A Ribosomal Frameshifting Structure in the CCR5 mRNA Leads to Mirna-Stimulated Nonsense-Mediated mRNA Decay

Abstract

RNA structure-based signals are used by viruses to affect programmed ribosomal frameshifting (PRF) yielding extended fusion protein products in a fraction of translation processes. Computationally identified −1 PRF signals in cellular mRNAs have been predicted to lead to premature termination of translation in the vast majority of cases. We found that a −1 PRF signal predicted in the mRNA of the human CCR5 cytokine receptor is a pseudoknotted structure that is responsible for redirecting translation toward a premature termination codon (PTC), ultimately destabilizing the mRNA via the nonsense mediated mRNA decay pathway (NMD) and possibly another decay pathway. A chemokine receptor, CCR5 is also a co-receptor used by HIV-1 to enter its target CD4+ T-cells. We built a 3D model of the −1 PRF structure and validated its stability in molecular dynamics simulations (MD). The structure is a two-stemmed pseudoknot, with the larger of the two stem domains consisting of multiple half-turn helical segments, separated by asymmetric single strands, which enable bending of the larger stem region and bridging of the two stems. MD predicted this larger region and the 3’ end of the structure to be very stable, which is consistent with the experimental results indicating that it may form triple base interactions with miR-1224. Such interactions can increase the stability of the whole −1 PRF structure, ultimately resulting in an increased fraction of paused ribosomes. Another miRNA, miR-141, is also predicted to interact with the same region. Experiments have also demonstrated that several other cytokine receptor mRNA −1 PRF signals are controlled via miRNAs. Altogether these results indicate a novel mechanism of cellular gene expression regulation via a −1 PRF structural signal further refined by the sequence-specific miRNA interactions.Funded in part by HHSN261200800001E.