Three-dimensional model of the potyviral genome-linked protein.

Abstract

The full sequence of the genome-linked viral protein (VPg) cistron located in the central part of potato virus Y (common strain) genome has been identified. The VPg gene codes for a protein of 188 amino acids, with significant homology to other known potyviral VPg polypeptides. A three-dimensional model structure of VPg is proposed on the basis of similarity of hydrophobic-hydrophilic residue distribution to the sequence of malate dehydrogenase of known crystal structure. The 5'. end of the viral RNA can be fitted to interact with the protein through the exposed hydroxyl group of Tyr-64, in agreement with experimental data. The complex favors stereochemically the formation of a phosphodiester bond [5'-(04-tyrosylphospho) The genome-linked viral protein (VPg) covalently bound to a 5'-terminal nucleotide of the genome has been identified for several animal and plant viruses, with both DNA and RNA genomes (1). Among positive-sense RNA viruses five families-luteoviruses, picornaviruses, comoviruses, nepoviruses, and potyviruses-are known to contain 5'-terminal VPg (1).The latter four families also share other similarities in RNA structure [3'-terminal poly(A) tail], genome organization (the presence of a characteristic cluster of replication genes), and strategy of expression (expression of viral RNA as a single polyprotein undergoing self-processing), and they are therefore often arranged in a supergroup of picornavirus-like viruses (2). In the potyvirus family, the area of our interest, genomic RNAs carry at their 5' end a VPg of molecular mass 22-24 kDa (3-5). As in polioviruses (6, 7), potyviral VPg binds to the 5'-phosphate through the hydroxyl group of a tyrosine (8). Sequencing the potato virus Y, common strain (PVYO), we detected a part of the viral open reading frame covering the putative VPg cistron, which translates into a protein of molecular mass equal to 25 kDa. In a study of the sequences of phenotypically different PVY strains, the PVY variants were recently classified into three phylogenetic groups (9). Strikingly, the first 20 5'-proximal RNA bases, covering the fragment which could be implicated in interaction with VPg, seem to be fully conserved in representatives of all subgroups (9). The distal 5' nontranslated region varies significantly between the strains. The conservation of the 5' terminus and of tyrosine implicated in RNA binding (8) suggests that constraints are imposed on their interaction.It can be inferred from the data on poliovirus (10, 11) that VPg binding to RNA is intimately related to the synthesis of progeny plus and minus RNA strands. It is suggested that a covalent [5'-(04-tyrosylphospho)adenylate] bond could be formed during potyviral RNA replication either by transesterification with nascent RNA chain or as a result of adenylylation of specific VPg tyrosine. Such VPg mono-(or oligo)adenylate could prime the progeny RNA synthesis. The two mechanisms are believed not to be mutually exclusive and could reflect the role of VPg in differentiation of viral plus and minus ...

Potato virus A genome-linked protein VPg is an intrinsically disordered molten globule-like protein with a hydrophobic core

“…In the latter case the secondary structure element prediction correlated well with our prediction including the amphiphilic central α-helix. As Roudet-Tavert et al 2007, we noted obvious discrepancies between our secondary structure prediction and the three dimensional model made by Płochocka et. al.…”

“…Experimental data obtained supports the presence of large unstructured regions, which is in contrast with an earlier model of PVY VPg structure. This structure was constructed with the aid of a template protein sharing 52% amino acid sequence similarity with PVY VPg, and the modeling resulted into a highly ordered structure (Płochocka et al, 1996). We approached the structural features of PVA VPg with partially overlapping experimental setup as in Grezela et al, 2008.…”

A Cysteine-Rich Plant Protein Potentiates Potyvirus Movement through an Interaction with the Virus Genome-Linked Protein VPg

“…A putative three-dimensional structure for the potyvirus VPg has been published (20). The VPg amino acid sequence showed the greatest structural homology to the folded structure for the enzyme malate dehydrogenase.…”

“…The VPg amino acid sequence showed the greatest structural homology to the folded structure for the enzyme malate dehydrogenase. This placed the N-terminal 16 aa on the surface of the folded VPg (20). In this location, F12 would be available for a surface interaction with PVIPs.…”

Structural Flexibility Allows the Functional Diversity of Potyvirus Genome-Linked Protein VPg

“…These difficulties have been reported, together with other problems in VPg structure determination (16,40,41). The structure of PVY VPg has been modeled based on a nonhomologous template (33), which was selected on the basis of similarity in the hydrophobic-hydrophilic residue distribution. Recent advances in homology-modeling algorithms and the increasing number of template structures enabled us to achieve a plausible model of PVA VPg structure in spite of its apparently being on the border between order and disorder.…”