scholarly journals Norovirus infection results in assembly of virus-specific G3BP1 granules and evasion of eIF2α signaling

2018 ◽  
Author(s):  
Michèle Brocard ◽  
Valentina Iadevaia ◽  
Philipp Klein ◽  
Belinda Hall ◽  
Glenys Lewis ◽  
...  
Keyword(s):  
Host Cell ◽  
Rna Binding ◽  
Viral Gene Expression ◽  
Stress Granules ◽  
Viral Gene ◽  
Murine Norovirus ◽  
Initiation Factors ◽  
Protein Synthesis Machinery ◽  
Signaling Axis ◽  
Efficient Replication

ABSTRACTDuring viral infection, the accumulation of RNA replication intermediates or viral proteins imposes major stress on the host cell. In response, cellular stress pathways can rapidly impose defence mechanisms by shutting off the protein synthesis machinery, which viruses depend on, and triggering the accumulation of mRNAs into stress granules to limit the use of energy and nutrients. Because this threatens viral gene expression, viruses need to evade these pathways to propagate. Human norovirus is responsible for gastroenteritis outbreaks worldwide. Previously we showed that murine norovirus (MNV) regulates the activity of eukaryotic initiation factors (eIFs). Here we examined how MNV interacts with the eIF2α signaling axis controlling translation and stress granules accumulation. We show that while MNV infection represses host cell translation, it results in the assembly of virus-specific granules rather than stress granules. Further mechanistic analyses revealed that eIF2α signaling is uncoupled from translational stalling. Moreover the interaction of the RNA-binding protein G3BP1 with viral factors together with a redistribution of its cellular interacting partners could explain norovirus evasion of stress granules assembly. These results identify novel strategies by which norovirus ensure efficient replication propagation by manipulating the host stress response.

Protein-RNA interactome analysis reveals wide association of KSHV ORF57 with host non-coding RNAs and polysomes

2021 ◽  
Author(s):  
Beatriz Alvarado-Hernandez ◽  
Yanping Ma ◽  
Nishi R. Sharma ◽  
Vladimir Majerciak ◽  
Alexei Lobanov ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Splicing ◽  
Rna Binding ◽  
Viral Gene Expression ◽  
Viral Gene ◽  
28S Rrna ◽  
Protein Coding ◽  
Infected Cells ◽  
Non Coding Rnas ◽  
Rna Interaction

Kaposi’s sarcoma-associated herpesvirus (KSHV) ORF57 is an RNA-binding post-transcriptional regulator. We recently applied an affinity-purified anti-ORF57 antibody to conduct ORF57-CLIP (Cross-linking Immunoprecipitation) in combination with RNA-sequencing (CLIP-seq) and analyzed the genome-wide host RNA transcripts in association with ORF57 in BCBL-1 cells with lytic KSHV infection. Mapping of the CLIPed RNA reads to the human genome (GRCh37) revealed that most of the ORF57-associated RNA reads were from rRNAs. The remaining RNA reads mapped to several classes of host non-coding and protein-coding mRNAs. We found ORF57 binds and regulates expression of a subset of host lncRNAs, including LINC00324, LINC00355, and LINC00839 which are involved in cell growth. ORF57 binds snoRNAs responsible for 18S and 28S rRNA modifications, but does not interact with fibrillarin and NOP58. We validated ORF57 interactions with 67 snoRNAs by ORF57-RNA immunoprecipitation (RIP)-snoRNA-array assays. Most of the identified ORF57 rRNA binding sites (BS) overlap with the sites binding snoRNAs. We confirmed ORF57-snoRA71B RNA interaction in BCBL-1 cells by ORF57-RIP and Northern blot analyses using a 32 P-labeled oligo probe from the 18S rRNA region complementary to snoRA71B. Using RNA oligos from the rRNA regions that ORF57 binds for oligo pulldown-Western blot assays, we selectively verified ORF57 interactions with 5.8S and 18S rRNAs. Polysome profiling revealed that ORF57 associates with both monosomes and polysomes and its association with polysomes increases PABPC1 binding to, but prevent Ago2 from polysomes. Our data indicate a functional correlation with ORF57 binding and suppression of Ago2 activities for ORF57 promotion of gene expression. Significance As an RNA-binding protein, KSHV ORF57 regulates RNA splicing, stability, and translation and inhibits host innate immunity by blocking the formation of RNA granules in virus infected cells. In this report, ORF57 was found to interact many host non-coding RNAs, including lncRNAs, snoRNAs and ribosomal RNAs to carry out additional unknown functions. ORF57 binds a group of lncRNAs via the identified RNA motifs by ORF57 CLIP-seq to regulate their expression. ORF57 associates with snoRNAs independently of fibrillarin and NOP58 proteins, and with ribosomal RNA in the regions that commonly bind snoRNAs. Knockdown of fibrillarin expression decreases the expression of snoRNAs and CDK4, but not affect viral gene expression. More importantly, we found that ORF57 binds translationally active polysomes and enhances PABPC-1 but prevents Ago2 association with polysomes. Data provide a compelling evidence on how ORF57 in KSHV infected cells might regulate protein synthesis by blocking Ago2’s hostile activities on translation.

