Identification of structural domains involved in astrovirus capsid biology

Abstract

Coat proteins of non-enveloped, icosahedral viruses must perform a variety of functions during their life cycle such as assembly of the coat protein subunits into a closed shell, specific encapsidation of the viral nucleic acid, maturation of the capsid, interaction with host receptors, and disassembly to deliver the genetic information into the newly infected cell. A thorough understanding of the multiple capsid properties at the molecular level is required in order to identify potential targets for antiviral therapy and the prevention of viral disease. The system we have chosen for study is the astrovirus, a family of icosahedral, single-stranded RNA viruses that cause disease in mammals and birds. Very little is known about what regions of the coat protein contribute to the diverse capsid functions. This review will present novel structural predictions for the coat protein sequence of different astrovirus family members. Based on these predictions, we hypothesize that the assembly and RNA packaging functions of the astrovirus coat protein constitutes an individual domain distinct from the determinants required for receptor binding and internalization. Information derived from these structural predictions will serve as an important tool in designing experiments to understand astrovirus biology.

FIG. 1

Genomic organization and morphogenesis of HAstV-1 prototype (Oxford strain). (A) Genomic and subgenomic RNA are indicated by the solid black line with their length indicated in nucleotides (nt). The open reading frames (ORF) along with their protein products are shown as rectangles. ORF1a encodes a 3C-like serine protease motif (stippled box) along with a nuclear localization (NLS) motif (horizontally striped box). The asterisk (*) denotes the ribosomal frameshifting signal. ORF1b encodes the viral polymerase and the polymerase motif is indicated (box with diagonal lines). ORF2 encodes the coat protein. The first half of the coat protein sequence (amino acids 1 to 415, heavily shaded) is highly conserved among all known members of the Astroviridae whereas the last half of the coat protein (amino acids 416–787, no shading) is highly variable. The arrowhead (▾) indicates the approximate location of putative caspase cleavage site(s) conserved among astrovirus capsid proteins (42). The numbers below the rectangles refer to length of the protein products in amino acids. (B) Cleavage cascade of the coat protein precursor as described in the text. Trypsin treatment cleaves the particle into its mature products of VP34 (of which two species are predicted), VP26 and VP29.

FIG. 2

Proposed functional domains of the astrovirus coat protein. The coat protein is illustrated with the conserved region in the first half (heavily shaded) and the variable region in the last half (no shading) of the molecule. The positively charged N terminus of the coat protein proposed to be involved in viral RNA packaging is indicated (+++) along with the approximate location of trypsin cleavage sites (T▾) and putative caspase cleavage site(s) (C▾). Based on the structural predictions outlined in the text, we propose that the conserved region of the coat protein encodes the assembly domain (AD) required to form the viral capsid and encapsidate the viral RNA whereas the variable region encodes the receptor-interaction domain (RID) that binds to specific receptors on the surface of the host cell.