apoplastic fluids devoid of EVs are enriched in sRNAs able of inducing silent expression in genes with matching sequences, which led to hypothesise on the existence of two independent pathways for sRNA export, with or without EVs as vehicles (Baldrich et al, 2019). Analysis of whole tissue sRNA public datasets in repositories revealed the overrepresentation of tyRNAs in plants compared to mammals.…”

Bacterium-Mediated RNA Interference: Potential Application in Plant Protection

“…OMVs may also be of relevance to bmRNAi, and merit further investigation-one could surmise from both size and functional similarity to RNA secretion systems in eukaryotes-which have been shown to harbor micro RNA [87], that they could contain dsRNA along with other ncRNA. Hypothetically, OMVs would not only assist in partitioning dsRNA away from extracellular ribonucleases increasing its persistence in the plant, but also facilitate its uptake into eukaryotic cells [84].…”