Virus–host interactions in persistently FMDV-infected cells derived from bovine pharynx

AbstractViral infection is usually studied at the level of cell populations, averaging over hundreds of thousands of individual cells. Moreover, measurements are typically done by analyzing a few time points along the infection process. While informative, such measurements are limited in addressing how cell variability affects infection outcome. Here we employ dynamic proteomics to study virus-host interactions, using the human pathogen Herpes Simplex virus 1 as a model. We tracked >50,000 individual cells as they respond to HSV1 infection, allowing us to model infection kinetics and link infection outcome (productive or not) with the cell state at the time of initial infection. We find that single cells differ in their preexisting susceptibility to HSV1, and that this is partially mediated by their cell-cycle position. We also identify specific changes in protein levels and localization in infected cells, attesting to the power of the dynamic proteomics approach for studying virus-host interactions.

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System-Based Approaches to Delineate the Antiviral Innate Immune Landscape

Viruses ◽

10.3390/v12101196 ◽

2020 ◽

Vol 12 (10) ◽

pp. 1196

Author(s):

Karsten Krey ◽

Aleksandra W. Babnis ◽

Andreas Pichlmair

Keyword(s):

Large Scale ◽

Innate Immune ◽

Host Interactions ◽

Interferon Stimulated Genes ◽

Cellular Processes ◽

Virus Inhibition ◽

Cellular Factors ◽

Functional Factors ◽

Infected Cells ◽

Screening Approaches

Viruses pose substantial challenges for society, economy, healthcare systems, and research. Their distinctive pathologies are based on specific interactions with cellular factors. In order to develop new antiviral treatments, it is of central importance to understand how viruses interact with their host and how infected cells react to the virus on a molecular level. Invading viruses are commonly sensed by components of the innate immune system, which is composed of a highly effective yet complex network of proteins that, in most cases, mediate efficient virus inhibition. Central to this process is the activity of interferons and other cytokines that coordinate the antiviral response. So far, numerous methods have been used to identify how viruses interact with cellular processes and revealed that the innate immune response is highly complex and involves interferon-stimulated genes and their binding partners as functional factors. Novel approaches and careful experimental design, combined with large-scale, high-throughput methods and cutting-edge analysis pipelines, have to be utilized to delineate the antiviral innate immune landscape at a global level. In this review, we describe different currently used screening approaches, how they contributed to our knowledge on virus–host interactions, and essential considerations that have to be taken into account when planning such experiments.

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Isolation of a TRAIL Antagonist from the Serum of HIV-infected Patients

Journal of Biological Chemistry ◽

10.1074/jbc.m111.274639 ◽

2011 ◽

Vol 286 (41) ◽

pp. 35742-35754 ◽

Cited By ~ 12

Author(s):

David J. Schnepple ◽

Brett Shepard ◽

Gary D. Bren ◽

Nathan W. Cummins ◽

Sekar Natesampillai ◽

...

Keyword(s):

Hiv Infection ◽

Defense Mechanisms ◽

Receptor Interaction ◽

Adaptive Mechanism ◽

Apoptosis Resistance ◽

Host Interactions ◽

Adaptive Mechanisms ◽

Trail Receptors ◽

Infected Cells ◽

Selection Of

Virus-host interactions are characterized by the selection of adaptive mechanisms by which to evade pathogenic and defense mechanisms, respectively. In primary T cells infected with HIV, HIV infection up-regulates TNF-related apoptosis inducing ligand (TRAIL) and death-inducing TRAIL receptors, but blockade of TRAIL:TRAIL receptor interaction does not alter HIV-induced cell death. Instead, HIV infection results in a novel splice variant that we call TRAIL-short (TRAIL-s), which antagonizes TRAIL-R2. In HIV patients, plasma TRAIL-s concentration increases with increasing viral load and renders cells resistant to TRAIL-induced death. Knockdown of TRAIL-s abrogates this resistance. We propose that TRAIL-s is a novel adaptive mechanism of apoptosis resistance acquired by HIV-infected cells to avoid their elimination by TRAIL-dependent effector mechanism.

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Visualization of viral infection dynamics in a unicellular eukaryote and quantification of viral production using VirusFISH

10.1101/849455 ◽

2019 ◽

Author(s):

Yaiza M. Castillo ◽

Marta Sebastián ◽

Irene Forn ◽

Nigel Grimsley ◽

Sheree Yau ◽

...

