Conserved RNA secondary structures in Picornaviridae genomes

• Published in: Nucleic acids research 2001-12, Vol.29 (24), p.5079-5089
• Main Authors: Witwer, C, Rauscher, S, Hofacker, I L, Stadler, P F
• Format: Article
• Language: English
• Subjects: 5' Untranslated Regions - chemistry; 5' Untranslated Regions - genetics; Base Sequence; Conserved Sequence - genetics; Foot-and-mouth disease virus; Genome, Viral; Hepatitis A virus; Molecular Sequence Data; Nucleic Acid Conformation; Picornaviridae; Picornaviridae - genetics; Picornavirus; RNA, Viral - chemistry; RNA, Viral - genetics; Sequence Homology, Nucleic Acid
• ISSN: 1362-4962; 0305-1048; 1362-4962
• DOI: 10.1093/nar/29.24.5079

The family Picornaviridae contains important pathogens including, for example, hepatitis A virus and foot-and-mouth disease virus. The genome of these viruses is a single messenger-active (+)-RNA of 7200-8500 nt. Besides coding for the viral proteins, it also contains functionally important RNA secondary structures, among them an internal ribosomal entry site (IRES) region towards the 5'-end. This contribution provides a comprehensive computational survey of the complete genomic RNAs and a detailed comparative analysis of the conserved structural elements in seven of the currently nine genera in the family PICORNAVIRIDAE: Compared with previous studies we find: (i) that only smaller sections of the IRES region than previously reported are conserved at single base-pair resolution and (ii) that there is a number of significant structural elements in the coding region. Furthermore, we identify potential cis-acting replication elements in four genera where this feature has not been reported so far.