Viral N6-methyladenosine upregulates replication and pathogenesis of human respiratory syncytial virus: m6A-seq of vesicular stomatitis virus
Ontology highlight
ABSTRACT:
ORGANISM(S): Vesicular stomatitis virus
PROVIDER: GSE162339 | GEO | 2020/12/01
REPOSITORIES: GEO
Similar Datasets
Project description:N6-methyladenosine (m6A) is the most abundant internal RNA modification catalyzed by host RNA methyltransferases. As obligate intracellular parasites, many viruses acquire m6A methylation in their RNAs. However, the biological functions of viral m6A methylation are poorly understood. Here, we found that viral m6A methylation serves as a molecular marker for host innate immunity to discriminate self from nonself RNA and that this novel biological function of viral m6A methylation is universally conserved in non-segmented negative-sense (NNS) RNA viruses. Using m6A methyltransferase (METTL3)-knockout cells, we produced m6A-deficient virion RNA from the representative members of the families Pneumoviridae, Paramyxoviridae, and Rhabdoviridae and found that these m6A-deficient viral RNAs triggered significantly higher levels of type I interferon compared to the m6A-sufficient viral RNAs, in a RIG-I dependent manner. Reconstitution of the RIG-I pathway revealed that m6A-deficient virion RNA induced higher expression of RIG-I, bound to RIG-I more efficiently, enhanced RIG-I ubiquitination, and facilitated RIG-I conformational rearrangement and oligomerization. Furthermore, the m6A binding protein YTHDF2 sequesters m6A-sufficient virion RNA which suppresses type I interferon signaling pathway. Collectively, our results suggest that NNS RNA viruses acquire m6A in viral RNA as a common strategy to evade host innate immunity.
2021-01-16 | GSE164882 | GEO
Project description:Internal N6-methyladenosine (m6A) modification of RNA is one of the most common and abundant modifications in eukaryotic cells as well as in viruses. However, the biological role(s) of RNA m6A in virus-host interaction remains elusive. Using human metapneumovirus (hMPV), a medically important non-segmented negative-sense RNA virus as a model, we demonstrate that m6A serves as a molecular marker for innate immune discrimination self and nonself RNAs. We show that hMPV RNAs are m6A methylated and that viral m6A methylation promotes hMPV replication and gene expression. HMPV infection leads to differential expression of interferon-related genes involved in innate immune signaling pathways. Inactivating these m6A sites with synonymous mutations resulted in m6A deficient recombinant hMPVs that induced significantly higher expression of type I interferon that restricted viral replication. Notably, the induction of type I interferons by m6A-deficient rhMPVs and virion RNA was dependent on the cytoplasmic RNA sensor RIG-I, not MDA5. Mechanistically, m6A-deficient virion RNA induces higher expression of RIG-I, enhances its binding affinity to RIG-I, and facilitates the conformational change of RIG-I, leading to enhanced induction of type I IFN expression. The replication of m6A-deficient rhMPVs was attenuated in wild type A459 cells but was restored in cells knocked out for RIG-I and MAVS. Furthermore, m6A-deficient rhMPVs triggered higher type I interferon in vivo and were significantly attenuated in the lower respiratory tract yet retained high immunogenicity in cotton rats. Collectively, our results highlight that (i) virus acquires m6A in their RNAs as a means of mimicking cellular RNA to avoid the detection by innate immunity; and (ii) viral m6A RNA can serve as a novel target to attenuate hMPV for vaccine purposes.
