Storing genetic material as DNA or RNA is all well and good for life on Earth, but it would be entirely pointless if we couldn’t do anything with it. To use our genetic blueprints, all organisms need to translate the message from their nucleic acid forms into protein, which then become the building blocks that make up each organism. Because this is such a critical part of life, ribosomes—the machinery responsible for the translation of RNA into protein—are fairly conserved across all living things.
Yet despite their similar functions across domains (Bacteria, Archaea, and Eukarya), ribosomes and ribosomal subunits can still be somewhat different from one another and can have modifications that help modulate their functions.
In a new paper from the lab of Doug Mitchell, the William Kelly Warren Sr. Professor of Biochemistry, postdocs and first authors Andrew Rice and Yanqing Xue conducted bioinformatics analyses and determined, for the first time, which is enzyme responsible for the thioamidation of uL16 in the bacteria Escherichia coli.
Previously, scientists had determined that the thioamidated archaeal protein was modified by an enzyme called YcaO. Rice, Xue, and colleagues used AlphaFold3 to assess whether YcaO might also modify uL16.
Using AlphaFold3, “We began by individually predicting the structures of all E. coli proteins complexed with YcaO,” Xue said. The results suggested, with high confidence, that YcaO is the protein responsible for the thioamidation of uL16 and that, out of all ~4,400 proteins in E. coli, it only thioamidates uL16.
“It was exciting that uL16 was the only [protein] that landed in that [high] confidence range,” Rice said.
Rice, Xue, and their team went on to show in their paper that YcaO has the same activity in two pathogenic bacteria, Klebsiella pneumoniae and Pseudomonas aeruginosa. They believe that neither thioamidation nor YcaO are present in eukaryotes but are widespread in a major group of bacteria that includes these clinically relevant human pathogens.
Identifying bacterial- or pathogen-specific features is always a welcome finding as they could one day become potential therapeutic targets. Although such a road is a long way away considering how little we know about thioamidation in general or its potential role in regulating ribosomal activity and protein synthesis, knowing that it is involved in a critical aspect of a bacterial process but not in its human counterpart means that it could one day be harnessed to treat bacterial infections.
Go deeper
The paper “Backbone Thioamidation of a Ribosomal Subunit Protein in Pseudomonadota” was published in Biochemistry in March 2026.
Funding
This research used funds from the National Institutes of Health and the National Science Foundation.
School of Medicine Basic Sciences shared resources
This research made use of the Mass Spectrometry Research Center.
Open access
The study was published open access through a transformative agreement negotiated by Vanderbilt University’s Jean and Alexander Heard Libraries. Transformative agreements eliminate traditional paywalls and remove the obstacle of article processing charges, ensuring immediate and unrestricted access to research worldwide. Vanderbilt authors can learn more about the Heard Libraries’ agreements supporting open access publishing in this research guide.