Genome complexity: RNA as a messenger (Introduction)

by David Turell , Thursday, September 26, 2024, 22:50 (25 days ago) @ David Turell

Latest findings:

https://www.quantamagazine.org/cells-across-the-tree-of-life-exchange-text-messages-usi...

"For a molecule of RNA, the world is a dangerous place. Unlike DNA, which can persist for millions of years in its remarkably stable, double-stranded form, RNA isn’t built to last — not even within the cell that made it. Unless it’s protectively tethered to a larger molecule, RNA can degrade in minutes or less. And outside a cell? Forget about it. Voracious, RNA-destroying enzymes are everywhere, secreted by all forms of life as a defense against viruses that spell out their genetic identity in RNA code. (my bold)

"There is one way RNA can survive outside a cell unscathed: in a tiny, protective bubble. For
decades, researchers have noticed cells releasing these bubbles of cell membrane, called extracellular vesicles (EVs), packed with degraded RNA, proteins and other molecules.
But these sacs were considered little more than trash bags that whisk broken-down molecular
junk out of a cell during routine decluttering.

"Since then, a wealth of evidence has emerged supporting this theory, enabled by improvements in sequencing technology that allow scientists to detect and decode increasingly small RNA segments. Since Valadi published his experiments, other researchers have also seen EVs filled with complex RNA combinations. These RNA sequences can contain detailed information about the cell that authored them and trigger specific effects in recipient cells. The findings have led some researchers to suggest that RNA may be a molecular lingua franca that transcends traditional taxonomic boundaries and can therefore encode messages that remain intelligible across the tree of life.

"In 2024, new studies have exposed additional layers of this story, showing, for example, that
along with bacteria and eukaryotic cells, archaea also exchange vesicle-bound RNA, which confirms that the phenomenon is universal to all three domains of life. Another study has expanded our understanding of cross-kingdom cellular communication by showing that plants and infecting fungi can use packets of havoc-wreaking RNA as a form of coevolutionary information warfare: Ann enemy cell reads the RNA and builds self-harming protein with its own molecular
machinery.

***

"The microbiologist Susanne Erdmann recently found archaea enclosing RNA in life, which features cells built differently from bacteria or eukaryotes like us.n Because EVs are the same size and density as the virus particles Erdmann’s team studies at the Max Planck Institute for Marine nMicrobiology in Germany, they “always pop up nwhen you isolate and purify viruses, ” she said. Eventually, her group got curious and decided to peek at what’s inside. ncellular bubbles and dispatching it into the environment. Her discovery extended our
knowledge of this messaging ability to all three domains of life.

***

"That suggested to her that the RNA wasn’t ending up in the EVs by chance, and that the
process wasn’t just waste disposal. “It’s very unlikely that [archaea] use them for cell-to-cell communication, ” she said. “Why else would you invest so much energy in throwing out
random RNA in vesicles?”

***

"As a message, RNA is transient. This is a feature, not a bug: It can have only short-term
effects on other cells before it degrades. And since the RNA inside a cell is constantly
changing, n“the message that 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 etched in stone or a formal memo on
letterhead.

***

"However, its flexible backbone lets RNA fold into a number of shapes that can impact cell
biology. It can act as an enzyme to accelerate chemical reactions within cells. It can bind to DNA to activate or silence the expression of genes. And competing strands of RNA can
tangle up mRNA instructions in a process called RNA interference that prevents the production of new proteins.

***

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

***

"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 lots of other systems, once people start looking for it."

Comment: note my bold. This fragility of RNA makes it a very unlikely candidate to start life. On the other hand, it is amazing how useful it is. Another example for design.