# bib

id: cord-002689-qakbp4dz
author: Brisse, Morgan
title: Viral inhibitions of PACT-induced RIG-I activation
date: 2017-07-03
extension: .txt
mime: text/plain
words: 1050
sentence: 35
flesch: 39
cache: cache/cord-002689-qakbp4dz.txt
txt: txt/cord-002689-qakbp4dz.txt
summary:
  The dsRNA binding region of 4a has a high degree of sequence homology to other coronaviral dsRNA binding proteins. key: cord-002689-qakbp4dz authors: Brisse, Morgan; Ly, Hinh title: Viral inhibitions of PACT-induced RIG-I activation date: 2017-07-03 journal: Oncotarget DOI: 10.18632/oncotarget.18928 sha: doc_id: 2689 cord_uid: qakbp4dz nan Viral infections are usually detected by toll-like receptors (e.g., TLR3, TLR7/8) and cytosolic RIG-I-like receptors (RLRs), such as RIG-I and MDA5.


id: cord-285339-pwy1ry4n
author: Tarigan, Ronald
date: 2020-06-18
extension: .txt
mime: text/plain
words: 3178
sentence: 111
flesch: 47
cache: cache/cord-285339-pwy1ry4n.txt
txt: txt/cord-285339-pwy1ry4n.txt
title:
  Role of pattern recognition receptors and interferon-beta in protecting bat cell lines from encephalomyocarditis virus and Japanese encephalitis virus infection

summary:
  key: cord-285339-pwy1ry4n authors: Tarigan, Ronald; Shimoda, Hiroshi; Doysabas, Karla Cristine C.; Ken, Maeda; Iida, Atsuo; Hondo, Eiichi title: Role of pattern recognition receptors and interferon-beta in protecting bat cell lines from encephalomyocarditis virus and Japanese encephalitis virus infection date: 2020-06-18 journal: Biochem Biophys Res Commun DOI: 10.1016/j.bbrc.2020.04.060 sha: doc_id: 285339 cord_uid: pwy1ry4n Bats are potential natural hosts of Encephalomyocarditis virus (EMCV) and Japanese encephalitis virus (JEV). The knockdown of TLR3, RIG-I, and MDA5 in Rhinolophus bat cell line using antisense RNA oligonucleotide led to decrease IFN-β expression and increased viral replication.


id: cord-328549-r56lih8j
author: Okamoto, Masaaki
title: Regulation of RIG-I Activation by K63-Linked Polyubiquitination
date: 2018-01-05
extension: .txt
mime: text/plain
words: 3651
sentence: 134
flesch: 37
cache: cache/cord-328549-r56lih8j.txt
txt: txt/cord-328549-r56lih8j.txt
summary:
  Considering that mass spectrometry analysis revealed the covalent binding of RIG-I with K63-linked polyubiquitin chains, these observations indicate that either covalent or non-covalent binding with polyubiquitin chains is sufficient for RIG-I 2CARDs activation (23, 26) . However, subsequent studies have reported that Riplet, MEX3C, and TRIM4 ubiquitin ligases are also involved in K63-linked polyubiquitination and the activation of RIG-I. MEX3C and TRIM4 mediate polyubiquitination of the 2CARDs.


id: cord-257052-cik2wmlk
author: Ban, Junsu
date: 2018-12-14
extension: .txt
mime: text/plain
words: 3925
sentence: 160
flesch: 38
cache: cache/cord-257052-cik2wmlk.txt
txt: txt/cord-257052-cik2wmlk.txt
title:
  Human Respiratory Syncytial Virus NS 1 Targets TRIM25 to Suppress RIG-I Ubiquitination and Subsequent RIG-I-Mediated Antiviral Signaling

summary:
  These results suggest that RSV NS1 expression diminishes the interaction between RIG-I and MAVS by interfering with TRIM25-mediated RIG-I ubiquitination. RSV NS1 and NS2 have been shown to interfere with RIG-I-mediated antiviral signaling.


id: cord-299964-sn5o3ugb
author: Xue, Qiao
date: 2018-11-05
extension: .txt
mime: text/plain
words: 4082
sentence: 176
flesch: 51
cache: cache/cord-299964-sn5o3ugb.txt
txt: txt/cord-299964-sn5o3ugb.txt
title:
  Seneca Valley Virus 3C protease negatively regulates the type I interferon pathway by acting as a viral deubiquitinase

summary:
  Therefore, the three mutants, namely the single-site mutants H48A or C160A, and the doublesites mutants H48A/C160A (3Cdm) (Xue et al., 2018) , were used to confirm whether the Cys and His residues are involved in the DUB activity of SVV 3C pro . Taken together, these results indicate that the catalytic Cys and His residues of SVV 3C pro are required for its DUB activity.


id: cord-305737-bnzd7b25
author: Rehwinkel, Jan
title: Targeting the viral Achilles’ heel: recognition of 5′-triphosphate RNA in innate anti-viral defence
date: 2013-05-23
extension: .txt
mime: text/plain
words: 4140
sentence: 167
flesch: 47
cache: cache/cord-305737-bnzd7b25.txt
txt: txt/cord-305737-bnzd7b25.txt
summary:
  Selfpropagation allows for sensitive detection of minute amounts of viral RNA: it has been estimated that 20 molecules of 5PPP RNA are sufficient to activate IRF3 via the RIG-I/MAVS pathway IFITs control translation initiation, cell proliferation and cell migration, and exert anti-viral effects against a variety of RNA viruses and human papillomavirus


id: cord-288390-p1q3v1ie
author: Habjan, Matthias
title: Cytoplasmic sensing of viral nucleic acids
date: 2015-02-07
extension: .txt
mime: text/plain
words: 4050
sentence: 161
flesch: 39
cache: cache/cord-288390-p1q3v1ie.txt
txt: txt/cord-288390-p1q3v1ie.txt
summary:
  dsRNA could be either the result of replication intermediates (for RNA viruses), generation of genomic RNA (for dsRNA viruses), convergent transcription (for DNA viruses), or of the presence of secondary structures found in viral RNAs (e.g. the IRES structure of ssRNA viruses) I interferon signalling Protein kinase PKR and RNA adenosine deaminase ADAR1: new roles for old players as modulators of the interferon response Bevilacqua PC: 5'-Triphosphate-dependent activation of PKR by RNAs with short stem-loops AIM2 activates the inflammasome and cell death in response to cytoplasmic DNA Recognition of RNA virus by RIG-I results in activation of CARD9 and inflammasome signaling for interleukin 1 beta production The DHX33 RNA helicase senses cytosolic RNA and activates the NLRP3 inflammasome IFIT1 is an antiviral protein that recognizes 5 0 -triphosphate RNA Structural basis for viral 5 0 -PPP-RNA recognition by human IFIT proteins Inhibition of translation by IFIT family members is determined by their ability to interact selectively with the 5 0 -terminal regions of cap0-, cap1-and


id: cord-254549-ev0oesu0
author: Kutikhin, Anton G
title: C-type lectin receptors and RIG-I-like receptors: new points on the oncogenomics map
date: 2012-02-24
extension: .txt
mime: text/plain
words: 4456
sentence: 114
flesch: 22
cache: cache/cord-254549-ev0oesu0.txt
txt: txt/cord-254549-ev0oesu0.txt
summary:
  For instance, it was suggested that variant alleles of MRC1 rs2477637, rs2253120, rs2477664, rs692527, rs1926736, and rs691005 gene polymorphisms are associated with development of asthma 13 (eg, variant A allele of rs1926736 was connected with decreased asthma risk). Some polymorphisms may be valued as the most promising for further oncogenomic investigations on the basis of their association with cancer risk or because of their substantial functional consequences on the molecular level according to the following concept: Gene polymorphism may be included on the short list for further oncogenomic studies if: • The single nucleotide polymorphism leads to substantial functional consequences at the molecular level (for instance, it strongly affects transcription, splicing, translation, stability and transport of pre-mRNA, mRNA, noncoding RNA, or protein encoding by the gene, or it noticeably influences signaling of synthesized protein)


id: cord-287855-jfrg9soy
author: Gaur, Pratibha
title: Influenza virus and cell signaling pathways
date: 2011-06-01
extension: .txt
mime: text/plain
words: 4434
sentence: 190
flesch: 37
cache: cache/cord-287855-jfrg9soy.txt
txt: txt/cord-287855-jfrg9soy.txt
summary:
  A virus NS1 protein binds p85beta and activates phosphatidylinositol-3-kinase signaling A new player in a deadly game: influenza viruses and the PI3K/Akt signalling pathway Influenza virus propagation is impaired by inhibition of the Raf/MEK/ERK signalling cascade Ringing the alarm bells: signalling and apoptosis in influenza virus infected cells The cellular inhibitor of the PKR protein kinase, P58 (IPK), is an influenza virus-activated co-chaperone that modulates heat shock protein 70 activity Entry of influenza viruses into cells is inhibited by a highly specific protein kinase C inhibitor Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I NF-kappaB signaling differentially regulates influenza virus RNA synthesis Binding of influenza virus HA protein to host cell surface receptor activates PKC


id: cord-257886-ytlnhyxr
author: Zhao, Kuan
date: 2019-05-03
extension: .txt
mime: text/plain
words: 4903
sentence: 216
flesch: 49
cache: cache/cord-257886-ytlnhyxr.txt
txt: txt/cord-257886-ytlnhyxr.txt
title:
  Nucleocapsid protein of porcine reproductive and respiratory syndrome virus antagonizes the antiviral activity of TRIM25 by interfering with TRIM25-mediated RIG-I ubiquitination

summary:
  Furthermore, N protein inhibits the expression of TRIM25 and TRIM25-mediated RIG-I ubiquitination to suppress interferon β production. Furthermore, with increasing TRIM25 expression, the inhibitory effect of N protein on the ubiquitination of RIG-I diminished.


