scholarly journals Global analysis of protein-RNA interactions in SARS-CoV-2 infected cells reveals key regulators of infection

2020 ◽  
Author(s):  
Wael Kamel ◽  
Marko Noerenberg ◽  
Berati Cerikan ◽  
Honglin Chen ◽  
Aino I. Järvelin ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Metabolic Pathways ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Global Analysis ◽  
Viral Proteins ◽  
Antiviral Therapies ◽  
Infected Cells ◽  
Host Virus Interactions ◽  
Virus Interactions

ABSTRACTSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19. SARS-CoV-2 relies on cellular RNA-binding proteins (RBPs) to replicate and spread, although which RBPs control SARS-CoV-2 infection remains largely unknown. Here, we employ a multi-omic approach to identify systematically and comprehensively which cellular and viral RBPs are involved in SARS-CoV-2 infection. We reveal that the cellular RNA-bound proteome is remodelled upon SARS-CoV-2 infection, having widespread effects on RNA metabolic pathways, non-canonical RBPs and antiviral factors. Moreover, we apply a new method to identify the proteins that directly interact with viral RNA, uncovering dozens of cellular RBPs and six viral proteins. Amongst them, several components of the tRNA ligase complex, which we show regulate SARS-CoV-2 infection. Furthermore, we discover that available drugs targeting host RBPs that interact with SARS-CoV-2 RNA inhibit infection. Collectively, our results uncover a new universe of host-virus interactions with potential for new antiviral therapies against COVID-19.

scholarly journals Poxviral Strategies to Overcome Host Cell Apoptosis

Pathogens ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 6
Author(s):  
Chathura D. Suraweera ◽  
Mark G. Hinds ◽  
Marc Kvansakul
Keyword(s):  
Viral Infections ◽  
B Cell Lymphoma ◽  
Intrinsic Apoptosis ◽  
Host Cell Apoptosis ◽  
Successful Infection ◽  
Infected Cells ◽  
Host Virus Interactions ◽  
Almost All ◽  
Virus Interactions ◽  
Multicellular Organisms

Apoptosis is a form of cellular suicide initiated either via extracellular (extrinsic apoptosis) or intracellular (intrinsic apoptosis) cues. This form of programmed cell death plays a crucial role in development and tissue homeostasis in multicellular organisms and its dysregulation is an underlying cause for many diseases. Intrinsic apoptosis is regulated by members of the evolutionarily conserved B-cell lymphoma-2 (Bcl-2) family, a family that consists of pro- and anti-apoptotic members. Bcl-2 genes have also been assimilated by numerous viruses including pox viruses, in particular the sub-family of chordopoxviridae, a group of viruses known to infect almost all vertebrates. The viral Bcl-2 proteins are virulence factors and aid the evasion of host immune defenses by mimicking the activity of their cellular counterparts. Viral Bcl-2 genes have proved essential for the survival of virus infected cells and structural studies have shown that though they often share very little sequence identity with their cellular counterparts, they have near-identical 3D structures. However, their mechanisms of action are varied. In this review, we examine the structural biology, molecular interactions, and detailed mechanism of action of poxvirus encoded apoptosis inhibitors and how they impact on host–virus interactions to ultimately enable successful infection and propagation of viral infections.

scholarly journals The Sub-Nuclear Localization of RNA-Binding Proteins in KSHV-Infected Cells

Cells ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1958
Author(s):  
Ella Alkalay ◽  
Chen Gam Ze Letova Refael ◽  
Irit Shoval ◽  
Noa Kinor ◽  
Ronit Sarid ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Viral Infections ◽  
Rna Binding Proteins ◽  
Nuclear Periphery ◽  
Lytic Cycle ◽  
Splicing Factors ◽  
Nuclear Speckles ◽  
Viral Rnas ◽  
Infected Cells

