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

Abstract

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 all-atoms 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.

In-silico prediction and validation of Carica papaya protein domains interaction with the Papaya leaf curl virus and associated betasatellite encoded protein

“…The phosphorylation sites of viral proteins have also been discovered (Table 1). These sites represent variable serine, threonine, and tyrosine sites for phosphorylation, which is crucial for controlling a viral protein's stability, activity, and interactions with other viral and cellular proteins [13].…”

“…Statistical tests are applied to assess the significance of identified interactions, and the results are visualized using graphical tools. Gaining insights into the structural determinants of protein-protein interactions holds the key to a deeper understanding of biological functions, diseases, and the development of therapeutics [13].…”

Use of response surface methodology to optimise vacuum impregnation of β-carotene from Daucus carota in Pachyrhizus erosus

“…However, due to its moisture content ranging from 80 to 85 % (w.b. ), it requires storage in a cool and dry place to avoid spoilage [1][2][3] . Therefore, drying processes have been used to increase its shelf life.…”

“…), it requires storage in a cool and dry place to avoid spoilage. [1][2][3] Therefore, drying processes have been used to increase its shelf life. Some quality problems of dried jicama are browning (enzymatic browning), avour (sweetness) losses, and nutritional value reduction (regarding vitamins, minerals, and antioxidant content).…”

“…Pachyrhizus erosus is known as Mexican yam, Mexican turnip, yam bean, or “jicama”. 1 It is rich in fibre, vitamins (C and B6), and minerals (K, Ca, and P, among others). However, due to its moisture content ranging from 80 to 85% (w.b.…”