Molecular insights into RNA and DNA helicase evolution from the determinants of specificity for a DEAD-box RNA helicase.

Anna L Mallam,David J Sidote,Alan M Lambowitz

doi:10.7554/elife.04630

Abstract

How different helicase families with a conserved catalytic 'helicase core' evolved to function on varied RNA and DNA substrates by diverse mechanisms remains unclear. In this study, we used Mss116, a yeast DEAD-box protein that utilizes ATP to locally unwind dsRNA, to investigate helicase specificity and mechanism. Our results define the molecular basis for the substrate specificity of a DEAD-box protein. Additionally, they show that Mss116 has ambiguous substrate-binding properties and interacts with all four NTPs and both RNA and DNA. The efficiency of unwinding correlates with the stability of the 'closed-state' helicase core, a complex with nucleotide and nucleic acid that forms as duplexes are unwound. Crystal structures reveal that core stability is modulated by family-specific interactions that favor certain substrates. This suggests how present-day helicases diversified from an ancestral core with broad specificity by retaining core closure as a common catalytic mechanism while optimizing substrate-binding interactions for different cellular functions.

Highlights

Helicases of superfamilies (SFs) 1 and 2 use ATP or other NTPs to bind, unwind, or remodel RNA or DNA in essentially all facets of nucleic acid metabolism (Preugschat et al, 1996; Tanaka and Schwer, 2005; Singleton et al, 2007; Fairman-Williams et al, 2010; Jarmoskaite and Russell, 2014)
We investigated how Mss116 specifies for ATP during local unwinding by comparing the ability of the helicase core (D1D2, residues 88–597) to use different nucleotides to catalyze RNA unwinding
Our results elucidate the basis for the physiological preference of the DEAD-box protein Mss116 for ATP and RNA, and show that the helicase core has a surprising degree of substrate ambiguity

Summary

Introduction

Helicases of superfamilies (SFs) 1 and 2 use ATP or other NTPs to bind, unwind, or remodel RNA or DNA in essentially all facets of nucleic acid metabolism (Preugschat et al, 1996; Tanaka and Schwer, 2005; Singleton et al, 2007; Fairman-Williams et al, 2010; Jarmoskaite and Russell, 2014). They contain a conserved ‘helicase core’ of two RecA-like domains but act on varied substrates by different mechanisms.

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Conclusion