scholarly journals Variation in RNA Virus Mutation Rates across Host Cells

2014 ◽  
Vol 10 (1) ◽  
pp. e1003855 ◽  
Author(s):  
Marine Combe ◽  
Rafael Sanjuán
Keyword(s):  
Rna Virus ◽  
Host Cells ◽  
Mutation Rates

scholarly journals Host proteostasis modulates influenza evolution

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Angela M Phillips ◽  
Luna O Gonzalez ◽  
Emmanuel E Nekongo ◽  
Anna I Ponomarenko ◽  
Sean M McHugh ◽  
...  
Keyword(s):  
Rna Viruses ◽  
Rna Virus ◽  
Viral Evolution ◽  
Virus Evolution ◽  
Critical Force ◽  
Host Cells ◽  
Mutation Rates ◽  
Biophysical Properties ◽  
And Function ◽  
Protein Variants

Predicting and constraining RNA virus evolution require understanding the molecular factors that define the mutational landscape accessible to these pathogens. RNA viruses typically have high mutation rates, resulting in frequent production of protein variants with compromised biophysical properties. Their evolution is necessarily constrained by the consequent challenge to protein folding and function. We hypothesized that host proteostasis mechanisms may be significant determinants of the fitness of viral protein variants, serving as a critical force shaping viral evolution. Here, we test that hypothesis by propagating influenza in host cells displaying chemically-controlled, divergent proteostasis environments. We find that both the nature of selection on the influenza genome and the accessibility of specific mutational trajectories are significantly impacted by host proteostasis. These findings provide new insights into features of host–pathogen interactions that shape viral evolution, and into the potential design of host proteostasis-targeted antiviral therapeutics that are refractory to resistance.

scholarly journals Native Structure-Based Peptides as Potential Protein–Protein Interaction Inhibitors of SARS-CoV-2 Spike Protein and Human ACE2 Receptor

Molecules ◽  
2021 ◽  
Vol 26 (8) ◽  
pp. 2157
Author(s):  
Norbert Odolczyk ◽  
Ewa Marzec ◽  
Maria Winiewska-Szajewska ◽  
Jarosław Poznański ◽  
Piotr Zielenkiewicz
Keyword(s):  
Drug Development ◽  
Protein Interactions ◽  
Rna Virus ◽  
Antiviral Drug ◽  
Host Protein ◽  
Host Cells ◽  
Cell Surface Receptor ◽  
Short Peptides ◽  
Virus Protein ◽  
Positive Strand Rna

Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is a positive-strand RNA virus that causes severe respiratory syndrome in humans, which is now referred to as coronavirus disease 2019 (COVID-19). Since December 2019, the new pathogen has rapidly spread globally, with over 65 million cases reported to the beginning of December 2020, including over 1.5 million deaths. Unfortunately, currently, there is no specific and effective treatment for COVID-19. As SARS-CoV-2 relies on its spike proteins (S) to bind to a host cell-surface receptor angiotensin-converting enzyme-2(ACE2), and this interaction is proved to be responsible for entering a virus into host cells, it makes an ideal target for antiviral drug development. In this work, we design three very short peptides based on the ACE2 sequence/structure fragments, which may effectively bind to the receptor-binding domain (RBD) of S protein and may, in turn, disrupt the important virus-host protein–protein interactions, blocking early steps of SARS-CoV-2 infection. Two of our peptides bind to virus protein with affinity in nanomolar range, and as very short peptides have great potential for drug development.

scholarly journals Identifying SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of Nsp12/7/8 RNA-dependent RNA Polymerase

2021 ◽  
Author(s):  
Agustina P. Bertolin ◽  
Florian Weissmann ◽  
Jingkun Zeng ◽  
Viktor Posse ◽  
Jennifer C. Milligan ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Virus ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Etiologic Agent ◽  
Host Cells ◽  
Rdrp Activity ◽  
Chemical Library ◽  
Rna Dependent Rna Polymerase

SummaryThe coronavirus disease 2019 (COVID-19) global pandemic has turned into the largest public health and economic crisis in recent history impacting virtually all sectors of society. There is a need for effective therapeutics to battle the ongoing pandemic. Repurposing existing drugs with known pharmacological safety profiles is a fast and cost-effective approach to identify novel treatments. The COVID-19 etiologic agent is the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a single-stranded positive-sense RNA virus. Coronaviruses rely on the enzymatic activity of the replication-transcription complex (RTC) to multiply inside host cells. The RTC core catalytic component is the RNA-dependent RNA polymerase (RdRp) holoenzyme. The RdRp is one of the key druggable targets for CoVs due to its essential role in viral replication, high degree of sequence and structural conservation and the lack of homologs in human cells. Here, we have expressed, purified and biochemically characterised active SARS-CoV-2 RdRp complexes. We developed a novel fluorescence resonance energy transfer (FRET)-based strand displacement assay for monitoring SARS-CoV-2 RdRp activity suitable for a high-throughput format. As part of a larger research project to identify inhibitors for all the enzymatic activities encoded by SARS-CoV-2, we used this assay to screen a custom chemical library of over 5000 approved and investigational compounds for novel SARS-CoV-2 RdRp inhibitors. We identified 3 novel compounds (GSK-650394, C646 and BH3I-1) and confirmed suramin and suramin-like compounds as in vitro SARS-CoV-2 RdRp activity inhibitors. We also characterised the antiviral efficacy of these drugs in cell-based assays that we developed to monitor SARS-CoV-2 growth.