id: cord-268438-bjs5oliw
author: Jin, Yilin
date: 2019-12-03
extension: .txt
mime: text/plain
words: 5084
sentence: 186
flesch: 40
cache: cache/cord-268438-bjs5oliw.txt
txt: txt/cord-268438-bjs5oliw.txt
title:
  Zebrafish TRIM25 Promotes Innate Immune Response to RGNNV Infection by Targeting 2CARD and RD Regions of RIG-I for K63-Linked Ubiquitination

summary:
  Retinoic acid inducible gene-I (RIG-I)-like receptors (RLRs), as intracellular PRRs, composed of RIG-I, MDA5, and LGP2, recognize non-self signatures of viral RNAs in the cytosol of cells. RIG-I, as an important component of RLR signaling pathway, can detect viral dsRNAs in the cytoplasm and induce type I IFN production and the secretion of pro-inflammatory cytokines to suppress virus spread during virus infection (22) .


id: cord-312886-o3ipzn05
author: Onomoto, Koji
title: Antiviral innate immunity and stress granule responses
date: 2014-08-19
extension: .txt
mime: text/plain
words: 5143
sentence: 169
flesch: 27
cache: cache/cord-312886-o3ipzn05.txt
txt: txt/cord-312886-o3ipzn05.txt
summary:
  The mitochondrial targeting chaperone 14-3-3epsilon regulates a RIG-I translocon that mediates membrane association and innate antiviral immunity Reconstitution of the RIG-I pathway reveals a signaling role of unanchored polyubiquitin chains in innate immunity RIG-I forms signaling-competent filaments in an ATP-dependent, ubiquitin-independent manner Structural basis for ubiquitin-mediated antiviral signal activation by RIG-I Type I interferon gene induction by the interferon regulatory factor family of transcription factors Antiviral effect of the mammalian translation initiation factor 2alpha kinase GCN2 against RNA viruses Encephalomyocarditis virus disrupts stress granules, the critical platform for triggering antiviral innate immune responses Inhibition of cytoplasmic mRNA stress granule formation by a viral proteinase Production of a dominant-negative fragment due to G3BP1 cleavage contributes to the disruption of mitochondriaassociated protective stress granules during CVB3 infection Mammalian orthoreovirus particles induce and are recruited into stress granules at early times postinfection Importance of eIF2alpha phosphorylation and stress granule assembly in alphavirus translation regulation Dynamic oscillation of translation and stress granule formation mark the cellular response to virus infection Regulation of PKR by HCV IRES RNA: importance of domain II and NS5A Hepatitis C virus (HCV) induces formation of stress granules whose proteins regulate HCV RNA replication and virus assembly and egress The leader protein of cardioviruses inhibits stress granule assembly The mengovirus leader protein blocks interferon-alpha/beta gene transcription and inhibits activation of interferon regulatory factor 3 Stress granule formation induced by measles virus is protein kinase PKR dependent and impaired by RNA adenosine deaminase ADAR1 Measles virus nonstructural C protein modulates viral RNA polymerase activity by interacting with host protein Quantitative analysis of Argonaute protein reveals microRNA-dependent localization to stress granules Argonaute 2/RISC resides in sites of mammalian mRNA decay known as cytoplasmic bodies The translational regulator CPEB1 provides a link between dcp1 bodies and stress granules The DEAD-box RNA helicase DDX3 associates with export messenger ribonucleoproteins as well as tip-associated protein and participates in translational control Determination of the role of DDX3 a factor involved in mammalian RNAi pathway using an shRNA-expression library Cellular microRNA and P bodies modulate host-HIV-1 interactions RNA-associated protein 55 (RAP55) localizes to mRNA processing bodies and stress granules The dsRNA protein kinase PKR: virus and cell control PKR; a sentinel kinase for cellular stress Identification and characterization of pancreatic eukaryotic initiation factor 2 alpha-subunit kinase, PEK, involved in translational control Protein translation and folding are coupled by an endoplasmic-reticulum-resident kinase Regulation of protein synthesis by hypoxia via activation of the endoplasmic reticulum kinase PERK and phosphorylation of the translation initiation factor eIF2alpha Uncharged tRNA activates GCN2 by displacing the protein kinase moiety from a bipartite tRNA-binding domain Heme-regulated inhibitor kinase-mediated phosphorylation of eukaryotic translation initiation factor 2 inhibits translation, induces stress granule formation, and mediates survival upon arsenite exposure Regulation of protein synthesis by heme-regulated eIF-2 alpha kinase Analysis of subcellular G3BP redistribution during rubella virus infection Cell proteins TIA-1 and TIAR interact with the 3 0 stem-loop of the West Nile virus complementary minus-strand RNA and facilitate virus replication Modulation of hepatitis C virus RNA abundance and virus release by dispersion of processing bodies and enrichment of stress granules Hepatitis C virus hijacks P-body and stress granule components around lipid droplets The polypyrimidine tract-binding protein affects coronavirus RNA accumulation levels and relocalizes viral RNAs to novel cytoplasmic domains different from replication-transcription sites Mouse hepatitis coronavirus replication induces host translational shutoff and mRNA decay, with concomitant formation of stress granules and processing bodies Induction of stress granule-like structures in vesicular stomatitis virus-infected cells Respiratory syncytial virus induces host RNA stress granules to facilitate viral replication Activation of protein kinase R is required for induction of stress granules by respiratory syncytial virus but dispensable for viral replication Roles of the respiratory syncytial virus trailer region: effects of mutations on genome production and stress granule formation Arenavirus infection induces discrete cytosolic structures for RNA replication Mammalian orthoreovirus escape from host translational shutoff correlates with stress granule disruption and is independent of eIF2alpha phosphorylation and PKR Reovirus induces and benefits from an integrated cellular stress response Formation of antiviral cytoplasmic granules during orthopoxvirus infection Colocalization of transcription and translation within cytoplasmic poxvirus factories coordinates viral expression and subjugates host functions Modulation of stress granules and P bodies during dicistrovirus infection We were supported by the following grants: the Ministry of Education, Culture, Sports


id: cord-312075-asbt0mcj
author: Schulz, Katharina S.
title: Viral Evasion Strategies in Type I IFN Signaling – A Summary of Recent Developments
date: 2016-11-11
extension: .txt
mime: text/plain
words: 5784
sentence: 207
flesch: 33
cache: cache/cord-312075-asbt0mcj.txt
txt: txt/cord-312075-asbt0mcj.txt
summary:
  Macrophage (Houst) (2015) 2:e1009 Toscana virus NSs protein inhibits the induction of type I interferon by interacting with RIG-I Truncation of the C-terminal region of Toscana virus NSs protein is critical for interferon-beta antagonism and protein stability Foot-and-mouth disease virus viroporin 2B antagonizes RIG-I mediated antiviral effects by inhibition of its protein expression Hepatitis B virus inhibits intrinsic RIG-I and RIG-G immune signaling via inducing miR146a A phosphomimetic-based mechanism of dengue virus to antagonize innate immunity DDX60, a DEXD/H box helicase, is a novel antiviral factor promoting RIG-I-like receptor-mediated signaling DDX60 is involved in RIG-I-dependent and independent antiviral responses, and its function is attenuated by virus-induced EGFR activation A diverse range of gene products are effectors of the type I interferon antiviral response Mouse superkiller-2-like helicase DDX60 is dispensable for type I IFN induction and immunity to multiple viruses Dengue virus subverts host innate immunity by targeting adaptor protein MAVS Porcine reproductive and respiratory syndrome virus 3C protease cleaves the mitochondrial antiviral signalling complex to antagonize IFN-beta expression Hepatitis C virus protease NS3/4A cleaves mitochondrial antiviral signaling protein off the mitochondria to evade innate immunity Hepatitis C virus NS3-4A inhibits the peroxisomal MAVS-dependent antiviral signalling response Highly pathogenic porcine reproductive and respiratory syndrome virus Nsp4 cleaves VISA to impair antiviral responses mediated by RIG-I-like receptors Porcine epidemic diarrhea virus inhibits dsRNA-induced interferon-beta production in porcine intestinal epithelial cells by blockade of the RIG-I-mediated pathway SARS-coronavirus open reading frame-9b suppresses innate immunity by targeting mitochondria and the MAVS/TRAF3/TRAF6 signalosome PCBP2 mediates degradation of the adaptor MAVS via the HECT ubiquitin ligase AIP4 Oncogenic human T-cell lymphotropic virus type 1 tax suppression of primary innate immune signaling pathways Middle east respiratory syndrome coronavirus M protein suppresses type I interferon expression through the inhibition of TBK1-dependent phosphorylation of IRF3 Suppression of innate antiviral response by severe acute respiratory syndrome coronavirus M protein is mediated through the first transmembrane domain A firm hand on NFkappaB: structures of the IkappaBalpha-NFkappaB complex IkappaB kinases: key regulators of the NF-kappaB pathway Inducible degradation of IkappaBalpha by the proteasome requires interaction with the F-box protein h-betaTrCP Shaping the nuclear action of NF-kappaB Encephalomyocarditis virus 3C protease relieves TRAF family member-associated NF-kappaB activator (TANK) inhibitory effect on TRAF6-mediated NF-kappaB signaling through cleavage of TANK Porcine epidemic diarrhea virus 3C-like protease regulates its interferon antagonism by cleaving NEMO Hepatitis A virus 3C protease cleaves NEMO to impair induction of beta interferon Foot-and-mouth disease virus 3C protease cleaves NEMO to impair innate immune signaling NSP1 of human rotaviruses commonly inhibits NF-kappaB signalling by inducing beta-TrCP degradation IKKepsilon and TBK1 are essential components of the IRF3 signaling pathway Triggering the interferon antiviral response through an IKK-related pathway Regulation and function of IKK and IKK-related kinases Involvement of the ubiquitin-like domain of TBK1/IKK-i kinases in regulation of IFN-inducible genes IkappaB kinase epsilon (IKKepsilon): a therapeutic target in inflammation and cancer Regulation of TBK1 activity by optineurin contributes to cell cycle-dependent expression of the interferon pathway Negative regulation of TBK1-mediated antiviral immunity IRFs: master regulators of signalling by toll-like receptors and cytosolic pattern-recognition receptors The IRF family transcription factors in immunity and oncogenesis The IRF family transcription factors at the interface of innate and adaptive immune responses Direct triggering of the type I interferon system by virus infection: activation of a transcription factor complex containing IRF-3 and CBP/ Viruses target RIG-I directly or indirectly to block the type I IFN response.


