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.

Fig 1. The evolutionary relationship of taxa of YBMV CP and other closely related organisms using the NJ method.

The bootstrap test (1000 repetitions) showed the percentage of replicate trees where the related taxa were grouped. The analysis was conducted using MEGA version 6.0 software.

Fig 2. Target-template alignment of YMBV CP (coat protein) sequence with 5ODV using ESPript 3.0 software.

Fig 3

(A) The three-dimensional structure of YBMV CP N-terminal region (red); C-terminal region (blue). (B) The protein is visualized as a solid ribbon representing β‐sheets, α‐helices, and coils.

Fig 4

(A) Ramachandran plot of the YBMV CP model. The plot was created using the PROCHECK program. (B) Protein Structure Analysis (ProSA) of model YBMV CP. The overall quality of the YBMV CP model shows the z-score value of -3.75 (Native conformation to its template).

Fig 5

Oligomeric assembly of 24 identical subunits of CP with RNA (A) top, (B) front and (C) surface representation).

Fig 6. Interaction analysis of YBMV CP with RNA binding reorganization.

(A) Wild type; (B) R124A mutant.

Fig 7. Conformational stability of YBMV CP of apo and complex through MD simulation.

(A) Backbone RMSD (B) C-alpha RMSF YBMV CP (C) Radiation of gyration for YBMV CP; (D) Hydrogen bond analysis over 50 ns period concerning the index of the residue.

Fig 8. The H-bond occupancy of wild type YBMV CP with RNA throughout the trajectory.

(A) 2D interaction of RNA with YBMV CP during simulation (B) the amino acid residues involved in the interactions (C) the overall interaction of the protein with RNA.

Fig 9. Conformational stability of YBMV CP of R124A_Apo and R124_Complex through MD simulation.

(A) Backbone RMSD (B) C-alpha RMSF YBMV CP (C) Radiation of gyration for YBMV CP; (D) comparison of Hydrogen bond analysis between wild type and R124A mutant over 50 ns period concerning the index of the residue.

Fig 10. The H-bond occupancy of mutant type YBMV CP with RNA throughout the trajectory.

(A) 2D interaction of RNA with YBMV CP during simulation (B) the amino acid residues involved in the interactions (C) the overall interaction of the protein with RNA.