Roles of RNA Structures in the Genome Translation of (+) Sense RNA Viruses

Abstract

Positive (+) sense RNA viruses include many important pathogens that exploit noncanonical translation mechanisms to express their genomes within the host cells. Unlike DNA or negative (-) sense RNA viruses, (+) sense RNA viruses can directly function as mRNAs, even though they lack typical features of host mRNAs, such as the 5' cap structure required for canonical translation initiation. Instead, they exploit structured RNA elements to recruit host translational machinery without the 5' cap, bypassing the canonical translation initiation mechanism. Prominent examples include internal ribosome entry sites (IRESs) and 3' cap-independent translation enhancers (3' CITEs). These RNA modules facilitate translation initiation by recruiting the ribosomal subunits, either directly or through initiation factors, and mediating long-range RNA-RNA interactions. Other regulatory motifs, such as frameshifting signals, allow the ribosome to shift reading frames to regulate protein output. All these RNA elements function through RNA-protein interactions and often utilize host and virus-encoded proteins to hijack the host’s translational apparatus. Over the past several years, various structural biology approaches, including biochemical and enzymatic probing, X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryogenic electron microscopy (cryo-EM), have revealed the unique structural roles of these viral RNA elements and their protein complexes. Although a few structures of IRES and CITE domains have been solved through these methods, the structures of these RNA elements and their structure-function relationship have remained largely unknown. This review discusses the current understanding of translation-related RNA structures in (+) sense RNA viruses, the critical RNA-protein interactions they mediate, and various structural biology approaches used to study them. Since the genome of these viruses serves as a template for two mutually exclusive virological processes, namely genome translation and replication, the review also discusses how viruses can utilize RNA structure-based strategies to regulate the switch between genome translation and replication, highlighting future directions for exploring these fundamental virological processes to develop antiviral therapeutics able to combat diseases caused by these pathogens.