Plants use a variety of mechanisms to communicate with other organisms, including one another. Volatile compounds can signal flowering and attract pollinators, for instance, and mycorrhizal fungal networks can transmit warnings or transfer resources. Small RNAs are on that list of communication molecules, and new findings confirm their potential: according to a paper published October 14 in Nature Plants, the plant Arabidopsis thaliana secretes microRNAs (miRNAs)—a type of small, single-stranded RNAs—into its liquid growth medium. Nearby individuals then take up these RNAs, which alter their gene expression patterns by binding to messenger RNAs and preventing certain genes from being translated into proteins (a process known as RNA interference).
Hailing Jin, a plant molecular geneticist at the University of California, Riverside, who was not involved in the study, says it’s exciting to see that plants can take up microRNAs from the environment, including those “secreted by other plants through the roots.”
That small RNAs can be exchanged between different organisms is not new. In addition to their role as regulators of gene expression within an individual—as part of development or in response to stress—they have been implicated in defense against pathogens in recent years. For instance, Arabidopsis cells infected with the pathogenic fungus Botrytis cinerea secrete small RNAs packed in extracellular vesicles that, when delivered into their attacker, inhibit its virulence. Plants are also able to take up sprayed RNA molecules targeting genes from pathogens. The recent findings are the first evidence of plants taking up RNA secreted by other plants into the environment.
“The results were totally unexpected,” Pierdomenico Perata, a plant physiologist at the Sant’Anna School of Advanced Studies in Pisa, Italy, and coauthor on the study, writes in an email to The Scientist. Given RNAs’ reputation as “highly unstable” molecules outside of a cell, he writes his team “expected miRNA to be incompatible with a non-sterile environment such as the growth medium.”
Perata relates that his team was working “on a totally unrelated topic”—exploring the role of RNA interference under limited oxygen availability—and it was for that purpose that they hydroponically grew Arabidopsis plants engineered to produce large quantities of specific miRNAs. As they simply wanted them to produce seeds, he adds, the researchers “didn’t care about placing different plant lines in separate trays.” But then they noticed that wildtype plants sharing the mutants’ hydroponic solution had phenotypes different from those expected—for example, those growing next to mutants that overexpressed miRNAs targeting developmental genes had their own flowering time altered. According to Perata, that’s when he and his colleagues wondered “if miRNAs could be released in the liquid growth medium, thereby affecting the phenotype of wildtype plants.”
The researchers tested the hydroponic solution, and lo and behold, they detected miRNAs. These miRNAs were present regardless of whether the plants growing in the solution were wildtype or mutated to overexpress them, although more RNAs were detected in the mutants’ solution. Furthermore, cultivating both lines in the same solution resulted in wildtype plants with notably lower expression levels of the genes targeted by the mutants’ boosted miRNA molecules. Applying miRNAs extracted from the mutants or chemically synthesized equivalents also reduced gene expression.
Why would a plant need to affect another plant’s gene expression? One possibility, Perata posits, is that “sharing information by exchanging RNA would allow plants experiencing a stress to warn nearby plants, not yet affected by the stress.” Competition could be another explanation, he writes; for instance, if a plant releasing miRNAs “could inhibit physiological functions in a nearby plant,” it could gain “a competitive advantage for the use of resources.”
One unanswered question is how the plants take up these tiny molecules from the environment. Previous work studying RNA exchange between plants and pathogens suggests that exosomes, a type of vesicles that can act as delivery vehicles, might be involved in the process. However, the researchers found that applying extracted, presumably naked miRNAs or synthetic RNAs had an effect in gene expression, suggesting that exosomes aren’t needed for uptake.
Hui-Shan Guo, a plant microbiologist at the Institute of Microbiology at the Chinese Academy of Sciences, says the study’s evidence for naked RNA uptake confirms previous reports of gene silencing via sprayed-on RNA. She suggests in an email to The Scientist that, as with nutrients, plants might actively assimilate small RNAs from the environment. But unlike the substances plants are known to import, naked RNA molecules “were thought instable,” she says, so “RNA uptake was ignored or underestimated.”
Jin agrees that the evidence in the paper supports the hypothesis that plants can uptake naked miRNA, but she says she wonders whether their secretion still occurs via exosomes from roots—a question the authors did not explore. She adds she also suspects that these vesicles could protect the miRNAs, helping the plants to accomplish a more efficient uptake. Otherwise, the molecules could be more easily degraded in the soil and in the environment, she speculates.
Guo points out that, as this mechanism has only been explored in hydroponically grown plants, it’s not yet clear “whether seedlings growing in soil . . . would have effects on regulation of gene expression in [nearby] plants”—something future studies could examine.
Jin adds that these new findings open a lot of new questions, and that there is likely much more to learn about the role of RNA in plant communication. What we currently know about it is just the “tip of the iceberg,” she concludes.