Nature Invented the RNA Drug Trick First: Archaea Fortify Their RNA With Sulfur

Some of the most valuable chemistry in modern medicine is a simple atomic swap: replacing one oxygen atom with sulfur in the backbone of RNA. That single substitution shields RNA therapeutics from enzymes that would otherwise chew them apart inside the body. Now it turns out nature got there first. A large international team reports in the journal Cell that heat-loving archaea naturally carry these phosphorothioate modifications in their own RNA, the first phosphate-backbone modification ever confirmed in a living organism.

The finding lands at an awkward and fascinating moment for the field. More than 150 natural chemical modifications of RNA have been catalogued, from methylation to pseudouridine, and every single one sits on the nucleobase or the ribose sugar. The phosphate backbone that links the building blocks together was considered untouched by nature, a blank scaffold. In contrast, the sulfur-substituted version of that backbone has been a workhorse of human drug design for decades. The new work, led by corresponding authors Masato Taoka of Tokyo Metropolitan University, Thomas J. Santangelo of Colorado State University, Schraga Schwartz of the Weizmann Institute of Science, and Dina Grohmann of the University of Regensburg, closes that gap by showing the two chemistries are one and the same.

A claim that had to be proven twice

This is not the first time someone has claimed to find sulfur in the RNA backbone. In 2020, a paper reported thiophosphate-modified linkers in the RNA of prokaryotes and eukaryotes, only for a 2021 rebuttal to argue the result was an artifact, warning of common pitfalls in RNA modification analysis by mass spectrometry. Many researchers walked away convinced that thiophosphate linkers simply do not exist in natural RNA. The new team clearly knew that history, because they built their case the hard way.

The researchers developed sequencing and mass-spectrometry methods that map phosphorothioates at single-nucleotide resolution, with the sensitivity to distinguish one modified linker from the rest. Applied across diverse archaeal species, the methods found stereospecific sulfur modifications clustered at hotspots in ribosomal RNA and transfer RNA. And the stereochemistry was unambiguous: every naturally occurring modified linker was the R-isomer, one of the two mirror-image forms possible around the phosphorus atom. A random chemical artifact would not sort itself into a single mirror image across species. That is the signature of an enzyme at work.

The collaboration behind the evidence was broad: Tokyo Metropolitan University, the Weizmann Institute, Colorado State University, the University of Regensburg, plus teams at Virginia Tech, Tel Aviv University, the University of Strasbourg, Jagiellonian University, the Medical University of Vienna, Christian Albrecht University, and the US National Cancer Institute. Samples came from the extensive strain collection of the German Archaea Center at the University of Regensburg, grown under tightly controlled conditions.

Microbes that tune their chemistry to the heat

The organisms carrying these modifications are hyperthermophiles, archaea that thrive in environments that would cook most life. Their RNA modification load is unusually high, and it responds to the environment. The amount of phosphorothioate modification shifted with the sulfur available in the growth medium, and several of the modified linkers increased as growth temperature rose, suggesting the microbes dial the chemistry up as the heat mounts.

The placement is telling. In ribosomal RNA, the sulfur-modified linkers concentrated in two critical neighborhoods: the region that reads the genetic code carried by messenger RNA, and the peptidyl transferase center, the ribosome's core where new amino acids are stitched onto a growing protein chain. Those are the spots where a mistake or a wobble would be most costly, which is exactly where extra structural reinforcement pays off. In transfer RNA, the modifications were found to be necessary for maintaining the molecule's stability.

This is not just an ornamental detail. When the researchers removed the enzymes responsible, some archaeal species could not survive at all, while others grew conspicuously more slowly at high temperatures. The modification behaves less like a decoration and more like load-bearing architecture.

The most important chemical trick in modern RNA medicine was invented by microbes living near boiling water.

Esti-A and Esti-B, the enzymes that do the writing

Finding a modification is one thing; finding the machinery that installs it is what turns an observation into biology. The team hunted for the responsible enzymes by tracking the evolutionary distribution of proteins suspected of having related functions, looking for genes whose presence across species matched the presence of the sulfur modifications. That search produced two new enzymes, named Esti-A and Esti-B, which perform the stereoselective replacement of oxygen with sulfur in the RNA linker.

The enzymes are selective about their substrates, targeting specific tRNA and rRNA molecules rather than modifying RNA indiscriminately. The knockout experiments confirmed the assignment: species that lost these enzymes lost the modifications and paid for it in viability or heat tolerance. The result establishes both the first natural RNA phosphate-backbone modification and the writer machinery that produces it, a complete package that had been missing from the field.

Why drugmakers should pay attention

Phosphorothioate chemistry is central to RNA therapeutics, used in nearly all RNA drugs except mRNA products to improve stability and efficacy in the body. The catch is manufacturing. Drugmakers want stereoselective synthesis, producing only the desired three-dimensional form of the molecule, but there is currently no convenient commercial method for doing it. The newly discovered enzymes, which naturally build only the R-form, look like a promising starting point for exactly that technology. If Esti-A and Esti-B can be adapted to make synthetic RNA drugs in a chosen stereochemical form, they could streamline a step that currently limits production.

There is also a broader lesson. The archaea had this chemistry long before medicine did, as Dina Grohmann put it: they had already developed this form of RNA stabilization before it became usable in the age of RNA therapeutics, and as so often happens with archaea, they were one step ahead. Biology keeps a deeper catalog of chemical tricks than drug design has explored, and extremophiles are where the catalog gets interesting. The next time a manufacturing problem in RNA medicine looks intractable, the search for a solution might start in a hot spring.