Structure of sacbrood honeybee virus reveals evolution of capsid protein features important for Iflavirus cell entry

M. Procházková¹, T. Füzik¹, K. Škubník¹, J. Moravcová¹, Z. Ubiparip¹, A. Přidal², P. Plevka¹

¹ Structural Virology, CEITEC Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic

² Department of Zoology, Fishery, Hydrobiology, and Apidology, Faculty of Agronomy, Mendel University in Brno, Zemědělská 1/1665, 613 00 Brno, Czech Republic

            Infection by sacbrood virus (SBV) from the family Iflaviridae is lethal to honeybee larvae and causes the collapse of honeybee colonies [1]. Despite the negative effect of the virus on honeybee populations, the structure of its virion and mechanism of its genome delivery are unknown. Here we present the crystal structure of SBV virion and show that it contains sixty copies of a minor capsid protein (MiCP) attached to the virion surface. No similar minor capsid proteins have been previously observed in any of the related picornaviruses. The location of the MiCP coding sequence within the SBV genome indicates that MiCP evolved from a C-terminal extension of a major capsid protein VP3 by the introduction of a cleavage site for a virus protease. Other Iflaviruses (deformed wing virus and slow bee paralysis virus) contain, instead of MiCP, C-terminal extensions of capsid protein VP3 [2,3]. These globular C-terminal domains form protruding crown-like structures at five-fold symmetry axes of these viruses. In contrast, MiCP is positioned closer to three-fold axis, similarly to the “knob” and ”puff” structures in enteroviruses [4,5], rendering the virion surface of SBV smooth.

The exposure of SBV to low pH, which the virus probably encounters during cell entry, induces the formation of pores at threefold and fivefold symmetry axes of the capsid that are 7.8 and 12.5 Å in diameter, respectively. This is in contrast to vertebrate picornaviruses, in which the pores along twofold icosahedral symmetry axes are generally considered the most likely sites for genome release. SBV virions lack VP4 subunits that facilitate the genome delivery of many related dicistro- and picornaviruses [6–8]. However, MiCP subunits induce liposome disruption in vitro, indicating that they are functional analogues of VP4 subunits and enable the virus genome to escape across the endosome membrane into the cell cytoplasm.

1.        Ellis JD, Munn PA. The worldwide health status of honey bees. Bee World. 2005;86: 88–101. doi:10.1080/0005772X.2005.11417323.

2.        Škubník K, Nováček J, Füzik T, Přidal A, Paxton RJ, Plevka P. Structure of deformed wing virus, a major honey bee pathogen. Proc Natl Acad Sci U S A. 2017;114: 201615695. doi:10.1073/pnas.1615695114

3.        Kalynych S, Přidal A, Pálková L, Levdansky Y, de Miranda JR, Plevka P. Virion Structure of Iflavirus Slow Bee Paralysis Virus at 2.6-Angstrom Resolution. Williams B, editor. J Virol. American Society for Microbiology; 2016;90: 7444–7455. doi:10.1128/JVI.00680-16

4.        Rossmann MG, Arnold E, Erickson JW, Frankenberger EA, Griffith JP, Hecht HJ, et al. Structure of a human common cold virus and functional relationship to other picornaviruses. Nature. 1985;317: 145–153. doi:10.1038/317145a0

5.        Rossmann MG. Viral cell recognition and entry. Protein Sci. Wiley-Blackwell; 1994;3: 1712–1725. doi:10.1002/pro.5560031010

6.        Tate J, Liljas L, Scotti P, Christian P, Lin T, Johnson JE, et al. The crystal structure of cricket paralysis virus: the first view of a new virus family. Nat Struct Biol. Nature Publishing Group; 1999;6: 765–774. doi:10.1038/11543

7.           Squires G, Pous J, Agirre J, Rozas-Dennis GS, Costabel MD, Marti GA, et al. Structure of the Triatoma virus capsid. Acta Crystallogr Sect D Biol Crystallogr. 2013;69: 1026–1037. doi:10.1107/S0907444913004617

8.           Panjwani A, Strauss M, Gold S, Wenham H, Jackson T, Chou JJ, et al. Capsid Protein VP4 of Human Rhinovirus Induces Membrane Permeability by the Formation of a Size-Selective Multimeric Pore. Rey FA, editor. PLoS Pathog. Public Library of Science; 2014;10: e1004294. doi:10.1371/journal.ppat.1004294