An anti-prion system that cures infected cells

Most yeast prions (infectious proteins) are amyloids, linear β-sheet-rich polymers of a single protein with the β-strands perpendicular to the long axis of the filament. A single prion protein can form any of many different prion variants, differing in structure and biological properties, but with the same amino acid sequence. The folded parallel β-sheet architecture shown for several yeast prions explains how a given prion variant can be propagated stably, how a protein can template its conformation, just as DNA can template its sequence.

Prion protein conformation templating mechanism

A recent paper in PLoS Pathogens describes an anti-prion system that sequesters prion seeds, preventing their even distribution to daughter cells. The recent discovery of a cellular anti-prion system that cures most arising prions of the yeast Ure2 protein offers a possible direction to look for treatments of amyloidoses such as Alzheimer disease, Parkinson disease, and others. While an array of methods have been found to cure yeast prions by over- or underproduction of various chaperones and other proteins and by various conditions, the system described in this paper cures the [URE3] prion at normal expression levels, indicating that this is a cellular anti-prion system. Information gleaned from yeast systems may have applications in efforts to control human prions and amyloidoses.

Yeast Prions: Proteins Templating Conformation and an Anti-prion System. (2015) PLoS Pathog 11(2): e1004584. doi:10.1371/journal.ppat.1004584

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Oncogenes and RNA splicing of human tumor viruses

Approximately 10.8% of human cancers are associated with infection by an oncogenic virus. These viruses include human papillomavirus (HPV), Epstein–Barr virus (EBV), Merkel cell polyomavirus (MCV), human T-cell leukemia virus 1 (HTLV-1), Kaposi’s sarcoma-associated herpesvirus (KSHV), hepatitis C virus (HCV) and hepatitis B virus (HBV). These oncogenic viruses, with the exception of HCV, require the host RNA splicing machinery in order to exercise their oncogenic activities, a strategy that allows the viruses to efficiently export and stabilize viral RNA and to produce spliced RNA isoforms from a bicistronic or polycistronic RNA transcript for efficient protein translation. Infection with a tumor virus affects the expression of host genes, including host RNA splicing factors, which play a key role in regulating viral RNA splicing of oncogene transcripts. A current prospective focus is to explore how alternative RNA splicing and the expression of viral oncogenes take place in a cell- or tissue-specific manner in virus-induced human carcinogenesis.

Oncogenes and RNA splicing of human tumor viruses. (2014) Emerging Microbes & Infections, 3(9), e63

Oncogenic human viruses and viral oncogenes

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Morbillivirus Infections: An Introduction

Measles Virus The genus Morbillivirus belongs to the virus family Paramyxoviridae, a group of enveloped viruses with non-segmented, negative strand RNA genomes. It contains viruses that are highly infectious, spread via the respiratory route, cause profound immune suppression, and have a propensity to cause large outbreaks associated with high morbidity and mortality in previously unexposed populations. In populations with endemic virus circulation, the epidemiology changes to that of a childhood disease, as hosts that survive the infection normally develop lifelong immunity.

Research on morbillivirus infections has led to exciting developments in recent years. Global measles vaccination coverage has increased, resulting in a significant reduction in measles mortality. In 2011 rinderpest virus was declared globally eradicated – only the second virus to be eradicated by targeted vaccination. Identification of new cellular receptors and implementation of recombinant viruses expressing fluorescent proteins in a range of model systems have provided fundamental new insights into the pathogenesis of morbilliviruses, and their interactions with the host immune system. Nevertheless, both new and well-studied morbilliviruses are associated with significant disease in wildlife and domestic animals. This illustrates the need for robust surveillance and a strategic focus on barriers that restrict cross-species transmission. Recent and ongoing measles outbreaks also demonstrate that maintenance of high vaccination coverage for these highly infectious agents is critical. This article summarizes the most important current research topics in this field.

The identification of cellular receptors and improvement of animal models has provided important new insights into the pathogenesis of morbillivirus infections. It has become clear that all morbilliviruses initially infect cells of the immune system, before they spread to epithelial, endothelial and/or neuronal cells. Morbilliviruses remain a potential cause of disease outbreaks in previously unexposed populations. However, they can also be used to our advantage, as vaccine vectors or as oncolytic viruses. Sustained vaccination coverage and surveillance of circulating morbilliviruses will remain of critical importance for years to come.

Morbillivirus Infections: An Introduction. (2015) Viruses 7(2): 699-706. doi: 10.3390/v7020699

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A Short History of the Discovery of Viruses

A Short History of the Discovery of Viruses Free online book:

  • Part 1: Filters and Discovery
  • Part 2: The Ultracentrifuge, Eggs and Flu
  • Part 3: Phages, Cell Culture and Polio
  • Part 4: RNA Genomes and Modern Virology

Edward P Rybicki and Russell Kightley (2015) A Short History of the Discovery of Viruses

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Silencing the alarms: Innate immune antagonism by rotaviruses

This review discusses the structural and mechanistic basis of innate immune antagonism by two direct effectors, the Rotavirus NSP1 and VP3 proteins. It starts with a nice overview of Rotavirus biology then goes on to describe how the structural and mechanistic properties of NSP1 and VP3 allow these proteins to directly antagonize host innate immune responses.

NSP1 is a putative E3 ubiquitin ligase that mediates the degradation of a wide range of cellular targets, including those that function as innate immune sensors (RIG-I), signaling intermediates (TRAF2, MAVS, and β-TrCP), transcription factors (IRFs), and mediators of host survival pathways (PI3K and p53). In many respects, VP3 is like two proteins in one: it caps viral transcripts as they emerge from RV DLPs, which likely prevents activation of host RNA sensors, and it directly antagonizes the dsRNA-responsive OAS/RNase L pathway by cleaving the signaling molecule 2-5A. VP3 may also function in two distinct regions of the cell during infection: within a viral particle as the capping enzyme and perhaps also within the cytoplasm as a direct innate immune antagonist.

