High-Order Epistasis and Functional Coupling of Infection Steps Drive Virus Evolution toward Independence from a Host Pathway

Microbiology Spectrum ◽

10.1128/spectrum.00800-21 ◽

2021 ◽

Author(s):

Minetaro Arita

Keyword(s):

Viral Replication ◽

Rna Virus ◽

Virus Evolution ◽

High Order ◽

Host Factors ◽

Functional Coupling

Each virus has a different strategy for its replication, which requires different host factors. Enterovirus, a model RNA virus, requires host factors PI4KB and OSBP, which form an obligatory functional axis to support viral replication.

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Network-Guided Discovery of Influenza Virus Replication Host Factors

mBio ◽

10.1128/mbio.02002-18 ◽

2018 ◽

Vol 9 (6) ◽

Cited By ~ 14

Author(s):

Emily E. Ackerman ◽

Eiryo Kawakami ◽

Manami Katoh ◽

Tokiko Watanabe ◽

Shinji Watanabe ◽

...

Keyword(s):

Influenza Virus ◽

Viral Replication ◽

Virus Replication ◽

Drug Targets ◽

Antiviral Drug ◽

Viral Proteins ◽

Host Factors ◽

Ppi Network ◽

Host Proteins ◽

Influenza Virus Replication

ABSTRACTThe positions of host factors required for viral replication within a human protein-protein interaction (PPI) network can be exploited to identify drug targets that are robust to drug-mediated selective pressure. Host factors can physically interact with viral proteins, be a component of virus-regulated pathways (where proteins do not interact with viral proteins), or be required for viral replication but unregulated by viruses. Here, we demonstrate a method of combining human PPI networks with virus-host PPI data to improve antiviral drug discovery for influenza viruses by identifying target host proteins. Analysis shows that influenza virus proteins physically interact with host proteins in network positions significant for information flow, even after the removal of known abundance-degree bias within PPI data. We have isolated a subnetwork of the human PPI network that connects virus-interacting host proteins to host factors that are important for influenza virus replication without physically interacting with viral proteins. The subnetwork is enriched for signaling and immune processes distinct from those associated with virus-interacting proteins. Selecting proteins based on subnetwork topology, we performed an siRNA screen to determine whether the subnetwork was enriched for virus replication host factors and whether network position within the subnetwork offers an advantage in prioritization of drug targets to control influenza virus replication. We found that the subnetwork is highly enriched for target host proteins—more so than the set of host factors that physically interact with viral proteins. Our findings demonstrate that network positions are a powerful predictor to guide antiviral drug candidate prioritization.IMPORTANCEIntegrating virus-host interactions with host protein-protein interactions, we have created a method using these established network practices to identify host factors (i.e., proteins) that are likely candidates for antiviral drug targeting. We demonstrate that interaction cascades between host proteins that directly interact with viral proteins and host factors that are important to influenza virus replication are enriched for signaling and immune processes. Additionally, we show that host proteins that interact with viral proteins are in network locations of power. Finally, we demonstrate a new network methodology to predict novel host factors and validate predictions with an siRNA screen. Our results show that integrating virus-host proteins interactions is useful in the identification of antiviral drug target candidates.

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Structural and Functional Characterization of Host FHL1 Protein Interaction with Hypervariable Domain of Chikungunya Virus nsP3 Protein

Journal of Virology ◽

10.1128/jvi.01672-20 ◽

2020 ◽

Vol 95 (1) ◽

Author(s):

Tetyana Lukash ◽

Tatiana Agback ◽

Francisco Dominguez ◽

Nikita Shiliaev ◽

Chetan Meshram ◽

...

Keyword(s):