scholarly journals Viral RNA at Two Stages of Reovirus Infection Is Required for the Induction of Necroptosis

2017 ◽  
Vol 91 (6) ◽  
Author(s):  
Angela K. Berger ◽  
Bradley E. Hiller ◽  
Deepti Thete ◽  
Anthony J. Snyder ◽  
Encarnacion Perez ◽  
...  
Keyword(s):  
Cell Death ◽  
Immune System ◽  
Virus Infection ◽  
De Novo ◽  
Rna Virus ◽  
Viral Rna ◽  
Host Cells ◽  
Type I ◽  
Tissue Destruction ◽  
Reovirus Infection

ABSTRACT Necroptosis, a regulated form of necrotic cell death, requires the activation of the RIP3 kinase. Here, we identify that infection of host cells with reovirus can result in necroptosis. We find that necroptosis requires sensing of the genomic RNA within incoming virus particles via cytoplasmic RNA sensors to produce type I interferon (IFN). While these events that occur prior to the de novo synthesis of viral RNA are required for the induction of necroptosis, they are not sufficient. The induction of necroptosis also requires late stages of reovirus infection. Specifically, efficient synthesis of double-stranded RNA (dsRNA) within infected cells is required for necroptosis. These data indicate that viral RNA interfaces with host components at two different stages of infection to induce necroptosis. This work provides new molecular details about events in the viral replication cycle that contribute to the induction of necroptosis following infection with an RNA virus. IMPORTANCE An appreciation of how cell death pathways are regulated following viral infection may reveal strategies to limit tissue destruction and prevent the onset of disease. Cell death following virus infection can occur by apoptosis or a regulated form of necrosis known as necroptosis. Apoptotic cells are typically disposed of without activating the immune system. In contrast, necroptotic cells alert the immune system, resulting in inflammation and tissue damage. While apoptosis following virus infection has been extensively investigated, how necroptosis is unleashed following virus infection is understood for only a small group of viruses. Here, using mammalian reovirus, we highlight the molecular mechanism by which infection with a dsRNA virus results in necroptosis.

Following the very initial growth of biological RNA viral clones

2005 ◽  
Vol 86 (2) ◽  
pp. 435-443 ◽  
Author(s):  
José M. Cuevas ◽  
Andrés Moya ◽  
Rafael Sanjuán
Keyword(s):  
Environmental Changes ◽  
Rna Virus ◽  
Growth Dynamics ◽  
Direct Consequence ◽  
Mutation Rates ◽  
Initial Growth ◽  
Virus Population ◽  
High Genetic Diversity ◽  
Viral Yield ◽  
Fitness Parameters

Due to their extremely high genetic diversity, which is a direct consequence of high mutation rates, RNA viruses are often described as molecular quasispecies. According to this theory, RNA virus populations cannot be understood in terms of individual viral clones, as they are clouds of interconnected mutants, but this prediction has not yet been demonstrated experimentally. The goal of this study was to determine the fitness of individual clones sampled from a given RNA virus population, a necessary previous step to test the above prediction. To do so, limiting dilutions of a vesicular stomatitis virus population were employed to isolate single viral clones and their initial growth dynamics were followed, corresponding to the release of the first few hundred viral particles. This technique is useful for estimating basic fitness parameters, such as intracellular growth rate, viral yield per cell, rate at which cells are infected and time spent in cell-to-cell transmission. A combination of these parameters allows estimation of the fitness of individual clones, which seems to be determined mainly by their ability to complete infection cycles more quickly. Interestingly, fitness was systematically higher for initial clones than for their derived populations. In addition to environmental changes, such as cellular defence mechanisms, these differences are attributable to high RNA virus mutation rates.

scholarly journals An overview of RNA virus-encoded microRNAs

ExRNA ◽  
2019 ◽  
Vol 1 (1) ◽  
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.

scholarly journals Symbiosis Comes of Age at the 10th Biennial Meeting of Wolbachia Researchers

2019 ◽  
Vol 85 (8) ◽  
Author(s):  
Irene L. G. Newton ◽  
Barton E. Slatko
Keyword(s):  
Cell Biology ◽  
Rna Virus ◽  
Host Cells ◽  
Human Pathogens ◽  
Content Type ◽  
New Science ◽  
Successful Infection ◽  
Filarial Nematodes ◽  
Insect Populations ◽  
Basic Biology