id: cord-343824-00mqmpzw
author: Qian, Wei
date: 2017-07-03
extension: .txt
mime: text/plain
words: 6262
sentence: 223
flesch: 41
cache: cache/cord-343824-00mqmpzw.txt
txt: txt/cord-343824-00mqmpzw.txt
title:
  The C-Terminal Effector Domain of Non-Structural Protein 1 of Influenza A Virus Blocks IFN-β Production by Targeting TNF Receptor-Associated Factor 3

summary:
  Although all types of influenza virus NS1 proteins interact with TRIM25, only part of NS1 prevents IRF3 activation, indicating that TRIM25 is not required for the inhibition of IRF3 activation. It is noteworthy that cells infected with viruses expressing NS1 proteins in seasonal H3N2 and H2N2 viruses do not inhibit IRF3 activation.


id: cord-000125-uvf5qzfd
author: Kenworthy, Rachael
date: 2009-09-03
extension: .txt
mime: text/plain
words: 6664
sentence: 215
flesch: 43
cache: cache/cord-000125-uvf5qzfd.txt
txt: txt/cord-000125-uvf5qzfd.txt
title:
  Short-hairpin RNAs delivered by lentiviral vector transduction trigger RIG-I-mediated IFN activation

summary:
  Moreover, activation of IRF-3 ( Figure 1E ) and IFN promoters ( Figure 1F ) in 293FT cells, which do not contain a functional TLR3 signaling pathway (42) , indicates that TLR3 plays a negligible role, if any, in IFN induction by sh-B971. These results demonstrate that sh-B971 is a potent activator of IRF-3 and IRF-7, master regulators of IFN expression in human cells.


id: cord-001129-gi2kswai
author: Lemos de Matos, Ana
title: Positive Evolutionary Selection On the RIG-I-Like Receptor Genes in Mammals
date: 2013-11-27
extension: .txt
mime: text/plain
words: 6982
sentence: 274
flesch: 42
cache: cache/cord-001129-gi2kswai.txt
txt: txt/cord-001129-gi2kswai.txt
summary:
  For RIG-I, the greatest number of codons identified as candidates under selective pressures were located in known protein functional domains, which might reveal the pressure imposed by the great number of viruses recognized by this RLR The coding region of the three RLR genes, RIG-I, MDA5 and LGP2, were collected for different mammalian species from NCBI (http://www.ncbi.nlm.nih.gov) and Ensembl (http:// www.ensembl.org/index.html) databases (Table S1 ).


id: cord-301362-f3lp10lm
author: Delgui, Laura R.
date: 2017-01-20
extension: .txt
mime: text/plain
words: 7023
sentence: 192
flesch: 26
cache: cache/cord-301362-f3lp10lm.txt
txt: txt/cord-301362-f3lp10lm.txt
title:
  A Novel Mechanism Underlying the Innate Immune Response Induction upon Viral-Dependent Replication of Host Cell mRNA: A Mistake of +sRNA Viruses' Replicases

summary:
  It was shown that several poliovirus and host proteins are involved in the membrane rearrangements that are essential for virus RNA replication (reviewed by Jackson, 2014) . Other +sRNA viruses such as the enterovirus Coxsackievirus (Kemball et al., 2010) , Hepatitis C virus (Flaviviridae family) (Sir et al., 2012) , or Coronavirus such as MVH (Reggiori et al., 2010) also usurp the autophagy pathway and induce remarkably alterations in intracellular membranous components to harbor the sites for viral RNA replication.


id: cord-252485-cxi3cr15
author: Yoshida, Asuka
date: 2015-08-04
extension: .txt
mime: text/plain
words: 7105
sentence: 198
flesch: 38
cache: cache/cord-252485-cxi3cr15.txt
txt: txt/cord-252485-cxi3cr15.txt
title:
  IFN-β-inducing, unusual viral RNA species produced by paramyxovirus infection accumulated into distinct cytoplasmic structures in an RNA-type-dependent manner

summary:
  The SG-like structures have been suggested to serve as the sites at which the RLRs encounter viral RNA and subsequently activate the IFN signaling pathways in infections by RNA viruses (Onomoto et al., 2012; Yoo et al., 2014) . In spite of the large number of studies conducted in this field, it remains unknown what kinds of viral RNA species are recognized by RLRs and where the sites of recognition are in real infections by RNA viruses.


id: cord-007689-0vpp3xdl
author: Schlee, M.
title: Beyond Double-Stranded RNA-Type I IFN Induction by 3pRNA and Other Viral Nucleic Acids
date: 2007
extension: .txt
mime: text/plain
words: 7770
sentence: 251
flesch: 38
cache: cache/cord-007689-0vpp3xdl.txt
txt: txt/cord-007689-0vpp3xdl.txt
summary:
  With notable exceptions such as the Picornavirus family (see below), viral RNA-dependent RNA polymerases (RdRp) initiate polymerase activity de novo, without a specific primer (Kao et al. 2001) . Both activated PKR and OAS were found to block translation of viral RNA by distinct mechanisms.


id: cord-261532-q923xxn2
author: Chen, Huihui
title: The essential adaptors of innate immune signaling
date: 2012-09-21
extension: .txt
mime: text/plain
words: 7451
sentence: 251
flesch: 34
cache: cache/cord-261532-q923xxn2.txt
txt: txt/cord-261532-q923xxn2.txt
summary:
  On the other hand, RNA virus infection triggers STING activation through STING-MAVS interaction on MAVS-resident MAM or peroxisomal (Pex) membrane; activated STING then dissociates with MAVS and recruits STAT6 and TBK1, leading to STAT6 activation. Then JAKs further phosphorylate STAT6 at the receptor: activated STAT6 dimerizes through SH2 domain and translocates into nucleus to function as a transcriptional factor, regulating IL-4/IL-13-dependent signaling such as Th2 differentiation, immunoglobulin E (IgE) and chemokine production and mucus generation.


id: cord-306533-lvm11o4r
author: Woo, Bean
title: Regulatory interplay between deubiquitinating enzymes and cytokines
date: 2019-06-08
extension: .txt
mime: text/plain
words: 7634
sentence: 359
flesch: 45
cache: cache/cord-306533-lvm11o4r.txt
txt: txt/cord-306533-lvm11o4r.txt
summary:
  When HEK293 T cells were transfected with markers of co-IP and UL36USP or the C40A (a DUB motif mutant) and then infected with SeV, the result showed reduction of ubiquitination of TRAF3 in cells with WT UL36USP, while C40A has no reduction of UL36USP's ubiquitination [48] . A study by Leznicki et al. introduced three isoforms of USP3 in HEK293 cells:


id: cord-254492-42d77vxf
author: Heaton, Steven M.
title: Ubiquitin in the activation and attenuation of innate antiviral immunity
date: 2016-01-11
extension: .txt
mime: text/plain
words: 7459
sentence: 253
flesch: 25
cache: cache/cord-254492-42d77vxf.txt
txt: txt/cord-254492-42d77vxf.txt
summary:
  USP4 is a DUb that sustains RLR signaling by specifically removing such chains (Wang et al., 2013a) . NEDD4 family-interacting protein 1 (Ndfip1) binds MAVS and recruits Smurf1 and possibly Smurf2, facilitating ubiquitination of unknown sites within MAVS (Wang et al., 2012c; Pan et al., 2014) .


id: cord-284156-btb4oodz
author: Liu, Yiliu
title: Host and Viral Modulation of RIG-I-Mediated Antiviral Immunity
date: 2017-01-03
extension: .txt
mime: text/plain
words: 7075
sentence: 211
flesch: 23
cache: cache/cord-284156-btb4oodz.txt
txt: txt/cord-284156-btb4oodz.txt
summary:
  ISGF3 then translocates to the nucleus and coordinates the transcription of hundreds of ISGs including RIG-I, thus generating an amplifying loop leading to the accumulation of RIG-I during several types of infections (8) (Figure 1B ). On the other hand, some viruses encode enzymes that directly deubiquitinate RIG-I. For instance, KSHV encoded deubiquitinase ORF64 cleaves Lys63-ubiquination chains on CARDs, blocks CARDs interaction between RIG-I and MAVS, thereby downregulating RIG-I signaling (105) .


id: cord-342653-bpyc2gbl
author: Wang, Hai-Tao
title: Substrate recognition by TRIM and TRIM-like proteins in innate immunity
date: 2020-10-20
extension: .txt
mime: text/plain
words: 8610
sentence: 365
flesch: 44
cache: cache/cord-342653-bpyc2gbl.txt
txt: txt/cord-342653-bpyc2gbl.txt
summary:
  The tripartite motif family identifies cell compartments Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties The tripartite motif: structure and function The interferon-inducible ubiquitin-protein isopeptide ligase (E3) EFP also functions as an ISG15 E3 ligase Innate immunity to RNA virus is regulated by temporal and reversible sumoylation of RIG-I and MDA5 Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity Mechanism of TRIM25 catalytic activation in the antiviral RIG-I pathway Mechanism of B-box 2 domain-mediated higher-order assembly of the retroviral restriction factor TRIM5alpha Structural determinants of TRIM protein function Structural insights into the TRIM family of ubiquitin E3 ligases The tripartite motif coiled-coil is an elongated antiparallel hairpin dimer Molecular mechanism of influenza A NS1-mediated TRIM25 recognition and inhibition TRIM5alpha SPRY/coiled-coil interactions optimize avid retroviral capsid recognition Ubiquitin-dependent and -independent roles of E3 ligase RIPLET in innate immunity Hierarchical assembly governs TRIM5alpha recognition of HIV-1 and retroviral capsids TRIM family: pleiotropy and diversification through homomultimer and heteromultimer formation TRIM family proteins and their emerging roles in innate immunity TRIM family proteins: roles in autophagy, immunity, and carcinogenesis Genomics and evolution of the TRIM gene family Relationship between SPRY and B30.2 protein domains. Thus, TRIM CC plays diverse functions in regulating the overall architecture and functions of TRIM proteins.


