Elsevier

Current Opinion in Immunology

Volume 66, October 2020, Pages 90-97
Current Opinion in Immunology

Deciphering flavivirus–host interactions using quantitative proteomics

https://doi.org/10.1016/j.coi.2020.06.002Get rights and content

Highlights

  • Mass spectrometry (MS)-based proteomics is a powerful tool to investigate flavivirus-host interactions.

  • MS coupled with genetic screens can identify host proteins that physically interact with flaviviruses and impact viral replication.

  • MS can elucidate mechanisms of dysregulation and post-translational modifications of host proteins in flavivirus-infected cells.

Flaviviruses are a group of important emerging and re-emerging human pathogens that cause worldwide epidemics with thousands of deaths annually. Flaviviruses are small, enveloped, positive-sense, single-stranded RNA viruses that are obligate intracellular pathogens, relying heavily on host cell machinery for productive replication. Proteomic approaches have become an increasingly powerful tool to investigate the mechanisms by which viruses interact with host proteins and manipulate cellular processes to promote infection. Here, we review recent advances in employing quantitative proteomics techniques to improve our understanding of the complex interplay between flaviviruses and host cells. We describe new findings on our understanding of how flaviviruses impact protein–protein interactions, protein–RNA interactions, protein abundance, and post-translational modifications to modulate viral infection.

Introduction

Flaviviruses are a large group of medically relevant viruses that cause significant disease in humans and animals. These include dengue virus (DENV), Japanese encephalitis virus (JEV), West Nile virus (WNV), and Zika virus (ZIKV) [1,2]. Flavivirus virions contain the structural proteins, an envelope as well as a positive-sense, single-stranded RNA genome of approximately 11 kb in length. The incoming flavivirus genome encodes a single open reading frame that is translated on the endoplasmic reticulum (ER) into a single polyprotein. This polyprotein is subsequently cleaved into three structural proteins (capsid, prM and envelope) and seven non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5) by viral and host proteases. The structural proteins form the viral particles, while the non-structural proteins are required for intracellular viral propagation and immune evasion [1,2].

Given their limited protein repertoire, flaviviruses rely on the host cell machinery for many steps in their life cycle. Identification of host proteins that are required for viral replication can inform the development of effective host-directed therapeutics and new innate antiviral mechanisms. Recent advances in mass spectrometry (MS)-based proteomics have increased the sensitivity and specificity and allow for the systematic identification and quantification of proteins in a high-throughput manner (Box 1) [3]. This technology is being widely used in many fields, and has been used to identify host proteins that are involved in viral replication including flaviviral infection (Figure 1). Here, we review how proteomic approaches have improved our understanding of flavivirus–host interactions, highlighting the mechanisms by which flaviviruses manipulate host cellular processes to promote infection.

Section snippets

Mapping virus–host protein–protein interactions (PPIs)

Viruses hijack host machinery to ensure efficient viral replication. This is often achieved via physical interactions between viral and host proteins. By employing affinity purification-mass spectrometry (AP-MS) coupled with RNA interference (RNAi) screening, Li et al. generated WNV-host PPIs map and identified 26 virus-interacting host proteins that impact WNV infection [4••]. In particular, it was shown that WNV capsid interacts with PYM1, a host protein involved in the exon-junction complex

Identifying the interactomes of individual viral proteins

While some groups have taken a broad approach to identify a comprehensive flavivirus–host interactome, others have defined the interactors of an individual viral protein critical for infection. The non-structural proteins of flaviviruses play diverse roles in viral replication and assembly and in antagonizing the host immune response, including type I IFN signaling and RNA interference (RNAi). The flaviviral non-structural protein, NS2A, was shown to suppress RNAi in both mammals and

Identifying host proteins that associate with viral RNA

By performing comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS), Ooi et al. identified 464 host proteins that interact with DENV or ZIKV genomic RNA [32••]. Complementary CRISPR and haploid genetic screens with multiple clinical isolates of DENV and ZIKV revealed overlap between these approaches. Indeed, a subset of ER-associated proteins that play an important role during viral infection including RRBP1 and vigilin, were shown to bind to the viral genomic

Detecting host protein dysregulation upon viral infection

While we have a deep understanding of the changes in the gene expression landscape during infection, we have a much poorer understanding of how the proteome changes. Several groups have employed MS to define the changes in host protein abundance during flaviviral infection. Dong et al. used MS to quantify differential regulation of host proteins during DENV infection in 293T cells and found that DDX21 levels are decreased in infected cells. Upon infection, DDX21 translocates from the nucleus to