scholarly journals Identification of Specific Cellular Genes Up-Regulated Late in Adenovirus Type 12 Infection

2005 ◽  
Vol 79 (4) ◽  
pp. 2404-2412 ◽  
Author(s):  
Andreas Dorn ◽  
Hongxing Zhao ◽  
Frederik Granberg ◽  
Marianna Hösel ◽  
Dennis Webb ◽  
...  
Keyword(s):  
Gene Expression ◽  
Host Cell ◽  
Late Phase ◽  
Viral Gene Expression ◽  
Adenovirus Type ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Viral Gene ◽  
Cell Functions ◽  
Cellular Genes

ABSTRACT The infection of human cells by adenoviruses leads to a gradual reduction in the activity of host cell functions while viral gene expression progresses in a regulated way. We used the DNA microarray technique to determine the transcriptional activity profiles of cellular genes upon infection with adenovirus type 12 (Ad12). The microarray data were validated by quantitative real-time PCR for genes which showed significant alterations after Ad12 infection. At 12 h postinfection, there is a striking up-regulation between 10- and 30-fold in the expression of the G1P2, IFIT1, and IFIT2 cellular immune response genes compared to mock-infected cells. At later stages of infection, when the majority of regulated cellular genes has been turned down, a limited number of cellular genes exhibit increased activities by factors of 3 or less. These genes belong to the signal transduction or transcriptional regulator classes or are active in protein degradation, like ANPEP, an aminopeptidase. The SCD and CYP2S1 genes function in lipid metabolism. The eucaryotic translation initiation factor 4 is up-regulated, and one of the major histocompatibility complex genes is diminished in activity. For two of the genes, one up-regulated (CTSF gene) and one down-regulated (CYR61 gene), alterations in gene activity were confirmed at the protein level by Western blotting experiments. Increased genetic activity of cellular genes late in adenovirus infection has not been reported previously and demonstrates that Ad12 has a sustained control of host cell gene expression well into the late phase of infection.

scholarly journals CCCTC-Binding Factor Recruitment to the Early Region of the Human Papillomavirus 18 Genome Regulates Viral Oncogene Expression

2015 ◽  
Vol 89 (9) ◽  
pp. 4770-4785 ◽  
Author(s):  
Christian Paris ◽  
Ieisha Pentland ◽  
Ian Groves ◽  
David C. Roberts ◽  
Simon J. Powis ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Risk ◽  
Host Cell ◽  
Viral Gene Expression ◽  
Early Gene ◽  
Ctcf Binding ◽  
Ctcf Binding Site ◽  
Viral Gene ◽  
Genome Wide ◽  
High Risk Hpv

