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Open Access Research article

Intra-specific variability and biological relevance of P3N-PIPO protein length in potyviruses

Julia Hillung1, Santiago F Elena12 and José M Cuevas13*

Author Affiliations

1 Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València 46022, Spain

2 The Santa Fe Institute, 87501, Santa Fe, NM, USA

3 Present address: Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València 46980, Spain

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BMC Evolutionary Biology 2013, 13:249  doi:10.1186/1471-2148-13-249

Published: 13 November 2013



Pipo was recently described as a new ORF encoded within the genome of the Potyviridae family members (PNAS 105:5897–5902, 2008). It is embedded within the P3 cistron and is translated in the +2 reading frame relative to the potyviral long ORF as the P3N-PIPO fusion protein. In this work, we first collected pipo nucleotide sequences available for different isolates of 48 Potyvirus species. Second, to determine the biological implications of variation in pipo length, we measured infectivity, viral accumulation, cell-to-cell and systemic movements for two Turnip mosaic virus (TuMV) variants with pipo alleles of different length in three different susceptible host species, and tested for differences between the two variants.


In addition to inter-specific variation, there was high variation in the length of the PIPO protein among isolates within species (ranging from 1 to 89 amino acids). Furthermore, selection analyses on the P3 cistron did not account for the existence of stop codons in the pipo ORF, but showed that positive selection was significant in the overlapping region for Potato virus Y (PVY) and TuMV. In some cases, variability in length was associated with host species, geographic provenance and/or other strain features. We found significant empirical differences among the phenotypes associated with TuMV pipo alleles, though the magnitude and sign of the effects were host-dependent.


The combination of computational molecular evolution analyses and experiments stemming from these analyses provide clues about the selective pressures acting upon the different-length pipo alleles and show that variation in length may be maintained by host-driven selection.

Bayesian phylogenetic methods; Host-range determinants; Molecular evolution; Potyvirus; Virus evolution; Virus fitness components