Detection of potato virus Y P1 protein in infected cells and analysis of its cleavage site

Involvement of the P1 cistron in overcoming eIF4E-mediated recessive resistance against Clover yellow vein virus in pea

Two recessive genes (cyv1 and cyv2) are known to confer resistance against Clover yellow vein virus (ClYVV) in pea. cyv2 has recently been revealed to encode eukaryotic translation initiation factor 4E (eIF4E) and is the same allele as sbm1 and wlm against other potyviruses. Although mechanical inoculation with crude sap is rarely able to cause infection of a cyv2 pea, biolistic inoculation of the infectious ClYVV cDNA clone does. At the infection foci, the breaking virus frequently emerges, resulting in systemic infection. Here, a derived cleaved-amplified polymorphic sequence analysis showed that the breakings were associated with a single nonsynonymous mutation on the ClYVV genome, corresponding to an amino-acid substitution at position 24 (isoleucine to valine) on the P1 cistron. ClYVV with the point mutation was able to break the resistance. This is a first report demonstrating that P1 is involved in eIF4E-mediated recessive resistance.

Role of genetic recombination in the molecular architecture of Papaya ringspot virus

Papaya ringspot virus (PRSV) has a single-stranded RNA genome and causes severe economic losses both in cucurbits and papaya worldwide. The extent to which the genome of PRSV is shaped by recombination provides an understanding of the molecular evolution of PRSV and helps in studying features such as host specificity, geographic distribution, and its emergence as new epidemics. The PRSV-P-Indian isolate was completely sequenced and compared with 14 other isolates reported from the rest of the world for their phylogenetic survey of recombination events. Cistron-by-cistron sequence comparison and phylogenetic analysis based on full-genome polyprotein showed two distinct groupings of Asian and American isolates, although PRSV-P and W-India clustered along with the American isolates. Recombination sites were found throughout the genomes, except in the small 6K1 protein gene. A significant proportion of recombination hotspots was found in the P1 gene, followed by P3, cylindrical inclusion (CI), and helper component proteinase (HcPro). Correlations between the presence of recombination sites, geographic distribution, and phylogenetic relationship provide an opportunity to establish the molecular evolution and geographic route of PRSV.

A novel insertion site inside the potyvirus P1 cistron allows expression of heterologous proteins and suggests some P1 functions

The P1 cistron encodes the first and most variable part of the polyprotein of potyviruses. A site tolerant to a pentapeptide insertion at the N-terminus of Potato virus A P1 (Genome Res. 12, 584-594) was used to express heterologous proteins (insertions up to 783 nucleotides) with or without flanking new proteolytic sites. Aequorea victoria green fluorescent protein (GFP) accumulated to high levels when proteolytically released from P1 and showed strong fluorescence in leaves systemically infected with vector virus. Deletions in GFP and adjacent viral sequences emerged 2-4 weeks after infection, revealing putative recombination hot spots. The inserts in P1 diminished infectivity host-specifically, reduced virus accumulation in protoplasts and systemically infected leaves, alleviated symptoms and reduced accumulation of mRNA and HCpro in cis in a virus-free system. This heterologous protein expression site is the first within a protein-encoding cistron and the third in the genome of potyviruses.

Overview and analysis of the polyprotein cleavage sites in the family Potyviridae

SUMMARY The genomes of plant viruses in the family Potyviridae encode large polyproteins that are cut by virus-encoded proteases into ten mature proteins. Three different types of protease have been identified, each of which cuts at sites with a distinctive sequence pattern. The experimental evidence for this specificity is reviewed and the cleavage site patterns are compiled for all sequenced species within the family. Seven of the nine cleavage sites in each species are cut by the viral NIa-Pro and patterns around these sites are related where possible to the active site-substrate interactions recently deduced following the resolution of the crystal structure of Tobacco etch virus (TEV) NIa-Pro (Phan et al., 2002. J. Biol. Chem. 277, 50564-50572). In particular, a revised series of cleavage sites for Sweet potato mild mottle virus (genus Ipomovirus) is proposed with a conserved His at the P1 position. This is supported by homology modelling studies using the TEV structure as a template. The data also provide a standard to correct the annotation of some other published sequences and to help predict these sites in further virus sequences as they become available. Comprehensive data for all sequences of each virus in the family, together with some summaries, have been made available at http://www.rothamsted.bbsrc.ac.uk/ppi/links/pplinks/potycleavage/index.html.