ABSTRACTHost cell differentiation-dependent regulation of human papillomavirus (HPV) gene expression is required for productive infection. The host cell CCCTC-binding factor (CTCF) functions in genome-wide chromatin organization and gene regulation. We have identified a conserved CTCF binding site in the E2 open reading frame of high-risk HPV types. Using organotypic raft cultures of primary human keratinocytes containing high-risk HPV18 genomes, we show that CTCF recruitment to this conserved site regulates viral gene expression in differentiating epithelia. Mutation of the CTCF binding site increases the expression of the viral oncoproteins E6 and E7 and promotes host cell proliferation. Loss of CTCF binding results in a reduction of a specific alternatively spliced transcript expressed from the early gene region concomitant with an increase in the abundance of unspliced early transcripts. We conclude that high-risk HPV types have evolved to recruit CTCF to the early gene region to control the balance and complexity of splicing events that regulate viral oncoprotein expression.IMPORTANCEThe establishment and maintenance of HPV infection in undifferentiated basal cells of the squamous epithelia requires the activation of a subset of viral genes, termed early genes. The differentiation of infected cells initiates the expression of the late viral transcripts, allowing completion of the virus life cycle. This tightly controlled balance of differentiation-dependent viral gene expression allows the virus to stimulate cellular proliferation to support viral genome replication with minimal activation of the host immune response, promoting virus productivity. Alternative splicing of viral mRNAs further increases the complexity of viral gene expression. In this study, we show that the essential host cell protein CTCF, which functions in genome-wide chromatin organization and gene regulation, is recruited to the HPV genome and plays an essential role in the regulation of early viral gene expression and transcript processing. These data highlight a novel virus-host interaction important for HPV pathogenicity.

scholarly journals SARS-CoV-2 spike D614G variant exhibits highly efficient replication and transmission in hamsters

2020 ◽  
Author(s):  
Bobo Mok ◽  
Conor J. Cremin ◽  
Siu-Ying Lau ◽  
Shaofeng Deng ◽  
Pin Chen ◽  
...  
Keyword(s):  
Viral Gene Expression ◽  
Transmission Efficiency ◽  
Viral Gene ◽  
Infection Model ◽  
Diversity Analysis ◽  
Pathological Changes ◽  
Severe Respiratory Distress ◽  
Host Diversity ◽  
Efficient Replication ◽  
Asymptomatic Infections

Abstract SARS-CoV-2 causes disease varying in severity from asymptomatic infections to severe respiratory distress and death in humans. The viral factors which determine transmissibility and pathogenicity are not yet clearly characterized. We used the hamster infection model to compare the replication ability and pathogenicity of five SARS-CoV-2 strains isolated from early cases originating in Wuhan, China, in February, and infected individuals returning from Europe and elsewhere in March 2020. The HK-13 and HK-95 isolates showed distinct pathogenicity in hamsters, with higher virus titers and more severe pathological changes in the lungs observed compared to other isolates. HK-95 contains a D614G substitution in the spike protein and demonstrated higher viral gene expression and transmission efficiency in hamsters. Intra-host diversity analysis revealed that further quasi species were generated during hamster infections, indicating that strain-specific adaptive mutants with advantages in replication and transmission will continue to arise and dominate subsequent waves of SARS-CoV-2 dissemination.

scholarly journals Influenza Virus Usurps an Interferon-Induced Translational Program to Promote Viral Replication

Proceedings ◽  
2020 ◽  
Vol 50 (1) ◽  
pp. 134
Author(s):  
Mitchell P. Ledwith ◽  
Vy Tran ◽  
Thiprampai Thamamongood ◽  
Christina A. Higgins ◽  
Shashank Tripathi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Influenza Virus ◽  
Viral Replication ◽  
Rna Binding ◽  
Viral Gene Expression ◽  
Viral Gene ◽  
Translational Efficiency ◽  
A Genome ◽  
Cellular Mrnas ◽  
Stimulation Of