RNA-binding proteins, particularly splicing factors, localize to sub-nuclear domains termed nuclear speckles. During certain viral infections, as the nucleus fills up with replicating virus compartments, host cell chromatin distribution changes, ending up condensed at the nuclear periphery. In this study we wished to determine the fate of nucleoplasmic RNA-binding proteins and nuclear speckles during the lytic cycle of the Kaposi’s sarcoma associated herpesvirus (KSHV). We found that nuclear speckles became fewer and dramatically larger, localizing at the nuclear periphery, adjacent to the marginalized chromatin. Enlarged nuclear speckles contained splicing factors, whereas other proteins were nucleoplasmically dispersed. Polyadenylated RNA, typically found in nuclear speckles under regular conditions, was also found in foci separated from nuclear speckles in infected cells. Poly(A) foci did not contain lncRNAs known to colocalize with nuclear speckles but contained the poly(A)-binding protein PABPN1. Examination of the localization of spliced viral RNAs revealed that some spliced transcripts could be detected within the nuclear speckles. Since splicing is required for the maturation of certain KSHV transcripts, we suggest that the infected cell does not dismantle nuclear speckles but rearranges their components at the nuclear periphery to possibly serve in splicing and transport of viral RNAs into the cytoplasm.

scholarly journals Interferon-Induced Ifit Proteins: Their Role in Viral Pathogenesis

2014 ◽  
Vol 89 (5) ◽  
pp. 2462-2468 ◽  
Author(s):  
Volker Fensterl ◽  
Ganes C. Sen
Keyword(s):  
Host Defense ◽  
Viral Proteins ◽  
Viral Pathogenesis ◽  
Mechanisms Of Action ◽  
Tertiary Structures ◽  
Tetratricopeptide Repeats ◽  
Interferon Stimulated Genes ◽  
Multiple Copies ◽  
Host Virus Interactions ◽  
Virus Interactions

A major component of the protective antiviral host defense is contributed by the intracellular actions of the proteins encoded by interferon-stimulated genes (ISGs); among these are theinterferon-induced proteins withtetratricopeptide repeats (IFITs), consisting of four members in human and three in mouse. IFIT proteins do not have any known enzyme activity. Instead, they inhibit virus replication by binding and regulating the functions of cellular and viral proteins and RNAs. Although all IFITs are comprised of multiple copies of the degenerate tetratricopeptide repeats, their distinct tertiary structures enable them to bind different partners and affect host-virus interactions differently. The recent use ofIfitknockout mouse models has revealed novel antiviral functions of these proteins and new insights into the specificities of ISG actions. This article focuses on human and murine IFIT1 and IFIT2 by reviewing their mechanisms of action, their critical roles in protecting mice from viral pathogenesis, and viral strategies to evade IFIT action.

scholarly journals Use of Host-like Peptide Motifs in Viral Proteins Is a Prevalent Strategy in Host-Virus Interactions

Cell Reports ◽  
2014 ◽  
Vol 7 (5) ◽  
pp. 1729-1739 ◽  
Author(s):  
Tzachi Hagai ◽  
Ariel Azia ◽  
M. Madan Babu ◽  
Raul Andino
Keyword(s):  
Viral Proteins ◽  
Peptide Motifs ◽  
Host Virus Interactions ◽  
Virus Interactions

scholarly journals Identification of Proteins Bound to Dengue Viral RNA In Vivo Reveals New Host Proteins Important for Virus Replication

mBio ◽  
2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Stacia L. Phillips ◽  
Erik J. Soderblom ◽  
Shelton S. Bradrick ◽  
Mariano A. Garcia-Blanco
Keyword(s):  
Mass Spectrometry ◽  
Dengue Virus ◽  
Virus Replication ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Viral Rna ◽  
Host Proteins ◽  
Infected Cells

