Predictive Modeling of Proteins Encoded by a Plant Virus Sheds a New Light on Their Structure and Inherent Multifunctionality

Plant virus genomes encode proteins that are involved in replication, encapsidation, cell-to-cell, and long-distance movement, avoidance of host detection, counter-defense, and transmission from host to host, among other functions. Even though the multifunctionality of plant viral proteins is well d...

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Published in:Biomolecules (Basel, Switzerland) Vol. 14; no. 1; p. 62
Main Authors: Roy, Brandon G., Choi, Jiyeong, Fuchs, Marc F.
Format: Journal Article
Language:English
Published: Switzerland MDPI AG 01.01.2024
Subjects:
ABC transporter
Algorithms
Amino acids
Cell migration
Coat protein
Crystal structure
Disease transmission
DNA helicase
DNA Helicases
DNA topoisomerase
DNA Topoisomerases, Type I
DNA-directed RNA polymerase
Encapsidation
Endopeptidases
function
Genetic aspects
Genomes
in silico
Methods
modeling
Movement protein
Parathyroid hormone
Peptide Hydrolases
Physiological aspects
Plant Proteins - genetics
Plant viruses
Plant Viruses - genetics
prediction
Predictions
protein
Protein structure prediction
Protein transport
Proteins
RNA helicase
RNA polymerase
RNA viruses
RNA-directed RNA polymerase
RNA-mediated interference
Satellite RNA
Structure
Viral infections
Viral proteins
virus
Virus diseases of plants
United States
modeling
nepovirus
AlphaFold2
function
protein
prediction
in silico
virus
ISSN:2218-273X, 2218-273X
Online Access:Get full text
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Summary:Plant virus genomes encode proteins that are involved in replication, encapsidation, cell-to-cell, and long-distance movement, avoidance of host detection, counter-defense, and transmission from host to host, among other functions. Even though the multifunctionality of plant viral proteins is well documented, contemporary functional repertoires of individual proteins are incomplete. However, these can be enhanced by modeling tools. Here, predictive modeling of proteins encoded by the two genomic RNAs, i.e., RNA1 and RNA2, of grapevine fanleaf virus (GFLV) and their satellite RNAs by a suite of protein prediction software confirmed not only previously validated functions (suppressor of RNA silencing [VSR], viral genome-linked protein [VPg], protease [Pro], symptom determinant [Sd], homing protein [HP], movement protein [MP], coat protein [CP], and transmission determinant [Td]) and previously identified putative functions (helicase [Hel] and RNA-dependent RNA polymerase [Pol]), but also predicted novel functions with varying levels of confidence. These include a T3/T7-like RNA polymerase domain for protein 1AVSR, a short-chain reductase for protein 1BHel/VSR, a parathyroid hormone family domain for protein 1EPol/Sd, overlapping domains of unknown function and an ABC transporter domain for protein 2BMP, and DNA topoisomerase domains, transcription factor FBXO25 domain, or DNA Pol subunit cdc27 domain for the satellite RNA protein. Structural predictions for proteins 2AHP/Sd, 2BMP, and 3A? had low confidence, while predictions for proteins 1AVSR, 1BHel*/VSR, 1CVPg, 1DPro, 1EPol*/Sd, and 2CCP/Td retained higher confidence in at least one prediction. This research provided new insights into the structure and functions of GFLV proteins and their satellite protein. Future work is needed to validate these findings.
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ISSN:2218-273X
2218-273X
DOI:10.3390/biom14010062