Cutting In-line with Iron: Ribosomal Function and Non-oxidative RNA Cleavage

Ribosomes originated long before the Great Oxidation Event (GOE) and their structure and function are strongly dependent on divalent metals (M²⁺). Thus, understanding ribosomal evolution requires characterization of ribosomal interactions with M²⁺ ions under pre-GOE conditions: in the presence of abundant Fe²⁺ and in the absence of O₂. Here, we have shown for the first time that bacteria grown in these conditions contain functional ribosomes with tightly bound Fe atoms. We observe Fe²⁺ can exchange with Mg²⁺ (and vice versa) during purification; but, a small fraction of the associated Fe²⁺ is not exchangeable, presumably because those ions are tightly coordinated by rRNA and deeply buried in the ribosome. In extant aerobic life, Mg²⁺ appears to be the primary M²⁺ ion in translation and can facilitate RNA folding and assembly, but also cuts RNA by in-line cleavage. Before GOE, anoxia would have stabilized Fe²⁺ for such interactions, yet Fe²⁺’s activity with RNA is still poorly understood. We recently reported that anoxic Fe²⁺ can fold RNA and mediate in vitro translation under pre-GOE conditions, albeit at a lower rate compared to Mg²⁺. Here we show that anoxic Fe²⁺ cleaves RNA far more rapidly and extensively than Mg²⁺. Our experiments showed nearly identical banding patterns and cleavage reaction products for Mg²⁺ and anoxic Fe²⁺, pointing to a common in-line cleavage mechanism. The cleavage potency of Fe²⁺ may lead to decreased longevity of Fe²⁺-containing ribosomes. These results have significant implications for the evolution of RNA and iron toxicity in disease. The balance between insufficient and excessive M²⁺ may be at a lower concentration for Fe²⁺ relative to Mg²⁺, potentially conditioning RNA to access more functions using less metal while the high cleavage activity of Fe²⁺ could cause rapid recycling of RNA especially for unstable molecules. Therefore, Fe²⁺ may have been a force for accelerated RNA evolution on early Earth.

Guth-Metzler, R., Bray, M. S., Frenkel-Pinter, M., Suttapitugsakul, S., Montllor-Albalate, C., Bowman, J. C., Wu, R., Reddi, A. R., Okafor, C. D., Glass, J. B., & Williams, L. D. (2020). Cutting in-line with iron: ribosomal function and non-oxidative RNA cleavage. Nucleic acids research, 48(15), 8663–8674. https://doi.org/10.1093/nar/gkaa586