ABSTRACT Dengue virus is the most prevalent cause of arthropod-borne infection worldwide. Due to the limited coding capacity of the viral genome and the complexity of the viral life cycle, host cell proteins play essential roles throughout the course of viral infection. Host RNA-binding proteins mediate various aspects of virus replication through their physical interactions with viral RNA. Here we describe a technique designed to identify such interactions in the context of infected cells using UV cross-linking followed by antisense-mediated affinity purification and mass spectrometry. Using this approach, we identified interactions, several of them novel, between host proteins and dengue viral RNA in infected Huh7 cells. Most of these interactions were subsequently validated using RNA immunoprecipitation. Using small interfering RNA (siRNA)-mediated gene silencing, we showed that more than half of these host proteins are likely involved in regulating virus replication, demonstrating the utility of this method in identifying biologically relevant interactions that may not be identified using traditional in vitro approaches. IMPORTANCE Dengue virus is the most prevalent cause of arthropod-borne infection worldwide. Viral RNA molecules physically interact with cellular RNA-binding proteins (RBPs) throughout the course of infection; the identification of such interactions will lead to the elucidation of the molecular mechanisms of virus replication. Until now, the identification of host proteins bound to dengue viral RNA has been accomplished using in vitro strategies. Here, we used a method for the specific purification of dengue viral ribonucleoprotein (RNP) complexes from infected cells and subsequently identified the associated proteins by mass spectrometry. We then validated a functional role for the majority of these proteins in mediating efficient virus replication. This approach has broad relevance to virology and RNA biology, as it could theoretically be used to purify any viral RNP complex of interest.

scholarly journals Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis

2020 ◽  
Author(s):  
Mariana Ferrarini ◽  
Avantika Lal ◽  
Rita Rebollo ◽  
Andreas Gruber ◽  
Andrea Guarracino ◽  
...  
Keyword(s):  
Transposable Element ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Meta Analysis ◽  
Host Factors ◽  
Differentially Expressed ◽  
Nonstructural Proteins ◽  
Sequencing Data ◽  
Genome Wide ◽  
Infected Cells

Abstract The novel betacoronavirus named Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) caused a worldwide pandemic (COVID-19) after initially emerging in Wuhan, China. Here we applied a novel, comprehensive bioinformatic strategy to public RNA sequencing and viral genome sequencing data, to better understand how SARS-CoV-2 interacts with human cells. To our knowledge, this is the first meta-analysis to predict host factors that play a specific role in SARS-CoV-2 pathogenesis, distinct from other respiratory viruses. We identified differentially expressed genes, isoforms and transposable element families specifically altered in SARS-CoV-2 infected cells. Well-known immunoregulators including CSF2, IL-32, IL-6 and SERPINA3 were differentially expressed, while immunoregulatory transposable element families were overexpressed. We predicted conserved interactions between the SARS-CoV-2 genome and human RNA-binding proteins such as hnRNPA1, PABPC1 and eIF4b, which may play important roles in the viral life cycle. We also detected four viral sequence variants in the spike, polymerase, and nonstructural proteins that correlate with severity of COVID-19. The host factors we identified likely represent important mechanisms in the disease profile of this pathogen, and could be targeted by prophylactics and/or therapeutics against SARS-CoV-2.

scholarly journals Reovirus Nonstructural Protein μNS Recruits Viral Core Surface Proteins and Entering Core Particles to Factory-Like Inclusions

2004 ◽  
Vol 78 (4) ◽  
pp. 1882-1892 ◽  
Author(s):  
Teresa J. Broering ◽  
Jonghwa Kim ◽  
Cathy L. Miller ◽  
Caroline D. S. Piggott ◽  
Jason B. Dinoso ◽  
...  
Keyword(s):  
Rna Binding ◽  
Core Protein ◽  
Nonstructural Protein ◽  
Viral Proteins ◽  
Surface Proteins ◽  
Core Surface ◽  
Viral Core ◽  
The Core ◽  
Infected Cells ◽  
Core Particles

ABSTRACT Mammalian reoviruses are thought to assemble and replicate within cytoplasmic, nonmembranous structures called viral factories. The viral nonstructural protein μNS forms factory-like globular inclusions when expressed in the absence of other viral proteins and binds to the surfaces of the viral core particles in vitro. Given these previous observations, we hypothesized that one or more of the core surface proteins may be recruited to viral factories through specific associations with μNS. We found that all three of these proteins—λ1, λ2, and σ2—localized to factories in infected cells but were diffusely distributed through the cytoplasm and nucleus when each was separately expressed in the absence of other viral proteins. When separately coexpressed with μNS, on the other hand, each core surface protein colocalized with μNS in globular inclusions, supporting the initial hypothesis. We also found that λ1, λ2, and σ2 each localized to filamentous inclusions formed upon the coexpression of μNS and μ2, a structurally minor core protein that associates with microtubules. The first 40 residues of μNS, which are required for association with μ2 and the RNA-binding nonstructural protein σNS, were not required for association with any of the three core surface proteins. When coexpressed with μ2 in the absence of μNS, each of the core surface proteins was diffusely distributed and displayed only sporadic, weak associations with μ2 on filaments. Many of the core particles that entered the cytoplasm of cycloheximide-treated cells following entry and partial uncoating were recruited to inclusions of μNS that had been preformed in those cells, providing evidence that μNS can bind to the surfaces of cores in vivo. These findings expand a model for how viral and cellular components are recruited to the viral factories in infected cells and provide further evidence for the central but distinct roles of viral proteins μNS and μ2 in this process.