ABSTRACT Wolbachia pipientis is an alphaproteobacterial obligate intracellular microbe and arguably the most successful infection on our planet, colonizing 40% to 60% of insect species. Wolbachia spp. are also present in most, but not all, filarial nematodes, where they are obligate mutualists and are the targets for antifilarial drug discovery. Although Wolbachia spp. are related to important human pathogens, they do not infect mammals but instead are well known for their reproductive manipulations of insect populations, inducing the following phenotypes: male killing, feminization, parthenogenesis induction, and cytoplasmic incompatibility (CI). The most common of these, CI, results in a sperm-egg incompatibility and increases the relative fecundity of infected females in a population. In the last decade, Wolbachia spp. have also been shown to provide a benefit to insects, where the infection can inhibit RNA virus replication within the host. Wolbachia spp. cannot be cultivated outside host cells, and no genetic tools are available in the symbiont, limiting approaches available for their study. This means that many questions fundamental to our understanding of Wolbachia basic biology remained unknown for decades. The 10th biennial international Wolbachia conference, Wolbachia Evolution, Ecology, Genomics and Cell Biology: A Chronicle of the Most Ubiquitous Symbiont, was held on 17 to 22 June 2018 in Salem, MA. In this review, we highlight the new science presented at the meeting, link it to prior efforts to answer these questions across the Wolbachia genus, and present the importance of these findings to the field of symbiosis. The topics covered in this review are based on the presentations at the conference.

Increase of SARS-CoV 3CL peptidase activity due to macromolecular crowding effects in the milieu composition

2010 ◽  
Vol 391 (12) ◽  
Author(s):  
Debora N. Okamoto ◽  
Lilian C.G. Oliveira ◽  
Marcia Y. Kondo ◽  
Maria H.S. Cezari ◽  
Zoltán Szeltner ◽  
...  
Keyword(s):  
Rna Virus ◽  
Antiviral Agents ◽  
Fine Tuning ◽  
Host Cells ◽  
Respiratory Syndrome Virus ◽  
Peptidase Activity ◽  
Buffer Solutions ◽  
Tuning Mechanism ◽  
Positive Strand Rna Virus ◽  
Positive Strand Rna

Abstract The 3C-like peptidase of the severe acute respiratory syndrome virus (SARS-CoV) is strictly required for viral replication, thus being a potential target for the development of antiviral agents. In contrast to monomeric picornavirus 3C peptidases, SARS-CoV 3CLpro exists in equilibrium between the monomer and dimer forms in solution, and only the dimer is proteolytically active in dilute buffer solutions. In this study, the increase of SARS-CoV 3CLpro peptidase activity in presence of kosmotropic salts and crowding agents is described. The activation followed the Hofmeister series of anions, with two orders of magnitude enhancement in the presence of Na2SO4, whereas the crowding agents polyethylene glycol and bovine serum albumin increased the hydrolytic rate up to 3 times. Kinetic determinations of the monomer dimer dissociation constant (K d) indicated that activation was a result of a more active dimer, without significant changes in K d values. The activation was found to be independent of substrate length and was derived from both k cat increase and K m decrease. The viral peptidase activation described here could be related to the crowded intracellular environment and indicates a further fine-tuning mechanism for biological control, particularly in the microenvironment of the vesicles that are induced in host cells during positive strand RNA virus infection.

scholarly journals Role of an Internal and Two 3′-Terminal RNA Elements in Assembly of Tombusvirus Replicase

2005 ◽  
Vol 79 (16) ◽  
pp. 10608-10618 ◽  
Author(s):  
Zivile Panaviene ◽  
Tadas Panavas ◽  
Peter D. Nagy
Keyword(s):  
Rna Virus ◽  
Viral Rna ◽  
Host Cells ◽  
Replication Proteins ◽  
Rna Sequences ◽  
Alternative Structures ◽  
Recognition Element ◽  
Rna Elements

ABSTRACT Plus-strand RNA virus replication requires the assembly of the viral replicase complexes on intracellular membranes in the host cells. The replicase of Cucumber necrosis virus (CNV), a tombusvirus, contains the viral p33 and p92 replication proteins and possible host factors. In addition, the assembly of CNV replicase is stimulated in the presence of plus-stranded viral RNA (Z. Panaviene et al., J. Virol. 78:8254-8263, 2004). To define cis-acting viral RNA sequences that stimulate replicase assembly, we performed a systematic deletion approach with a model tombusvirus replicon RNA in Saccharomyces cerevisiae, which also coexpressed p33 and p92 replication proteins. In vitro replicase assays performed with purified CNV replicase preparations from yeast revealed critical roles for three RNA elements in CNV replicase assembly: the internal p33 recognition element (p33RE), the replication silencer element (RSE), and the 3′-terminal minus-strand initiation promoter (gPR). Deletion or mutagenesis of these elements reduced the activity of the CNV replicase to a minimal level. In addition to the primary sequences of gPR, RSE, and p33RE, formation of two alternative structures among these elements may also play a role in replicase assembly. Altogether, the role of multiple RNA elements in tombusvirus replicase assembly could be an important factor to ensure fidelity of template selection during replication.

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