Timing Is Everything: Coordinated Control of Host Shutoff by Influenza A Virus NS1 and PA-X Proteins

Like all viruses, influenza viruses (IAVs) use host translation machinery to decode viral mRNAs. IAVs ensure efficient translation of viral mRNAs through host shutoff, a process whereby viral proteins limit the accumulation of host proteins through subversion of their biogenesis. Despite its small genome, the virus deploys multiple host shutoff mechanisms at different stages of infection, thereby ensuring successful replication while limiting the communication of host antiviral responses. In this Gem, we review recent data on IAV host shutoff proteins, frame the outstanding questions in the field, and propose a temporally coordinated model of IAV host shutoff.

Download Full-text

Different Subtypes of Influenza Viruses Target Different Human Proteins and Pathways Leading to Different Pathogenic Phenotypes

BioMed Research International ◽

10.1155/2019/4794910 ◽

2019 ◽

Vol 2019 ◽

pp. 1-7

Author(s):

Yujie Wang ◽

Ting Song ◽

Kaiwu Li ◽

Yuan Jin ◽

Junjie Yue ◽

...

Keyword(s):

Protein Interactions ◽

Influenza A ◽

Viral Proteins ◽

Influenza Viruses ◽

Host Protein ◽

Protein Protein Interactions ◽

Influenza A Viruses ◽

Host Proteins ◽

Pathogenic Mechanisms ◽

Human Proteins

Different subtypes of influenza A viruses (IAVs) cause different pathogenic phenotypes after infecting human bodies. Analysis of the interactions between viral proteins and the host proteins may provide insights into the pathogenic mechanisms of the virus. In this paper, we found that the same proteins (nucleoprotein and neuraminidase) of H1N1 and H5N1 have different impacts on the NF-κB activation. By further examining the virus–host protein–protein interactions, we found that both NP and NA proteins of the H1N1 and H5N1 viruses target different host proteins. These results indicate that different subtypes of influenza viruses target different human proteins and pathways leading to different pathogenic phenotypes.

Download Full-text

Host Shutoff in Influenza A Virus: Many Means to an End

Viruses ◽

10.3390/v10090475 ◽

2018 ◽

Vol 10 (9) ◽

pp. 475 ◽

Cited By ~ 14

Author(s):

Rachel Levene ◽

Marta Gaglia

Keyword(s):

Immune Responses ◽

Influenza A Virus ◽

Influenza A ◽

Rna Synthesis ◽

Viral Proteins ◽

Host Gene Expression ◽

Structural Protein ◽

Infected Cells ◽

Host Shutoff ◽

Virus Replication Cycle

Influenza A virus carries few of its own proteins, but uses them effectively to take control of the infected cells and avoid immune responses. Over the years, host shutoff, the widespread down-regulation of host gene expression, has emerged as a key process that contributes to cellular takeover in infected cells. Interestingly, multiple mechanisms of host shutoff have been described in influenza A virus, involving changes in translation, RNA synthesis and stability. Several viral proteins, notably the non-structural protein NS1, the RNA-dependent RNA polymerase and the endoribonuclease PA-X have been implicated in host shutoff. This multitude of host shutoff mechanisms indicates that host shutoff is an important component of the influenza A virus replication cycle. Here we review the various mechanisms of host shutoff in influenza A virus and the evidence that they contribute to immune evasion and/or viral replication. We also discuss what the purpose of having multiple mechanisms may be.

Download Full-text

A systematic view on influenza induced host shutoff

eLife ◽

10.7554/elife.18311 ◽

2016 ◽

Vol 5 ◽

Cited By ~ 58

Author(s):

Adi Bercovich-Kinori ◽

Julie Tai ◽

Idit Anna Gelbart ◽

Alina Shitrit ◽

Shani Ben-Moshe ◽

...