scholarly journals Reovirus σNS Protein Localizes to Inclusions through an Association Requiring the μNS Amino Terminus

2003 ◽  
Vol 77 (8) ◽  
pp. 4566-4576 ◽  
Author(s):  
Cathy L. Miller ◽  
Teresa J. Broering ◽  
John S. L. Parker ◽  
Michelle M. Arnold ◽  
Max L. Nibert
Keyword(s):  
Rna Binding ◽  
Nonstructural Protein ◽  
Viral Proteins ◽  
Rnase A ◽  
The Other ◽  
Amino Terminus ◽  
Primary Determinant ◽  
Infected Cells ◽  
Necessary And Sufficient ◽  
Similar Phase

ABSTRACT Cells infected with mammalian reoviruses contain phase-dense inclusions, called viral factories, in which viral replication and assembly are thought to occur. The major reovirus nonstructural protein μNS forms morphologically similar phase-dense inclusions when expressed in the absence of other viral proteins, suggesting it is a primary determinant of factory formation. In this study we examined the localization of the other major reovirus nonstructural protein, σNS. Although σNS colocalized with μNS in viral factories during infection, it was distributed diffusely throughout the cell when expressed in the absence of μNS. When coexpressed with μNS, σNS was redistributed and colocalized with μNS inclusions, indicating that the two proteins associate in the absence of other viral proteins and suggesting that this association may mediate the localization of σNS to viral factories in infected cells. We have previously shown that μNS residues 1 to 40 or 41 are both necessary and sufficient for μNS association with the viral microtubule-associated protein μ2. In the present study we found that this same region of μNS is required for its association with σNS. We further dissected this region, identifying residues 1 to 13 of μNS as necessary for association with σNS, but not with μ2. Deletion of σNS residues 1 to 11, which we have previously shown to be required for RNA binding by that protein, resulted in diminished association of σNS with μNS. Furthermore, when treated with RNase, a large portion of σNS was released from μNS coimmunoprecipitates, suggesting that RNA contributes to their association. The results of this study provide further evidence that μNS plays a key role in forming the reovirus factories and recruiting other components to them.

scholarly journals Restriction of Retroviral Replication by Tetherin/BST-2

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Jason Hammonds ◽  
Jaang-Jiun Wang ◽  
Paul Spearman
Keyword(s):  
Restriction Factor ◽  
Initial Report ◽  
Host Restriction ◽  
Host Restriction Factor ◽  
Infected Cells ◽  
Important Host ◽  
Retroviral Replication ◽  
Host Virus Interactions ◽  
And Function ◽  
Virus Interactions

Tetherin/BST-2 is an important host restriction factor that limits the replication of HIV and other enveloped viruses. Tetherin is a type II membrane glycoprotein with a very unusual domain structure that allows it to engage budding virions and retain them on the plasma membrane of infected cells. Following the initial report identifying tetherin as the host cell factor targeted by the HIV-1 Vpu gene, knowledge of the molecular, structural, and cellular biology of tetherin has rapidly advanced. This paper summarizes the discovery and impact of tetherin biology on the HIV field, with a focus on recent advances in understanding its structure and function. The relevance of tetherin to replication and spread of other retroviruses is also reviewed. Tetherin is a unique host restriction factor that is likely to continue to provide new insights into host-virus interactions and illustrates well the varied ways by which host organisms defend against viral pathogens.

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