Conserved tertiary structural elements in the 5' nontranslated region of cardiovirus, aphthovirus and hepatitis A virus RNAs

• Published in: Nucleic acids research 1993-05, Vol.21 (10), p.2445-2451
• Main Authors: Le, S.Y, Chen, J.H, Sonenberg, N, Maizel, J.V. Jr
• Format: Article
• Language: English
• Subjects: Aphthovirus; Aphthovirus - genetics; Base Composition; Base Sequence; Biological and medical sciences; Cardiovirus; comparisons; Conserved Sequence; Encephalomyocarditis virus; Encephalomyocarditis virus - genetics; Foot-and-mouth disease virus; Fundamental and applied biological sciences. Psychology; Genetics; Hepatitis A virus; Hepatovirus - genetics; Humans; Maus Elberfeld virus - genetics; Microbiology; molecular conformation; Molecular Sequence Data; Monte Carlo method; Nucleic Acid Conformation; nucleotide sequences; protein tertiary structure; Rhinovirus; RNA; RNA, Ribosomal, 18S - chemistry; RNA, Viral - chemistry; simulation models; structural motifs; Theiler's encephalomyelitis virus; unusual folding regions; Virology
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/21.10.2445

Statistical analyses of RNA folding in 5' nontranslated regions (5'NTR) of encephalomyocarditis virus, Theiler's murine encephalomyelitis virus, foot-and-mouth disease virus, and hepatitis A virus indicate that two highly significant folding regions occur in the 5' and 31 portions of the 5'NTR. The conserved tertiary structural elements are predicted in the unusual folding regions (UFR) for these viral RNAs. The theoretical, common structural elements predicted in the 31 parts of the 5'NTR occur in a cis-acting element that is critical for internal ribosome binding. These structural motifs are expected to be highly significant from extensive Monte Carlo simulations. Nucleotides (nt) in the conserved single-stranded polypyrimidine tract for these RNAs are involved in a distinctively tertiary interaction that is located at about 15 nt prior to the initiator AUG. Intriguingly, the proposed common tertiary structure in this study shares a similar structural feature to that proposed in human enteroviruses and rhinoviruses. Based on these common structural features, plausible base pairing models between these viral RNAs and 18 S rRNA are suggested, which are consistent with a general mechanism for regulation of internal initiation of cap-independent translation.