The varied functions of NSP1 and VP3 highlight the diversity and importance of cellular innate immune defenses to RNA viruses and reflect the compactness of a viral genome.

Innate immune antagonism by Rotavirus NSP1 and VP3

Silencing the alarms: Innate immune antagonism by rotavirus NSP1 and VP3. Virology. 24 Feb 2015 doi: 10.1016/j.virol.2015.01.006
TThe innate immune response involves a broad array of pathogen sensors that stimulate the production of interferons (IFNs) to induce an antiviral state. Rotavirus, a significant cause of childhood gastroenteritis and a member of the Reoviridae family of segmented, double-stranded RNA viruses, encodes at least two direct antagonists of host innate immunity: NSP1 and VP3. NSP1, a putative E3 ubiquitin ligase, mediates the degradation of cellular factors involved in both IFN induction and downstream signaling. VP3, the viral capping enzyme, utilizes a 2H-phosphodiesterase domain to prevent activation of the cellular oligoadenylate synthase (OAS)/RNase L pathway. Computational, molecular, and biochemical studies have provided key insights into the structural and mechanistic basis of innate immune antagonism by NSP1 and VP3 of group A rotaviruses (RVA). Future studies with non-RVA isolates will be essential to understand how other rotavirus species evade host innate immune responses.

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T cell exhaustion during persistent viral infections

Why does the immune system fail to clear some virus (and other infections) and allow a state of chronic infection to occur? And when it does, how are immune responses different from a non-infected individual? This article describes the processes involved in T cell exhaustion and considers what can be done to reconstitute the immune system in chronic infections, including HIV.

T cell exhaustion during persistent viral infections

T cell exhaustion during persistent viral infections. (2015) Virology. 22 Jan. doi: 10.1016/j.virol.2014.12.033
Although robust and highly effective anti-viral T cells contribute to the clearance of many acute infections, viral persistence is associated with the development of functionally inferior, exhausted, T cell responses. Exhaustion develops in a step-wise and progressive manner, ranges in severity, and can culminate in the deletion of the anti-viral T cells. This disarming of the response is consequential as it compromises viral control and potentially serves to dampen immune-mediated damage. Exhausted T cells are unable to elaborate typical anti-viral effector functions. They are characterized by the sustained upregulation of inhibitory receptors and display a gene expression profile that distinguishes them from prototypic effector and memory T cell populations. In this review we discuss the properties of exhausted T cells; the virological and immunological conditions that favor their development; the cellular and molecular signals that sustain the exhausted state; and strategies for preventing and reversing exhaustion to favor viral control.

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Life in Our Phage World

Life in Our Phage World In 1915 Frederick Twort made the first scientific observations on bacteriophages (followed shortly after by Félix d’Herelle). In the century that has followed, phage research has revolutionized our understanding of biology.

“[the] molecular biology of higher organisms does not stand on the shoulder of giants, but on the shoulder of dwarfs like phage T4 and lambda.”
Harald Brüssow

Phage and other viruses outnumber all other organic entities on our planet, with an estimated numbers at a mind-boggling 1031. To celebrate 100 years of phage research, a conference was held in San Diego in January and all the contributions were captured on the 2015 year of the Phage website. This includes a 400 page book which describes in detail 30 diverse phages, including, where on Earth they’ve been found, who their close relatives are, how their genomes are structured, and how they trick their hosts into submission. Researchers who have devoted their lives to phage also recount their experiences. You can download a free copy of the book from the website, and it’s well worth reading.

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HIV Rev – Really Exasperating Virus protein

HIV Rev When viruses infect cells, they often use specialized proteins that hijack the host cell’s proteins to carry out essential tasks. For example, human immunodeficiency virus (HIV) needs to transport copies of its RNA out of the nucleus of the host cell and into the cell’s cytoplasm in order to create important viral proteins. To do this, a protein in HIV called Rev hijacks a transporter protein that carries cargo across the membrane that surrounds the cell nucleus. As a biochemical entity, Rev has proven to be truly exasperating over the last two miserable decades due to its propensity to generally misbehave – by aggregating or forming fibrils or oligomers – when studied in the laboratory. Now, in eLife, two papers provide a more detailed structural picture of how Rev works.

eLife: Really exasperating viral protein from HIV

Related articles:

RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev-Rev response element complex. (2014) eLife 3: e04120. doi: 10.7554/eLife.04120

The export receptor Crm1 forms a dimer to promote nuclear export of HIV RNA. (2014) eLife 3: e04121. doi: 10.7554/eLife.04121

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Paramyxovirus polymerase: transcription or replication?

Paramyxovirus polymerase -   transcription or replication

The paramyxovirus family has a genome consisting of a single strand of negative sense RNA. This genome acts as a template for two distinct processes: transcription to generate subgenomic, capped and polyadenylated mRNAs, and genome replication. These viruses only encode one polymerase. Thus, an intriguing question is, how does the viral polymerase initiate and become committed to either transcription or replication? By answering this we can begin to understand how these two processes are regulated.

This review article presents recent findings from studies on the paramyxovirus, respiratory syncytial virus, which show how its polymerase is able to initiate transcription and replication from a single promoter and discusses how these findings apply to other paramyxoviruses. It also examines how trans-acting proteins and promoter secondary structure might serve to regulate transcription and replication during different phases of the paramyxovirus replication cycle.

Initiation and regulation of paramyxovirus transcription and replication. Virology. 12 Feb 2015 doi: 10.1016/j.virol.2015.01.014

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