Hosts mount prudently tuned responses to viral infection in an attempt to block nearly every step of the replication cycle. Viruses must adapt to replicate in this hostile antiviral cellular state. Interferon stimulation or pathogen challenge robustly induces expression of IFIT (interferon-induced proteins with tetratricopeptide repeats) proteins. IFITs are a family of proteins that bind RNA and play antiviral roles during infection. Thus, we were surprised to identify the IFIT family as top candidate proviral host factors for influenza A virus (IAV) in a genome-wide CRISPR–Cas9 knockout screen. We validated the proviral activity of IFIT2 by showing that IFIT2-deficient cells support lower levels of IAV replication and exhibit defects in viral gene expression. The molecular functions of IFIT2, let alone how they are used by influenza virus, are unknown. Using CLIP-seq, we showed that IFIT2 binds directly to viral and cellular mRNAs in AU-rich regions largely in the 3’UTR, with a preference for a subset of interferon-stimulated mRNAs. IFIT2 also associates with actively translating ribosomes in infected cells to facilitate the translation of viral messages. IFIT2-responsive elements from an IAV mRNA were sufficient to confer translational enhancement to exogenous transcripts in cis. Conversely, mutation of these elements or the use of an IFIT2 RNA-binding mutant ablated stimulation of viral gene expression. Together, these data link the RNA-binding capability of IFIT2 to changes in translational efficiency of target viral mRNAs and the stimulation of viral replication. They establish a model for the normal function of IFIT2 as an antiviral protein affecting the post-transcriptional fate of cellular mRNAs and explain how influenza virus repurposes IFIT2 to support viral replication. Our work highlights a new node for the regulation of translation during interferon responses and highlights how canonical antiviral responses may be repurposed to support viral replication.

Exploring the COVID-19 Potential Targets: Big Challenges to Quest Specific Treatment

2021 ◽  
Vol 21 ◽  
Author(s):  
Harekrishna Roy ◽  
Asha Gummadi ◽  
Bhabani Shankar Nayak ◽  
Sisir Nandi ◽  
Anil Kumar Saxena
Keyword(s):  
Host Cell ◽  
Viral Genome ◽  
Specific Treatment ◽  
Viral Gene Expression ◽  
Protein S ◽  
Complete Recovery ◽  
Viral Gene ◽  
S Protein ◽  
N Protein ◽  
Terminal Domain

Background: The novel strain SARS-CoV-2 of coronavirus diseases (COVID-19) became pandemic in end of 2019 with an unprecedented global crisis by infecting around 11 million people in more than 200 countries. The condition has now been provoked by the demand, supply, and liquidity shocks that COVID-19 has attacked lives of an incredible population. Objective: Therefore, researchers are trying to encode and understand the viral genome sequence along with various potential targets to explore the transmission mechanism and the mode of treatment for COVID-19. The important structural proteins such as nucleocapsid protein (N), membrane protein (M), an envelope protein (E), and spike protein (S) related to covid-19 are discussed in this manuscript. Methods: The topology of these various targets has been explored utilizing structure-based design and crystallographic studies. Results: The literature reported that the N protein process viral genome to the host cell during replication. The “N terminal domain” and “C terminal domain” contribute towards the localization in the endoplasmic region and dimerization respectively. The M protein determines the shape of coronavirus and also assists the S protein to integrate with the Golgi-endoplasmic region complex leading to the stabilization of the virion. The smallest hydrophobic viroporin termed “E” takes part in morphogenesis and pathogenesis during intracellular infection. The viral spike (S) protein attaches the cellular receptors and initiates virus-cell membrane fusions. The main protease in the proteolytic process during viral gene expression and replication has also been discussed. Conclusion: Currently there is no permanent cure and treatment of COVID-19 hence researchers are repurposing the suitable combination of drugs including antiviral, antimalarial, antiparasitic, and antibacterial, hypertensive receptor blockers, immunosuppressant, anti-arthritis drug, including ayurvedic formulations. In brief, it is justified that, for complete recovery, there is a need for deep and elaborate studies on genomic sequences and invading mechanisms in the host cell.

scholarly journals Nuclear Export Signal Masking Regulates HIV-1 Rev Trafficking and Viral RNA Nuclear Export

