title: Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements.
abstract: The function of Internal Ribosome Entry Site (IRES) elements is intimately linked to their RNA structure. Viral IRES elements are organized in modular domains consisting of one or more stem-loops that harbor conserved RNA motifs critical for internal initiation of translation. A conserved motif is the pyrimidine-tract located upstream of the functional initiation codon in type I and II picornavirus IRES. By computationally designing synthetic RNAs to fold into a structure that sequesters the polypyrimidine tract in a hairpin, we establish a correlation between predicted inaccessibility of the pyrimidine tract and IRES activity, as determined in both in vitro and in vivo systems. Our data supports the hypothesis that structural sequestration of the pyrimidine-tract within a stable hairpin inactivates IRES activity, since the stronger the stability of the hairpin the higher the inhibition of protein synthesis. Destabilization of the stem-loop immediately upstream of the pyrimidine-tract also decreases IRES activity. Our work introduces a hybrid computational/experimental method to determine the importance of structural motifs for biological function. Specifically, we show the feasibility of using the software RNAiFold to design synthetic RNAs with particular sequence and structural motifs that permit subsequent experimental determination of the importance of such motifs for biological function.
authors.affiliation: Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas -Universidad Autonoma de Madrid, Nicolas Cabrera 1, 28049 Madrid, Spain.
authors.forename: Javier
authors.initials: J
authors.lastname: Fernandez-Chamorro
authors.affiliation: Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas -Universidad Autonoma de Madrid, Nicolas Cabrera 1, 28049 Madrid, Spain.
authors.forename: Gloria
authors.initials: G
authors.lastname: Lozano
authors.affiliation: Biology Department, Boston College, 140 Commonwealth Ave, Chestnut Hill, MA 02467, USA.
authors.forename: Juan Antonio
authors.initials: JA
authors.lastname: Garcia-Martin
authors.affiliation: Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas -Universidad Autonoma de Madrid, Nicolas Cabrera 1, 28049 Madrid, Spain.
authors.forename: Jorge
authors.initials: J
authors.lastname: Ramajo
authors.affiliation: Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, Barcelona, Spain.
authors.forename: Ivan
authors.initials: I
authors.lastname: Dotu
authors.affiliation: Biology Department, Boston College, 140 Commonwealth Ave, Chestnut Hill, MA 02467, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Clote
authors.affiliation: Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas -Universidad Autonoma de Madrid, Nicolas Cabrera 1, 28049 Madrid, Spain.
authors.forename: Encarnacion
authors.initials: E
authors.lastname: Martinez-Salas
mesh_terms: D001483:Base Sequence; D000067556:Internal Ribosome Entry Sites / Q000235:genetics*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs / Q000235:genetics*; D010802:Phylogeny; D010849:Picornaviridae / Q000235:genetics*; D014176:Protein Biosynthesis / Q000235:genetics; D011743:Pyrimidines / Q000737:chemistry / Q000378:metabolism; D012367:RNA, Viral / Q000138:chemical synthesis / Q000145:classification / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid
chemical_list: D000067556:Internal Ribosome Entry Sites; D011743:Pyrimidines; D012367:RNA, Viral; C030986:pyrimidine