Keyword(s):

Burst Size ◽

Axenic Culture ◽

Cell Lysis ◽

Unicellular Eukaryote ◽

Viral Ecology ◽

Host Interactions ◽

Infection Dynamics ◽

Specific Virus ◽

Infected Cells ◽

The Impact

ABSTRACTOne of the major challenges in viral ecology is to assess the impact of viruses in controlling the abundance of specific hosts in the environment. For this, techniques that enable the detection and quantification of virus–host interactions at the single-cell level are essential. With this goal in mind, we implemented VirusFISH (Virus Fluorescence in situ Hybridization) using as a model the marine picoeukaryote Ostreococcus tauri and its virus OtV5. VirusFISH allowed the visualization and quantification of the fraction of infected cells during an infection experiment. We were also able to quantify the abundance of free viruses released during cell lysis and assess the burst size of our non-axenic culture, because we could discriminate OtV5 from phages. Our results showed that although the major lysis of the culture occurred between 24 and 48 h after OtV5 inoculation, some new viruses were produced between 8 and 24 h, propagating the infection. Nevertheless, the production of viral particles increased drastically after 24 h. The burst size for the O. tauri–OtV5 system was 7±0.4 OtV5 per cell, which was consistent with the estimated amount of viruses inside the cell prior to cell lysis. With this work we demonstrate that VirusFISH is a promising technique to study specific virus–host interactions in non-axenic cultures, and set the ground for its application in complex natural communities.

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Rubella Viruses Shift Cellular Bioenergetics to a More Oxidative and Glycolytic Phenotype with a Strain-Specific Requirement for Glutamine

Journal of Virology ◽

10.1128/jvi.00934-18 ◽

2018 ◽

Vol 92 (17) ◽

Cited By ~ 8

Author(s):

Nicole C. Bilz ◽

Kristin Jahn ◽

Mechthild Lorenz ◽

Anja Lüdtke ◽

Judith M. Hübschen ◽

...

Keyword(s):

Virus Infection ◽

Host Cell ◽

Metabolic Activity ◽

Mammalian Cells ◽

Energy Demand ◽

Umbilical Vein ◽

Natural Infection ◽

Host Interactions ◽

Infected Cells ◽

Cellular Bioenergetics

ABSTRACTThe flexible regulation of cellular metabolic pathways enables cellular adaptation to changes in energy demand under conditions of stress such as posed by a virus infection. To analyze such an impact on cellular metabolism, rubella virus (RV) was used in this study. RV replication under selected substrate supplementation with glucose, pyruvate, and glutamine as essential nutrients for mammalian cells revealed its requirement for glutamine. The assessment of the mitochondrial respiratory (based on the oxygen consumption rate) and glycolytic (based on the extracellular acidification rate) rate and capacity by respective stress tests through Seahorse technology enabled determination of the bioenergetic phenotype of RV-infected cells. Irrespective of the cellular metabolic background, RV infection induced a shift of the bioenergetic state of epithelial cells (Vero and A549) and human umbilical vein endothelial cells to a higher oxidative and glycolytic level. Interestingly there was a RV strain-specific, but genotype-independent demand for glutamine to induce a significant increase in metabolic activity. While glutaminolysis appeared to be rather negligible for RV replication, glutamine could serve as donor of its amide nitrogen in biosynthesis pathways for important metabolites. This study suggests that the capacity of RVs to induce metabolic alterations could evolve differently during natural infection. Thus, changes in cellular bioenergetics represent an important component of virus-host interactions and could complement our understanding of the viral preference for a distinct host cell population.IMPORTANCERV pathologies, especially during embryonal development, could be connected with its impact on mitochondrial metabolism. With bioenergetic phenotyping we pursued a rather novel approach in virology. For the first time it was shown that a virus infection could shift the bioenergetics of its infected host cell to a higher energetic state. Notably, the capacity to induce such alterations varied among different RV isolates. Thus, our data add viral adaptation of cellular metabolic activity to its specific needs as a novel aspect to virus-host evolution. In addition, this study emphasizes the implementation of different viral strains in the study of virus-host interactions and the use of bioenergetic phenotyping of infected cells as a biomarker for virus-induced pathological alterations.

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Catch me if you can – the crosstalk of ZIKV and the restriction factor Tetherin

Journal of Virology ◽

10.1128/jvi.02117-21 ◽

2021 ◽

Author(s):

Marie-Luise Herrlein ◽

Paul Schmanke ◽

Fabian Elgner ◽

Catarina Sabino ◽

Sami Akhras ◽

...

