VirusMapper: open-source nanoscale mapping of viral architecture through super-resolution microscopy.

Robert D M Gray,Jason Mercer,Kathrin Maria Scherer,Ricardo Henriques,Jerzy Samolej,Pedro Matos Pereira,Christopher Karl Ernst Bleck,Corina Beerli

doi:10.1038/srep29132

Robert D M Gray, Jason Mercer + Show 6 more

Open Access

https://doi.org/10.1038/srep29132

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Abstract

The nanoscale molecular assembly of mammalian viruses during their infectious life cycle remains poorly understood. Their small dimensions, generally bellow the 300nm diffraction limit of light microscopes, has limited most imaging studies to electron microscopy. The recent development of super-resolution (SR) light microscopy now allows the visualisation of viral structures at resolutions of tens of nanometers. In addition, these techniques provide the added benefit of molecular specific labelling and the capacity to investigate viral structural dynamics using live-cell microscopy. However, there is a lack of robust analytical tools that allow for precise mapping of viral structure within the setting of infection. Here we present an open-source analytical framework that combines super-resolution imaging and naïve single-particle analysis to generate unbiased molecular models. This tool, VirusMapper, is a high-throughput, user-friendly, ImageJ-based software package allowing for automatic statistical mapping of conserved multi-molecular structures, such as viral substructures or intact viruses. We demonstrate the usability of VirusMapper by applying it to SIM and STED images of vaccinia virus in isolation and when engaged with host cells. VirusMapper allows for the generation of accurate, high-content, molecular specific virion models and detection of nanoscale changes in viral architecture.

Highlights

The nanoscale molecular assembly of mammalian viruses during their infectious life cycle remains poorly understood
We have demonstrated the method with structured illumination microscopy (SIM) and stimulated emission depletion (STED) microscopy and the method is expected to work for high quality single-molecule localization microscopy (SMLM) data, as long as the labelling and localisation density is high enough
To determine the structural model generation ability of VirusMapper we applied it to the prototypic poxvirus, vaccinia virus (VACV)[8]

Summary

Introduction

The nanoscale molecular assembly of mammalian viruses during their infectious life cycle remains poorly understood. We present an open-source analytical framework that combines superresolution imaging and naïve single-particle analysis to generate unbiased molecular models. This tool, VirusMapper, is a high-throughput, user-friendly, ImageJ-based software package allowing for automatic statistical mapping of conserved multi-molecular structures, such as viral substructures or intact viruses. Probing viral structure often provides novel insight into the structure-function relationship of protein localization within viral particles[1,2] This information is key to understanding viral organization, and the mechanisms of virus metastability that dictate virus assembly and disassembly in host cells[3]. VirusMapper is an open-source, user-friendly software that provides researchers with a powerful tool to create accurate, detailed virus models thereby opening new doors to further our understanding of virus structure-function relationships

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