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Recent investigations have underscored the potential role of cilia within the respiratory tracts of infected hosts, particularly regarding the entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the mechanisms by which other CoVs exert their virulence through ciliary interactions remain inadequately elucidated. In this context, our research has demonstrated that porcine epidemic diarrhea virus (PEDV) and porcine deltacoronavirus (PDCoV) induce ciliary disassembly within six hours post-infection during the early infection stage. Utilizing mass spectrometry, we identified histone deacetylases 6 (HDAC6) or Aurora A (AurA) as binding partners of PEDV or PDCoV membrane (M) proteins. Immunofluorescence studies corroborated that the AurA-HDAC6 axis serves as a principal regulator of ciliary disassembly. Additionally, M proteins from all four CoV genera\u2014PEDV, SARS-CoV-2, PDCoV, and infectious bronchitis virus (IBV)\u2014were observed to congregate at the ciliary base. Molecular techniques, including immunoprecipitation and molecular docking combined with molecular mechanics\/generalized born surface area (MM\/GBSA) free energy decomposition analysis, further revealed that CoV M proteins interact with both AurA and HDAC6. These interactions depend on conserved residues at the transmembrane-cytosolic junction of M proteins, essential for their binding to the AurA-HDAC6 axis. Mutations disrupting these residues significantly impaired the binding affinity, thus inhibiting the associated ciliary disassembly process. Collectively, our findings illuminate a conserved regulatory mechanism involving CoV M proteins across all four genera, contributing to ciliary disassembly during early infection. This work enhances our understanding of the fundamental interactions between CoVs and host cells, positioning AurA and HDAC6 as potential therapeutic targets for a broad spectrum of CoV infections.<\/jats:p>","DOI":"10.1371\/journal.ppat.1013515","type":"journal-article","created":{"date-parts":[[2025,9,12]],"date-time":"2025-09-12T17:59:13Z","timestamp":1757699953000},"page":"e1013515","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["Coronavirus M protein impairs cilium during early infection by enhancing the AurA-HDAC6 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