RNA modifications. While oxidation of RNA is typically detrimental, E. coli surprisingly encodes a dedicated enzyme that adds a 5-hydroxyl-group to cytidine C2501 in close proximity the active site. We investigated this dynamic rRNA modification both in vivo through genetic manipulation, modification quantification, and from a mechanistic perspective through in vitro experiments. We found this modification to be highly dynamic and growth phase-dependent, with high oxidation levels helping E. coli adapt to oxidative stress. These findings provided first functional insights into the role of this unique rRNA modification and showcase a novel mechanism for how bacteria adapt to oxidative stress. 

Further reading:

• Dynamic 23S rRNA modification ho5C2501 benefits Escherichia coli under oxidative stress, Fasnacht ... Willi & Polacek, NAR 2022

•  Ribosomal RNA modification enzymes stimulate large ribosome subunit assembly in E. coli, Ero, Leppik, Reier, Liiv & Remme, NAR 2024

RNA sequence diversity. The E. coli genome encodes seven copies of the ribosomal RNAs 23S, 16S, and 5S. These copies are not identical; they differ in about 1.4% of their sequence. Do these small variations matter? Evidence from the Blanchard group suggests yes: in 2018 they showed that 16S rRNA variant H is an important regulator of the bacterium's stress response. This means that ribosome variation can directly affect how it functions. We set out to investigate these ribosomal differences further, and found that 23S rRNA variant A has higher protein yields than other variants. What's more, reducing the ribosome variety to only "A-type" ribosomes resulted in a highly active cell lysate, with the potential of boosting bio-production (patent filed). The Willi lab's latest project looks at ribosomal variants' sensitivity to antibiotics. We are actively investigating how these sequence differences could give infectious bacteria an edge in surviving treatment and developing antimicrobial resistance. This project is supported by funding from the Banting Research Foundation.

Further reading:

• Ribosome Pool Engineering Increases Protein Biosynthesis Yields, Kofman, Willi, Karim & Jewett, ACS Cent. Sci. 2024

• Endogenous rRNA Sequence Variation Can Regulate Stress Response Gene Expression and Phenotype, Kurylo ... Blanchard, Cell Rep. 2018

• Ribosome heterogeneity: another level of complexity in bacterial translation regulation, Byrgazov, Vesper & Moll, Curr Opin Microbiol. 2013

RNA structural adaptations. Octopuses are unique, right down to their ribosomes. The respective teams of Amy Lee and Nicholas Bellono found that octopuses of the highly intelligent incirrate suborder have an unique ribosomal adaptation: a programmed RNA break within ribosome’s core at helix 88. This rRNA break allows ribosomes to make fewer errors and make proteins that do not aggregate, allowing for a more complex nervous system. The Willi lab collaborated with the Lee and Bellono teams to make an artificial E. coli ribosome with the characteriztic octopus Helix 88 break - and found that this chimeric ribosome also gained the high-fidelity and low-aggregation powers. So while the Helix 88 break is an unuqiely octopus invention, it uses a mechanism that is shared among many life forms - just like the ribosome.

Further reading:

• Evolution of a core ribosomal innovation in octopus, Mitra et al., Curr. Biol. 2026

• Science News: A molecular quirk unique to octopuses makes them better at building proteins by Sara Reardon 

• Nature Daily briefing: Mutation lets octopuses make proteins with precision by Jacob Smith