Keyword(s):

Oxidative Phosphorylation ◽

Influenza A ◽

Mrna Translation ◽

Cellular Protein ◽

Ribosome Profiling ◽

Viral Mrnas ◽

Viral Propagation ◽

Mrna Pool ◽

Common Strategy ◽

Host Shutoff

Host shutoff is a common strategy used by viruses to repress cellular mRNA translation and concomitantly allow the efficient translation of viral mRNAs. Here we use RNA-sequencing and ribosome profiling to explore the mechanisms that are being utilized by the Influenza A virus (IAV) to induce host shutoff. We show that viral transcripts are not preferentially translated and instead the decline in cellular protein synthesis is mediated by viral takeover on the mRNA pool. Our measurements also uncover strong variability in the levels of cellular transcripts reduction, revealing that short transcripts are less affected by IAV. Interestingly, these mRNAs that are refractory to IAV infection are enriched in cell maintenance processes such as oxidative phosphorylation. Furthermore, we show that the continuous oxidative phosphorylation activity is important for viral propagation. Our results advance our understanding of IAV-induced shutoff, and suggest a mechanism that facilitates the translation of genes with important housekeeping functions.

Download Full-text

The influenza A virus endoribonuclease PA-X usurps host mRNA processing machinery to limit host gene expression

10.1101/442996 ◽

2018 ◽

Author(s):

Lea Gaucherand ◽

Brittany K. Porter ◽

Summer K. Schmaling ◽

Christopher Harley Rycroft ◽

Yuzo Kevorkian ◽

...

Keyword(s):

Gene Expression ◽

Influenza A Virus ◽

Rna Splicing ◽

Influenza A ◽

Host Gene ◽

Host Gene Expression ◽

Viral Control ◽

New Host ◽

Antiviral Responses ◽

Host Shutoff

SUMMARYMany viruses globally shut off host gene expression to inhibit activation of cell-intrinsic antiviral responses. However, host shutoff is not indiscriminate, since viral proteins and host proteins required for viral replication are still synthesized during shutoff. The molecular determinants of target selectivity in host shutoff remain incompletely understood. Here, we report that the influenza A virus shutoff factor PA-X usurps RNA splicing to selectively target host RNAs for destruction. PA-X preferentially degrades spliced mRNAs, both transcriptome-wide and in reporter assays. Moreover, proximity-labeling proteomics revealed that PA-X interacts with cellular proteins involved in RNA splicing. The interaction with splicing contributes to target discrimination and is unique among viral host shutoff nucleases. This novel mechanism sheds light on the specificity of viral control of host gene expression and may provide opportunities for development of new host-targeted antivirals.

Download Full-text

Dynamic phospho-modification of viral proteins as a crucial regulatory layer of influenza A virus replication and innate immune responses

Biological Chemistry ◽

10.1515/hsz-2021-0241 ◽

2021 ◽

Vol 0 (0) ◽

Author(s):

Yvonne Boergeling ◽

Linda Brunotte ◽

Stephan Ludwig

Keyword(s):

Influenza Virus ◽

Virus Replication ◽

Influenza A ◽

Current Knowledge ◽

Viral Proteins ◽

Transport Processes ◽

Influenza Viruses ◽

Innate Immune ◽

A Genome ◽

Influenza Virus Replication

Abstract Influenza viruses are small RNA viruses with a genome of about 13 kb. Because of this limited coding capacity, viral proteins have evolved to fulfil multiple functions in the infected cell. This implies that there must be mechanisms allowing to dynamically direct protein action to a distinct activity in a spatio-temporal manner. Furthermore, viruses exploit many cellular processes, which also have to be dynamically regulated during the viral replication cycle. Phosphorylation and dephosphorylation of proteins are fundamental for the control of many cellular responses. There is accumulating evidence that this mechanism represents a so far underestimated level of regulation in influenza virus replication. Here, we focus on the current knowledge of dynamics of phospho-modifications in influenza virus replication and show recent examples of findings underlining the crucial role of phosphorylation in viral transport processes as well as activation and counteraction of the innate immune response.

Download Full-text

Network analysis of host-pathogen protein interactions in microbe induced cardiovascular diseases

In Silico Biology ◽

10.3233/isb-210238 ◽

2021 ◽

pp. 1-19

Author(s):

Nirupma Singh ◽

Sneha Rai ◽

Rakesh Bhatnagar ◽

Sonika Bhatnagar

Keyword(s):

