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

Chun-Jung Chen^1,2,3,4*

¹Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, Taiwan
²Physics, Nationan Tsing Hua University, Hsinchu, Taiwan
³Biotechnology and Bioindustry Science, National Cheng Kung University, Tainan, Taiwan
⁴Biological Science & Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan

* Presenter:Chun-Jung Chen, email:cjchen@nsrrc.org.tw

Understanding the structural insight and 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 atomic resolutions in various pH environments [1]. 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. For a comparison, we also determine the structure of the T=3 delta-N48 LSV1 VLP. Delta-N48 LSV1 CP interacts with ssRNA via the positively charged domains of the rigid helix α1’, α1’–α1 loop, β-barrel domain, and C-arm. Cryo-EM reconstructions, combined with X-ray crystallographic and small-angle X-ray scattering analyses, indicate that pH affects capsid conformations by regulating reversible dynamic particle motions and sizes of LSV2 VLPs. C-arms with continuous densities exist in all LSV2 and delta-N48 LSV1 VLPs across varied pH conditions, indicating that autoproteolysis cleavage for γ peptide release, which was generally observed in other known T=4 and T=3 viruses, is not required for LSV maturation. Interestingly, an introduction of a double mutation of M83E/D461F on the LSV2 CP, mimicking the key residues at the autoproteolysis sites from other tetraviruses, potentially triggers a self-cleavage process on the specific scissile bond of LSV2 CP. Moreover, 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 [2, 3, 4].

[1] Chen, N.-C., Wang, C.-H., Yoshimura, M., Yeh, Y.-Q., Guan, H.-H., Chuankhayan, P., Lin, C.-C., Lin, P.-J., Huang, Y.-C., Wakatsuki, S., Ho, M.-C. & Chen, C.-J. (2023). Nat. Commun. 14, 545.
[2] Cox-Foster, D. et al. (2007). Science 318, 283–287.
[3] Daughenbaugh, K., Martin, M., Brutscher, L. M., Cavigli, I., Garcia, E., Lavin, M. & Flenniken, M. L. (2015) Viruses, 7, 3285–3309.
[4] Simenc, L., Kuhar, U., Jamnikar-Ciglenecki, U. & Toplak, I. (2020). J. Econ. Entomol. 113, 1055–1061.

Keywords: honeybee-infecting virus, capsid assembly, dynamics, cryo-EM, X-ray structure