In silico Characterization and Homology Modelling of Potato Leaf Roll Virus (PLRV) Coat Protein
Jitesh Kumar
Department of Molecular Biology and Genetic Engineering, Bihar Agricultural University, Sabour-813210, India.
Tushar Ranjan
Department of Molecular Biology and Genetic Engineering, Bihar Agricultural University, Sabour-813210, India.
Ravi Ranjan Kumar *
Department of Molecular Biology and Genetic Engineering, Bihar Agricultural University, Sabour-813210, India.
Mohammad Ansar
Department of Plant Pathology, Bihar Agricultural University, Sabour-813210, India.
Kumari Rajani
Department of Seed Science and Technology, Bihar Agricultural University, Sabour-813210, India.
Mahesh Kumar
Department of Molecular Biology and Genetic Engineering, Bihar Agricultural University, Sabour-813210, India.
Vinod Kumar
Pulse Research Centre, Mokama, Bihar Agricultural University (BAU), Sabour, India.
Anand Kumar
Department of Plant Breeding and Genetics, Bihar Agricultural University, Sabour-813210, India.
*Author to whom correspondence should be addressed.
Abstract
Polerovirus (Family-Luteoviridae) are one of the most destructive viruses causing detrimental diseases in vegetable crops in tropical regions of the world including India. Four species viz. potato leaf roll virus (PLRV), potato virus Y(PVY), potato virus X(PVX) and potato virus S(PVS) are known to cause different diseases in potato crops. Of the various viral diseases inflicting potato crops, potato leaf roll disease is the most destructive and widely distributed. They cause huge agro-economical losses (90%) worldwide and thus are the subjects of immense concern. PLRV is a phloem-limited spherical virus transmitted by several aphid species in a persistent manner. A study was performed in order to detect the infection of potato leaf roll virus from different regions of Bihar. These infected samples were diagnosed first using DAS-ELISA for the PLRV infection and later, coat protein was amplified and sequenced from PLRV positive sample. Phylogenetic tree deduced based on the nucleotide sequence of the coat protein gene gene showed a distinct divergence of PLRV isolates in two major clades. The molecular weight of the predicted protein sequence of 203 amino acids was found 22617.06 daltons while theoretical pI was 5.22. The extinction coefficient of predicted coat protein was 0.836. An attempt was taken in order to illustrate the 3D model of the coat protein which was further verified using Ramachandran plot. The model structure obtained using Swiss-Model had 92.9% residues in the most favourable region of the Ramachandran plot (Fig. 3c) and showed Z-score for bond angles, chi-1/chi-2 correlation and Ramachandran Z-score were 1.457, 1.773 and -2.633 respectively which exhibited considerably good model quality.
Keywords: Coat protein, potato leaf roll virus, phylogenetic analysis, structural analysis, homology modeling