2019-10-18 | GSE136139 | GEO
Project description:Viruses employ various strategies to evade innate immunity. Despite many studies on host or viral gene expression, how the cellular proteome responds to internal or external cues, has not been fully investigated. Using a Hepatitis B Virus (HBV) replication model, we performed proteomic analyses of HBV-replicating cells in G1/S and G2/M phases, as a function of IFN-alpha, providing specific information of how HBV infection, in combination with IFN-alpha, alters the hepatocyte proteome. We identified the conserved LSm (Like-Sm1-8) proteins were differentially expressed as a function of HBV replication and IFN-alpha. Specifically, in G2/M, IFN-alpha increased protein level of LSm1, the unique subunit of cytoplasmic LSm1-7 complex involved in mRNA decay. By contrast, IFN-alpha decreased LSm8, the unique subunit of nuclear LSm2-8 complex, a chaperone of U6 spliceosomal RNA. These results suggest cytoplasmic LSm1-7 has antiviral role, whereas nuclear LSm2-8 complex is pro-viral. Employing HBV replication and infection models, siRNA-mediated knockdown of LSm1 increased the level of all viral RNAs. Conversely, knockdown of LSm8 reduced viral RNA levels, dependent on N6-adenosine methylation (m6A) of the epsilon stem-loop at the 5 end of pre-Core/pregenomic (preC/pg) RNA. Methylated RNA immunoprecipitation (MeRIP) assays demonstrated reduced viral RNA methylation upon LSm8 knockdown, dependent on the m6A modification, suggesting the LSm2-8 complex has a role in mediating this modification. Interestingly, splicing inhibitor Cp028 acting upstream of LSm2-8 complex, suppressed levels of viral RNAs without reducing the m6A modification. This observation suggests Cp028 has novel antiviral effects, likely potentiating IFN-alpha -mediated suppression of HBV biosynthesis.
2022-06-03 | MSV000089600 | MassIVE
Project description:N6-methyladenosine (m6A) is the most prevalent internal modification of mRNAs in most eukaryotes. Likewise, viral RNAs may acquire m6A methylation during replication within these cells. Here we show that RNAs of human respiratory syncytial virus (RSV), a medically important non-segmented negative-sense (NNS) RNA virus, are modified by m6A within discreet regions and that these modifications enhance viral replication and pathogenesis. Overexpression of m6A binding proteins significantly enhanced RSV replication and gene expression. Knockdown of m6A methyltransferases decreased viral replication and gene expression whereas knockdown of m6A demethylases had the opposite effect. The G gene contained the most abundant m6A modifications. Recombinant RSV expressing a G gene lacking different m6A sites, resulted in RSVs with various degrees of defects in replication in A549 cells, primary well differentiated human airway epithelial (HAE) cultures, upper and lower respiratory tract of cotton rats, and were also less pathogenic to the lungs of cotton rats. One of the m6A-deficient rgRSVs, rgRSV-G12, was completely attenuated yet retained high immunogenicity in cotton rats. Moreover, a small molecule that inhibits S-adenosyl-L-homocysteine (SAH) hydrolase, thereby reducing the cellular SAH pool and viral RNA m6A, also inhibited RSV replication in HAE cells. Collectively, our results demonstrate viral m6A methylation upregulates RSV replication and pathogenesis and identify viral m6A methylation as a target for rational design of live attenuated vaccine candidates and for novel antiviral therapeutic agents for RSV.
2019-09-10 | GSE125803 | GEO
Project description:It is urgent and important to understand the relationship of the widespread severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2) with host immune response and study the underlying molecular mechanism. RNA modification landscape of SARS-CoV-2 and its functional relevance to host cell innate immune response remain unknown. N6-methylation of adenosine (m6A) in RNA regulates many physiological and disease processes. Here, we investigated m6A modification of SARS-CoV-2 gene in regulating host cell innate immune response. Our data showed that SARS-CoV-2 virus has m6A modification enriched in 3' region of the viral genome. We also found that host cell m6A methyltransferase METTL3 depletion reduced viral load in infected cells, decreased m6A levels in SARS-CoV-2 and host genes, and m6A reduction in viral RNA increased RIG-1 binding and subsequently enhanced downstream innate immune signaling pathway and inflammatory gene expression. METTL3 expression is reduced and inflammatory genes are induced in severe COVID-19 patients. These findings will aid to understand the COVID-19 pathogenesis and help in designing future studies of regulating innate immunity for COVID-19 treatment.