Protein Interactions ◽

Ribosomal Proteins ◽

Influenza A ◽

Large Scale ◽

Viral Proteins ◽

Alpha Synuclein ◽

System Level ◽

Host Proteins ◽

Cardiac Damage ◽

Tata Box Binding Protein

Large-scale visualization and analysis of HPIs involved in microbial CVDs can provide crucial insights into the mechanisms of pathogenicity. The comparison of CVD associated HPIs with the entire set of HPIs can identify the pathways specific to CVDs. Therefore, topological properties of HPI networks in CVDs and all pathogens was studied using Cytoscape3.5.1. Ontology and pathway analysis were done using KOBAS 3.0. HPIs of Papilloma, Herpes, Influenza A virus as well as Yersinia pestis and Bacillus anthracis among bacteria were predominant in the whole (wHPI) and the CVD specific (cHPI) network. The central viral and secretory bacterial proteins were predicted virulent. The central viral proteins had higher number of interactions with host proteins in comparison with bacteria. Major fraction of central and essential host proteins interacts with central viral proteins. Alpha-synuclein, Ubiquitin ribosomal proteins, TATA-box-binding protein, and Polyubiquitin-C &B proteins were the top interacting proteins specific to CVDs. Signaling by NGF, Fc epsilon receptor, EGFR and ubiquitin mediated proteolysis were among the top enriched CVD specific pathways. DEXDc and HELICc were enriched host mimicry domains that may help in hijacking of cellular machinery by pathogens. This study provides a system level understanding of cardiac damage in microbe induced CVDs.

Download Full-text

The Development and Use of Reporter Influenza B Viruses

Viruses ◽

10.3390/v11080736 ◽

2019 ◽

Vol 11 (8) ◽

pp. 736 ◽

Cited By ~ 2

Author(s):

Rebekah E. Dumm ◽

Nicholas S. Heaton

Keyword(s):

Immune Responses ◽

Host Response ◽

Influenza A ◽

Genetically Modified ◽

Viral Proteins ◽

Influenza Viruses ◽

Influenza B ◽

Human Influenza ◽

Influenza A Viruses ◽

Viral Spread

Influenza B viruses (IBVs) are major contributors to total human influenza disease, responsible for ~1/3 of all infections. These viruses, however, are relatively less studied than the related influenza A viruses (IAVs). While it has historically been assumed that the viral biology and mechanisms of pathogenesis for all influenza viruses were highly similar, studies have shown that IBVs possess unique characteristics. Relative to IAV, IBV encodes distinct viral proteins, displays a different mutational rate, has unique patterns of tropism, and elicits different immune responses. More work is therefore required to define the mechanisms of IBV pathogenesis. One valuable approach to characterize mechanisms of microbial disease is the use of genetically modified pathogens that harbor exogenous reporter genes. Over the last few years, IBV reporter viruses have been developed and used to provide new insights into the host response to infection, viral spread, and the testing of antiviral therapeutics. In this review, we will highlight the history and study of IBVs with particular emphasis on the use of genetically modified viruses and discuss some remaining gaps in knowledge that can be addressed using reporter expressing IBVs.

Download Full-text

Next generation methodology for updating HA vaccines against emerging human seasonal influenza A(H3N2) viruses

Scientific Reports ◽

10.1038/s41598-020-79590-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

James D. Allen ◽

Ted M. Ross

Keyword(s):

Influenza Virus ◽

Immune Responses ◽

Influenza A ◽

Seasonal Influenza ◽

Influenza Viruses ◽

Next Generation ◽

Virus Infections ◽

Wild Type ◽

Influenza Hemagglutinin ◽

H3n2 Influenza

AbstractWhile vaccines remain the best tool for preventing influenza virus infections, they have demonstrated low to moderate effectiveness in recent years. Seasonal influenza vaccines typically consist of wild-type influenza A and B viruses that are limited in their ability to elicit protective immune responses against co-circulating influenza virus variant strains. Improved influenza virus vaccines need to elicit protective immune responses against multiple influenza virus drift variants within each season. Broadly reactive vaccine candidates potentially provide a solution to this problem, but their efficacy may begin to wane as influenza viruses naturally mutate through processes that mediates drift. Thus, it is necessary to develop a method that commercial vaccine manufacturers can use to update broadly reactive vaccine antigens to better protect against future and currently circulating viral variants. Building upon the COBRA technology, nine next-generation H3N2 influenza hemagglutinin (HA) vaccines were designed using a next generation algorithm and design methodology. These next-generation broadly reactive COBRA H3 HA vaccines were superior to wild-type HA vaccines at eliciting antibodies with high HAI activity against a panel of historical and co-circulating H3N2 influenza viruses isolated over the last 15 years, as well as the ability to neutralize future emerging H3N2 isolates.

