Small Luggage for a Long Journey: Transfer of Vesicle-Enclosed Small RNA in Interspecies Communication

Abstract

In the evolutionary arms race, symbionts have evolved means to modulate each other's physiology, oftentimes through the dissemination of biological signals. Beyond small molecules and proteins, recent evidence shows that small RNA molecules are transferred between organisms and transmit functional RNA interference signals across biological species. However, the mechanisms through which specific RNAs involved in cross-species communication are sorted for secretion and protected from degradation in the environment remain largely enigmatic. Over the last decade, extracellular vesicles have emerged as prominent vehicles of biological signals. They can stabilize specific RNA transcripts in biological fluids and selectively deliver them to recipient cells. Here, we review examples of small RNA transfers between plants and bacterial, fungal, and animal symbionts. We also discuss the transmission of RNA interference signals from intestinal cells to populations of the gut microbiota, along with its roles in intestinal homeostasis. We suggest that extracellular vesicles may contribute to inter-species crosstalk mediated by small RNA. We review the mechanisms of RNA sorting to extracellular vesicles and evaluate their relevance in cross-species communication by discussing conservation, stability, stoichiometry, and co-occurrence of vesicles with alternative communication vehicles.

Keywords: argonaute; communication; exosomes; extracellular vesicles; gene silencing; miRNA; small RNA.

Figure 1

Overview of sRNA biogenesis in mammals. Pri-miRNA is cleaved into pre-miRNA by the microprocessor complex, consisting of two nuclear proteins, Drosha and its cofactor DGCR8. Pre-miRNA is exported to the cytoplasm through Exportin-5 (Exp-5), then bound and processed into short dsRNA sequences of ~22 nt by the RBP Dicer and its associated factors TRBP and PACT. Structured ncRNA encompassing stretches of paired nucleotides such as tRNAs can also be recognized and processed as Dicer substrates. Dicer recruits AGO2 and its cleavage yields two single-stranded RNA sequences, called the leading strand and the guide strand (or miRNA^*). The leading strand is actively repositioned in the complex and loaded onto AGO2 to form a RISC, which can exert RNA silencing.

Figure 2

Host-induced hairpin RNA-mediated silencing confers resistance to the fungal pathogen Fusarium. (A) Host-induced hairpin RNA-mediated silencing enables plant to resist to the fungal pathogen Fusarium. In Arabidopsis, expression of a dsRNA construct complementary to fungal CYP51 transcripts can immunize transgenic plants to the pathogenic ascomycete Fusarium graminearum by inhibiting fungal growth (Koch et al., 2013). The vehicles through which transgenic dsRNA and/or sRNA is transferred are unknown and possibly include plant EVs, secreted RNPs and/or lipoproteins. (B) Botrytis cinerea sRNA populations hijack Arabidopsis RNAi pathways to suppress plant immunity. Populations of sRNA derived from a B. cinerea retrotransposon are shuttled to infected Arabidopsis and Solanum lycopersicum. In plants, fungal sRNA are loaded onto AGO1 and direct the silencing of diverse proteins, including Mitogen-activated kinases, which impact the host's immune response (Weiberg et al., 2013). The vehicles through which dsRNA and/or sRNA are transferred from fungus to plant are unknown and possibly include fungal EVs, secreted RNPs and/or lipoproteins.

Figure 3

Host miRNA targets microbiota gene expression. Gut epithelial cells release miRNAs that can be recovered in murine and human fecal matter. Fecal miRNA populations are likely stabilized through EVs and possibly through lipoproteins or RNPs containing AGO2. Host miRNA enters E. coli and F. nucleatum where it co-localizes with bacterial nucleic acids and impacts bacterial growth by interacting with nucleic acids (Liu et al., 2016).

Figure 4

Mechanisms of sRNA loading to EVs. Schematic view of a mammalian cell releasing sRNA through lipoproteins and AGO2 RNPs (left), exosomes (center), and membrane-shed microvesicles (right). Properties broadly associated with RNA targeting to EVs are listed on top (white font). Mechanisms, lipid structures and RBPs involved in sorting RNA molecules to exosome and microvesicles are portrayed.