Structural and Functional Insights into Viral Programmed Ribosomal Frameshifting

Abstract

Protein synthesis by the ribosome is the final stage of biological information transfer and represents an irreversible commitment to gene expression. Accurate translation of messenger RNA is therefore essential to all life, and spontaneous errors by the translational machinery are highly infrequent (∼1/100,000 codons). Programmed −1 ribosomal frameshifting (−1PRF) is a mechanism in which the elongating ribosome is induced at high frequency to slip backward by one nucleotide at a defined position and to continue translation in the new reading frame. This is exploited as a translational regulation strategy by hundreds of RNA viruses, which rely on −1PRF during genome translation to control the stoichiometry of viral proteins. While early investigations of −1PRF focused on virological and biochemical aspects, the application of X-ray crystallography and cryo–electron microscopy (cryo-EM), and the advent of deep sequencing and single-molecule approaches have revealed unexpected structural diversity and mechanistic complexity. Molecular players from several model systems have now been characterized in detail, both in isolation and, more recently, in the context of the elongating ribosome. Here we provide a summary of recent advances and discuss to what extent a general model for −1PRF remains a useful way of thinking. Expected final online publication date for the Annual Review of Virology, Volume 10 is September 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Possible involvement of three-stemmed pseudoknots in regulating translational initiation in human mRNAs

“…In situations where L3 is absent, the two stems, S1 and S2, have the potential to stack together coaxially, forming a quasi-continuous helical structure. These common structural features of H-type pseudoknots are illustrated in various NMR and crystal structures, as discussed in reviews by Hill and Brierley, as well as Peselis and Serganov [ 5 , 6 ].…”

Ribosome cooperativity promotes fast and efficient translation

“…Programmed translational pausing can also allow complex regulation of the mRNA, as is the case for the pause sequence in the Xbp1 mRNA, which is required for efficient mRNA processing during cellular stress (Yanagitani et al, 2011). RNA structures in mRNAs can also slow down translation, which is leveraged by viral RNAs to pause ribosomes at specific sites in their mRNA to induce programmed ribosome frameshifting (Hill and Brierley, 2023; Namy et al, 2006). In addition to regulated pauses, ribosome pausing can also occur on defective or damaged mRNA.…”

Shiftless Is a Novel Member of the Ribosome Stress Surveillance Machinery That Has Evolved to Play a Role in Innate Immunity and Cancer Surveillance

“…Despite strong limitations on spontaneous ribosomal frameshifting, many RNA viruses evade this by programming ribosomes to shift into alternate reading frames, often at frequencies of three orders of magnitude greater than the background rate, through a process called Programmed Ribosomal Frameshifting (PRF) [12][13][14][15]. It is generally accepted that RNA viruses use PRF to maximize their gene expression programs without altering their genomes [16].…”