id: cord-311823-85wj08gr
author: Katze, Michael G.
title: Innate immune modulation by RNA viruses: emerging insights from functional genomics
date: 2008
extension: .txt
mime: text/plain
words: 9163
sentence: 289
flesch: 28
cache: cache/cord-311823-85wj08gr.txt
txt: txt/cord-311823-85wj08gr.txt
summary:
  The role of RIg-I in the response to influenza virus infection has also been assessed 10 . A relevant observation in this regard is that early stimulation of the respiratory-tract B cells (within 48 hours of influenza virus infection) was shown to be strongly driven by virus-induced type


id: cord-254895-ym0jsir5
author: Eisenächer, Katharina
date: 2008-01-18
extension: .txt
mime: text/plain
words: 9107
sentence: 258
flesch: 31
cache: cache/cord-254895-ym0jsir5.txt
txt: txt/cord-254895-ym0jsir5.txt
title:
  The role of viral nucleic acid recognition in dendritic cells for innate and adaptive antiviral immunity

summary:
  TLR7 does not seem to play an essential role in the innate immune response to RNA virus infection in vivo. (Xu et al., 2005) and CARD adapter inducing IFN-b (CARDIF) (Meylan et al., 2005) , respectively.


id: cord-283096-qm7h4qui
author: Jeon, Young Joo
title: ISG15 and immune diseases
date: 2010-02-12
extension: .txt
mime: text/plain
words: 11213
sentence: 456
flesch: 38
cache: cache/cord-283096-qm7h4qui.txt
txt: txt/cord-283096-qm7h4qui.txt
summary:
  Like ubiquitin, ISG15 proteins in some species are synthesized as precursors that need to be processed before conjugation to target proteins (Fig. 2) While ISG15 molecules in human, mouse, and rat are translated as precursors containing the extensions of5-8 amino acids in their C-termini, ISG15 proteins in most other species, including fish and bovine, are synthesized as matured forms [46] .


id: cord-312892-p72zwmtb
author: Chen, Nanhua
title: RNA sensors of the innate immune system and their detection of pathogens
date: 2017-04-04
extension: .txt
mime: text/plain
words: 4243
sentence: 134
flesch: 31
cache: cache/cord-312892-p72zwmtb.txt
txt: txt/cord-312892-p72zwmtb.txt
summary:
  Cold Spring Harbor Perspect TLR8: the forgotten relative revindicated Master sensors of pathogenic RNA -RIG-I like receptors RIG-I in RNA virus recognition The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses Regulating intracellular antiviral defense and permissiveness to hepatitis C virus RNA replication through a cellular RNA helicase, RIG-I Filament assemblies in foreign nucleic acid sensors How RIG-I like receptors activate MAVS Sensing microbial RNA in the cytosol International Union of Basic and Clinical Pharmacology. RNA are the major PAMPs of RNA viruses, to which most severe disease causing viruses belong thus posing a tougher challenge to human and animal health.


id: cord-278523-djjtgbh6
author: Zhou, Bei-xian
date: 2020-06-05
extension: .txt
mime: text/plain
words: 11767
sentence: 500
flesch: 45
cache: cache/cord-278523-djjtgbh6.txt
txt: txt/cord-278523-djjtgbh6.txt
title:
  β-sitosterol ameliorates influenza A virus-induced proinflammatory response and acute lung injury in mice by disrupting the cross-talk between RIG-I and IFN/STAT signaling

summary:
  We confirmed the anti-apoptotic effect of βsitosterol by measuring the active caspase-3 and its substrate PARP, observing that these products were found in cells transfected with vRNA but not in those treated with β-sitosterol Fig. 4 (continued) β-Sitosterol ameliorates IAV-induced inflammation and ALI BX Zhou (Fig. 5b) . Moreover, β-sitosterol treatment attenuated RIG-I-mediated apoptotic injury of alveolar epithelial cells (AEC) via downregulation of pro-apoptotic factors.


id: cord-313957-hviv5zar
author: Masucci, Maria Grazia
title: Viral Ubiquitin and Ubiquitin-Like Deconjugases—Swiss Army Knives for Infection
date: 2020-08-01
extension: .txt
mime: text/plain
words: 11785
sentence: 403
flesch: 30
cache: cache/cord-313957-hviv5zar.txt
txt: txt/cord-313957-hviv5zar.txt
summary:
  Hence, UbL-regulated cellular functions are exploited for viral entry, transcription and replication of the viral genomes, synthesis of viral proteins, and assembly of new virions and for the maturation and exit of viral particles from the infected cell [32] [33] Thus, the ISGylation of de novo synthesized viral proteins may hinder their interaction with host proteins that are required for replication, may disrupt their catalytic function, or may alter the oligomerization of capsid proteins leading to a decrease in the number and infectivity of virus particles


id: cord-319501-a2x1hvkk
author: Wong, Lok-Yin Roy
title: A molecular arms race between host innate antiviral response and emerging human coronaviruses
date: 2016-01-15
extension: .txt
mime: text/plain
words: 7773
sentence: 261
flesch: 38
cache: cache/cord-319501-a2x1hvkk.txt
txt: txt/cord-319501-a2x1hvkk.txt
summary:
  In a previous study, MERS-CoV M is shown to impede IFN production by preventing IRF3 translocation into the nucleus (Yang et al., 2013) . Among the five accessory proteins, ORF4a, ORF4b and ORF5 show the ability to dampen IFN production (Yang et al., 2013) .


id: cord-323756-atnrw9ew
author: Vabret, Nicolas
title: Sensing Microbial RNA in the Cytosol
date: 2013-12-25
extension: .txt
mime: text/plain
words: 6419
sentence: 201
flesch: 31
cache: cache/cord-323756-atnrw9ew.txt
txt: txt/cord-323756-atnrw9ew.txt
summary:
  A structural basis for discriminating between self and nonself double-stranded RNAs in mammalian cells Length-dependent recognition of double-stranded ribonucleic acids by retinoic acid-inducible gene-I and melanoma differentiation-associated gene Nonself RNA-sensing mechanism of RIG-I helicase and activation of antiviral immune responses The thermodynamic basis for viral RNA detection by the RIG-I innate immune sensor RIG-I detects viral genomic RNA during negative-strand RNA virus infection Incoming RNA virus nucleocapsids containing a 5'-triphosphorylated genome activate RIG-I and antiviral signaling Differential roles of MDA5 and RIG-I helicases in the recognition of RNA viruses Innate immunity induced by composition-dependent RIG-I recognition of hepatitis C virus RNA Preference of RIG-I for short viral RNA molecules in infected cells revealed by next-generation sequencing Epstein-Barr virus-encoded small RNA induces IL-10 through RIG-I-mediated IRF-3 signaling Adenovirus virus-associated RNAs induce type I interferon expression through a RIG-I-mediated pathway The 5' ends of RNA oligonucleotides in Escherichia coli and mRNA degradation Extracellular and intracellular pattern recognition receptors cooperate in the recognition of Helicobacter pylori IFNgamma inhibits the cytosolic replication of Shigella flexneri via the cytoplasmic RNA sensor RIG-I Essential role of mda-5 in type I IFN responses to polyriboinosinic:polyribocytidylic acid and encephalomyocarditis picornavirus Structural basis for dsRNA recognition, filament formation, and antiviral signal activation by MDA5 Double-stranded RNA is produced by positive-strand RNA viruses and DNA viruses but not in detectable amounts by negative-strand RNA viruses Activation of MDA5 requires higher-order RNA structures generated during virus infection MDA5 detects the double-stranded RNA replicative form in picornavirus-infected cells Innate immune response after adenoviral gene delivery into skin is mediated by AIM2, NALP3, DAI and mda5 Visualisation of direct interaction of MDA5 and the dsRNA replicative intermediate form of positive strand RNA viruses Activation of IFN-&#946; expression by a viral mRNA through RNase L and MDA5 New insights into the role of RNase L in innate immunity Ribose 2'-O-methylation provides a molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5 MAVS forms functional prion-like aggregates to activate and propagate antiviral innate immune response Intracellular pathogen detection by RIG-I-like receptors The adaptor MAVS promotes NLRP3 mitochondrial localization and inflammasome activation Recognition of RNA virus by RIG-I results in activation of CARD9 and inflammasome signaling for interleukin 1 beta production Type I IFN triggers RIG-I/TLR3/NLRP3-dependent inflammasome activation in influenza A virus infected cells The RIG-I-like receptor LGP2 recognizes the termini of double-stranded RNA The regulatory domain of the RIG-I family ATPase LGP2 senses doublestranded RNA LGP2 is a positive regulator of RIG-I-and MDA5-mediated antiviral responses ATP hydrolysis enhances RNA recognition and antiviral signal transduction by the innate immune sensor, laboratory of genetics and physiology 2 (LGP2) RNA ligands can be generated by DNA viruses and retroviruses via genome transcription, or by synthesis of mRNA and replication intermediates by RNA-dependent RNA polymerases (RdRps) of RNA viruses (8) .


id: cord-328252-dk54w8z9
author: Kikkert, Marjolein
title: Innate Immune Evasion by Human Respiratory RNA Viruses
date: 2019-10-14
extension: .txt
mime: text/plain
words: 11567
sentence: 387
flesch: 34
cache: cache/cord-328252-dk54w8z9.txt
txt: txt/cord-328252-dk54w8z9.txt
summary:
  Although the exact mechanism of inhibition is still not clear for several of the viruses inhibited by Mx proteins, Mx GTPase family members bind to intracellular membranes, and in cytosolic +RNA virus infections Mx proteins could target the ROs As discussed in the beginning of this review, the type I IFN antiviral pathway is very relevant for RNA virus infections, and an essential adaptor that enables downstream signaling in this pathway is IPS-1 (also called MAVS).


id: cord-355839-o0m71kvw
author: Sedeyn, Koen
date: 2019-10-17
extension: .txt
mime: text/plain
words: 8217
sentence: 343
flesch: 41
cache: cache/cord-355839-o0m71kvw.txt
txt: txt/cord-355839-o0m71kvw.txt
title:
  Respiratory syncytial virus nonstructural proteins 1 and 2: Exceptional disrupters of innate immune responses

summary:
  RIG-I expression in A549 cells is strongly reduced in the presence of RSV NS1, either expressed separately or in the context of an RSV infection [51] . Another study concluded that RSV NS1 prevents GR nuclear translocation [88] .


