Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1110270 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28995100_1.fastq.gz | Fastqsanger.gz | |||
| SRR28995100_2.fastq.gz | Fastqsanger.gz | |||
| SRR28995101_1.fastq.gz | Fastqsanger.gz | |||
| SRR28995101_2.fastq.gz | Fastqsanger.gz | |||
| SRR28995102_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Influenza A virus (IAV) is a segmented negative-sense RNA virus and is the cause of major global epidemics and pandemics. The replication of IAV is complex, involving both transcription and replication, during which three distinct RNA species, namely mRNA, cRNA, and vRNA are generated for all eight genome segments. While understanding IAV replication kinetics is important for drug development and improving vaccine production, current methods for studying IAV kinetics has been limited by the ability to detect all three different RNA species in a scalable manner. Here were report the development of a novel pipeline using total stranded RNA-Seq, named Influenza Virus Enumerator of RNA Transcripts (InVERT) which allows for the simultaneous quantification of all three RNA species of IAV. Using InVERT provides a full landscape of the IAV replication kinetics, in which we found that different groups of viral genes followed different traits of kinetics. During a cycle of infection, the RNA-dependent RNA Polymerase (RdRP) produced more vRNA than mRNA while some other genes (NP, NS, HA) consistently make more mRNA than vRNA. vRNA expression levels do not correlate with the cRNA expression, suggesting complex regulations of vRNA synthesis. Furthermore, by studying the kinetics of a virus lacking the capacity to generate new polymerase complexes, we found evidence that further supports the model that cRNA synthesis requires newly synthesized RdRP and that incoming RdRP can only generate mRNA.
2021-02-19 | GSE162281 | GEO
Project description:Segment-specific kinetics of mRNA, cRNA and vRNA during influenza infection
| PRJNA681243 | ENA
Project description:During influenza A virus (IAV) infections, viral proteins are targeted by cellular E3 ligases for modification with ubiquitin. Here, we decipher and functionally explore the ubiquitin landscape of the IAV polymerase during infection of human alveolar epithelial cells by applying mass spectrometry analysis of immuno-purified K-ε-GG- (di-glycyl)-remnant-bearing peptides. We identified 59 modified lysines across all three subunits of the viral polymerase of which 17 distinctively affected mRNA transcription, vRNA replication and the generation of recombinant viruses via non-proteolytic mechanisms. Moreover, our results demonstrate that the ubiquitinated residue K578 in the PB1 thumb domain is crucial for the dynamic structural transitions of the viral polymerase that are required for vRNA replication. Mutations K578A and K578R impeded the steps of cRNA stabilization and vRNA transcription, respectively, and affected NP binding as well as polymerase dimerization. Collectively, our results indicate that ubiquitin-mediated disruption of the charge-dependent interaction between PB1-K578 and PB2-E72 is required to coordinate polymerase dimerization and facilitate vRNA replication, which demonstrates that IAV exploit the cellular ubiquitin system to modulate the activity of the viral polymerase for the regulation of viral replication.
2023-03-11 | PXD030816 | Pride
Project description:Influenza virus polymerase transcribes or replicates the segmented RNA genome (vRNA) into respectively viral mRNA or full-length copies and initiates RNA synthesis by binding the conserved 3' and 5' vRNA ends (the promoter). In recent structures of promoter-bound polymerase, the cap-binding and endonuclease domains are configured for cap snatching, which generates capped transcription primers. Here, we present a FluB polymerase structure with a bound complementary cRNA 5' end that exhibits a major rearrangement of the subdomains within the C-terminal two-thirds of PB2 (PB2-C). Notably, the PB2 nuclear localization signal (NLS)- containing domain translocates ~90 A ̊ to bind to the endonuclease domain. FluA PB2-C alone and RNA-free FluC polymerase are similarly arranged. Biophysical and cap-dependent endonuclease assays show that in solution the polymerase explores different conformational distributions depending on which RNA is bound. The inherent flexibility of the polymerase allows it to adopt alternative conformations that are likely important during polymerase maturation into active progeny RNPs.</br></br>Extra contact information:</br><a href="mailto:cusack@embl.fr">Stephen Cusack</a>, EMBL Grenoble Outstation, Unit of Virus Host-Cell Interactions, France ( corresponding author and lab head )
2016-01-04 | PXD002234 | Pride
Project description:Due to the RNA nature of their genomes, influenza viruses have to utilize many RNA-binding proteins (RBPs) of both viral and host origin, for their replication. To uncover the comprehensive vRNA-host protein interactions, we performed affinity purification coupled with mass spectrometry (AP-MS) analysis of influenza vRNA complexes. The eight vRNA segments of H7N9 were transcribed and individually labeled with biotin in vitro and incubated with IAV virus-infected THP-1 cells, and vRNA complexes were enriched streptavidin magnetic beads and analyzed by mass spectrometry
2021-03-25 | PXD020723 | Pride
Project description:Heldt2012 - Influenza Virus Replication
The model describes the life cycle of influenza A virus in a mammalian cell including the following steps: attachment of parental virions to the cell membrane, receptor-mediated endocytosis, fusion of the virus envelope with the endosomal membrane, nuclear import of vRNPs, viral transcription and replication, translation of the structural viral proteins, nuclear export of progeny vRNPs and budding of new virions. It also explicitly accounts for the stabilization of cRNA by viral polymerases and NP and the inhibition of vRNP activity by M1 protein binding. In short, the model focuses on the molecular mechanism that controls viral transcription and replication.
This model is described in the article:
Modeling the intracellular dynamics of influenza virus replication to understand the control of viral RNA synthesis.
Heldt FS, Frensing T, Reichl U.
J Virol.