2016 ◽  
Vol 91 (3) ◽  
Author(s):  
Ryan T. Behrens ◽  
Mounavya Aligeti ◽  
Ginger M. Pocock ◽  
Christina A. Higgins ◽  
Nathan M. Sherer
Keyword(s):  
Gene Expression ◽  
Nuclear Export ◽  
Rna Binding ◽  
Nuclear Export Signal ◽  
Viral Gene Expression ◽  
Viral Gene ◽  
Virion Production ◽  
Export Signal ◽  
Hiv 1 ◽  
Rev Protein

ABSTRACT HIV-1's Rev protein forms a homo-oligomeric adaptor complex linking viral RNAs to the cellular CRM1/Ran-GTP nuclear export machinery through the activity of Rev's prototypical leucine-rich nuclear export signal (NES). In this study, we used a functional fluorescently tagged Rev fusion protein as a platform to study the effects of modulating Rev NES identity, number, position, or strength on Rev subcellular trafficking, viral RNA nuclear export, and infectious virion production. We found that Rev activity was remarkably tolerant of diverse NES sequences, including supraphysiological NES (SNES) peptides that otherwise arrest CRM1 transport complexes at nuclear pores. Rev's ability to tolerate a SNES was both position and multimerization dependent, an observation consistent with a model wherein Rev self-association acts to transiently mask the NES peptide(s), thereby biasing Rev's trafficking into the nucleus. Combined imaging and functional assays also indicated that NES masking underpins Rev's well-known tendency to accumulate at the nucleolus, as well as Rev's capacity to activate optimal levels of late viral gene expression. We propose that Rev multimerization and NES masking regulates Rev's trafficking to and retention within the nucleus even prior to RNA binding. IMPORTANCE HIV-1 infects more than 34 million people worldwide causing >1 million deaths per year. Infectious virion production is activated by the essential viral Rev protein that mediates nuclear export of intron-bearing late-stage viral mRNAs. Rev's shuttling into and out of the nucleus is regulated by the antagonistic activities of both a peptide-encoded N-terminal nuclear localization signal and C-terminal nuclear export signal (NES). How Rev and related viral proteins balance strong import and export activities in order to achieve optimal levels of viral gene expression is incompletely understood. We provide evidence that multimerization provides a mechanism by which Rev transiently masks its NES peptide, thereby biasing its trafficking to and retention within the nucleus. Targeted pharmacological disruption of Rev-Rev interactions should perturb multiple Rev activities, both Rev-RNA binding and Rev's trafficking to the nucleus in the first place.

scholarly journals Human Cytomegalovirus Infection Leads to Accumulation of Geminin and Inhibition of the Licensing of Cellular DNA Replication

2003 ◽  
Vol 77 (4) ◽  
pp. 2369-2376 ◽  
Author(s):  
Nilima Biswas ◽  
Veronica Sanchez ◽  
Deborah H. Spector
Keyword(s):  
Dna Replication ◽  
Host Cell ◽  
Human Cytomegalovirus ◽  
Human Fibroblasts ◽  
Viral Gene Expression ◽  
Viral Gene ◽  
Early Protein ◽  
Infected Cells ◽  
Mcm Proteins ◽  
Cellular Dna

ABSTRACT Previous studies have shown that infection of G0-synchronized human fibroblasts by human cytomegalovirus (HCMV) results in a block to cellular DNA synthesis. In this study, we have examined the effect of viral infection on the formation of the host cell DNA prereplication complex (pre-RC). We found that the Cdc6 protein level was significantly upregulated in the virus-infected cells and that there was a delay in the expression of the Mcm family of proteins. The loading of the Mcm proteins onto the DNA pre-RC complex also appeared to be defective in the virus-infected cells. This inhibition of DNA replication licensing was associated with the accumulation of geminin, a replication inhibitor. Cdt1, which participates in the loading of the Mcm proteins, was also downregulated and modified differentially in the infected cells. Early viral gene expression was sufficient for the virus-induced alteration of the pre-RC, and the immediate-early protein IE1 was not required. These studies show that the inhibition of replication licensing in HCMV-infected cells is one of the multiple pathways by which the virus dysregulates the host cell cycle.

