Analysis of host protein interactions in plant viruses: an in silico study using Sesbania mosaic virus

Virus Genes ◽  
2020 ◽  
Vol 56 (6) ◽  
pp. 756-766
Author(s):  
Mariya Rashid ◽  
Shubham Mittal ◽  
Sangita Venkataraman
Keyword(s):  
Mosaic Virus ◽  
Protein Interactions ◽  
In Silico ◽  
Plant Viruses ◽  
Host Protein ◽  
In Silico Study

scholarly journals How Computational Epitope Mapping Identifies the Interactions between Nanoparticles Derived from Papaya Mosaic Virus Capsid Proteins and Immune System

2019 ◽  
Vol 20 (3) ◽  
pp. 214-225
Author(s):  
Mahbobeh Zamani-Babgohari ◽  
Kathleen L. Hefferon ◽  
Tsu Huang ◽  
Mounir G. AbouHaidar
Keyword(s):  
Immune System ◽  
Mosaic Virus ◽  
In Silico ◽  
Computational Study ◽  
Vaccine Design ◽  
Plant Viruses ◽  
Capsid Proteins ◽  
Virus Capsid ◽  
Empty Capsid ◽  
Papaya Mosaic Virus

Background: Nanoparticles derived from plant viruses possess fascinating structures, versatile functions and safe properties, rendering them valuable for a variety of applications. Papaya mosaic Virus-Like Particles (VLPs) are nanoparticles that contain a repetitive number of virus capsid proteins (PMV-CP) and are considered to be promising platforms for vaccine design. Previous studies have reported the antigenicity of PMV nanoparticles in mammalian systems. Materials and Methods: As experiments that concern vaccine development require careful design and can be time consuming, computational experiments are of particular importance. Therefore, prior to expressing PMV-CP in E. coli and producing nanoparticles, we performed an in silico analysis of the virus particles using software programs based on a series of sophisticated algorithms and modeling networks as useful tools for vaccine design. A computational study of PMV-CP in the context of the immune system reaction allowed us to clarify particle structure and other unknown features prior to their introduction in vitro. Results: The results illustrated that the produced nanoparticles can trigger an immune response in the absence of fusion with any foreign antigen. Conclusion: Based on the in silico analyses, the empty capsid protein was determined to be recognised by different B and T cells, as well as cells which carry MHC epitopes.

scholarly journals In Silico Study on Spice-Derived Antiviral Phytochemicals Against SARS-CoV-2 TMPRSS2 Target

2020 ◽  
Author(s):  
Pradeep Kumar Yadav ◽  
Amit Jaiswal ◽  
Rajiv Kumar Singh
Keyword(s):  
Molecular Simulation ◽  
In Silico ◽  
Catalytic Domain ◽  
Host Protein ◽  
Dynamics Simulation ◽  
Spike Protein ◽  
Potential Inhibitor ◽  
In Silico Study

We predicted the structure of TMPRSS2 (transmembrane protease serine 2), a host protein that truncates spike protein of SARS-CoV-2. Then we docked 18 anti-viral compounds found in Indian spices against the catalytic domain of TMPRSS2. We then performed rigorous molecular simulation dynamics simulation to screen the best natural phytochemical which could act as a potential inhibitor of TMPRSS2 activation. <br>

scholarly journals The Potyvirus Silencing Suppressor Protein VPg Mediates Degradation of SGS3 via Ubiquitination and Autophagy Pathways

2016 ◽  
Vol 91 (1) ◽  
Author(s):  
Xiaofei Cheng ◽  
Aiming Wang
Keyword(s):  
Mosaic Virus ◽  
Rna Silencing ◽  
Plant Viruses ◽  
Turnip Mosaic Virus ◽  
Host Protein ◽  
Ubiquitin Proteasome ◽  
Cellular Pathways ◽  
Viral Suppressors ◽  
Interfering Rna ◽  
Innate Antiviral Immunity

ABSTRACT RNA silencing is an innate antiviral immunity response of plants and animals. To counteract this host immune response, viruses have evolved an effective strategy to protect themselves by the expression of viral suppressors of RNA silencing (VSRs). Most potyviruses encode two VSRs, helper component-proteinase (HC-Pro) and viral genome-linked protein (VPg). The molecular biology of the former has been well characterized, whereas how VPg exerts its function in the suppression of RNA silencing is yet to be understood. In this study, we show that infection by Turnip mosaic virus (TuMV) causes reduced levels of suppressor of gene silencing 3 (SGS3), a key component of the RNA silencing pathway that functions in double-stranded RNA synthesis for virus-derived small interfering RNA (vsiRNA) production. We also demonstrate that among 11 TuMV-encoded viral proteins, VPg is the only one that interacts with SGS3. We furthermore present evidence that the expression of VPg alone, independent of viral infection, is sufficient to induce the degradation of SGS3 and its intimate partner RNA-dependent RNA polymerase 6 (RDR6). Moreover, we discover that the VPg-mediated degradation of SGS3 occurs via both the 20S ubiquitin-proteasome and autophagy pathways. Taken together, our data suggest a role for VPg-mediated degradation of SGS3 in suppression of silencing by VPg. IMPORTANCE Potyviruses represent the largest group of known plant viruses and cause significant losses of many agriculturally important crops in the world. In order to establish infection, potyviruses must overcome the host antiviral silencing response. A viral protein called VPg has been shown to play a role in this process, but how it works is unclear. In this paper, we found that the VPg protein of Turnip mosaic virus (TuMV), which is a potyvirus, interacts with a host protein named SGS3, a key protein in the RNA silencing pathway. Moreover, this interaction leads to the degradation of SGS3 and its interacting and functional partner RDR6, which is another essential component of the RNA silencing pathway. We also identified the cellular pathways that are recruited for the VPg-mediated degradation of SGS3. Therefore, this work reveals a possible mechanism by which VPg sabotages host antiviral RNA silencing to promote virus infection.

