Identification of Cryptic Putative IRESs Initiating the Translation of Nonstructural Proteins Encoded by the HRV16 Genome

Abstract Cap-dependent initiation of translation is a canonical mechanism adopted by eukaryotic cells. Internal ribosome entry site (IRES)-dependent translation is a mechanism distinct from 5′ cap-dependent translation. IRES elements are located mainly in the 5′-untranslated regions (UTRs) of viral and eukaryotic mRNAs. In addition, IRESs are found in the coding regions of some viral and eukaryotic genomes and initiate the translation of some functional truncated isoforms. Here, via IRES-initiated expression of proteins, bicistronic vectors and ribosome profiling of the human rhinovirus 16 (HRV16), we found that the coding region of the nonstructural proteins P2 and P3 contained 5 putative IRES elements. These 5 putative IRESs were located within nucleotides 4286-4585, 5002-5126, 6245-6394, 6619-6718 and 6629-6778 and initiated green fluorescent protein (GFP) expression in vitro. This alternative mechanism might be effective and economical for eliminating the time and raw material required to synthesize the full-length polyprotein.