The sequence and model structure analysis of three Polish peanut stunt virus strains

Abstract

Peanut stunt virus (PSV) belongs to the Cucumovirus genus of the family Bromoviridae and is widely distributed worldwide, also in Poland. PSV is a common pathogen of a wide range of economically important plants. Its coat protein (CP), similarly as in other viruses, plays an important role in many processes during viral life cycle and has great impact on the infectivity. In this study, we present the results of sequence-structure analysis of CP derived from three Polish strains of PSV: PSV Ag, G, and P. Sequences were determined using RT-PCR amplification followed by sequencing and compared with each other and also with CP from other known PSV viruses. We analyzed their phylogenetic relationship, based on CP sequence, using bioinformatic tools as well as their spatial model using homology-modeling approach with combination of ROSETTA algorithm for de novo modeling. We compared our model with those recently obtained for other cucumoviruses including PSV-Er. Our results have shown that all Polish strains probably belong to the first subgroup of PSV viruses. Homology level between strains Ag and G proved very high. Using theoretical modeling approach we obtained a model very similar to the one resolved previously with the differences caused by slightly different amino acid sequence. We have also undertaken an attempt to analyze its distant regions; however, results are not unequivocal. Analysis of symptoms and their correlation with specific amino acid position was also performed on the basis of results published elsewhere. The definite interpretation is impeded by the presence of satellite RNAs in Ag and P strains modulating symptoms' severity, though.

Effect of temperature on the pathogenesis, accumulation of viral and satellite RNAs and on plant proteome in peanut stunt virus and satellite RNA-infected plants

“…As with some CMV strains, some PSV strains may be associated with satRNA. One of the best known examples is the PSV-P strain (Pospieszny, 1987 ), later sequenced and classified in subgroup I of PSV (Obrępalska-Stęplowska et al, 2008a , b ). SatRNAs of PSV are linear, ssRNA molecules varying in length between 391 and 393 nt and do not encode any functional proteins (Obrępalska-Stęplowska et al, 2008a , 2012 ).…”

Analysis of Coat Protein of Peanut stunt virus Subgroup II Isolates from Alfalfa Fields in West Iran

“…RT‐PCRs were performed using specific primers designed in the PSV‐CP gene (Obrepalska‐Steplowska et al. ), and DNA amplicons were sequenced in both directions. Amino acid sequences corresponding to CP were aligned using clustal x 2 (Larkin et al.…”

“…The broad host range and the large number of vector species make cucumoviruses a serious threat to plant health (Obrepalska‐Steplowska et al. ). Isolates and strains of PSV have been differentiated by symptomology and serology (Xu et al.…”

Architecture and Assembly of Virus Particles

“…Modeling the CP structure demonstrated that the structures of various strains of CMV and PSV are similar though there are some differences which possibly related to differences in function (Gellért et al, 2006;Obrepalska-Steplowska et al, 2008).…”