Collaborative Research: Ideas Lab: The Role of Extracellular RNA in Intercellular and Interkingdom Communication

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This project is a collaboration among seven laboratories with diverse and complementary expertise. The overarching goal of the project is to understand the role of extracellular RNA (exRNA) in communication between cells and in shaping the community of microbes, especially bacteria, that live on and inside plants, insects, and humans. These collections of microbes are often referred to as microbiomes and are critical for the health of plants and animals, including humans. A healthy microbiome promotes a healthy immune system, but how healthy microbiomes are maintained is poorly understood. This project will test the hypothesis that RNA secreted by host cells plays a central role in maintaining health both through communication among cells and by modifying the microbiome. RNA is best known for its key role in protein production inside cells, such as in RNA-based COVID vaccines. However, not all RNA encodes proteins, and cells produce more non-coding RNA than coding RNA, some of which is actively pushed into the environment by cells. This secreted RNA appears to be taken up by other cells, including bacteria and fungi, where it could potentially impact their growth. Understanding how exRNAs shape communication between cells and organisms will enable manipulation of exRNA communication in both agriculture and medicine, which will lead to development of environmentally friendly pesticides, as well as treatments that promote formation of healthy microbiomes in both plants and animals. This knowledge will also enable development of diagnostic and therapeutic tools for early detection and/or treatment of disease.All cellular organisms secrete RNAs. The functions of these extracellular RNAs (exRNAs), however, are poorly understood. Two likely functions are intercellular and interkingdom communication. Open questions abound in exRNA biology: how are exRNAs selected for secretion, how are they targeted to recipient cells, and what are their roles in normal health and organismal fitness? Arabidopsis leaf exRNA isolates are highly enriched in the post-transcriptional modification N6-methyladenosine (m6A) (as compared to total cellular RNA) suggesting that post-transcriptional modifications may tag specific RNAs for export. Consistent with this, human exosomal microRNAs are enriched with m6A (relative to cytosolic microRNAs). Interestingly, a large number of mammalian small non-coding RNAs (ncRNAs) that localize to the external cell surface were recently found to harbor specific sialylated glycan modifications. These observations suggest that specific RNA modifications tag RNAs for cellular export and direct entry into appropriate recipient cells. This project will 1) test the hypothesis that exRNAs have specific features marking them for secretion and uptake, both within and among species, 2) determine how exRNAs are transferred from signaler to receiver cells, and 3) assess the impact of exRNA on microbiome health and composition through examining human gut, insect gut, and leaf surface models.This project was co-funded by the Directorate for Biological Sciences, and the Plant Genome Research Program and the Plant Biotic Interactions Program in the Division of Integrative Organismal Systems.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.