Raw data related to S2 Fig.

Coronaviruses (CoVs) are implicated in human outbreaks and significant economic losses in the porcine and avian industries. 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—PEDV, SARS-CoV-2, PDCoV, and infectious bronchitis virus (IBV)—were 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.冠状病毒（Coronaviruses, CoVs）可引发人类暴发疫情，并给猪类与禽类养殖业造成巨额经济损失。近期研究凸显了感染宿主呼吸道内纤毛的潜在作用，尤其是在严重急性呼吸综合征冠状病毒2（Severe Acute Respiratory Syndrome Coronavirus 2, SARS-CoV-2）的入侵过程中。然而，其他冠状病毒通过纤毛互作发挥毒力的具体机制，目前仍未得到充分阐明。在此背景下，本研究证实，猪流行性腹泻病毒（Porcine Epidemic Diarrhea Virus, PEDV）与猪德尔塔冠状病毒（Porcine Deltacoronavirus, PDCoV）可在感染早期的6小时内诱导纤毛解体。本研究采用质谱分析法（Mass Spectrometry），鉴定出猪流行性腹泻病毒或猪德尔塔冠状病毒的膜（Membrane, M）蛋白的结合伴侣分别为组蛋白去乙酰化酶6（Histone Deacetylases 6, HDAC6）与极光激酶A（Aurora A, AurA）。免疫荧光（Immunofluorescence）实验证实，AurA-HDAC6信号轴是调控纤毛解体的核心通路。此外，冠状病毒四个属的膜蛋白——猪流行性腹泻病毒、严重急性呼吸综合征冠状病毒2、猪德尔塔冠状病毒以及传染性支气管炎病毒（Infectious Bronchitis Virus, IBV）的M蛋白——均会聚集于纤毛基部。后续通过免疫沉淀（Immunoprecipitation）、分子对接（Molecular Docking）结合分子力学/广义玻恩表面积（Molecular Mechanics/Generalized Born Surface Area, MM/GBSA）自由能分解分析等分子生物学技术，进一步证实冠状病毒M蛋白可同时与AurA及HDAC6发生相互作用。此类相互作用依赖于冠状病毒M蛋白跨膜-胞质连接区域的保守残基，而该区域正是其结合AurA-HDAC6信号轴的关键位点。破坏此类保守残基的突变可显著降低其结合亲和力，进而抑制相关的纤毛解体过程。综上，本研究揭示了冠状病毒四个属中均存在的、由M蛋白介导的保守调控机制，该机制可在感染早期引发纤毛解体。本研究加深了人们对冠状病毒与宿主细胞基础互作机制的理解，并将AurA与HDAC6确立为广谱冠状病毒感染的潜在治疗靶点。