scholarly journals In Silico Study on Spice-Derived Antiviral Phytochemicals Against SARS-CoV-2 TMPRSS2 Target

2020 ◽  
Author(s):  
Pradeep Kumar Yadav ◽  
Amit Jaiswal ◽  
Rajiv Kumar Singh
Keyword(s):  
Molecular Simulation ◽  
In Silico ◽  
Catalytic Domain ◽  
Host Protein ◽  
Dynamics Simulation ◽  
Spike Protein ◽  
Potential Inhibitor ◽  
In Silico Study

We predicted the structure of TMPRSS2 (transmembrane protease serine 2), a host protein that truncates spike protein of SARS-CoV-2. Then we docked 18 anti-viral compounds found in Indian spices against the catalytic domain of TMPRSS2. We then performed rigorous molecular simulation dynamics simulation to screen the best natural phytochemical which could act as a potential inhibitor of TMPRSS2 activation. <br>

Identification of Plant Virus Movement-Host Protein Interactions

2001 ◽  
Vol 56 (9-10) ◽  
pp. 669-679 ◽  
Author(s):  
Jan-Wolfhard Kellmann
Keyword(s):  
Protein Interactions ◽  
Plant Virus ◽  
Molecular Mechanisms ◽  
Plant Viruses ◽  
Host Protein ◽  
Virus Movement ◽  
Plant Tissues ◽  
Host Proteins ◽  
Movement Proteins ◽  
Systemic Spread

Abstract After the discovery of ‘movement proteins’ as a peculiarity of plant viruses and with the help of novel methods for the detection and isolation of interacting host proteins new insights have been obtained to understand the mechanisms of virus movement in plant tissues. Rapid progress in studying the molecular mechanisms of systemic spread of plant infecting viruses revealed an interrelation between virus movement and macromolecular trafficking in plant tissues. This article summarizes current explorations on plant virus movement proteins (MPs) and introduces the state of the art in the identification and isolation of MP interacting host proteins.

scholarly journals An in silico study on plant-derived inhibitors against a prognostic Biomarker, Jab1

2019 ◽  
Vol 10 (2) ◽  
pp. 1058-1061
Author(s):  
Fahad Khan ◽  
Pratibha Pandey ◽  
Rashmi Mishra ◽  
Niraj Kumar Jha ◽  
Shweta Sharma
Keyword(s):  
Protein Interactions ◽  
In Silico ◽  
Natural Compounds ◽  
Multiple Protein ◽  
In Silico Study ◽  
Low Toxicity ◽  
Systemic Drug Delivery ◽  
Cancerous Cells ◽  
Systemic Drug

Cancer kills millions of people worldwide every year. The main form of treatment at this point is chemotherapy, which comprises of systemic drug delivery so that they can kill the cancerous cells more effectively. But most of these drugs cause severe side effects in patients and, therefore there is a strong need to focus on identifying natural compounds as a potent phytoinhibitors using various in silico and in vitro approaches. Natural compounds pose low toxicity, hence render them to be an excellent alternative to the basis for the development of new anti-cancerous drugs. Our study considers an effective therapeutic target, Jab1 (c-Jun activation domain-binding protein-1) or a c-Jun coactivator, which has been implicated in multiple protein interactions that play a significant role in various stages of carcinogenesis. Hence we have performed screening of 1500 natural compounds having anticancerous activity by applying various in silico approaches including Lipinski rule of five, ADME, and various Molecular Docking tools. In this study, we have identified two potent phytoinhibitors against Jab1 which needs to be further validated through in vitro approaches.

scholarly journals A comprehensive physical interaction map between the Turnip mosaic potyvirus and Arabidopsis thaliana proteomes

2021 ◽  
Author(s):  
Fernando Martínez ◽  
Christina Toft ◽  
Julia Hillung ◽  
Silvia Giménez-Santamarina ◽  
Lynne Yenush ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Protein Interactions ◽  
Mode Of Action ◽  
Plant Viruses ◽  
Host Protein ◽  
Bimolecular Fluorescence Complementation ◽  
Virus Protein ◽  
Physical Interaction ◽  
Protein Protein Interactions ◽  
Disease Etiology

Abstract Viruses are obligate intracellular parasites that have co-evolved with their hosts to establish an intricate network of protein-protein interactions. Yet, the systems-level mode of action of plant viruses remains poorly understood. Here, we followed a high-throughput yeast two-hybrid screening to identify 378 novel virus-host protein-protein interactions between Turnip mosaic virus (TuMV), a representative plant RNA virus, and Arabidopsis thaliana, one of its natural hosts. We found the RNA-dependent RNA polymerase NIb as the virus protein with the largest number of contacts. We verified a subset of 25 selected interactions in planta by bimolecular fluorescence complementation assays. We then constructed a comprehensive network comprising 399 TuMV-A. thaliana interactions to perform, together with intravirus and intrahost connections, detailed computational analyses. In particular, we found that the host proteins targeted by the virus participate in a higher number of infection-related functions, are more connected and have an increased capacity to spread information throughout the cell proteome, display higher expression levels, and have been subject to stronger purifying selection than expected by chance. Overall, our results provide a comprehensive mechanistic description of a plant virus-host interplay, with potential impact on disease etiology, and reveal that plant and animal viruses share fundamental features in their mode of action.

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