Record Details

Structural insights into the RNA interaction with Yam bean Mosaic virus (coat protein) from Pachyrhizus erosus using bioinformatics approach

KRISHI: Publication and Data Inventory Repository

View Archive Info
 
 
Field Value
 
Title Structural insights into the RNA interaction with Yam bean Mosaic virus (coat protein) from Pachyrhizus erosus using bioinformatics approach
Not Available
 
Creator Varsha Acharya
R. Arutselvan
Kalidas Pati
Ajaya Kumar Rout
Budheswar Dehury
V. B. S. Chauhan
M. Nedunchezhiyan
 
Subject Potyvirus
Coat protein
Yam bean mosaic virus
RNA binding
MD Simulation
 
Description Not Available
Plants are constantly threatened by a virus infection, i.e., Potyviruses, the second largest
genus of plant viruses which results in several million-dollar losses in various essential
crops globally. Yam bean (Pachyrhizus erosus) is considered to be one of the essential
tuberous legume crops holding a great potential source of starch. Yam Bean Mosaic Virus
(YBMV) of Potyvirus group belonging to the family potyviridae affects Yam bean and several
angiosperms both in the tropical and sub-tropical regions causing large economical losses
in crops. In this study, we attempted to understand the sequence-structure relationship and
mode of RNA binding mechanism in YBMV CP using in silico integrative modeling and allatoms
molecular dynamics (MD) simulations. The assembly of coat protein (CP) subunits
from YBMV and the plausible mode of RNA binding were compared with the experimental
structure of CP from Watermelon mosaic virus potyvirus (5ODV). The transmembrane helix
region is present in the YBMV CP sequence ranging from 76 to 91 amino acids. Like the
close structural-homolog, 24 CPs monomeric sub-units formed YBMV a conserved fold.
Our computational study showed that ARG124, ARG155
, and TYR151 orient towards the inner side of the virion, while, THR122, GLN125, SER92, ASP94 reside towards the outer side of the virion. Despite sharing very low sequence similarity with CPs from other plant viruses, the strongly conserved residues Ser, Arg, and Asp within the RNA binding pocket of YBMV CP
indicate the presence of a highly conserved RNA binding site in CPs from different families. Using several bioinformatics tools and comprehensive analysis from MD simulation, our
study has provided novel insights into the RNA binding mechanism in YBMV CP. Thus, we
anticipate that our findings from this study will be useful for the development of new therapeutic
agents against the pathogen, paving the way for researchers to better control this
destructive plant virus.
Not Available
 
Date 2022-08-24T09:18:19Z
2022-08-24T09:18:19Z
2022-07-22
 
Type Article
 
Identifier Acharya V, Arutselvan R, Pati K, Rout AK, Dehury B, Chauhan VBS, et al. (2022) Structural insights into the RNA interaction with Yam bean Mosaic virus (coat protein) from Pachyrhizus erosus using bioinformatics approach. PLoS ONE 17(7): e0270534
1932-6203
http://krishi.icar.gov.in/jspui/handle/123456789/73839
 
Language English
 
Relation Not Available;
 
Publisher PLOS ONE