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

Abstract

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.

The evolutionary and molecular history of a chikungunya virus outbreak lineage

“…Mutation L136F is located on the surface of domain I, I317V is located on the surface of domain III, and mutation D284E is situated in the linker region between domains I and III. This junction region undergoes substantial rearrangement upon conversion of E1 to the fusion form [66, 67], but given the conservative nature of the mutation, the rearrangement is unlikely to be affected by the identified mutation. As the surface mutations found in domains I and III are positioned at the outer surface of the spike, they could also affect the packing of neighbouring spike complexes into the icosahedral viral lattice.…”

Comparative Virucidal Activities of Essential Oils and Alcohol-Based Solutions against Enveloped Virus Surrogates: In Vitro and In Silico Analyses

“…As for CHIKV, seventeen EO compounds docked the E1-E2-E3 glycoprotein complex. Some bound to the E2 protein in a pocket of the β-ribbon connector peptides, which play a role during virus entry, helping to trigger E1 conformational changes during the fusion process [ 37 ]. Other EO compounds bound to the E1 protein of CHIKV near the hydrophobic fusion loop, which mediates membrane fusion [ 37 ].…”

“…Some bound to the E2 protein in a pocket of the β-ribbon connector peptides, which play a role during virus entry, helping to trigger E1 conformational changes during the fusion process [ 37 ]. Other EO compounds bound to the E1 protein of CHIKV near the hydrophobic fusion loop, which mediates membrane fusion [ 37 ]. According to the docking score values, EO compounds exhibited better binding affinities against DENV-2 than against CHIKV, which could partly explain the differences in sensitivity to the test solutions revealed in the virucidal disinfectant assays.…”

IFITM3 blocks influenza virus entry by sorting lipids and stabilizing hemifusion

“…Interestingly, viral membrane curvature at the hemifusion sites appeared largely intact, likely reflecting the rigidity and pressure difference between the virus and cell membrane. The M1 layer was still partially or fully intact in most cases (91%), and it might still provide additional rigidity to the virus envelope that favors the initial bent shape of the virus, as commonly seen in virus-liposome fusion in vitro 50,51,53 . No fused IAV or vRNPs were observed in the cytosol, illustrating that IFITM3 can effectively block the membrane fusion of most incoming viruses.…”