Cells in the tree of life exchange ‘text messages’ using RNA

“I was expecting DNA,” Erdmann recalls, following reports that other archaeal species were packing DNA into EVs. Instead, her lab found a whole smorgasbord of RNA — specifically noncoding RNAs, mysterious stretches of nucleotides with no known function in archaea. These noncoding RNA sequences were far more abundant in the EVs than in the archaeal cells themselves. “It was the first time we’d found RNA in EVs in archaea,” she said.

Erdmann wondered if there was a purpose for the archaeal EVs. A cell can spontaneously make vesicles when its membrane pinches in on itself to form a small bubble that then detaches. But other mechanisms involve more active and purposeful processes, similar to those that move molecules around in the cell. Erdmann’s group identified an archaeal protein that was essential for the production of RNA-containing EVs.

That suggested to her that the RNA wasn’t getting into the EVs by chance, and that the process wasn’t just waste disposal. “It’s very likely that (archaea) are using them for cell-to-cell communication,” she said. “Otherwise, why would you put so much energy into throwing out random RNA in vesicles?”

Erdmann is not sure why the Haloferax Microbes fill their vesicles with RNA, while other archaea prefer DNA. But she suspects it has to do with how time-sensitive the molecular message is. “RNA is a different language than DNA,” she said, and it serves a fundamentally different purpose, both inside and outside cells.

An organism’s DNA should be stable and relatively unchanging throughout its life. It can pick up spontaneous mutations or even extra genes, but it takes generations of natural selection for temporary changes in DNA sequences to take root in a population. RNA, on the other hand, is constantly in flux, responding to dynamic conditions inside and outside the cell. RNA signals don’t last long, but they don’t have to, because they can become irrelevant so quickly.

As a message, RNA is ephemeral. This is a feature, not a bug: It can have only short-term effects on other cells before it breaks down. And because the RNA in a cell is constantly changing, “the message you can send to your neighboring cell” can also change very quickly, Erdmann said. In that sense, it’s more like a quick text message or email meant to communicate timely information than, say, runes carved in stone or a formal memo on letterhead.

While it appears that neighboring archaea are taking up and internalizing EVs from their fellow cells, it’s not yet clear whether the messages are affecting them. Erdmann also wonders what happens to these vesicles in the wild, where many different organisms might be within earshot of the messages they’re carrying.

“How many other organisms in the same environment could pick up this message?” she asked. “And do they just eat it and use the RNA as food, or do they actually detect the signal?”

While that may still be a mystery to Haloferaxother researchers have shown that cells from different species, kingdoms, and even domains of life can send and receive remarkably targeted molecular messages.

Biological crosstalk

Although RNA is short-lived, it has emerged as a molecular marvel that can change shape. It is best known for helping cells produce new proteins by copying DNA instructions (as messenger RNA, or mRNA) and passing them to the ribosome for construction. However, its flexible backbone allows RNA to fold into a number of shapes that can affect cell biology. It can act as an enzyme to speed up chemical reactions in cells. It can bind to DNA to turn genes on or off. And competing strands of RNA can confuse mRNA instructions in a process called RNA interference, which prevents the production of new proteins.

As researchers increasingly appreciate how RNA alters cell activity, they’ve been studying strategies to use this mutable small molecule as an experimental tool, a disease treatment, and even the basis for the Covid-19 mRNA vaccine. All of these applications require delivering RNA into cells, but evolution seems to have gotten ahead of us: EVs ship RNA even to cells that might not want to receive the message.

About 10 years ago, molecular geneticist Hailing Jin and her lab at the University of California, Riverside discovered that two organisms from different kingdoms — a plant and a fungus — exchange RNA as a form of warfare. Jin studied Botrytis cinereaa fluffy gray mold that devastates crops like strawberries and tomatoes, when she saw it exchanging RNA with the plant Arabidopsis (sand rocket) during infection. The Botrytis fungus delivered RNA that prevented the plant from fighting the infection. Later research showed that the plant cells could respond with their own burst of RNA that damaged the fungus.

In this “co-evolutionary arms race,” as Jin described it, both organisms used EVs as vehicles for these delicate but damaging RNA messages. Previously, scientists interested in host-pathogen dynamics have focused primarily on proteins and metabolites, Jin said, because those molecules are easier to study. But it makes sense that organisms have multiple ways to cope with environmental challenges, she said, including using RNA to interact with distant evolutionary relatives.

In the past decade, more scientists have discovered examples of cross-kingdom RNA exchange as an offensive strategy during infection. Parasitic worms living in mouse intestines release RNA in EVs that disable host defensive immune proteins. Bacteria can send messages to human cells that suppress antibacterial immune responses. The fungus Candida albicans has even learned to twist a message from human electric vehicles to its own advantage: it uses human RNA to promote its own growth.

Interkingdom correspondence isn’t always hate mail. These interactions have been seen in friendly (or neutral) relationships, too, Jin said. For example, bacteria living symbiotically in the roots of legumes send RNA messages to promote nodulation — the growth of small bumps where the bacteria live and fix nitrogen for the plant.

How can RNA from one branch of the tree of life be understood by organisms on another branch? It’s a common language, Buck said. RNA has likely been around since the beginning of life. As organisms have evolved and diversified, their RNA-reading mechanisms have remained largely the same. “RNA already has a meaning in every cell,” Buck said. “And it’s a pretty simple code.”

So simple, in fact, that a receiving cell can open and interpret the message before realizing it might be dangerous, just as we instinctively click on a link in an email before noticing the suspicious sender’s address. Earlier this year, Jin’s lab showed that Arabidopsis Plant cells can send seemingly innocent RNA instructions that have a surprising impact on a hostile fungus. In experiments, Jin’s team saw the Botrytis The fungus reads the invading mRNA along with its own molecules and unknowingly creates proteins that compromise its infectious capabilities.

It’s almost as if the plants are creating a “pseudovirus,” Jin says: little packets of RNA that infect a cell and then use that cell’s machinery to make proteins.

“This is a pretty powerful mechanism,” she said. “One mRNA can be translated into many, many copies of proteins. … It’s much more effective than transporting the protein itself.”

To her knowledge, Jin said, this is the first time she’s seen evidence of organisms across kingdoms exchanging mRNA messages and reading them into proteins. But she thinks it’s likely to be seen in many other systems, once people start looking for it.

The field feels young, Buck said, and that’s exciting. There’s still a lot to learn: for example, whether the other molecules in EVs help deliver the RNA message. “It’s a fun challenge to figure all that out,” she said. “We should be inspired by how incredibly powerful and dynamic RNA is, and how we’re still discovering all the ways it shapes and regulates life.”