Download Full-text

An evaluation of the InDevR FluChip-8G insight microarray assay in characterizing influenza a viruses

Tropical Diseases Travel Medicine and Vaccines ◽

10.1186/s40794-021-00133-7 ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Emily S. Bailey ◽

Xinye Wang ◽

Mai-juan Ma ◽

Guo-lin Wang ◽

Gregory C. Gray

Keyword(s):

Influenza A ◽

Influenza Viruses ◽

Time Range ◽

Influenza B ◽

Influenza A Viruses ◽

Laboratory Methods ◽

Duke University ◽

Multiple Viral Strains ◽

Rapid Characterization

AbstractInfluenza viruses are an important cause of disease in both humans and animals, and their detection and characterization can take weeks. In this study, we sought to compare classical virology techniques with a new rapid microarray method for the detection and characterization of a very diverse, panel of animal, environmental, and human clinical or field specimens that were molecularly positive for influenza A alone (n = 111), influenza B alone (n = 3), both viruses (n = 13), or influenza negative (n = 2) viruses. All influenza virus positive samples in this study were first subtyped by traditional laboratory methods, and later evaluated using the FluChip-8G Insight Assay (InDevR Inc. Boulder, CO) in laboratories at Duke University (USA) or at Duke Kunshan University (China). The FluChip-8G Insight multiplexed assay agreed with classical virologic techniques 59 (54.1%) of 109 influenza A-positive, 3 (100%) of the 3 influenza B-positive, 0 (0%) of 10 both influenza A- and B-positive samples, 75% of 24 environmental samples including those positive for H1, H3, H7, H9, N1, and N9 strains, and 80% of 22 avian influenza samples. It had difficulty with avian N6 types and swine H3 and N2 influenza specimens. The FluChip-8G Insight assay performed well with most human, environmental, and animal samples, but had some difficulty with samples containing multiple viral strains and with specific animal influenza strains. As classical virology methods are often iterative and can take weeks, the FluChip-8G Insight Assay rapid results (time range 8 to 12 h) offers considerable time savings. As the FluChip-8G analysis algorithm is expected to improve over time with addition of new subtypes and sample matrices, the FluChip-8G Insight Assay has considerable promise for rapid characterization of novel influenza viruses affecting humans or animals.

Download Full-text

Performance of BioFire array or QuickVue influenza A + B test versus a validation qPCR assay for detection of influenza A during a volunteer A/California/2009/H1N1 challenge study

Virology Journal ◽

10.1186/s12985-021-01516-0 ◽

2021 ◽

Vol 18 (1) ◽

Author(s):

David R. McIlwain ◽

Han Chen ◽

Maria Apkarian ◽

Melton Affrime ◽

Bonnie Bock ◽

...

Keyword(s):

Influenza A ◽

Rapid Test ◽

Influenza Viruses ◽

Qpcr Assay ◽

Superior Performance ◽

Qrt Pcr ◽

Challenge Study ◽

Test Kit ◽

2009 H1n1 ◽

B Test

Abstract Background Influenza places a significant burden on global health and economics. Individual case management and public health efforts to mitigate the spread of influenza are both strongly impacted by our ability to accurately and efficiently detect influenza viruses in clinical samples. Therefore, it is important to understand the performance characteristics of available assays to detect influenza in a variety of settings. We provide the first report of relative performance between two products marketed to streamline detection of influenza virus in the context of a highly controlled volunteer influenza challenge study. Methods Nasopharyngeal swab samples were collected during a controlled A/California/2009/H1N1 influenza challenge study and analyzed for detection of virus shedding using a validated qRT-PCR (qPCR) assay, a sample-to-answer qRT-PCR device (BioMerieux BioFire FilmArray RP), and an immunoassay based rapid test kit (Quidel QuickVue Influenza A + B Test). Results Relative to qPCR, the sensitivity and specificity of the BioFire assay was 72.1% [63.7–79.5%, 95% confidence interval (CI)] and 93.5% (89.3–96.4%, 95% CI) respectively. For the QuickVue rapid test the sensitivity was 8.5% (4.8–13.7%, 95% CI) and specificity was 99.2% (95.6–100%, 95% CI). Conclusion Relative to qPCR, the BioFire assay had superior performance compared to rapid test in the context of a controlled influenza challenge study.

Download Full-text