The newly emerged Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome CoV (SARS-CoV) represent highly pathogenic human CoVs that share a property to inhibit host gene expression at the posttranscriptional level. Similar to the nonstructural protein 1 (nsp1) of SARS-CoV that inhibits host gene expression at the translational level, we report that MERS-CoV nsp1 also exhibits a conserved function to negatively regulate host gene expression by inhibiting host mRNA translation and inducing the degradation of host mRNAs. Furthermore, like SARS-CoV nsp1, the mRNA degradation activity of MERS-CoV nsp1, most probably triggered by its ability to induce an endonucleolytic RNA cleavage, was separable from its translation inhibitory function. Despite these functional similarities, MERS-CoV nsp1 used a strikingly different strategy that selectively targeted translationally competent host mRNAs for inhibition. While SARS-CoV nsp1 is localized exclusively in the cytoplasm and binds to the 40S ribosomal subunit to gain access to translating mRNAs, MERS-CoV nsp1 was distributed in both the nucleus and the cytoplasm and did not bind stably to the 40S subunit, suggesting a distinctly different mode of targeting translating mRNAs. Interestingly, consistent with this notion, MERS-CoV nsp1 selectively targeted mRNAs, which are transcribed in the nucleus and transported to the cytoplasm, for translation inhibition and mRNA degradation but spared exogenous mRNAs introduced directly into the cytoplasm or virus-like mRNAs that originate in the cytoplasm. Collectively, these data point toward a novel viral strategy wherein the cytoplasmic origin of MERS-CoV mRNAs facilitates their escape from the inhibitory effects of MERS-CoV nsp1. (1) and has spread to several other countries in the Middle East, North Africa, Europe, and Asia. MERS-CoV appears to have originated in bats (2), while accumulating evidence has also pointed to the dromedary camels as the potential animal reservoir (3, 4). MERS-CoV infection generally causes fever, cough, and pneumonia, leading to respiratory failure, and the reported case fatality rate is ϳ40%. Some MERS patients develop acute renal failure. MERS-CoV can be transmitted from person to person (5-7), and many cases have occurred in persons with chronic underlying medical conditions or immunosuppression (8). The mechanisms governing the virulence and pathogenesis of MERSCoV are largely unknown (9).Upon entry into host cells, CoV genome expression is initiated by the translation of two large precursor polyproteins, pp1a and pp1ab, which are processed by viral proteinases into 15 to 16 mature proteins; the alpha and beta CoVs encodes 16 mature nonstructural proteins (nsp1 to nsp16), while the gamma and delta CoVs lack nsp1, the most N-terminal cleavage product, and encode only 15 nsp's (10-12). While many of these proteins play an Citation Lokugamage KG, Narayanan K, Nakagawa K, Terasaki K, Ramirez SI, Tseng CK, Makino S. 2015. Middle East respiratory syndrome coro...