Biologists at Indiana University Bloomington have shown that the surfaces of plant leaves are coated with a variety of RNA molecules. The finding suggests that RNA present on the surface of leaves may play a role in shaping the microbial communities that inhabit them, potentially influencing plant health and interactions in their environment, according to a new study.
The study, Diverse plant RNAs coat Arabidopsis leaves and are distinct from apoplastic RNAs, was published on January 3, 2025 in Proceedings of the National Academy of Sciences. The first authors are Lucía Borniego and Meenu Singla-Rastogi, postdoctoral fellows in the Department of Biology at Indiana University College of Arts and Sciences. The senior author is Roger Innes, Distinguished Professor of Biology.
What excites us most about this discovery is that it indicates that plants can control their microbiomes, in part, by regulating gene expression in microbes using cross-kingdom RNA interference, also known as RNAi. RNA interference is a well-known type of gene regulation in which cells can reduce the expression of a gene by expressing a small RNA that can base pair with the RNA of the target gene. This type of gene regulation appears to occur in almost all living organisms, but only recently has it been shown that RNAs produced by one organism can be taken up by another organism and then paired with RNA in the recipient organism.”
Roger Innes, Distinguished Professor of Biology, Senior Author, Indiana University Bloomington
RNA is extremely fragile and therefore breaks down quickly if not protected. The study produces some of the first evidence that plants can secrete viable RNA onto their leaf surfaces.
The paper found abundant RNAs on leaf surfaces that are surprisingly stable. The data presented in the paper suggest that this stability may be related to the ability of RNA to form condensates with polysaccharides, such as pectin. By discovering that plant leaves are coated with RNA, this work shows that microbes that colonize leaf surfaces are exposed to plant RNA and likely interact with that RNA. In turn, this likely affects gene expression in these microbes, which could affect microbes that thrive on leaf surfaces.
“Manipulation of microbial communities by environmental RNA is likely to occur in our own guts as well, with RNA secreted by our intestinal epithelial cells,” said Innes. “It is also very possible that RNA on the surfaces of leaves, such as lettuce, could affect our gut microbiomes.”
Additional contributors to the paper were Megha Hastantram Sampangi-Ramaiah and Hana Zand Karimi of Indiana University’s Department of Biology, Patricia Baldrich and Blake C. Meyers of the University of California–Davis, and Madison McGregor of the Donald Danforth Plant Science Center.
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Journal Reference:
Borniego, ML, et al. (2025). Diverse coverage of plant RNAs Arabidopsis leaves and distinguished from apoplastic RNAs. Proceedings of the National Academy of Sciences. doi.org/10.1073/pnas.2409090121.
