Interrogating Host Antiviral Environments Driven by Nuclear DNA Sensing: A Multiomic Perspective.

Timothy R Howard,Ileana M Cristea

doi:10.3390/biom10121591

Abstract

Nuclear DNA sensors are critical components of the mammalian innate immune system, recognizing the presence of pathogens and initiating immune signaling. These proteins act in the nuclei of infected cells by binding to foreign DNA, such as the viral genomes of nuclear-replicating DNA viruses herpes simplex virus type 1 (HSV-1) and human cytomegalovirus (HCMV). Upon binding to pathogenic DNA, the nuclear DNA sensors were shown to initiate antiviral cytokines, as well as to suppress viral gene expression. These host defense responses involve complex signaling processes that, through protein–protein interactions (PPIs) and post-translational modifications (PTMs), drive extensive remodeling of the cellular transcriptome, proteome, and secretome to generate an antiviral environment. As such, a holistic understanding of these changes is required to understand the mechanisms through which nuclear DNA sensors act. The advent of omics techniques has revolutionized the speed and scale at which biological research is conducted and has been used to make great strides in uncovering the molecular underpinnings of DNA sensing. Here, we review the contribution of proteomics approaches to characterizing nuclear DNA sensors via the discovery of functional PPIs and PTMs, as well as proteome and secretome changes that define a host antiviral environment. We also highlight the value of and future need for integrative multiomic efforts to gain a systems-level understanding of DNA sensors and their influence on epigenetic and transcriptomic alterations during infection.

Highlights

Eukaryotic cells are relentlessly assailed by a myriad of pathogens, thereby needing to constantly evolve and expand their mechanisms for pathogen detection and host defense
Pathogens bring foreign sugars, lipids, proteins, and nucleic acids into host cells. These foreign molecules can act as pathogen-associated molecular patterns (PAMPs), and the ability of the cell to detect them is critical for the initiation of host defense mechanisms and the inhibition of virus production and spread
By comparing temporal proteome changes during WT and d106 herpes simplex virus type 1 (HSV-1) infections, we discovered the upregulation of several proteins involved in innate immunity and apoptosis, and integration with cGAS Immunoaffinity purification (IP)-Mass spectrometry (MS) led to the discovery of OASL-mediated cGAS inhibition [51]

Summary

Introduction

Eukaryotic cells are relentlessly assailed by a myriad of pathogens, thereby needing to constantly evolve and expand their mechanisms for pathogen detection and host defense. Four proteins have been shown to have the ability to perform nuclear DNA sensing—in chronological order of discovery of nuclear function: interferon-inducible protein 16 (IFI16 [9,10,11]), interferon-inducible protein X (IFIX [12]), cyclic GMP-AMP synthase (cGAS [13,14,15,16]), and heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNPA2B1 [17]) The structures of these four proteins and their currently understood mechanisms for induction of antiviral responses are Biomoillelcuusletsra20te2d0, i1n0,F1i5g9u1re 1. HSV-1 genome biotinylation and AP-MS was integrated with a characterization of the nuclear and cytoplasmic proteomes following cellular fractionation This allowed the authors to identify hnRNPA2B1 as a protein that both binds to viral DNA and shuttles to the nucleus to activate STING–TBK1–IRF3 signaling. IP studies followed by targeted assays were valuable for identifying other mechanisms of virus immune evasion, such as the inhibition of cGAMP production by the KSHV virion protein ORF52 [72] and the HSV-1 tegument protein pUL37 (detailed in the PTM section below) [39] (Figure 3)

Post-Translational Modifications for Finely Tuning DNA Sensor Function

Defining the Cellular Landscape Representative of Immune Activation

The Missing Link

Concluding Remarks