Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway

Programmed −1 ribosomal frameshift (−1 PRF) signals redirect translating ribosomes to slip back one base on messenger RNAs. Although well characterized in viruses, how these elements may regulate cellular gene expression is not understood. Here we describe a −1 PRF signal in the human mRNA encoding CCR5, the HIV-1 co-receptor. CCR5 mRNA-mediated −1 PRF is directed by an mRNA pseudoknot, and is stimulated by at least two microRNAs. Mapping the mRNA–miRNA interaction suggests that formation of a triplex RNA structure stimulates −1 PRF. A −1 PRF event on the CCR5 mRNA directs translating ribosomes to a premature termination codon, destabilizing it through the nonsense-mediated mRNA decay pathway. At least one additional mRNA decay pathway is also involved. Functional −1 PRF signals that seem to be regulated by miRNAs are also demonstrated in mRNAs encoding six other cytokine receptors, suggesting a novel mode through which immune responses may be fine-tuned in mammalian cells. Programmed −1 ribosomal frameshifting (−1 PRF) is a process by which a signal in a messenger RNA causes a translating ribosome to shift by one nucleotide, thus changing the reading frame; here −1 PRF in the mRNA for the co-receptor for HIV-1, CCR5 , is stimulated by two microRNAs and leads to degradation of the transcript by nonsense-mediated decay and at least one other decay pathway. Ribosomal frameshift tunes the immune response This paper reports the identification of an operational programmed minus one ribosomal frameshift (−1 PRF) signal that shifts elongating ribosomes into a premature termination codon in the human CCR5 mRNA, suggesting that it may destabilize the CCR5 mRNA through the nonsense-mediated mRNA decay pathway. PRF events, in which a signal in an mRNA causes a translating ribosome to shift by one nucleotide, thereby changing the reading frame, have been widely studied in viruses but less is known about how they act in mammalian cells. In the experiments described here, CCR5-mediated −1 PRF is enhanced by two microRNAs, one of which binds the −1 PRF signal directly and results in its structural reorganization. Other cytokine receptors also exhibit the potential for miRNA-regulated −1 PRF. These findings demonstrate a novel mechanism for fine-tuning immune responses in mammalian cells.