Abstract:
Influenza viruses transcribe and replicate their negative-sense RNA genome inside the nucleus of host cells via three viral RNA species. In the course of an infection, these RNAs show distinct dynamics, suggesting that differential regulation takes place. To investigate this regulation in a systematic way, we developed a mathematical model of influenza virus infection at the level of a single mammalian cell. It accounts for key steps of the viral life cycle, from virus entry to progeny virion release, while focusing in particular on the molecular mechanisms that control viral transcription and replication. We therefore explicitly consider the nuclear export of viral genome copies (vRNPs) and a recent hypothesis proposing that replicative intermediates (cRNA) are stabilized by the viral polymerase complex and the nucleoprotein (NP). Together, both mechanisms allow the model to capture a variety of published data sets at an unprecedented level of detail. Our findings provide theoretical support for an early regulation of replication by cRNA stabilization. However, they also suggest that the matrix protein 1 (M1) controls viral RNA levels in the late phase of infection as part of its role during the nuclear export of viral genome copies. Moreover, simulations show an accumulation of viral proteins and RNA toward the end of infection, indicating that transport processes or budding limits virion release. Thus, our mathematical model provides an ideal platform for a systematic and quantitative evaluation of influenza virus replication and its complex regulation.
With the current parameter set, the model reproduces an infection at a multiplicity of infection (MOI) of 10. Figure 2A of the paper is reproduced here, with parameters kDegRnp and kSynP changed to zeros.
Initial conditions and parameter changes that were used to obtain specific figures in the article can be found in Table A2.
The model has the correct value for kAttLo as 4.55e-04. The value of this parameter mentioned as 4.55e-02 in Table 1 of the paper is incorrect. This is checked with the author.
This model is hosted on BioModels Database
and identified
by: MODEL1307270000
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource
for published quantitative kinetic models
.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to the public
domain worldwide. Please refer to CC0 Public Domain
Dedication
for more information.
2024-09-02 | BIOMD0000000463 | BioModels
Project description:Encoding only ten major proteins, Influenza A virus (IAV) gains access to both the cell and nucleus, replicates its eight genomic segments, then enters the cytoplasm to assemble and egress. This is achieved through an expansive network of interactions with the host and a coordinated production of viral components. Here we show that upon infection, primary transcription of the virus results in the accumulation of the splice product, Nuclear Export Protein (NEP), which associates with the viral polymerase leading to the synthesis of segment-specific small viral RNAs (svRNAs). Here we demonstrate that svRNA biology is responsible for coordinating segment-specific amplification and is predominantly required for amplification of the three larger polymerase segments. Generation of svRNA ambiguity results in predictable changes in segment-specific vRNA levels and up to a five log attenuation. Together, these data elucidate the molecular function of svRNAs as essential mediators responsible for maintaining a stoichiometric balance between genomic segments and establish these small RNAs as functional components of the virus.
2017-06-14 | GSE83289 | GEO
Project description:We defined the major transcriptional responses in primary human bronchial epithelial cells (HBECs) after either infection with influenza or treatment with relevant ligands. We used four different strategies, each highlighting distinct aspects of the response. (1) cells were infected with the wild-type PR8 influenza virus that can mount a complete replicative cycle. (2) cells were transfected with viral RNA (âvRNAâ) isolated from influenza particles. This does not result in the production of viral proteins or particles and identifies the effect of RNA-sensing pathways (e.g., RIG-I.). (3) Cells were treated with interferon beta (IFNb), to distinguish the portion of the response which is mediated through Type I IFNs. (4) Cells were infected with a PR8 virus lacking the NS1 gene (âDNS1â). The NS1 protein normally inhibits vRNA- or IFNb-induced pathways, and its deletion can reveal an expanded response to infection. HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNÃ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ?NS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated
2010-04-13 | E-GEOD-19392 | biostudies-arrayexpress
Project description:Assembly of infectious influenza A viruses (IAV) is a complex process involving transport from the nucleus to the plasma membrane. Rab11A containing recycling endosomes have been identified as a platform for intracellular transport of viral RNA (vRNA). Using high spatiotemporal resolution light-sheet microscopy (~1.4 volumes/s, 330 nm isotropic spatial resolution), we quantify Rab11A and vRNA movement in live cells during IAV infection. Here we report that IAV infection decreases speed and increases arrest of Rab11A. Unexpectedly, infection with RSV alters Rab11A motion in a manner opposite to IAV, suggesting that Rab11A is a common host component that is differentially manipulated by respiratory RNA viruses. Using two-color imaging we demonstrate co-transport between Rab11A and IAV vRNA in infected cells and provide direct evidence that vRNA-associated Rab11A have altered transport. The mechanism of altered Rab11A movement is likely related to a decrease in dynein motors bound to Rab11A vesicles during IAV infection.
2020-01-14 | PXD016331 | Pride
Project description:We defined the major transcriptional responses in primary human bronchial epithelial cells (HBECs) after either infection with influenza or treatment with relevant ligands. We used four different strategies, each highlighting distinct aspects of the response. (1) cells were infected with the wild-type PR8 influenza virus that can mount a complete replicative cycle. (2) cells were transfected with viral RNA (‘vRNA’) isolated from influenza particles. This does not result in the production of viral proteins or particles and identifies the effect of RNA-sensing pathways (e.g., RIG-I.). (3) Cells were treated with interferon beta (IFNb), to distinguish the portion of the response which is mediated through Type I IFNs. (4) Cells were infected with a PR8 virus lacking the NS1 gene (‘DNS1’). The NS1 protein normally inhibits vRNA- or IFNb-induced pathways, and its deletion can reveal an expanded response to infection.
2010-03-30 | GSE19392 | GEO