Viral Replication ◽

Binding Site ◽

Cell Lines ◽

Binding Sites ◽

Chikungunya Virus ◽

Biological Significance ◽

Host Factors ◽

Published Data ◽

Wide Range ◽

Infection Spread

ABSTRACT Decades of insufficient control have resulted in unprecedented spread of chikungunya virus (CHIKV) around the globe, and millions have suffered from the highly debilitating disease. Nevertheless, the current understanding of CHIKV-host interactions and adaptability of the virus to replication in mosquitoes and mammalian hosts is still elusive. Our new study shows that four-and-a-half LIM domain protein (FHL1) is one of the host factors that interact with the hypervariable domain (HVD) of CHIKV nsP3. Unlike G3BPs, FHL1 is not a prerequisite of CHIKV replication, and many commonly used cell lines do not express FHL1. However, its expression has a detectable stimulatory effect(s) on CHIKV replication, and Fhl1 knockout (KO) cell lines demonstrate slower infection spread. Nuclear magnetic resonance (NMR)-based studies revealed that the binding site of FHL1 in CHIKV nsP3 HVD overlaps that of another proviral host factor, CD2AP. The structural data also demonstrated that FHL1-HVD interaction is mostly determined by the LIM1 domain of FHL1. However, it does not mirror binding of the entire protein, suggesting that other LIM domains are involved. In agreement with previously published data, our biological experiments showed that interactions of CHIKV HVD with CD2AP and FHL1 have additive effects on the efficiency of CHIKV replication. This study shows that CHIKV mutants with extensive modifications of FHL1- or both FHL1- and CD2AP-binding sites remain viable and develop spreading infection in multiple cell types. Our study also demonstrated that other members of the FHL family can bind to CHIKV HVD and thus may be involved in viral replication. IMPORTANCE Replication of chikungunya virus (CHIKV) is determined by a wide range of host factors. Previously, we have demonstrated that the hypervariable domain (HVD) of CHIKV nsP3 contains linear motifs that recruit defined families of host proteins into formation of functional viral replication complexes. Now, using NMR-based structural and biological approaches, we have characterized the binding site of the cellular FHL1 protein in CHIKV HVD and defined the biological significance of this interaction. In contrast to previously described binding of G3BP to CHIKV HVD, the FHL1-HVD interaction was found to not be a prerequisite of viral replication. However, the presence of FHL1 has a stimulatory effect on CHIKV infectivity and, subsequently, the infection spread. FHL1 and CD2AP proteins were found to have overlapping binding sites in CHIKV HVD and additive proviral functions. Elimination of the FHL1-binding site in the nsP3 HVD can be used for the development of stable, attenuated vaccine candidates.

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BPIFB3 interacts with ARFGAP1 and TMED9 to regulate non-canonical autophagy and RNA virus infection

Journal of Cell Science ◽

10.1242/jcs.251835 ◽

2020 ◽

pp. jcs.251835

Author(s):

Azia S. Evans ◽

Nicholas J. Lennemann ◽

Carolyn B. Coyne

Keyword(s):

Mass Spectrometry ◽

Mammalian Cells ◽

Viral Infections ◽

Rna Viruses ◽

Rna Virus ◽

Negative Regulator ◽

Host Factors ◽

Important Negative Regulator ◽

Cellular Components

Autophagy is a degradative cellular pathway that targets cytoplasmic contents and organelles for turnover by the lysosome. Various autophagy pathways play key roles in the clearance of viral infections, and many families of viruses have developed unique methods for avoiding degradation. Some positive stranded RNA viruses, such as enteroviruses and flaviviruses, usurp the autophagic pathway to promote their own replication. We previously identified the endoplasmic reticulum-localized protein BPIFB3 as an important negative regulator of non-canonical autophagy that uniquely impacts the replication of enteroviruses and flaviviruses. Here, we find that many components of the canonical autophagy machinery are not required for BPIFB3 depletion induced autophagy and identify the host factors that facilitate its role in the replication of enteroviruses and flaviviruses. Using proximity-dependent biotinylation (BioID) followed by mass spectrometry, we identify ARFGAP1 and TMED9 as two cellular components that interact with BPIFB3 to regulate autophagy and viral replication. Importantly, our data demonstrate that non-canonical autophagy in mammalian cells can be controlled outside of the traditional pathway regulators and define the role of two proteins in BPIFB3 depletion mediated non-canonical autophagy.

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An overview of RNA virus-encoded microRNAs

ExRNA ◽

10.1186/s41544-019-0037-6 ◽

2019 ◽

Vol 1 (1) ◽

Cited By ~ 5

Author(s):

Xihan Li ◽

Xiaoping Zou

Keyword(s):

Gene Expression ◽

Gene Regulation ◽

Viral Replication ◽

Potential Role ◽

Rna Viruses ◽

Rna Virus ◽

Host Cells ◽

Basic Pattern ◽

Double Stranded Dna ◽

Non Coding Rnas

Abstract MicroRNAs (miRNAs) are a number of small non-coding RNAs playing a regulatory part in gene expression. Many virus-encoded miRNAs have been found, which manifests that viruses as well apply the basic pattern of gene regulation, however, mostly in viruses transcribed from double-stranded DNA genomes. It is still in dispute if RNA viruses could encode miRNAs because the excision of miRNA might result in the cleavage of viral RNA genome. We will focus on the miRNAs encoded by RNA virus and discuss their potential role in viral replication cycle and host cells.

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Host factors determine differential disease progression after infection with nef-deleted simian immunodeficiency virus

Journal of General Virology ◽

10.1099/vir.0.066563-0 ◽

2014 ◽

Vol 95 (10) ◽

pp. 2273-2284 ◽

Cited By ~ 2

Author(s):

Sieghart Sopper ◽

Kerstin Mätz-Rensing ◽

Thorsten Mühl ◽

Jonathan Heeney ◽

Christiane Stahl-Hennig ◽

...

