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              <p>Nonsense-mediated mRNA decay (NMD) is a translation-dependent RNA degradation pathway involved in many cellular pathways and crucial for telomere maintenance and embryo development. Core NMD factors Upf1, Upf2 and Upf3 are conserved from yeast to mammals, but a universal NMD model is lacking. We used affinity purification coupled with mass spectrometry and an improved data analysis protocol to obtain the first large-scale quantitative characterization of yeast NMD complexes in yeast (112 experiments). Unexpectedly, we identified two distinct complexes associated with Upf1: Detector (Upf1/2/3) and Effector. Effector contained the mRNA decapping enzyme, together with Nmd4 and Ebs1, two proteins that globally affected NMD and were critical for RNA degradation mediated by the Upf1 C-terminal helicase region. The fact that Nmd4 association to RNA was dependent on Detector components and the similarity between Nmd4/Ebs1 and mammalian Smg5-7 proteins suggest that NMD operates through successive Upf1-bound Detector and Effector complexes in other species. This model can be extended to accommodate steps that are missing in yeast, and thus serve for mechanistic studies of NMD in all eukaryotes. Running title: The Detector/Effector NMD model</p>
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              <org type="consortium">We thank Magalie Duchateau, Julia Chamot‐Rooke and Mariette Matondo of the Mass Spectrometry for Biology UtechS at the Pasteur Institute for access to the mass spectrometry facility, Jean‐Yves Coppée, from the Transcriptome and Epigenome, Biomics platform for access to the sequencing facility. We thank Giorgio Dieci, University of Parma, Italy, for the Rps8 antibodies. We thank members of the Genetics of Macromolecular Interactions Unit: Gwenael Badis for providing RNA sequencing results for the upf1Δ strain, helpful discussions and critical reading of the manuscript; Antonia Doyen for performing initial affinity purification experiments and for building strains; Frank Feuerbach for providing strains, reagents, critical suggestions, advice and support in writing the manuscript; and Micheline Fromont‐Racine for discussions and critical reading of the manuscript. We thank Christophe Malabat from the Bioinformatics and Biostatistics hub, Pasteur Institute, for help with data analysis and support in making the results available through a web interface.</org>
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