Rewriting the Rulebook of RNA

RNA modifications are a fundamental mechanism regulating biological processes in all living cells. An international research team, including Sebastian Glatt of the University of Veterinary Medicine Vienna (Vetmeduni), has identified the first naturally occurring modification of the RNA phosphate backbone. The results have been published in Cell, one of the world's most prestigious scientific journals.

A Blind Spot in RNA Biology

All living organisms require precise regulatory mechanisms for their RNA molecules. Science has recognized over 150 post-transcriptional chemical modifications of RNA, but all were mapped exclusively to the nucleobases or ribose sugars - the phosphate backbone itself was long considered chemically invariant and immune to natural enzymatic editing.

In the new study, a team led by Schraga Schwartz from the Weizmann Institute of Science (Israel) demonstrated that a natural backbone modification - phosphorothioate (PS), the stereospecific replacement of a non-bridging oxygen atom with sulfur - is widespread in nature. Using newly developed sequencing- and mass spectrometry-based approaches, the researchers mapped these modifications at single-nucleotide resolution across diverse archaeal species, identifying PS marks at conserved rRNA and tRNA hotspots regulated by sulfur availability and temperature. They also discovered a novel enzyme family, named Esti, responsible for their installation - loss of these enzymes causes phenotypes ranging from cell death to temperature-sensitive growth defects.

"Understanding the biological significance of this revolutionary modification required complex and unique in vitro biophysical analyses," comments Sebastian Glatt, professor for system genetics at the Department of Biological Sciences and Pathobiology at Vetmeduni , who led the interpretation of the biophysical data. Applying the innovative method DyRNA Thermometry, developed by Jakub Nowak and Sebastian Glatt, the team measured the melting profiles and dynamics of modified nucleic acids, demonstrating that the sulfur atom acts as a microscopic thermal stabilizer.

"Until now, epitranscriptomics has focused entirely on chemical marks added to the sugars or nucleobases," emphasizes Glatt. "This discovery overturns that central dogma. The backbone itself is subject to strictly regulated, evolutionarily conserved enzymatic editing. Phosphorothioates in archaea drastically stabilize the translational machinery - an elegant survival strategy in hostile environments, proving that RNA regulation is far more complex than we assumed."

From Archaeal Evolution to Modern Therapeutics

Phosphorothioate is already the cornerstone of synthetic RNA therapeutics such as antisense oligonucleotides (ASOs) and siRNAs, increasing their resistance to degradation. However, chemical synthesis yields random stereoisomer mixtures, limiting efficacy. The natural Esti enzymes introduce this modification stereospecifically, opening new biotechnological perspectives as programmable tools for producing highly stable nucleic acid therapeutics.
 

The work was coordinated by Prof. Schraga Schwartz (Weizmann Institute of Science, Israel) and involved researchers at Colorado State University (USA), Tokyo Metropolitan University (Japan), Christian-Albrechts-Universität zu Kiel (Germany), Virginia Tech (USA), Tel Aviv University (Israel), the University of Regensburg (Germany), the Jagiellonian University Krakow (Poland) and the Université de Strasbourg (France). Prof. Glatt's contribution was funded by the European Research Council (ERC) under Horizon 2020 (Grant No. 101001394).

The article "Phosphate backbone epitranscriptomics: Discovery of natural RNA phosphorothioates and their writer machinery." by Maman, A., Nobe, Y., Fluke, K.A., et al. was published in Cell.

Scientific article

Scientific contact:       
Prof. Dr. Sebastian Glatt          
Systemgenetik
Veterinärmedizinische Universität Wien 
Sebastian.Glatt@vetmeduni.ac.at