Keyword(s):

Viral Load ◽

Viral Replication ◽

Disease Progression ◽

Simian Immunodeficiency Virus ◽

Mhc Class Ii ◽

Cell Activation ◽

Host Factors ◽

Immunological Parameters ◽

Set Point ◽

Immunodeficiency Virus

Infection of macaques with live attenuated simian immunodeficiency virus (SIV) usually results in long-lasting efficient protection against infection with pathogenic immunodeficiency viruses. However, attenuation by deletion of regulatory genes such as nef is not complete, leading to a high viral load and fatal disease in some animals. To characterize immunological parameters and polymorphic host factors, we studied 17 rhesus macaques infected with attenuated SIVmac239ΔNU. Eight animals were able to control viral replication, whereas the remaining animals (non-controllers) displayed variable set-point viral loads. Peak viral load at 2 weeks post-infection (p.i.) correlated significantly with set-point viral load (P<0.0001). CD4+ T-cell frequencies differed significantly soon after infection between controllers and non-controllers. Abnormal B-cell activation previously ascribed to Nef function could already be observed in non-controllers 8 weeks after infection despite the absence of Nef. Two non-controllers developed an AIDS-like disease within 102 weeks p.i. Virus from these animals transmitted to naïve animals replicated at low levels and the recipients did not develop immunodeficiency. This suggested that host factors determined differential viral load and subsequent disease course. Known Mhc class I alleles associated with disease progression in SIV WT infection only marginally influenced the viral load in Δnef-infected animals. Protection from SIVmac251 was associated with homozygosity for MHC class II in conjunction with a TLR7 polymorphism and showed a trend with initial viral replication. We speculated that host factors whose effects were usually masked by Nef were responsible for the different disease courses in individual animals upon infection with nef-deleted viruses.

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A phase I study of reolysin given intravenously to patients with advanced malignancies

Journal of Clinical Oncology ◽

10.1200/jco.2006.24.18_suppl.3064 ◽

2006 ◽

Vol 24 (18_suppl) ◽

pp. 3064-3064 ◽

Cited By ~ 4

Author(s):

L. Vidal ◽

H. Pandha ◽

J. Spicer ◽

K. J. Harrington ◽

S. Allen ◽

...

Keyword(s):

Antitumor Activity ◽

Viral Replication ◽

Tumor Necrosis ◽

Rna Virus ◽

Maximum Tolerated Dose ◽

Systemic Delivery ◽

Double Stranded Rna ◽

Infectious Dose ◽

Viral Shedding

3064 Background: Reovirus is a double-stranded RNA virus with minimal pathogenicity in humans that selectively replicates in cells with activated Ras. Activated Ras inhibits the anti-viral effects of double stranded RNA-activated protein kinase (PKR). Reovirus serotype 3 Dearing has selective antitumor activity, in vitro and in tumour xenograft models. Methods: Reolysin was administered as a 1-hr IV infusion every 4-weeks initially for one day; then 3 days then 5-days every 4 weeks. The starting dose was 1×108 tissue culture infectious dose (TCID50) increasing in successive cohorts until observation of drug-related toxicity ≥ grade 2. Endpoints were safety, viral replication, viral shedding, evaluation of immune response and antitumor activity. Results: 24 patients (pts) (median age 60; ECOG 1, 16 males) have been entered into the first 7 cohorts at the following dose levels: 1×108 for 1-day, 1×108 for 3-days and 1×108, 3×108, 1×109, 3×109 and 1×1010 TCID50 for 5-days. A maximum tolerated dose (MTD) has not been reached and no dose-limiting toxicities have been observed. Toxicities have been mild (grade 1 or 2) and have included chills, fever, headache, runny nose, fatigue and myelosuppression. Reverse transcription polymerase chain reaction (RT-PCR) studies of blood, urine, stool and sputum post reovirus administration were negative for viral shedding for all treated pts. All but one pt had neutralising anti-reovirus antibodies detectable pre-treatment. Titres increased after 1-week of treatment and remained high during subsequent courses of treatment. Two pts with metastatic colorectal cancer treated at 3×108 and 3×109 TCID50 had CEA tumour marker reduction by 60% and 27% receiving 6 and 3 courses of treatment respectively. One pt with metastatic pancreatic cancer received 4 courses of treatment with stable disease. One pt with metastatic prostate cancer had a 50% decrease in PSA after treatment at 3×109 TCID50, with evidence of tumor necrosis on CT scanning. Intratumoral reovirus replication has been detected by electron microscopy in tumur biopsies. Conclusions: Reolysin is well tolerated with minimal toxicity. No viral shedding has been detected. Virus-induced tumor necrosis associated with intratumor viral replication after systemic delivery has been observed. [Table: see text]

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