Is the Glycoprotein Responsible for the Differences in Dispersal Rates between Lettuce Necrotic Yellows Virus Subgroups?

Abstract

Lettuce necrotic yellows virus is a type of species in the Cytorhabdovirus genus and appears to be endemic to Australia and Aotearoa New Zealand (NZ). The population of lettuce necrotic yellows virus (LNYV) is made up of two subgroups, SI and SII. Previous studies demonstrated that SII appears to be outcompeting SI and suggested that SII may have greater vector transmission efficiency and/or higher replication rate in its host plant or insect vector. Rhabdovirus glycoproteins are important for virus-insect interactions. Here, we present an analysis of LNYV glycoprotein sequences to identify key features and variations that may cause SII to interact with its aphid vector with greater efficiency than SI. Phylogenetic analysis of glycoprotein sequences from NZ isolates confirmed the existence of two subgroups within the NZ LNYV population, while predicted 3D structures revealed the LNYV glycoproteins have domain architectures similar to Vesicular Stomatitis Virus (VSV). Importantly, changing amino acids at positions 244 and 247 of the post-fusion form of the LNYV glycoprotein altered the predicted structure of Domain III, glycosylation at N248 and the overall stability of the protein. These data support the glycoprotein as having a role in the population differences of LNYV observed between Australia and New Zealand.

Keywords: LNYV; cytorhabdovirus; glycoprotein; lettuce necrotic yellows virus; plant virus; rhabdovirus; virus–insect interaction.

Figure 1

LNYV SI and SI samples collected from New Zealand sites. (A) Map of NZ illustrating the locations of samples. Black pins indicate major NZ cities, and green pins indicate sample sites. Blue text represents isolates that were diagnosed as LNYV subgroup I and red text represents isolates that were diagnosed as LNYV subgroup II. Modified with permission from Darling [18]. (B,C) Maximum likelihood analysis of glycoprotein nt and aa sequences, respectively, with LYMoV as the outgroup. Bootstrap values greater than 50 are indicated at the branch nodes. The scales indicate the number of substitutions per site.

Figure 2

LNYV SI and SI samples collected from New Zealand sites. (A) Comparison of the topology of the pre-fusion forms of LNYV and VSV glycoproteins. (B) Comparison of the domain structure of the post-fusion forms of LNYV and VSV glycoproteins. (C) Ribbon models of the predicted 3D structures for the post-fusion glycoproteins of VSV, LNYV subgroups I (HV33) and SII (HV19) as well as the in silico DIII mutant of HV19. Domains are coloured according to that shown in (B).

Figure 3

Tertiary and secondary structures of each domain of each post-fusion glycoprotein. (A,C,E,G) Predicted 3D structures for Domain I (DI), Domain II (DII), Domain III (DIII) and Domain IV (DIV), respectively. (B,D,F,H) Alignments of the predicted secondary structures for DI, DII, DIII and DIV, respectively. (B) Alignment of DI aa positions 1–16 and 300–405; (D) alignment of DII aa positions 15–35, 259–304 and 405–478; (F) alignment of DIII aa positions 34–51 and 180–261; (H) alignment of DIV aa positions DIV, 49–181. Amino acids that are not conserved are marked in yellow. The low-possibility glycosylation sites are marked in blue in the alignment and blue stars in the 3D structure. The high-potential glycosylation sites are marked in red in the alignment and red stars in the 3D structure. Disulphide bonds are marked by yellow lines and loops by red lines. The altered amino acids are marked in purple.

Figure 3

Tertiary and secondary structures of each domain of each post-fusion glycoprotein. (A,C,E,G) Predicted 3D structures for Domain I (DI), Domain II (DII), Domain III (DIII) and Domain IV (DIV), respectively. (B,D,F,H) Alignments of the predicted secondary structures for DI, DII, DIII and DIV, respectively. (B) Alignment of DI aa positions 1–16 and 300–405; (D) alignment of DII aa positions 15–35, 259–304 and 405–478; (F) alignment of DIII aa positions 34–51 and 180–261; (H) alignment of DIV aa positions DIV, 49–181. Amino acids that are not conserved are marked in yellow. The low-possibility glycosylation sites are marked in blue in the alignment and blue stars in the 3D structure. The high-potential glycosylation sites are marked in red in the alignment and red stars in the 3D structure. Disulphide bonds are marked by yellow lines and loops by red lines. The altered amino acids are marked in purple.