id: cord-007382-5kb16qb7
author: Hartmann, G.
title: Nucleic Acid Immunity
date: 2016-12-15
extension: .txt
mime: text/plain
words: 16190
sentence: 498
flesch: 33
cache: cache/cord-007382-5kb16qb7.txt
txt: txt/cord-007382-5kb16qb7.txt
summary:
  The involvement of SAMHD1 in innate immunity was initially proposed based on its mouse ortholog Mg11 which is IFN-inducible in macrophages and dendritic cells (Li et al., 2000) , hence the alternative name dendritic cell-derived IFN-Î³-induced protein. TLR7 and TLR8 are preferentially activated by polyU or by G-and U-rich sequences (Diebold et al., 2004; Heil et al., 2004; Hornung et al., 2005; Judge et al., 2005) .


id: cord-321607-3r736dnk
author: Ezelle, Heather J.
title: The Roles of RNase-L in Antimicrobial Immunity and the Cytoskeleton-Associated Innate Response
date: 2016-01-08
extension: .txt
mime: text/plain
words: 11712
sentence: 424
flesch: 34
cache: cache/cord-321607-3r736dnk.txt
txt: txt/cord-321607-3r736dnk.txt
summary:
  Fractionation of the endonucleaseint system into two macromolecular components; role of a small molecule in nuclease activation Expression cloning of 2-5A-dependent RNaase: A uniquely regulated mediator of interferon action Germline mutations in the ribonuclease L gene in families showing linkage with HPC1 The role of 2 1 -5 1 oligoadenylate-activated ribonuclease L in apoptosis A study of the interferon antiviral mechanism: Apoptosis activation by the 2-5A system A dominant negative mutant of 2-5A-dependent RNase suppresses antiproliferative and antiviral effects of interferon Interferon action and apoptosis are defective in mice devoid of 2 1 ,5 1 -oligoadenylate-dependent RNase L Ribonuclease L proteolysis in peripheral blood mononuclear cells of chronic fatigue syndrome patients Characterization of a 2 1 ,5 1 -oligoadenylate (2-5A)-dependent 37-kDa RNase L: Azido photoaffinity labeling and 2-5A-dependent activation Biochemical evidence for a novel low molecular weight 2-5A-dependent RNase L in chronic fatigue syndrome Role of 2-5A-dependent RNase-L in senescence and longevity Defects in TLR3 expression and RNase L activation lead to decreased mnsod expression and insulin resistance in muscle cells of obese people RNase L controls terminal adipocyte differentiation, lipids storage and insulin sensitivity via CHOP10 mRNA regulation RNase L mediated protection from virus induced demyelination RNase-L deficiency exacerbates experimental colitis and colitis-associated cancer RNase L contributes to experimentally induced type 1 diabetes onset in mice RNase-L control of cellular mRNAs: Roles in biologic functions and mechanisms of substrate targeting An essential role for the antiviral endoribonuclease, RNase-L, in antibacterial immunity Small self-RNA generated by RNase L amplifies antiviral innate immunity RNase L interacts with filamin a to regulate actin dynamics and barrier function for viral entry RNase L induces autophagy via c-jun N-terminal kinase and double-stranded RNA-dependent protein kinase signaling pathways RNase L cleavage products promote switch from autophagy to apoptosis by caspase-mediated cleavage of beclin-1 Skin allograft rejection is suppressed in mice lacking the antiviral enzyme, 2 1 ,5 1 -oligoadenylate-dependent RNase L Lack of RNase L attenuates macrophage functions Interferons at age 50: Past, current and future impact on biomedicine Interferon-inducible antiviral effectors The human 2 1 ,5 1 -oligoadenylate synthetase family: Interferon-induced proteins with unique enzymatic properties The human 2 1 -5 1 oligoadenylate synthetase family: Unique bond formation Antiviral activity of human OASL protein is mediated by enhancing signaling of the RIG-I RNA sensor Activation of 2 1 -5 1 oligoadenylate synthetase by single-stranded and double-stranded RNA aptamers Selection and cloning of poly(rC)-binding protein 2 and raf kinase inhibitor protein RNA activators of 2 1 ,5 1 -oligoadenylate synthetase from prostate cancer cells Heterogeneous nuclear RNA from hairy cell leukemia patients activates 2 1 ,5 1 -oligoadenylate synthetase Ribosomal protein mRNAs are primary targets of regulation in RNase-L-induced senescence Germline mutation in RNase L predicts increased risk of head and neck, uterine cervix and breast cancer A bipartite model of 2-5A-dependent RNase L radiobinding and hplc analysis of 2-5A and related oligonucleotides from intact cells Identification of 2 1 -phosphodiesterase, which plays a role in the 2-5A system regulated by interferon Synthesis, characterization and properties of ppp(A2 1 p)nApCp and related high-specific-activity 32P-labelled derivatives of ppp(A2 1 p)nA The role of phosphodiesterase 12 (PDE12) as a negative regulator of the innate immune response and the discovery of antiviral inhibitors Structure of human RNase L reveals the basis for regulated RNA decay in the IFN response Innate immune messenger 2-5A tethers human RNase L into active high-order complexes Dimeric structure of pseudokinase RNase L bound to 2-5A reveals a basis for interferon-induced antiviral activity Interferon action: RNA cleavage pattern of a (2 1 -5 1 )oligoadenylate-dependent endonuclease Interferon action-Sequence specificity of the ppp(A2 1 p)nA-dependent ribonuclease RNase L mediates the antiviral effect of interferon through a selective reduction in viral RNA during encephalomyocarditis virus infection RNase L attenuates mitogen-stimulated gene expression via transcriptional and post-transcriptional mechanisms to limit the proliferative response A transcriptional signaling pathway in the IFN system mediated by 2 1 -5 1 -oligoadenylate activation of RNase L Mapping of the human RNase L promoter and expression in cancer and normal cells Overexpression of the transcription factor sp1 activates the OAS-RNase L-RIG-I pathway Regulation of human RNase-L by the mir-29 family reveals a novel oncogenic role in chronic myelogenous leukemia Post-transcriptional regulation of RNase-L expression is mediated by the 3 1 -untranslated region of its mRNA Posttranscriptional regulation of cancer traits by HuR Proteasome-mediated degradation of RNase L in response to phorbol-12-myristate-13-acetate (PMA) treatment of mouse l929 cells Decreased proteasomal activity causes age-related phenotypes and promotes the development of metabolic abnormalities Proteomics-based identification of novel factor inhibiting hypoxia-inducible factor (FIH) substrates indicates widespread asparaginyl hydroxylation of ankyrin repeat domain-containing proteins Cloning and characterization of a RNase L inhibitor. RNase L inhibitor is induced during human immunodeficiency virus type 1 infection and down regulates the 2-5A/RNase L pathway in human T cells RNase L inhibitor (RLI) antisense constructions block partially the down regulation of the 2-5A/RNase L pathway in encephalomyocarditisvirus-(EMCV)-infected cells A newly discovered function for RNase L in regulating translation termination 2 1 ,5 1 -oligoadenylate-dependent RNase L is a dimer of regulatory and catalytic subunits Eukaryotic release factors (ERFS) history RNase Lregulates the stability of mitochondrial DNA-encoded mRNAs in mouse embryo fibroblasts Regulation of mitochondrial mRNA stability by RNase L is translation-dependent and controls IFNα-induced apoptosis Ultrastructural localization of interferon-inducible double-stranded RNA-activated enzymes in human cells Human 2 1 -phosphodiesterase localizes to the mitochondrial matrix with a putative function in mitochondrial RNA turnover The mRNA-destabilizing protein tristetraprolin is suppressed in many cancers, altering tumorigenic phenotypes and patient prognosis TTP): Interactions with mRNA and proteins, and current thoughts on mechanisms of action Zinc-finger antiviral protein mediates retinoic acid inducible gene I-like receptor-independent antiviral response to murine leukemia virus mRNA degradation by the endoribonuclease Regnase-1/ZC3H12a/MCPIP-1 RNase L activates the NLRP3 inflammasome during viral infections Enteropathogenic escherichia coli inhibits type I interferon-and RNase L-mediated host defense to disrupt intestinal epithelial cell barrier function Viral encounters with 2 1 ,5 1 -oligoadenylate synthetase and RNase L during the interferon antiviral response Interferon action: Binding of viral RNA to the 40-kilodalton 2 1 -5 1 -oligoadenylate synthetase in interferon-treated hela cells infected with encephalomyocarditis virus Natural occurrence of 2-5A in interferon-treated emc virus-infected l cells A phylogenetically conserved RNA structure in the poliovirus open reading frame inhibits the antiviral endoribonuclease RNase L Evasion of antiviral innate immunity by theiler's virus l* protein through direct inhibition of RNase L A viral RNA competitively inhibits the antiviral endoribonuclease domain of RNase L A putative loop E motif and an H-H kissing loop interaction are conserved and functional features in a group C enterovirus RNA that inhibits ribonuclease L Activation and evasion of the antiviral 2 1 -5 1 oligoadenylate synthetase/ribonuclease L pathway by hepatitis c virus mRNA Hepatitis c virus RNA: Dinucleotide frequencies and cleavage by RNase L Clinical relevance of the 2 1 -5 1 -oligoadenylate synthetase/RNase L system for treatment response in chronic hepatitis c RNase L targets distinct sites in influenza a virus RNAs The primary function of RNA binding by the influenza A virus NS1 protein in infected cells: Inhibiting the 2 1 -5 1 oligo (A) synthetase/RNase L pathway Mechanisms of IFN resistance by influenza virus Diagnostic value of the determination of an interferon-induced enzyme activity: Decreased 2 1 ,5 1 -oligoadenylate dependent binding protein activity in aids patient lymphocytes Antagonism of the interferon-induced OAS-RNase L pathway by murine coronavirus ns2 protein is required for virus replication and liver pathology Inhibition of the OAS/RNase L pathway by viruses Caspase-dependent apoptosis by 2 1 ,5 1 -oligoadenylate activation of RNase L is enhanced by IFN-β Viruses and the autophagy pathway RNase L triggers autophagy in response to viral infections The crosstalk between autophagy and apoptosis: Where does this lead Regulation of antiviral T cell responses by type I interferons Transcription factor STAT3 and type I interferons are corepressive insulators for differentiation of follicular helper and T helper


id: cord-319729-6lzjhn8j
author: Tian, Bin
date: 2018-01-19
extension: .txt
mime: text/plain
words: 7820
sentence: 293
flesch: 42
cache: cache/cord-319729-6lzjhn8j.txt
txt: txt/cord-319729-6lzjhn8j.txt
title:
  Lab-Attenuated Rabies Virus Causes Abortive Infection and Induces Cytokine Expression in Astrocytes by Activating Mitochondrial Antiviral-Signaling Protein Signaling Pathway

summary:
  Notably, B2c titers were significantly increased in MAVS−/− astrocytes compared with wt astrocytes (Figures 5A,B) . Moreover, the cell numbers of immunofluorescence plaques in MAVS−/− astrocytes caused by B2c infection were significantly more than those in wt astrocytes (Figures 5E,F) .


