Variability of the PIPO protein within Sunflower chlorotic mottle virus (SuCMoV) and the Potato virus Y (PVY) subgroup members

BEJERMAN, NICOLÁS.; GIOLITTI, FABIÁN; DE BREUIL SOLEDAD; LENARDON, SERGIO

Congreso; 2do Congreso Argentino de Bioinformática y Biología Computacional; 2011

Sunflower chlorotic mottle virus (SuCMoV) is the most prevalent sunflower present in Argentina. Two biologically different strains of SuCMoV have been described: the common strain (C) and the chlorotic ringspot strain (CRS). Its complete genomic sequence has been determined [1]. SuCMoV belong to the Potato virus Y (PVY) subgroup into the Potyvirus genus. The genome of SuCMoV, similar to other members in the potyvirus, contains an open reading frame (ORF) encoding a single large polypeptide that is cleaved by three virus-encoded proteinases to produce ten mature proteins. However, in 2008 [2], a small ORF, embedded in the P3 cistron was discovered in the potyvirus and termed PIPO (Pretty Interesting Potyviridae ORF). To our knowledge, no studies have been conducted to study its variability intra and interspecies to compare with the variability found in the other potyviral proteins. Therefore, the purpose of this investigation was to study the PIPO´s variability between both SuCMoV strains, between each SuCMoV strain and the members of the PVY subgroup and also within each member of the PVY subgroup. Furthermore, we have constructed a phylogenetic tree of the PVY´s subgroup members PIPOs.          SucMoV´s PIPO contained 73 amino acids (aa), whereas the PIPO´s range size of the other member of the PVY subgroup was 64-93 aa. When pairwise comparisons were performed between both SuCMoV strains, a 94.6% identity at nucleotide (nt) level was found, whereas at aa level, the identity found was 89%. There were 1.5 nt changes for each aa change. Therefore PIPO is the least conserved protein of the SuCMoV genome.  When the C and CRS strains PIPO aa sequence was compared with those of the PVY´s subgroup members,  Pepper severe mosaic virus (PepSMV) shared the highest  identities (57.3% and 60%, respectively); whereas, Potato virus V (PVV) shared the lowest identities (20.5% and 24.7%, respectively). When the intraspecies variability of each PVY´s subgroup member was analyzed, a highest variability was found, being PIPO the most variable protein in sequence and size within the members of this subgroup.  The phylogenetic relationship between the SuCMoV strains and the other members of the PVY subgroup is illustrated in the Figure 1. When a MotifScan analysis was performed using as input the PIPO aa sequence of each SuCMoV strain, three possible phosphorilation sites were found.Taken together, the results obtained shows the importance of study the variability of this recently ORF discovered to deep the understanding of its functions.