RNA Folding and Catalysis Mediated by Iron (II)

Shreyas S Athavale,Nicholas V Hud,Caitlin D Prickett,Loren Dean Williams,Lively Lie,Stephen C Harvey,Chiaolong Hsiao,Roger M Wartell,Jessica C Bowman,Eric O'Neill,Anton S Petrov,Derrick Watkins,Chad R Bernier,J Jared Gossett,Alfred Lewin

doi:10.1371/journal.pone.0038024

Abstract

Mg2+ shares a distinctive relationship with RNA, playing important and specific roles in the folding and function of essentially all large RNAs. Here we use theory and experiment to evaluate Fe2+ in the absence of free oxygen as a replacement for Mg2+ in RNA folding and catalysis. We describe both quantum mechanical calculations and experiments that suggest that the roles of Mg2+ in RNA folding and function can indeed be served by Fe2+. The results of quantum mechanical calculations show that the geometry of coordination of Fe2+ by RNA phosphates is similar to that of Mg2+. Chemical footprinting experiments suggest that the conformation of the Tetrahymena thermophila Group I intron P4–P6 domain RNA is conserved between complexes with Fe2+ or Mg2+. The catalytic activities of both the L1 ribozyme ligase, obtained previously by in vitro selection in the presence of Mg2+, and the hammerhead ribozyme are enhanced in the presence of Fe2+ compared to Mg2+. All chemical footprinting and ribozyme assays in the presence of Fe2+ were performed under anaerobic conditions. The primary motivation of this work is to understand RNA in plausible early earth conditions. Life originated during the early Archean Eon, characterized by a non-oxidative atmosphere and abundant soluble Fe2+. The combined biochemical and paleogeological data are consistent with a role for Fe2+ in an RNA World. RNA and Fe2+ could, in principle, support an array of RNA structures and catalytic functions more diverse than RNA with Mg2+ alone.

Highlights

When large RNAs fold into compact structures, negatively charged phosphate groups achieve close proximity
We find that Fe2+ is an excellent Mg2+ mimic in the absence of O2, readily substituting for Mg2+ in RNA folding and catalysis
Quantum mechanical (QM) calculations show that RNA conformation and coordination geometry are conserved when Mg2+ is replaced by Fe2+ in first shell RNA-metal complexes

Summary

Introduction

When large RNAs fold into compact structures, negatively charged phosphate groups achieve close proximity. Folded RNAs are stabilized in part by inorganic cations that accumulate in and around the RNA envelope. ‘Diffuse’ cations remain hydrated and make primary contributions to global stability by mitigating electrostatic repulsion of the negatively charged backbone. Chelated ions are less frequent, but in some instances are essential for achieving specific local conformation of the RNA. A special importance of Mg2+ in tRNA folding was seen early on [1,2,3]. It is known that Mg2+ plays important roles in folding of essentially all large RNAs [4,5,6]. Mg2+ ions assist directly in stabilizing transition states of some ribozymes [7,8]

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Conclusion