Structures of honeybee-infecting Lake Sinai virus reveal domain functions and capsid assembly with dynamic motions

Nai-Chi Chen, Chun-Hsiung Wang, Masato Yoshimura, Yi-Qi Yeh, Hong-Hsiang Guan, Phimonphan Chuankhayan, Chien-Chih Lin, Pei-Ju Lin, Yen-Chieh Huang, Soichi Wakatsuki, Meng-Chiao Ho () and Chun-Jung Chen ()
Additional contact information
Nai-Chi Chen: National Synchrotron Radiation Research Center
Chun-Hsiung Wang: Academia Sinica
Masato Yoshimura: National Synchrotron Radiation Research Center
Yi-Qi Yeh: National Synchrotron Radiation Research Center
Hong-Hsiang Guan: National Synchrotron Radiation Research Center
Phimonphan Chuankhayan: National Synchrotron Radiation Research Center
Chien-Chih Lin: National Synchrotron Radiation Research Center
Pei-Ju Lin: National Synchrotron Radiation Research Center
Yen-Chieh Huang: National Synchrotron Radiation Research Center
Soichi Wakatsuki: Stanford University
Meng-Chiao Ho: Academia Sinica
Chun-Jung Chen: National Synchrotron Radiation Research Center

Nature Communications, 2023, vol. 14, issue 1, 1-15

Abstract: Abstract Understanding the structural diversity of honeybee-infecting viruses is critical to maintain pollinator health and manage the spread of diseases in ecology and agriculture. We determine cryo-EM structures of T = 4 and T = 3 capsids of virus-like particles (VLPs) of Lake Sinai virus (LSV) 2 and delta-N48 LSV1, belonging to tetraviruses, at resolutions of 2.3–2.6 Å in various pH environments. Structural analysis shows that the LSV2 capsid protein (CP) structural features, particularly the protruding domain and C-arm, differ from those of other tetraviruses. The anchor loop on the central β-barrel domain interacts with the neighboring subunit to stabilize homo-trimeric capsomeres during assembly. Delta-N48 LSV1 CP interacts with ssRNA via the rigid helix α1’, α1’–α1 loop, β-barrel domain, and C-arm. Cryo-EM reconstructions, combined with X-ray crystallographic and small-angle scattering analyses, indicate that pH affects capsid conformations by regulating reversible dynamic particle motions and sizes of LSV2 VLPs. C-arms exist in all LSV2 and delta-N48 LSV1 VLPs across varied pH conditions, indicating that autoproteolysis cleavage is not required for LSV maturation. The observed linear domino-scaffold structures of various lengths, made up of trapezoid-shape capsomeres, provide a basis for icosahedral T = 4 and T = 3 architecture assemblies. These findings advance understanding of honeybee-infecting viruses that can cause Colony Collapse Disorder.

Date: 2023
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DOI: 10.1038/s41467-023-36235-3

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