Keyword(s):

Life Cycle ◽

Protein Level ◽

Cellular Protein ◽

Viral Escape ◽

Restriction Factor ◽

Host Interactions ◽

Escape Strategy ◽

Tetherin Expression ◽

Elevated Protein ◽

Infected Cells

Zika virus (ZIKV) is a flavivirus that is mainly transmitted by Aedes mosquitos and normally causes mild symptoms. During the outbreak in the Americas in 2015, it was associated with more severe implications, like microcephaly in new-borns and the Gullain-Barré syndrome. The lack of specific vaccines and cures strengthen the need for a deeper understanding of the virus life cycle and virus-host interactions. The restriction factor tetherin (THN) is an interferon-inducible cellular protein with broad antiviral properties. It is known to inhibit the release of various enveloped viruses by tethering them to each other and to the cell membrane, thereby preventing their further spread. On the other hand, different viruses have developed various escape strategies against THN. Analysis of the crosstalk between ZIKV and THN revealed that in spite of a strong induction of THN mRNA expression in ZIKV-infected cells, this is not reflected by an elevated protein level of THN. Contrariwise, the THN protein level is decreased due to a reduced half-life. The increased degradation of THN in ZIKV infected cells involves the endo-lysosomal system, but does not depend on the early steps of autophagy. Enrichment of THN by depletion of the ESCRT-0 protein HRS diminishes ZIKV release and spread, which points out the capacity of THN to restrict ZIKV and explains the enhanced THN degradation in infected cells as an effective viral escape strategy. Importance Although tetherin expression is strongly induced by ZIKV infection there is a reduction in the amount of tetherin protein. This is due to an enhanced lysosomal degradation. However, if tetherin level is rescued release of ZIKV is impaired. This shows that tetherin is a restriction factor for ZIKV and the induction of an efficient degradation represents a viral escape strategy. To our knowledge this is the first study that describes and characterizes tetherin as an restriction factor for ZIKV life cycle.

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Deep Sequencing Identifies Noncanonical Editing of Ebola and Marburg Virus RNAs in Infected Cells

mBio ◽

10.1128/mbio.02011-14 ◽

2014 ◽

Vol 5 (6) ◽

Cited By ~ 44

Author(s):

Reed S. Shabman ◽

Omar J. Jabado ◽

Chad E. Mire ◽

Timothy B. Stockwell ◽

Megan Edwards ◽

...

Keyword(s):

Gene Expression ◽

Deep Sequencing ◽

Marburg Virus ◽

Cellular Mechanisms ◽

Viral Mrnas ◽

Protein Coding ◽

Genomic Rnas ◽

Host Interactions ◽

Adenosine Deaminase Activity ◽

Infected Cells

ABSTRACT Deep sequencing of RNAs produced by Zaire ebolavirus (EBOV) or the Angola strain of Marburgvirus (MARV-Ang) identified novel viral and cellular mechanisms that diversify the coding and noncoding sequences of viral mRNAs and genomic RNAs. We identified previously undescribed sites within the EBOV and MARV-Ang mRNAs where apparent cotranscriptional editing has resulted in the addition of non-template-encoded residues within the EBOV glycoprotein (GP) mRNA, the MARV-Ang nucleoprotein (NP) mRNA, and the MARV-Ang polymerase (L) mRNA, such that novel viral translation products could be produced. Further, we found that the well-characterized EBOV GP mRNA editing site is modified at a high frequency during viral genome RNA replication. Additionally, editing hot spots representing sites of apparent adenosine deaminase activity were found in the MARV-Ang NP 3′-untranslated region. These studies identify novel filovirus-host interactions and reveal production of a greater diversity of filoviral gene products than was previously appreciated. IMPORTANCE This study identifies novel mechanisms that alter the protein coding capacities of Ebola and Marburg virus mRNAs. Therefore, filovirus gene expression is more complex and diverse than previously recognized. These observations suggest new directions in understanding the regulation of filovirus gene expression.

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Translocation of Porphyromonas gingivalis Gingipain Adhesin Peptide A44 to Host Mitochondria Prevents Apoptosis

Infection and Immunity ◽

10.1128/iai.00187-10 ◽

2010 ◽

Vol 78 (8) ◽

pp. 3616-3624 ◽

Cited By ~ 12

Author(s):

Heike Boisvert ◽

Margaret J. Duncan

Keyword(s):

Porphyromonas Gingivalis ◽

Time Course ◽

Periodontal Diseases ◽

Cell Fractionation ◽

Host Interactions ◽

Cellular Environment ◽

Cell Clearance ◽

Mitochondrial Functions ◽

Infected Cells ◽

Induced Apoptosis

ABSTRACT Porphyromonas gingivalis, a Gram-negative oral anaerobe, is associated with periodontal diseases that, in some form, affect up to 80% of the U.S. population. The organism is highly proteolytic, and noncatalytic adhesin domains of the major proteases, gingipains, are involved in bacterium-host interactions. Recently, we showed that gingipain adhesin peptide A44 hijacks the host's clathrin-dependent endocytosis system, allowing the peptide and whole bacteria to be internalized by epithelial cells. In the present study, we found by cell fractionation assays and confocal microscopy that peptide A44 translocated to host mitochondria. Cell viability assays and quantitative real-time PCR showed that the peptide interacted with the cell death machinery by triggering upregulation of antiapoptotic factors bcl-2 and bcl-XL and prevented staurosporine-induced apoptosis for up to 12 h. We confirmed these findings with Western blot analyses of caspase-9 activation in time course experiments with staurosporine. Finally, we verified a similar antiapoptotic effect for P. gingivalis, showing for the first time that the organism manipulated mitochondrial functions during the first hours of infection, thus resisting host cell clearance by apoptosis of infected cells. This mechanism may enable the bacteria to persist in the protected cellular environment until the next step in pathogenesis, progression or resolution of infection.

