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

Chen, Nai-Chi; Wang, Chun-Hsiung; Yoshimura, Masato; Yeh, Yi-Qi; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Lin, Chien-Chih; Lin, Pei-Ju; Huang, Yen-Chieh; Wakatsuki, Soichi; Ho, Meng-Chiao; Chen, Chun-Jung

doi:10.1038/s41467-023-36235-3

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

Journal Article · Wed Feb 01 00:00:00 EST 2023 · Nature Communications

DOI:https://doi.org/10.1038/s41467-023-36235-3· OSTI ID:2005032

^[1]; Wang, Chun-Hsiung ^[2];

^[1];

^[1]; Chuankhayan, Phimonphan ^[1];

^[1]; Lin, Pei-Ju ^[3];

^[1]; Wakatsuki, Soichi ^[4];

^[2];

^[5]

National Synchrotron Radiation Research Center, Hsinchu (Taiwan)
Academia Sinica, Taipei (Taiwan)
National Synchrotron Radiation Research Center, Hsinchu (Taiwan); National Tsing Hua University, Hsinchu (Taiwan)
Stanford University, CA (United States); SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)
National Synchrotron Radiation Research Center, Hsinchu (Taiwan); National Tsing Hua University, Hsinchu (Taiwan); National Cheng Kung University, Tainan (Taiwan); National Yang Ming Chiao Tung University, Hsinchu (Taiwan)

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.

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Research Organization:: SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); National Science and Technology Council (NSTC)

Grant/Contract Number:: AC02-76SF00515; 105-2311-B-213-001-MY3; 107-2923-B-213-001-MY3; 108-2311-B-213-001-MY3; 111-2311-B-213-001

OSTI ID:: 2005032

Journal Information:: Nature Communications, Vol. 14, Issue 1; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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

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