Conserved RNA secondary structures in Picornaviridae genomes | Zendy

Christina Witwer | Zendy; Susanne Rauscher | Zendy; Ivo L. Hofacker | Zendy; Peter F. Stadler | Zendy

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Conserved RNA secondary structures in Picornaviridae genomes

Author(s) -

Christina Witwer,

Susanne Rauscher,

Ivo L. Hofacker,

Peter F. Stadler

Publication year - 2001

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/29.24.5079

Subject(s) - biology , picornaviridae , genome , genetics , rna , virology , computational biology , gene

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.

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