A Distinct Class of Internal Ribosomal Entry Site in Members of the Kobuvirus and Proposed

The 5=-untranslated regions (5=UTRs) of picornavirus genomes contain an internal ribosomal entry site (IRES) that promotes the end-independent initiation of translation. Picornavirus IRESs are classified into four structurally distinct groups, each with different initiation factor requirements. Here, we identify a fifth IRES class in members ofKobuvirus, Salivirus, and Paraturdivi-rus genera of Picornaviridae: Aichi virus (AV), bovine kobuvirus (BKV), canine kobuvirus (CKoV), mouse kobuvirus (MKoV), sheep kobuvirus (SKV), salivirus A (SV-A), turdivirus 2 (TV2), and TV3. The 410-nucleotide (nt)-long AV IRES comprises four domains (I to L), including a hairpin (L) that overlaps a Yn-Xm-AUG (pyrimidine tract/spacer/initiation codon) motif. SV-A, CKoV, andMKoV also contain these four domains, whereas BKV, SKV, and TV2/TV3 5=UTRs contain domains that are related to domain I and equivalent to domains J and K but lack an AV-like domain L. These IRESs are located at different relative posi-tions between a conserved 5=-terminal origin of replication and divergent coding sequences. Elements in these IRESs also occur elsewhere: domain J’s apical subdomain, which contains a GNRA tetraloop, matches an element in type 1 IRESs, and eIF4G-binding motifs in domain K and in type 2 IRESs are identical. Other elements are unique, and their presence leads to unique ini-tiation factor requirements. In vitro reconstitution experiments showed that like AV, but in contrast to other currently charac-terized IRESs, SV-A requires the DExH-box protein DHX29 during initiation, which likely ensures that the initiation codon sequestered in domain L is properly accommodated in the ribosomal mRNA-binding cleft. The genomes of RNA viruses contain structural elements thathave important roles in translation, replication, and encapsi