Cutting in-line with iron: ribosomal function and non-oxidative RNA cleavage.

Rebecca Guth-Metzler,Marcus S Bray,C Denise Okafor,Ronghu Wu,Jessica C Bowman,Amit R Reddi,Claudia Montllor-Albalate,Loren Dean Williams,Jennifer B Glass,Moran Frenkel-Pinter,Suttipong Suttapitugsakul

doi:10.1093/nar/gkaa586

Rebecca Guth-Metzler, Marcus S Bray + Show 9 more

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https://doi.org/10.1093/nar/gkaa586

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Abstract

Divalent metal cations are essential to the structure and function of the ribosome. Previous characterizations of the ribosome performed under standard laboratory conditions have implicated Mg2+ as a primary mediator of ribosomal structure and function. Possible contributions of Fe2+ as a ribosomal cofactor have been largely overlooked, despite the ribosome's early evolution in a high Fe2+ environment, and the continued use of Fe2+ by obligate anaerobes inhabiting high Fe2+ niches. Here, we show that (i) Fe2+ cleaves RNA by in-line cleavage, a non-oxidative mechanism that has not previously been shown experimentally for this metal, (ii) the first-order in-line rate constant with respect to divalent cations is >200 times greater with Fe2+ than with Mg2+, (iii) functional ribosomes are associated with Fe2+ after purification from cells grown under low O2 and high Fe2+ and (iv) a small fraction of Fe2+ that is associated with the ribosome is not exchangeable with surrounding divalent cations, presumably because those ions are tightly coordinated by rRNA and deeply buried in the ribosome. In total, these results expand the ancient role of iron in biochemistry and highlight a possible new mechanism of iron toxicity.

Highlights

The translation system is responsible for the synthesis of all coded proteins and contains life’s most conserved ribonucleic acids
In parallel with our experiments comparing Fe2+ and Mg2+ in-line cleavage, we investigated whether ribosomes from E. coli grown in pre-Great Oxidation Event (GOE) conditions associate functionally with Fe2+ in vivo
We could switch the mode of ribosomal RNA (rRNA) cleavage between Fenton and in-line mechanisms

Summary

Introduction

The translation system is responsible for the synthesis of all coded proteins and contains life’s most conserved ribonucleic acids. The common core of the ribosome is universal to all life [1,2]. Has been essentially invariant since the last universal common ancestor [3,4,5]. Ribosomes can be interrogated as molecular fossils [6,7,8]. Mg2+ appears to be the dominant M2+ ion in the translation system. Hundreds of Mg2+ ions mediate ribosomal RNA (rRNA) folding and ribosomal assembly, in some instances binding to specific sites in the universal rRNA common core by direct coordination [9,15,16,17]

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