id: cord-351520-c5fi2uoh
author: Zhong, Bo
title: Regulation of virus-triggered type I interferon signaling by cellular and viral proteins
date: 2010-02-01
extension: .txt
mime: text/plain
words: 10652
sentence: 327
flesch: 30
cache: cache/cord-351520-c5fi2uoh.txt
txt: txt/cord-351520-c5fi2uoh.txt
summary:
  However, over-produced type I IFNs cause excessive and harmful immune effects to the host (Theofilopoulos et al., 2005) . However, the overproduction of type I IFNs can cause unwanted or excessive immune responses that may lead to allergy, necrosis, autoimmune diseases and other harmful effects (Theofilopoulos et al., 2005) .


id: cord-327000-oyg3oyx1
author: Li, Shasha
title: Porcine Epidemic Diarrhea Virus and the Host Innate Immune Response
date: 2020-05-11
extension: .txt
mime: text/plain
words: 11139
sentence: 482
flesch: 41
cache: cache/cord-327000-oyg3oyx1.txt
txt: txt/cord-327000-oyg3oyx1.txt
summary:
  These cap structures enhance the initiation of translation of viral proteins, protect viral mRNAs against cellular 5 -3 -exoribonuclease and limit the recognition of viral RNA by host innate system [120, 121] . Although several studies have been performed to understand the pathogenicity of PEDV, there remains limited information about the interaction between viral proteins and host cell factors during viral infection.


id: cord-312001-8p7scli8
author: Majzoub, Karim
title: The Innate Antiviral Response in Animals: An Evolutionary Perspective from Flagellates to Humans
date: 2019-08-16
extension: .txt
mime: text/plain
words: 10087
sentence: 365
flesch: 37
cache: cache/cord-312001-8p7scli8.txt
txt: txt/cord-312001-8p7scli8.txt
summary:
  [corrected] gene induction by the interferon regulatory factor family of transcription factors Cutting edge: TNFR-associated factor (TRAF) 6 is essential for MyD88-dependent pathway but not toll/IL-1 receptor domain-containing adaptor-inducing IFN-beta (TRIF)-dependent pathway in TLR signaling Interferon-alpha induction through Toll-like receptors involves a direct interaction of IRF7 with MyD88 and TRAF6 Helical assembly in the MyD88-IRAK4-IRAK2 complex in TLR/IL-1R signalling Protein kinase IKKbeta-catalyzed phosphorylation of IRF5 at Ser462 induces its dimerization and nuclear translocation in myeloid cells An oligomeric signaling platform formed by the Toll-like receptor signal transducers MyD88 and IRAK-4 IKKbeta is an IRF5 kinase that instigates inflammation Interleukin-1 receptor-associated kinase-1 plays an essential role for Toll-like receptor (TLR)7-and TLR9-mediated interferon-{alpha} induction Structural basis of RNA recognition and activation by innate immune receptor RIG-I Structural basis for the activation of innate immune pattern-recognition receptor RIG-I by viral RNA MDA5 assembles into a polar helical filament on dsRNA Cooperative assembly and dynamic disassembly of MDA5 filaments for viral dsRNA recognition TRIM25 RING-finger E3 ubiquitin ligase is essential for RIG-I-mediated antiviral activity Ubiquitin-induced oligomerization of the RNA sensors RIG-I and MDA5 activates antiviral innate immune response Riplet/RNF135, a RING finger protein, ubiquitinates RIG-I to promote interferon-beta induction during the early phase of viral infection The ubiquitin ligase Riplet is essential for RIG-I-dependent innate immune responses to RNA virus infection IPS-1, an adaptor triggering RIG-I-and Mda5-mediated type I interferon induction Cardif is an adaptor protein in the RIG-I antiviral pathway and is targeted by hepatitis C virus Identification and characterization of MAVS, a mitochondrial antiviral signaling protein that activates NF-kappaB and IRF 3 Essential role of IPS-1 in innate immune responses against RNA viruses An autoinhibitory mechanism modulates MAVS activity in antiviral innate immune response MAVS forms functional prion-like aggregates to activate and propagate antiviral innate immune response Structural basis for the prion-like MAVS filaments in antiviral innate immunity MAVS recruits multiple ubiquitin E3 ligases to activate antiviral signaling cascades Activation of IKK by TNFalpha requires site-specific ubiquitination of RIP1 and polyubiquitin binding by NEMO Sensing of Lys 63-linked polyubiquitination by NEMO is a key event in NF-kappaB activation Key role of Ubc5 and lysine-63 polyubiquitination in viral activation of IRF3 STING is an endoplasmic reticulum adaptor that facilitates innate immune signalling The adaptor protein MITA links virus-sensing receptors to IRF3 transcription factor activation STING regulates intracellular DNA-mediated, type I interferon-dependent innate immunity STING is a direct innate immune sensor of cyclic di-GMP Coordinated regulation of accessory genetic elements produces cyclic di-nucleotides for V. cholerae virulence MPYS is required for IFN response factor 3 activation and type A conserved Toll-like receptor-to-NF-kappaB signaling pathway in the endangered coral Orbicella faveolata Genomic insights into the immune system of the sea urchin Massively parallel RNA sequencing identifies a complex immune gene repertoire in the lophotrochozoan Mytilus edulis Massive expansion and functional divergence of innate immune genes in a protostome Teleost TLR22 recognizes RNA duplex to induce IFN and protect cells from birnaviruses Adaptive evolution of virus-sensing toll-like receptor 8 in bats The evolution of bat nucleic acid-sensing Toll-like receptors Immune system modulation and viral persistence in bats: Understanding viral spillover Origin and evolution of the RIG-I like RNA helicase gene family Characterization of the mollusc RIG-I/MAVS pathway reveals an archaic antiviral signalling framework in invertebrates Retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) in fish: Current knowledge and future perspectives Chicken cells sense influenza A virus infection through MDA5 and CARDIF signaling involving LGP2 Association of RIG-I with innate immunity of ducks to influenza Genome of the Chinese tree shrew Loss of RIG-I leads to a functional replacement with MDA5 in the Chinese tree shrew The kinase IKKbeta regulates a STING-and NF-kappaB-dependent antiviral response pathway in Drosophila The Jak-STAT signaling pathway is required but not sufficient for the antiviral response of drosophila The RNA silencing endonuclease Argonaute 2 mediates specific antiviral immunity in Drosophila melanogaster Essential function in vivo for Dicer-2 in host defense against RNA viruses in drosophila Sensing viral RNAs by Dicer/RIG-I like ATPases across species The DExD/H-box helicase Dicer-2 mediates the induction of antiviral activity in drosophila Secreted Vago restricts West Nile virus infection in Culex mosquito cells by activating the Jak-STAT pathway Dicer-2-dependent activation of Culex Vago occurs via the TRAF-Rel2 signaling pathway Nucleic acid sensing in invertebrate antiviral immunity The RIG-I ATPase core has evolved a functional requirement for allosteric stabilization by the Pincer domain The selective footprints of viral pressures at the human RIG-I-like receptor family Evolution and functional impact of rare coding variation from deep sequencing of human exomes Cyclic di-nucleotide signaling enters the eukaryote domain Evolutionary origins of cGAS-STING signaling Toll signaling: The TIReless quest for specificity Analysis of Drosophila STING reveals an evolutionarily conserved antimicrobial function Modular architecture of the STING C-terminal tail allows interferon and NF-kappaB signaling adaptation Dampened STING-dependent interferon activation in bats Structure of human cGAS reveals a conserved family of second-messenger enzymes in innate immunity ] is the metazoan second messenger produced by DNA-activated cyclic GMP-AMP synthase Structural mechanism of cytosolic DNA sensing by cGAS Overlapping patterns of rapid evolution in the nucleic acid sensors cGAS


id: cord-299754-tgexahwd
author: van Tol, Sarah
title: The TRIMendous Role of TRIMs in Virus–Host Interactions
date: 2017-08-22
extension: .txt
mime: text/plain
words: 18335
sentence: 832
flesch: 37
cache: cache/cord-299754-tgexahwd.txt
txt: txt/cord-299754-tgexahwd.txt
summary:
  Additionally, several TRIMs directly restrict viral replication either through proteasome-mediated degradation of viral proteins or by interfering with different steps of the viral replication cycle. In addition to conferring an antiviral state indirectly by regulating cytokine production downstream of PRR signaling, TRIMs are capable of restricting the effectiveness of pathogens through direct interactions with viral proteins crucial to their entry, dissemination, or life cycle [6] .


id: cord-307598-p54p7enk
author: Schlee, Martin
title: Master sensors of pathogenic RNA – RIG-I like receptors
date: 2013-07-01
extension: .txt
mime: text/plain
words: 12877
sentence: 388
flesch: 39
cache: cache/cord-307598-p54p7enk.txt
txt: txt/cord-307598-p54p7enk.txt
summary:
  Hornung et al. , 2002 Judge et al. 2005; Krieg et al. 1995) , reviewed in (Barchet et al. 2008; Schlee et al. 2007 Schlee et al. , 2006 . In contrast to TLR7, 8 and 9, TLR3 is expressed in more cell types (e.g. endothelial cells, fibroblasts, astrocytes) (Barchet et al. 2008; Schlee et al. 2007) and was found to detect long double-stranded RNA (Alexopoulou et al. 2001) .


