In Vitro Molecular Characterization of RNA–Proteins Interactions During Initiation of Translation of a Wild-Type and a Mutant Coxsackievirus B3 RNAs

• Published in: Molecular biotechnology 2013-06, Vol.54 (2), p.515-527
• Main Authors: Souii, Amira, M’hadheb-Gharbi, Manel Ben, Aouni, Mahjoub, Gharbi, Jawhar
• Format: Article
• Language: English
• Subjects: Animals; binding capacity; Biochemistry; Biological Techniques; Biotechnology; Cell Biology; Cell Line, Tumor; Chemistry; Chemistry and Materials Science; Coxsackievirus B3; Cricetinae; crosslinking; Enterovirus B; Enterovirus B, Human - genetics; Enterovirus B, Human - metabolism; Eukaryotic Initiation Factors - genetics; genome; HeLa Cells; Human Genetics; Humans; Molecular Weight; mutants; Mutation; Peptide Chain Initiation, Translational - genetics; Phylogeny; polypeptides; Protein Interaction Domains and Motifs - genetics; Protein Science; ribosomes; Ribosomes - genetics; Ribosomes - metabolism; RNA; RNA, Viral - genetics; RNA, Viral - metabolism; RNA-binding proteins; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; translation (genetics)
• ISSN: 1073-6085; 1559-0305
• DOI: 10.1007/s12033-012-9592-x

Translation initiation of Coxsackievirus B3 (CVB3) RNA is directed by an internal ribosome entry site (IRES) within the 5′ untranslated region. Host cell factors involved in this process include some canonical translation factors and additional RNA-binding proteins. We have, previously, described that the Sabin3-like mutation (U475 → C) introduced in CVB3 genome led to a defective mutant with a serious reduction in translation efficiency. With the aim to identify proteins interacting with CVB3 wild-type and Sabin3-like IRESes and to study interactions between HeLa cell or BHK-21 protein extracts and CVB3 RNAs, UV-cross-linking assays were performed. We have observed a number of proteins that specifically interact with both RNAs. In particular, molecular weights of five of these proteins resemble to those of the eukaryotic translation initiation factors 4G, 3b, 4B, and PTB. According to cross-linking patterns obtained, we have demonstrated a better affinity of CVB3 RNA binding to BHK-21 proteins and a reduced interaction of the mutant RNA with almost cellular polypeptides compared to the wild-type IRES. On the basis of phylogeny of some initiation factors and on the knowledge of the initiation of translation process, we focused on the interaction of both IRESes with eIF3, p100 (eIF4G), and 40S ribosomal subunit by filter-binding assays. We have demonstrated a better affinity of binding to the wild-type CVB3 IRES. Thus, the reduction efficiency of the mutant RNA to bind to cellular proteins involved in the translation initiation could be the reason behind inefficient IRES function.