The enterovirus genome can be translated in an IRES-independent manner that requires the initiation factors eIF2A/eIF2D

• Published in: PLoS biology Vol. 21; no. 1; p. e3001693
• Main Authors: Kim, Hyejeong, Aponte-Diaz, David, Sotoudegan, Mohamad S., Shengjuler, Djoshkun, Arnold, Jamie J., Cameron, Craig E.
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 23.01.2023; Public Library of Science (PLoS)
• Subjects: Analysis; Biology and Life Sciences; Cytoplasm; DNA-directed RNA polymerase; Enterovirus - physiology; Enterovirus Infections - virology; Enteroviruses; Evolution; Genetic aspects; Genetic translation; Genomes; Host-Pathogen Interactions; Humans; Hypotheses; Identification and classification; Inactivation; Infections; Initiation factor eIF-2; Internal ribosome entry site; Internal Ribosome Entry Sites; Methods; Mutation; Peptide Initiation Factors - genetics; Polymerase chain reaction; Protein Biosynthesis; Recombination; Research and Analysis Methods; Ribonucleic acid; Ribosomes; RNA; RNA polymerase; RNA sequencing; RNA viruses; RNA, Viral - genetics; RNA, Viral - metabolism; RNA-directed RNA polymerase; Severe acute respiratory syndrome coronavirus 2; Vaccines; Viral infections; Viruses; United States; Netherlands
• ISSN: 1545-7885; 1544-9173; 1545-7885
• DOI: 10.1371/journal.pbio.3001693

RNA recombination in positive-strand RNA viruses is a molecular-genetic process, which permits the greatest evolution of the genome and may be essential to stabilizing the genome from the deleterious consequences of accumulated mutations. Enteroviruses represent a useful system to elucidate the details of this process. On the biochemical level, it is known that RNA recombination is catalyzed by the viral RNA-dependent RNA polymerase using a template-switching mechanism. For this mechanism to function in cells, the recombining genomes must be located in the same subcellular compartment. How a viral genome is trafficked to the site of genome replication and recombination, which is membrane associated and isolated from the cytoplasm, is not known. We hypothesized that genome translation was essential for colocalization of genomes for recombination. We show that complete inactivation of internal ribosome entry site (IRES)-mediated translation of a donor enteroviral genome enhanced recombination instead of impairing it. Recombination did not occur by a nonreplicative mechanism. Rather, sufficient translation of the nonstructural region of the genome occurred to support subsequent steps required for recombination. The noncanonical translation initiation factors, eIF2A and eIF2D, were required for IRES-independent translation. Our results support an eIF2A/eIF2D-dependent mechanism under conditions in which the eIF2-dependent mechanism is inactive. Detection of an IRES-independent mechanism for translation of the enterovirus genome provides an explanation for a variety of debated observations, including nonreplicative recombination and persistence of enteroviral RNA lacking an IRES. The existence of an eIF2A/eIF2D-dependent mechanism in enteroviruses predicts the existence of similar mechanisms in other viruses.