2021-04-27 | GSE167075 | GEO
Project description:Viruses package host RNAs in their virions which are associated with a range of functions in the viral life cycle. Previous transcriptomic profiling on host RNA packaging were mostly focused on retroviruses. Which host RNAs are packaged in other viruses at the transcriptome level has not been thoroughly examined. Here we apply both small RNA and large RNA sequencing of SARS-CoV-2 virions from six individual isolates in Vero cell cultures to profile packaging of host RNAs in a coronavirus and to explore SARS-CoV-2 genomic RNA modifications. We find selective packaging of specific tRNAs, tRNA fragments and signal recognition particle RNA into SARS-CoV-2 virions. Virions from all individual clones package the same set of host RNAs, suggesting a common mechanism of selective packaging. We estimate that a SARS-CoV-2 virion contains up to 1 SRP RNA and 4 tRNA molecules. We identify tRNA modification differences between the virion-packaged tRNAs and those in the uninfected host cells. Furthermore, we find subgenomic viral RNAs in the virions, and uncharacterized candidate modifications in the SARS-CoV-2 genomic RNA. Our results reveal an under-explored aspect of viral-host interaction that may be explored for viral therapeutics.
2022-03-06 | GSE182883 | GEO
Project description:N6-methyladenosine (m6A) modification is one of the most abundant post-transcriptional modifications that plays an important role in many pathophysiological conditions including host-pathogen interactions. A number of viruses were previously shown to manipulate the cellular m6A machinery usurping its function to their benefit during the course of their life cycle. Previously, we reported that EBV reprograms the host m6A system to regulate the stability of the viral transcripts and drive viral-mediated tumorigenesis by hijacking the functions of methyltransferase METTL14. We now report that during lytic reactivation EBV targets the RNA methylation system of the host to attenuate the innate immune response by suppressing the interferon response to facilitate a successful lytic replication.
2023-03-22 | GSE210618 | GEO
Project description:<p>Despite the nuclear localization of the m6A machinery, the genomes of multiple exclusively-cytoplasmic RNA viruses, such as chikungunya (CHIKV) and dengue (DENV), are reported to be extensively m6A-modified. However, these findings are mostly based on m6A-seq, an antibody-dependent technique with a high rate of false positives. Here, we addressed the presence of m6A in CHIKV and DENV RNAs. For this, we combined m6A-seq and the antibody-independent SELECT and nanopore direct RNA sequencing techniques with functional, molecular, and mutagenesis studies. Following this comprehensive analysis, we found no evidence of m6A modification in CHIKV or DENV transcripts. Furthermore, depletion of key components of the host m6A machinery did not affect CHIKV or DENV infection. Moreover, CHIKV or DENV infection had no effect on the m6A machinery’s localization. Our results challenge the prevailing notion that m6A modification is a general feature of cytoplasmic RNA viruses and underscore the importance of validating RNA modifications with orthogonal approaches.</p>
2024-01-25 | MTBLS6978 | MetaboLights
Project description:Viral infections involve packaging of the viral genome and proteins into virions. Knowing virion composition and structure is critical to understand viral pathogenesis. However, an integrated picture of virion proteome organization of large viruses, such as Herpesviruses, is lacking. Here we use cross-linking mass spectrometry to derive a spatially resolved structural interactome of intact human cytomegalovirus virions. We capture interactions of 82 host and 33 viral proteins, allowing us to de novo allocate them into distinct virion-layers and identify several host proteins as constitutive virion components recruited via specific protein interactions. The abundant viral protein pp150 forms domain-specific interactions with all virion layers and scaffolds numerous viral and host proteins such as PP1 phosphatase and 14-3-3 proteins, which are incorporated via nearby short linear motifs in pp150’s C-terminus. PP1 recruitment antagonizes 14-3-3 proteins and is pivotal during early and late viral replication steps. Collectively, this study gives a spatial and quantitative inventory of the system-wide organization and functional relevance of protein interactions inside native herpesvirus particles.
2023-06-14 | PXD031911 | 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.
2013-08-07 | BIOMD0000000463 | BioModels