Inter- and Intragenus Structural Variations in Caliciviruses and Their Functional Implications

Abstract

The family Caliciviridae is divided into four genera and consists of single-stranded RNA viruses with hosts ranging from humans to a wide variety of animals. Human caliciviruses are the major cause of outbreaks of acute nonbacterial gastroenteritis, whereas animal caliciviruses cause various host-dependent illnesses with a documented potential for zoonoses. To investigate inter-and intragenus structural variations and to provide a better understanding of the structural basis of host specificity and strain diversity, we performed structural studies of the recombinant capsid of Grimsby virus, the recombinant capsid of Parkville virus, and San Miguel sea lion virus serotype 4 (SMSV4), which are representative of the genera Norovirus (genogroup 2), Sapovirus, and Vesivirus, respectively. A comparative analysis of these structures was performed with that of the recombinant capsid of Norwalk virus, a prototype member of Norovirus genogroup 1. Although these capsids share a common architectural framework of 90 dimers of the capsid protein arranged on a T‫3؍‬ icosahedral lattice with a modular domain organization of the subunit consisting of a shell (S) domain and a protrusion (P) domain, they exhibit distinct differences. The distally located P2 subdomain of P shows the most prominent differences both in shape and in size, in accordance with the observed sequence variability. Another major difference is in the relative orientation between the S and P domains, particularly between those of noroviruses and other caliciviruses. Despite being a human pathogen, the Parkville virus capsid shows more structural similarity to SMSV4, an animal calicivirus, suggesting a closer relationship between sapoviruses and animal caliciviruses. These comparative structural studies of caliciviruses provide a functional rationale for the unique modular domain organization of the capsid protein with an embedded flexibility reminiscent of an antibody structure. The highly conserved S domain functions to provide an icosahedral scaffold; the hypervariable P2 subdomain may function as a replaceable module to confer host specificity and strain diversity; and the P1 subdomain, located between S and P2, provides additional fine-tuning to position the P2 subdomain.

Cryo-electron microscopy reconstructions of two types of wild rabbit hemorrhagic disease viruses characterized the structural features of Lagovirus

“…P2 subdomain shows obvious structural differences among RHDV, rNV and SMSV. RHDV has a hat-shaped prominency at P2 region, while rNV has an approximately rectangular platform on its top and SMSV exhibits an approximately parallelogram-shaped platform with a dent at the center as previously reported (Chen et al, 2004). The different shapes of P2 region implicate the difference in antigen structures and antibody binding sites of caliciviruses.…”

“…The 23 sequences of the capsid protein or protein precursors of caliciviruses were obtained from NCBI (National Center for Biotechnology Information, http://www.ncbi.nlm.nih.gov) as described (Chen et al, 2004), including AY269825 (RHDV NJ85), M87661 (NV), U22498 (Mexico), AJ004864 (GrV), U07611 (Hawaii), X86557 (Lordsdale), AB042808 (Chiba), L23828 (KY89), U04469 (Desert Shield virus), AJ011099 (bovine), AF181082 (VESV), M87482 (SMSV4), AF091736 (pan-1), M87481 (SMSV1), M86379 (FCV-F9), U13992 (FCV-CFI), D31836 (FCV-F4), U65427 (Sapporo), X86560 (Manchester), U73124 (PV), AF182760 (porcine), Z69620 (EBHSV) and AB00225 (canine). Multiple-sequence alignment against these 23 sequences was calculated by using the program CLUSTALW2 (http://www.ebi.ac.uk/Tools/clustalw2/) (Larkin et al, 2007).…”

“…Examples include the cryo-electron microscopy (cryo-EM) reconstruction of the primate calicivirus (~25 Å) (Prasad et al, 1994), San Miguel sea lion virus (SMSV) (22 Å) (Chen et al, 2004) and RHDV (32 Å) (Zheng et al, 2001). In addition, the recombinant VP60s of NV (Venkataram Prasad et al, 2000;Bertolotti-Ciarlet et al, 2002), Grimsby virus (GrV) (Chen et al, 2004), Parksville virus (PV) (Chen et al, 2004) and RHDV (Barcena et al, 2004) were heterogeneously expressed and assembled into VLPs whose 3D structures were successfully reconstructed by cryo-EM with the resolution about 20 Å.…”

“…Examples include the cryo-electron microscopy (cryo-EM) reconstruction of the primate calicivirus (~25 Å) (Prasad et al, 1994), San Miguel sea lion virus (SMSV) (22 Å) (Chen et al, 2004) and RHDV (32 Å) (Zheng et al, 2001). In addition, the recombinant VP60s of NV (Venkataram Prasad et al, 2000;Bertolotti-Ciarlet et al, 2002), Grimsby virus (GrV) (Chen et al, 2004), Parksville virus (PV) (Chen et al, 2004) and RHDV (Barcena et al, 2004) were heterogeneously expressed and assembled into VLPs whose 3D structures were successfully reconstructed by cryo-EM with the resolution about 20 Å. In addition, higher resolution cryo-EM reconstructions of Feline calicivirus (FCV) VLP (16 Å) (Bhella et al, 2008) and Murine Norovirus (MNV) VLP (12 Å) (Katpally et al, 2008), as well as the interactions between virion and receptor or antibody, fJAM-1-labeled FCV (18 Å) (Bhella et al, 2008), MNV-Fab (22 Å) (Katpally et al, 2008) and RHDV VLP/mAb-E3 (32 Å) (Thouvenin et al, 1997), were reported recently.…”

Genetic Analysis of Noroviruses in Chiba Prefecture, Japan, between 1999 and 2004

“…1B and For verification of these clusters and characterization of each subtype, we analyzed the nucleotide sequences of the P regions of 10 strains belonging to each GII-4 cluster. The range of the P region was determined as described by Chen et al (7). The resultant phylogenetic tree and amino acid alignment of the P region are shown in Fig.…”