scholarly journals Epigenetic Repression of Herpes Simplex Virus Infection by the Nucleosome Remodeler CHD3

mBio ◽  
2014 ◽  
Vol 5 (1) ◽  
Author(s):  
Jesse H. Arbuckle ◽  
Thomas M. Kristie
Keyword(s):  
Gene Expression ◽  
Herpes Simplex Virus ◽  
Herpes Simplex ◽  
Viral Infection ◽  
Host Cell ◽  
Viral Gene Expression ◽  
Viral Gene ◽  
Histone Marks ◽  
Viral Genomes ◽  
Simplex Virus

ABSTRACTUpon infection, the genome of herpes simplex virus is rapidly incorporated into nucleosomes displaying histone modifications characteristic of heterochromatic structures. The initiation of infection requires complex viral-cellular interactions that ultimately circumvent this repression by utilizing host cell enzymes to remove repressive histone marks and install those that promote viral gene expression. The reversion of repression and activation of viral gene expression is mediated by the cellular coactivator HCF-1 in association with histone demethylases and methyltransferases. However, the mechanisms and the components that are involved in the initial repression remain unclear. In this study, the chromatin remodeler chromodomain helicase DNA binding (CHD3) protein is identified as an important component of the initial repression of the herpesvirus genome. CHD3 localizes to early viral foci and suppresses viral gene expression. Depletion of CHD3 results in enhanced viral immediate early gene expression and an increase in the number of transcriptionally active viral genomes in the cell. Importantly, CHD3 can recognize the repressive histone marks that have been detected in the chromatin associated with the viral genome and this remodeler is important for ultimately reducing the levels of accessible viral genomes. A model is presented in which CHD3 represses viral infection in opposition to the actions of the HCF-1 coactivator complex. This dynamic, at least in part, determines the initiation of viral infection.IMPORTANCEChromatin modulation of herpesvirus infection is a dynamic process involving regulatory components that mediate suppression and those that promote viral gene expression and the progression of infection. The mechanisms by which the host cell employs the assembly and modulation of chromatin as an antiviral defense strategy against an invading herpesvirus remain unclear. This study defines a critical cellular component that mediates the initial repression of infecting HSV genomes and contributes to understanding the dynamics of this complex interplay between host cell and viral pathogen.

scholarly journals Translational Control of Viral Gene Expression in Eukaryotes

2000 ◽  
Vol 64 (2) ◽  
pp. 239-280 ◽  
Author(s):  
Michael Gale ◽  
Seng-Lai Tan ◽  
Michael G. Katze
Keyword(s):  
Host Cell ◽  
Translational Control ◽  
Viral Gene Expression ◽  
Viral Gene ◽  
Translational Efficiency ◽  
Viral Mrna ◽  
Translational Machinery ◽  
Intracellular Parasites ◽  
Selective Translation ◽  
Translational Strategies

SUMMARY As obligate intracellular parasites, viruses rely exclusively on the translational machinery of the host cell for the synthesis of viral proteins. This relationship has imposed numerous challenges on both the infecting virus and the host cell. Importantly, viruses must compete with the endogenous transcripts of the host cell for the translation of viral mRNA. Eukaryotic viruses have thus evolved diverse mechanisms to ensure translational efficiency of viral mRNA above and beyond that of cellular mRNA. Mechanisms that facilitate the efficient and selective translation of viral mRNA may be inherent in the structure of the viral nucleic acid itself and can involve the recruitment and/or modification of specific host factors. These processes serve to redirect the translation apparatus to favor viral transcripts, and they often come at the expense of the host cell. Accordingly, eukaryotic cells have developed antiviral countermeasures to target the translational machinery and disrupt protein synthesis during the course of virus infection. Not to be outdone, many viruses have answered these countermeasures with their own mechanisms to disrupt cellular antiviral pathways, thereby ensuring the uncompromised translation of virion proteins. Here we review the varied and complex translational programs employed by eukaryotic viruses. We discuss how these translational strategies have been incorporated into the virus life cycle and examine how such programming contributes to the pathogenesis of the host cell.

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