Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs

Abstract

SummaryThe rapid development of our understanding of the diverse biological roles fulfilled by non-coding RNA has motivated interest in the basic macromolecular behavior, structure, and function of RNA. We focus on two areas in the behavior of complex RNAs. First, we present advances in the understanding of how RNA folding is accomplished in vivo by presenting a mechanism for the action of DEAD-box proteins. Members of this family are intimately associated with almost all cellular processes involving RNA, mediating RNA structural rearrangements and chaperoning their folding. Next, we focus on advances in understanding and characterizing the basic biophysical forces that govern the folding of complex RNAs. Ultimately we expect that a confluence and synergy between these approaches will lead to profound understanding of RNA and its biology.The explosion in our knowledge about noncoding RNA (ncRNA) -RNA that is not translated into protein -has expanded interest in RNA beyond the traditional RNA community. Diverse ncRNAs include the recently-discovered riboswitches, whose novel gene-regulation function is induced by the binding of small metabolites [1]; most of the so-called "Human Accelerated Regions" (HAR) of the human genome, whose recent evolution may be linked to the emergence of the human brain [2]; and many ncRNAs of unknown function [3]. These discoveries underscore the need to understand the fundamental macromolecular behavior of RNA, its structure and dynamics, and how these RNAs are handled and exploited in biology.Study of catalytic RNAs, which allow detection of correct folding via activity measurements, has established basic thermodynamic and kinetic properties of RNA folding. Large catalytic RNAs such as the group I intron from Tetrahymena thermophila and the RNase P RNA from Bacillus subtilis fold at vastly different rates under different conditions upon addition of Mg 2+ and have been shown to fold via multiple parallel pathways, in which different molecules follow different routes with different rates and intermediates, to a common final folded structure [4,5]. These observations support the common view that RNAs traverse rugged energy landscapes as they fold [6,7]. However, little is known about the true shape of these

A DEAD-box RNA helicase promotes thermodynamic equilibration of kinetically trapped RNA structures in vivo

“…DEAD-box proteins exhibit little substrate specificity in vitro, but are usually found in large macromolecular complexes in vivo, such as spliceosomes and degradosomes, which direct their activities to specific pathways. However, some DEAD-box helicases have been shown to mediate nonspecific RNA unwinding both in vitro and in vivo (Rössler et al 2001;Yang and Jankowsky 2005;Uhlmann-Schiffler et al 2006;Halls et al 2007;), suggesting that they might act generally to promote RNA rearrangements (Herschlag 1995;Schroeder et al 2002;Rajkowitsch et al 2007;Chu and Herschlag 2008;Russell 2008;Russell et al 2013;. The general increase in mRNA structure observed in yeast after ATP depletion (Rouskin et al 2014) is consistent with the idea that ATP-dependent processes such as helix unwinding modulate RNA secondary structures.…”

Double-stranded RNA under force and torque: Similarities to and striking differences from double-stranded DNA

“…Our results provide a benchmark and challenge for quantitative models of nucleic acid mechanics and a comprehensive experimental foundation for modeling complex RNAs in vitro and in vivo. In addition, we envision our assay to enable a new class of quantitative single-molecule experiments to probe the proposed roles of twist and torque in RNA-protein interactions and processing (4,56).…”

3 Importance of Diffuse Metal Ion Binding to RNA

“…Extensive experimental findings suggest that the structural formation of the Tetrahymena ribozyme involves multi-state kinetics governed by a highly rugged energy landscape [54]. The folding rates and pathways are sensitive to the ionic condition of the solution [6]. For example, SAXS experiments with millisecond resolution indicate that Mg 2+ ions induce a rapid collapse in 10 ms with the global compactness decreasing from 75 Å to 55 Å.…”

“…Specifically, metal ions in the solution can cluster around the polyanionic RNA to effectively reduce the electrostatic energy and to promote folding and stabilize a folded RNA structure. Therefore, RNA structure and stability are strongly coupled to ion electrostatic interactions [1][2][3][4][5][6][7][8].…”

“…Due to the close interaction with specific RNA groups, a specifically bound ion could be energetically important (in addition to its catalytic role). However, due to the longrange nature of the Coulomb interaction, the (large number of) diffuse ions can result in a significant electrostatic force on the charged (phosphate) groups of RNA and have a critical impact on the structural formation of RNA [4][5][6][7][8].…”