Discovering post-translational modifications of host proteins in virus-infected cells

Post-translational modifications (PTMs) can regulate protein function, localization and stability. One strategy utilized by viruses to manipulate host proteins is to alter PTMs. Protein ubiquitylation is one of the most common PTMs that can play important roles in regulating protein stability and function. Following immunoprecipitation and MS analysis, Zhang et al. identified host proteins that are differentially ubiquitylated in DENV-infected cells [58]. AUP1, a lipid droplet-localized

Concluding remarks

The interplay between viruses and their hosts is complex. To investigate such interactions, it is important to obtain a comprehensive view of both viral and host proteins during infection, and not just at the RNA level. MS-based proteomics approaches can be used to quantify protein abundance, interactions, and PTMs upon viral infection and provide researchers with opportunities to better understand the mechanisms by which viral infection alters the host cellular machinery.

AP-MS is a robust

Conflict of interest statement

Nothing declared.

References and recommended reading

Papers of particular interest, published within the period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

Acknowledgements

This work was supported by grants from the National Institutes of Health to S.C. (5R01AI122749, 1R01AI140539, 1R01AI150246) and H.R. (1RO1AI143850). S.C. is a recipient of the Burroughs Wellcome Investigators in the Pathogenesis of Infectious Disease Award. We apologize to all colleagues whose contributions were not cited due to space limitations.

References (61)

  • S. Mukherjee et al.

    Japanese encephalitis virus induces human neural stem/progenitor cell death by elevating GRP78, PHB and hnRNPC through ER stress

    Cell Death Dis

    (2018)
  • G.H. Samuel et al.

    Yellow fever virus capsid protein is a potent suppressor of RNA silencing that binds double-stranded RNA

    Proc Natl Acad Sci U S A

    (2016)
  • A.A. Sher et al.

    Zika Virus infection disrupts astrocytic proteins involved in synapse control and axon guidance

    Front Microbiol

    (2019)
  • X. Jiang et al.

    Proteomic analysis of Zika virus infected primary human fetal neural progenitors suggests a role for Doublecortin in the pathological consequences of infection in the cortex

    Front Microbiol

    (2018)
  • P.P. Garcez et al.

    Zika virus disrupts molecular fingerprinting of human neurospheres

    Sci Rep

    (2017)
  • S. Mukhopadhyay et al.

    A structural perspective of the flavivirus life cycle

    Nat Rev Microbiol

    (2005)
  • C.J. Neufeldt et al.

    Rewiring cellular networks by members of the Flaviviridae family

    Nat Rev Microbiol

    (2018)
  • A. Bensimon et al.

    Mass spectrometry–based proteomics and network biology

    Annu Rev Biochem

    (2012)
  • M. Li et al.

    Identification of antiviral roles for the exon–junction complex and nonsense-mediated decay in flaviviral infection

    Nat Microbiol

    (2019)
  • F. Bono et al.

    Assembly, disassembly and recycling: the dynamics of exon junction complexes

    RNA Biol

    (2011)
  • F. Bono et al.

    Molecular insights into the interaction of PYM with the Mago–Y14 core of the exon junction complex

    EMBO Rep

    (2004)
  • K.A. Fontaine et al.

    The cellular NMD pathway restricts zika virus infection and is targeted by the viral capsid protein

    mBio

    (2018)
  • P.S. Shah et al.

    Comparative flavivirus-host protein interaction mapping reveals mechanisms of dengue and zika virus pathogenesis

    Cell

    (2018)
  • N.J. Krogan et al.

    The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation

    Mol Cell

    (2003)
  • P. Scaturro et al.

    An orthogonal proteomic survey uncovers novel Zika virus host factors

    Nature

    (2018)
  • Q. Liang et al.

    Zika Virus NS4A and NS4B proteins deregulate Akt-mTOR signaling in human fetal neural stem cells to inhibit neurogenesis and induce autophagy

    Cell Stem Cell

    (2016)
  • M.L. Hafirassou et al.

    A global interactome map of the dengue virus NS1 identifies virus restriction and dependency host factors

    Cell Rep

    (2017)
  • C.D. Marceau et al.

    Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens

    Nature

    (2016)
  • T. Dechtawewat et al.

    Mass spectrometric analysis of host cell proteins interacting with dengue virus nonstructural protein 1 in dengue virus-infected HepG2 cells

    Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

    (2016)
  • L. Chatel-Chaix et al.

    Dengue virus perturbs mitochondrial morphodynamics to dampen innate immune responses

    Cell Host Microbe

    (2016)
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