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Unveiling Infection Strategies across Diverse Marine Phage–Host Systems

Proceedings ◽

10.3390/proceedings2020050099 ◽

2020 ◽

Vol 50 (1) ◽

pp. 99

Author(s):

Cristina Howard-Varona ◽

Karin Holmfeldt ◽

Melissa B Duhaime ◽

Matthew B Sullivan

Keyword(s):

Model Systems ◽

Host Interactions ◽

Genome Wide ◽

Central Carbon ◽

Energy Consuming ◽

Infected Cells ◽

Marine Phage ◽

And Function ◽

Biological Entities ◽

Host Metabolism

Bacterial viruses (phages) are amongst the smallest, most powerful biological entities on Earth. Through infection, phages impact host metabolism, bacterial mortality, and evolution. In the oceans, 20–40% of surface microbes are infected, with 1023 new infections each second. Yet, infections remain virtually uncharacterized, as the available phage isolates underrepresent the diversity of marine phage–host interactions. Additionally, while sequencing efforts reveal “who is there?”, a gap between sequence and function prevents answering “what are they doing?” and “how?”. We have developed new Bacteroidetes and Proteobacteria marine phage–host model systems with which to connect genomes, infection strategies, and functions using both traditional and genome-wide “-omics” experiments. We ask: How do infections by genomically divergent phages compare? Are there links between phage–host genomes and infection strategies? Our findings are as follows. In Bacteroidetes, a phage infecting two nearly identical strains (host38 and host18) under identical conditions is more fit and efficient on host38. By contrast, on host18, it is less fit and, except for phage transcription, it fails at efficiently mastering all stages of the infection: from adsorption through to cell lysis. In Proteobacteria, genomically unrelated podovirus and siphovirus phages infecting the same strain reprogram host metabolisms very differently. Namely, siphovirus-infected cells hardly differ from uninfected and mainly repress energy-consuming processes such as motility and translation. By contrast, podovirus-infected cells greatly differ from uninfected cells in transcription and in uniquely shifting central carbon and energy metabolism. Additionally, the siphovirus is more complementary to the host than the podovirus in %GC, amino acids, and codon usage. We found that phage–host genome complementarity may drive the resource demand and fitness of a phage: the phage most complementary to its host easily accesses intracellular resources, infects with little reprogramming, and accomplishes the largest fitness, which has not previously been shown. Together, this work helps to uncover infection efficiency strategies, and connect genomes with metabolisms in marine phage–host systems.

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ILDR1 Promotes Influenza a Virus Replication Through Binding to PLSCR1

10.21203/rs.3.rs-1069522/v1 ◽

2021 ◽

Author(s):

Yueyue Liu ◽

Shuqian Lin ◽

Yunhui Xie ◽

Lu Zhao ◽

Haibo Du ◽

...

Keyword(s):

Influenza A Virus ◽

Virus Replication ◽

Influenza A ◽

Vital Role ◽

Host Interactions ◽

Phospholipid Scramblase ◽

Antiviral Function ◽

Siv Infection ◽

Infected Cells

Abstract As a natural antiviral regulator, phospholipid scramblase 1 (PLSCR1) has been shown to inhibit influenza virus replication in infected cells through interacting with NP of influenza A virus (IAV). But its antiviral function as well as the underlying regulatory mechanism has not been examined in vivo. In the present work, we show that PLSCR1 expression is decreased in H1N1 SIV-infected mice, and Plscr1−/−mice are more susceptible to H1N1 SIV infection. By performing yeast two-hybrid screening, we identified immunoglobulin-like domain-containing receptor 1 (ILDR1) as a novel PLSCR1-binding partner. ILDR1 is highly expressed in the lungs, and its expression level is increased after virus infection. Interestingly, ILDR1 could not directly interact with virus NP protein, but could combine with PLSCR1 competitively. Our data indicates that there is a previously unidentified PLSCR1-ILDR1-NP regulatory pathway playing a vital role in limiting IAV infection, which provides novel insights into IAV-host interactions.

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