Globally defining the effects of mutations in a picornavirus capsid.

Florian Mattenberger,Adi Stern,Victor Latorre,Omer Tirosh,Ron Geller

doi:10.7554/elife.64256

Florian Mattenberger, Adi Stern + Show 3 more

Open Access

https://doi.org/10.7554/elife.64256

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Abstract

The capsids of non-enveloped viruses are highly multimeric and multifunctional protein assemblies that play key roles in viral biology and pathogenesis. Despite their importance, a comprehensive understanding of how mutations affect viral fitness across different structural and functional attributes of the capsid is lacking. To address this limitation, we globally define the effects of mutations across the capsid of a human picornavirus. Using this resource, we identify structural and sequence determinants that accurately predict mutational fitness effects, refine evolutionary analyses, and define the sequence specificity of key capsid-encoded motifs. Furthermore, capitalizing on the derived sequence requirements for capsid-encoded protease cleavage sites, we implement a bioinformatic approach for identifying novel host proteins targeted by viral proteases. Our findings represent the most comprehensive investigation of mutational fitness effects in a picornavirus capsid to date and illuminate important aspects of viral biology, evolution, and host interactions.

Highlights

The capsids of non-enveloped viruses are among the most complex of any viral protein
These results suggest that the prediction of mutational fitness effects (MFE) in the coxsackievirus B3 (CVB3) capsid can be achieved at relatively high accuracy based on available structural and sequence information
To evaluate whether our approach can identify novel cellular targets for the viral protease, we examined the ability of 3CD protease (3CDpro) to cleave eight different proteins found in the data set, focusing on those with cellular functions of potential relevance to CVB3 biology and which could be readily detected in our cell culture assay

Summary

Introduction

The capsids of non-enveloped viruses are among the most complex of any viral protein. The assembled structure must be both sufficiently stable to protect the viral genome during its transition between cells yet readily disassemble upon entry to initiate subsequent infections For these functions to be achieved, viral capsids must encode the information for interacting with numerous cellular factors that are required to correctly fold and assemble around the genome (Callaway et al, 2001; Fields et al, 2013; Geller et al, 2007; Jiang et al, 2014; Macejak and Sarnow, 1992). We perform a comprehensive analysis of mutational fitness effects (MFE) across the complete capsid region of the human picornavirus coxsackievirus B3 (CVB3), analyzing >90% of all possible single amino acid mutations Using these data, we develop models to predict the effect of mutations with high accuracy from available sequence and structural information, improve evolutionary analyses of CVB3, and define the sequence preferences of several viral encoded motifs. Our data comprise the most comprehensive survey of MFE effects in a picornavirus capsid to date and provide important insights into virus biology, evolution, and interaction with the host

Results

Discussion

Materials and methods