Visualization of conformational changes and membrane remodeling leading to genome delivery by viral class-II fusion machinery

• Published in: Nature communications Vol. 13; no. 1; p. 4772
• Main Authors: Mangala Prasad, Vidya, Blijleven, Jelle S., Smit, Jolanda M., Lee, Kelly K.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 15.08.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 101/28; 631/326/596; 631/326/596/2116; 631/535/1258; 631/57/2270; 631/57/2271; Apposition; BASIC BIOLOGICAL SCIENCES; Chikungunya virus - genetics; Cytoplasm; electron microscopy; Fusion protein; Genomes; Glycoproteins; Glycoproteins - analysis; Humanities and Social Sciences; Humans; Intermediates; membrane biophysics; Membrane Fusion; Membrane proteins; membrane structure and assembly; Membranes; multidisciplinary; Nucleocapsids; pH effects; Proteins; Science; Science (multidisciplinary); Structural analysis; Tomography; Vector-borne diseases; Viral Envelope Proteins - chemistry; Viral Envelope Proteins - genetics; Viral Fusion Proteins - chemistry; Viral Fusion Proteins - genetics; viral membrane fusion; Virion - metabolism; Virions; virology; Virus Internalization; Viruses
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-022-32431-9

Chikungunya virus (CHIKV) is a human pathogen that delivers its genome to the host cell cytoplasm through endocytic low pH-activated membrane fusion mediated by class-II fusion proteins. Though structures of prefusion, icosahedral CHIKV are available, structural characterization of virion interaction with membranes has been limited. Here, we have used cryo-electron tomography to visualize CHIKV’s complete membrane fusion pathway, identifying key intermediary glycoprotein conformations coupled to membrane remodeling events. Using sub-tomogram averaging, we elucidate features of the low pH-exposed virion, nucleocapsid and full-length E1-glycoprotein’s post-fusion structure. Contrary to class-I fusion systems, CHIKV achieves membrane apposition by protrusion of extended E1-glycoprotein homotrimers into the target membrane. The fusion process also features a large hemifusion diaphragm that transitions to a wide pore for intact nucleocapsid delivery. Our analyses provide comprehensive ultrastructural insights into the class-II virus fusion system function and direct mechanistic characterization of the fundamental process of protein-mediated membrane fusion. Membrane fusion is essential for cellular entry of enveloped viruses. Here, authors use time-resolved cryo-electron tomography and subtomogram averaging to capture 3D organization and population evolution of intermediates during membrane fusion of CHIKV, a medically important alphavirus.