id: cord-341324-f9g9gitn
author: Rojas, José M.
title: Viral pathogen-induced mechanisms to antagonize mammalian interferon (IFN) signaling pathway
date: 2020-10-21
extension: .txt
mime: text/plain
words: 10861
sentence: 420
flesch: 35
cache: cache/cord-341324-f9g9gitn.txt
txt: txt/cord-341324-f9g9gitn.txt
summary:
  The measles virus V protein binding site to STAT2 overlaps with that of IRF9 STAT2 is a primary target for measles virus V protein-mediated alpha/ beta interferon signaling inhibition The interferon signaling antagonist function of yellow fever virus NS5 protein is activated by type I interferon Dengue virus co-opts UBR4 to degrade STAT2 and antagonize type I interferon signaling Nonstructural protein 11 of porcine reproductive and respiratory syndrome virus induces STAT2 degradation to inhibit interferon signaling The V protein of simian virus 5 inhibits interferon signalling by targeting STAT1 for proteasome-mediated degradation Association of mumps virus V protein with RACK1 results in dissociation of STAT-1 from the alpha interferon receptor complex The human papillomavirus type 16 E7 protein binds human interferon regulatory factor-9 via a novel PEST domain required for transformation Expression of hepatitis C virus proteins interferes with the antiviral action of interferon independently of PKR-mediated control of protein synthesis Herpes simplex virus 1 gene products occlude the interferon signaling pathway at multiple sites Human cytomegalovirus inhibits IFN-alpha-stimulated antiviral and immunoregulatory responses by blocking multiple levels of IFN-alpha signal transduction The polyoma virus T antigen interferes with interferon-inducible gene expression Foot-and-mouth disease virus leader protease cleaves G3BP1 and G3BP2 and inhibits stress granule formation Stress granule formation induced by measles virus is protein kinase PKR dependent and impaired by RNA adenosine deaminase ADAR1 G3BP1, G3BP2 and CAPRIN1 are required for translation of interferon stimulated mRNAs and are targeted by a dengue virus non-coding RNA Inhibitory activity for the interferoninduced protein kinase is associated with the reovirus serotype 1 sigma 3 protein Site-directed mutagenic analysis of reovirus sigma 3 protein binding to dsRNA Rift Valley fever virus NSs protein functions and the similarity to other bunyavirus NSs proteins RNA-specific adenosine deaminase ADAR1 suppresses measles virus-induced apoptosis and activation of protein kinase PKR Double-stranded RNA deaminase ADAR1 increases host susceptibility to virus infection ADAR1 interacts with PKR during human immunodeficiency virus infection of lymphocytes and contributes to viral replication Silencing the alarms: Innate immune antagonism by rotavirus NSP1 and VP3 Homologous 2',5'-phosphodiesterases from disparate RNA viruses antagonize antiviral innate immunity Rotavirus open cores catalyze 5′-capping and methylation of exogenous RNA: evidence that VP3 is a methyltransferase 2′-O methylation of the viral mRNA cap evades host restriction by IFIT family members Attenuation and restoration of severe acute respiratory syndrome coronavirus mutant lacking 2'-o-methyltransferase activity Biochemical and structural insights into the mechanisms of SARS coronavirus RNA ribose 2'-O-methylation by nsp16/nsp10 protein complex Middle East Respiratory Syndrome Coronavirus Nonstructural Protein 16 Is Necessary for Interferon Resistance and Viral Pathogenesis The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus Interferon induction of IFITM proteins promotes infection by human coronavirus OC43 HIV-1 mutates to evade IFITM1 restriction In vivo evasion of MxA by avian influenza viruses requires human signature in the viral nucleoprotein Irreversible inactivation of ISG15 by a viral leader protease enables alternative infection detection strategies Consecutive inhibition of ISG15 expression and ISGylation by cytomegalovirus regulators The abundant tegument protein pUL25 of human cytomegalovirus prevents proteasomal degradation of pUL26 and supports its suppression of ISGylation Transmembrane protein pUL50 of human cytomegalovirus inhibits ISGylation by downregulating UBE1L ISG15, a ubiquitin-like interferon-stimulated gene, promotes hepatitis C virus production in vitro: implications for chronic infection and response to treatment For instance, Ebola virus VP35 protein, Middle East respiratory syndrome Viral interference with accessory cellular components involved in PRR activation.


id: cord-313138-y485ev30
author: Magor, Katharine E.
title: Defense genes missing from the flight division
date: 2013-04-24
extension: .txt
mime: text/plain
words: 10647
sentence: 370
flesch: 40
cache: cache/cord-313138-y485ev30.txt
txt: txt/cord-313138-y485ev30.txt
summary:
  In comparison with mammals, birds have partial repertoires of pattern recognition receptors including TLR receptors (Boyd et al., 2007; Brownlie and Allan, 2011; Cormican et al., 2009 ) and RIG-like receptors (Barber et al., 2010; Karpala et al., 2012) . We demonstrated that ducks have a functional RIG-I (Barber et al., 2010) .


id: cord-346916-jj4l9ydl
author: Girardi, Erika
title: Roadblocks and fast tracks: How RNA binding proteins affect the viral RNA journey in the cell
date: 2020-08-23
extension: .txt
mime: text/plain
words: 13150
sentence: 502
flesch: 37
cache: cache/cord-346916-jj4l9ydl.txt
txt: txt/cord-346916-jj4l9ydl.txt
summary:
  genomic RNA Protein kinase r degradation is essential for rift valley fever virus infection and is regulated by SKP1-CUL1-F-box (SCF)FBXW11-NSs E3 ligase Viral encounters with 2',5'-oligoadenylate synthetase and RNase L during the interferon antiviral response New insights into the role of RNase L in innate immunity Molecular mechanisms for the adaptive switching between the OAS/RNase l and OASL/RIG-I pathways in birds and mammals Homologous 2',5'-phosphodiesterases from disparate RNA viruses antagonize antiviral innate immunity Attacked from all sides: RNA decay in antiviral defense The host nonsense-mediated mRNA decay pathway restricts Mammalian RNA virus replication Competing and noncompeting activities of miR-122 and the 5' exonuclease Xrn1 in regulation of hepatitis C virus replication Stabilization of hepatitis C virus RNA by an Ago2-miR-122 complex Zika virus produces noncoding RNAs using a multipseudoknot structure that confounds a cellular exonuclease The structural basis of pathogenic subgenomic flavivirus RNA (sfRNA) production RNA structures that resist degradation by Xrn1 produce a pathogenic Dengue virus RNA Full genome sequence and sfRNA interferon antagonist activity of zika virus from Recife, Brazil RNA structures required for production of subgenomic flavivirus RNA Dengue subgenomic RNA binds TRIM25 to inhibit interferon expression for epidemiological fitness A noncoding RNA produced by arthropod-borne flaviviruses inhibits the cellular exoribonuclease XRN1 and alters host mRNA stability A highly structured, nuclease-resistant, noncoding RNA produced by flaviviruses is required for pathogenicity An RNA pseudoknot is required for production of yellow fever virus subgenomic RNA by the host nuclease XRN1 Zika virus noncoding RNA suppresses apoptosis and is required for virus transmission by mosquitoes Noncoding flavivirus RNA displays RNA interference suppressor activity in insect and mammalian cells Viruses: overturning RNA turnover Stem-loop recognition by DDX17 facilitates miRNA processing and antiviral defense The zinc-finger antiviral protein recruits the RNA processing exosome to degrade the target mRNA CG dinucleotide suppression enables antiviral defence targeting non-self RNA KHNYN is essential for the zinc finger antiviral protein (ZAP) to restrict HIV-1 containing clustered CpG dinucleotides ZAP's stress granule localization is correlated with its antiviral activity and induced by virus replication RNA-binding activity of TRIM25 is mediated by its PRY/ SPRY domain and is required for ubiquitination TRIM25 enhances the antiviral action of zinc-finger antiviral protein (ZAP) MCPIP1 ribonuclease exhibits broad-spectrum antiviral effects through viral RNA binding and degradation MCPIP1 suppresses hepatitis C virus replication and negatively regulates virus-induced proinflammatory cytokine responses RNase L releases a small RNA from HCV RNA that refolds into a potent PAMP Activation and evasion of the antiviral 2'-5' oligoadenylate synthetase/ribonuclease L pathway by hepatitis C virus mRNA Essential function in vivo for Dicer-2 in host defense against RNA viruses in drosophila Cross-species comparative analysis of Dicer proteins during Sindbis virus infection RNA interference functions as an antiviral immunity mechanism in mammals Antiviral RNA interference in mammalian cells Flavivirus induces and antagonizes antiviral RNA interference in both mammals and mosquitoes The evolution of antiviral defense systems Human virus-derived small RNAs can confer antiviral immunity in mammals Induction and suppression of antiviral RNA interference by influenza A virus in mammalian cells Viruses and RNA interference: issues and controversies No evidence for viral small RNA production and antiviral function of Argonaute 2 in human cells RNase III nucleases from diverse kingdoms serve as antiviral effectors Making the mark: the role of adenosine modifications in the life cycle of RNA viruses Innate immune restriction and antagonism of viral RNA lacking 2‫-׳‬O methylation RNA modifications: what have we learned and where are we headed? Host factors in positive-strand RNA virus genome replication Human host factors required for influenza virus replication Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens Diverse roles of host RNA binding proteins in RNA virus replication CRISPR-Cas immunity in prokaryotes Antiviral immunity directed by small RNAs Combating emerging viral threats The global distribution and burden of dengue Virus: new clinical syndromes and its emergence in the western hemisphere Emergence of a novel human coronavirus threatening human health Sensing of RNA viruses: a review of innate immune receptors involved in recognizing RNA virus invasion The innate antiviral response in animals: an evolutionary perspective from flagellates to humans Discriminating self from non-self in nucleic acid sensing Toll-like receptor control of the adaptive immune responses Toll-like receptors in antiviral innate immunity Innate antiviral responses by means of TLR7-mediated recognition of single-stranded RNA Species-specific recognition of single-stranded RNA via toll-like receptor 7 and 8 Toll-like receptor 3 is an essential component of the innate stress response in virus-induced cardiac injury Human TLR3 recognizes dengue virus and modulates viral replication in vitro Zika virus depletes neural progenitors in human cerebral organoids through activation of the innate immune receptor TLR3 Toll-like receptor 3 in viral pathogenesis: friend or foe? RIG-I-like receptors: their regulation and roles in RNA sensing 5'-Triphosphate RNA is the ligand for RIG-I RIG-I-mediated antiviral responses to single-stranded RNA bearing 5'-phosphates Recognition of 5' triphosphate by RIG-I helicase requires short blunt double-stranded RNA as contained in panhandle of negative-strand virus 5'-triphosphate RNA requires base-paired structures to activate antiviral signaling via RIG-I Processing of genome 5' termini as a strategy of negative-strand RNA viruses to avoid RIG-I-dependent interferon induction Differential roles of MDA5 and RIG-I helicases in the recognition of RNA viruses Cell type-specific involvement of RIG-I in antiviral response RIG-I recognizes the 5' region of dengue and Zika virus genomes Balancing act: MDA5 in Antiviral Immunity and Autoinflammation MDA5 assembles into a polar helical filament on dsRNA Enterovirus 2Apro targets MDA5 and MAVS in infected cells MDA5 detects the double-stranded RNA replicative form in picornavirus-infected cells How flaviviruses activate and suppress the interferon response MDA5 is critical to host defense during infection with murine coronavirus LGP2 is a positive regulator of RIG-I-and MDA5-mediated antiviral responses The RNA helicase Lgp2 inhibits TLR-independent sensing of viral replication by retinoic acid-inducible gene-I Loss of DExD/H box RNA helicase LGP2 manifests disparate antiviral responses The RIG-I-like receptor LGP2 inhibits Dicer-dependent processing of long double-stranded RNA and blocks RNA interference in mammalian cells DEAD-box helicases: sensors, regulators, and effectors for antiviral defense Type 1 interferons and the virus-host relationship: a lesson in détente Interferon-inducible antiviral effectors Involvement of the interferon-regulated antiviral proteins PKR and RNase L in reovirus-induced shutoff of cellular translation Doublestranded RNA is produced by positive-strand RNA viruses and DNA viruses but not in detectable amounts by negative-strand RNA viruses RNA dimerization promotes PKR dimerization and activation Viral double-stranded RNAs from vaccinia virus early or intermediate gene transcripts possess PKR activating function, resulting in NF-kappaB activation, when the K1 protein is absent or mutated Regulation of innate immunity through RNA structure and the protein kinase PKR Translational control in virus-infected cells A cap-to-Tail guide to mRNA translation strategies in virus-infected cells Viral noncoding RNAs: more surprises Inhibition of the protein kinase PKR by the internal ribosome entry site of hepatitis C virus


id: cord-303189-ktl4jw8v
author: Coccia, Eliana M.
title: Early IFN type I response: Learning from microbial evasion strategies
date: 2015-03-31
extension: .txt
mime: text/plain
words: 15234
sentence: 527
flesch: 32
cache: cache/cord-303189-ktl4jw8v.txt
txt: txt/cord-303189-ktl4jw8v.txt
summary:
  Strategies, identified so far, include viral proteins that bind ISG15 or that remove ISG15 from target proteins (reviewed in [237] ). Similarly, some identified targets of viral proteins in PRR signaling pathways might be turned out to be new targets for treating a range of diseases.


id: cord-307914-lgprrwee
author: Bartok, Eva
title: Immune Sensing Mechanisms that Discriminate Self from Altered Self and Foreign Nucleic Acids
date: 2020-07-14
extension: .txt
mime: text/plain
words: 17786
sentence: 526
flesch: 34
cache: cache/cord-307914-lgprrwee.txt
txt: txt/cord-307914-lgprrwee.txt
summary:
  Unless modified nucleotides or specific sequences precluding the formation of the complementary strand are used, IVT can potentially generate RIG-I ligands from a variety of templates (Hornung et al., 2006; Kim et al., 2004; Schlee et al., 2009; Both sensors contribute to the immune response to dsRNA viruses, such as reoviridae (Loo et al., 2008) , but RIG-I-mediated sensing dominates the response to many (-) ssRNA viruses such as influenza, which form shorter dsRNA panhandles in their genomes (Rehwinkel et al., 2010; Schlee et al., 2009) , whereas MDA5 has a greater role in the host defense against (+) ssRNA viruses, many of which are known to generate large amounts of dsRNA during replication .


id: cord-350836-1enteev7
author: Brisse, Morgan
title: Comparative Structure and Function Analysis of the RIG-I-Like Receptors: RIG-I and MDA5
date: 2019-07-17
extension: .txt
mime: text/plain
words: 16397
sentence: 379
flesch: 23
cache: cache/cord-350836-1enteev7.txt
txt: txt/cord-350836-1enteev7.txt
summary:
  Front Immunol Molecular mechanisms of Dicer: endonuclease and enzymatic activity The RIG-I-like receptor LGP2 inhibits Dicer-dependent processing of long double-stranded RNA and blocks RNA interference in mammalian cells Virus sensor RIG-I represses RNA interference by interacting with TRBP through LGP2 in mammalian cells LGP2: positive about viral sensing MDA5 and LGP2: accomplices and antagonists of antiviral signal transduction Negative regulators of the RIG-I-like receptor signaling pathway Tissue-based map of the human proteome Structural basis for m7G recognition and 2'-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I Structural basis for dsRNA recognition, filament formation, and antiviral signal activation by MDA5 Molecular imprinting as a signal-activation mechanism of the viral RNA sensor RIG-I Parts, assembly and operation of the RIG-I family of motors The RNA helicase RIG-I has an essential function in doublestranded RNA-induced innate antiviral responses The C-terminal regulatory domain is the RNA 5'-triphosphate sensor of RIG-I 5 ′ -Triphosphate RNA is the ligand for RIG-I RIG-I-mediated antiviral responses to single-stranded RNA bearing 5'-Phosphates Nonself RNA-sensing mechanism of RIG-I helicase and activation of antiviral immune responses Cytosolic viral sensor RIG-I is a 5'-Triphosphate-dependent translocase on doublestranded RNA The structural basis of 5' triphosphate double-stranded RNA recognition by RIG-I C-terminal domain RIG-I detects viral genomic RNA during negative-strand RNA virus infection Structural and functional insights into 5'-ppp RNA pattern recognition by the innate immune receptor RIG-I The thermodynamic basis for viral RNA detection by the RIG-I innate immune sensor RIG-I ATPase activity and discrimination of self-RNA versus non-self-RNA Length-dependent recognition of doublestranded ribonucleic acids by retinoic acid -inducible gene-I and melanoma differentiation -associated gene 5 Activation of MDA5 requires higher-order RNA structures generated during virus infection MDA5 detects the double-stranded RNA replicative form in picornavirusinfected cells Visualisation of direct interaction of MDA5 and the dsRNA replicative intermediate form of positive strand RNA viruses A structure-based model of RIG-I activation Toward a crystal-clear view of the viral RNA sensing and response by RIG-I-like receptors Pattern recognition and signaling mechanisms of RIG-I and MDA5 Antiviral RNA recognition and assembly by RLR family innate immune sensors Post-translational control of intracellular pathogen sensing pathways Essential role of the N-terminal domain in the regulation of RIG-I ATPase activity Structural basis for the activation of innate immune pattern-recognition receptor RIG-I by viral RNA Structural and biochemical studies of RIG-I antiviral signaling Negative role of RIG-I serine 8 phosphorylation in the regulation of interferon-beta production Conventional protein kinase C-α (PKC-α) and PKC-β negatively regulate RIG-I antiviral signal transduction Phosphorylation of RIG-I by casein kinase II inhibits its antiviral response RIOK3-mediated phosphorylation of MDA5 interferes with its assembly and attenuates the innate immune response Dephosphorylation of the RNA sensors RIG-I and MDA5 by the phosphatase PP1 is essential for innate immune signaling Antagonism of the phosphatase PP1 by the measles virus V protein is required for innate immune escape of MDA5 HDAC6 regulates cellular viral RNA sensing by deacetylation of RIG-I The mechanism of ATP-dependent RNA unwinding by DEAD box proteins Mechanisms of RIG-I-like receptor activation and manipulation by viral pathogens The catcher in the RIG-I Viral RNA detection by RIG-I-like receptors MDA5 cooperatively forms dimers and ATP-sensitive filaments upon binding double-stranded RNA Riplet/RNF135, a RING finger protein, ubiquitinates RIG-I to promote interferon-beta induction during the early phase of viral infection REUL is a novel E3 ubiquitin ligase and stimulator of retinoic-acid-inducible gene-I A distinct role of Riplet-mediated K63-Linked polyubiquitination of the RIG-I repressor domain in human antiviral innate immune responses Ubiquitindependent and -independent roles of E3 ligase RIPLET in innate immunity TRIM25 RINGfinger ) RIG-I uses an ATPase-powered translocation-throttling mechanism for kinetic proofreading of RNAs and oligomerization Filament assemblies in foreign nucleic acid sensors IPS-1, an adaptor triggering RIG-I-and Mda5-mediated type I interferon induction VISA is an adapter protein required for virus-triggered IFN-β signaling Identification and characterization of MAVS, a mitochondrial antiviral signaling protein that activates NF-κB and IRF3 A common polymorphism in the caspase recruitment domain of RIG-I modifies the innate immune response of human dendritic cells Defective interfering particles with covalently linked [+/-]RNA induce interferon Structure and dynamics of the second CARD of human RIG-I provide mechanistic insights into regulation of RIG-I activation Pattern recognition receptors and inflammation Mitochondria in innate immunity Viral targeting of DEAD box protein 3 reveals its role in TBK1/IKKepsilon-mediated IRF activation Blockade of interferon beta, but not interferon alpha, signaling controls persistent viral infection The effects of dendritic cell hypersensitivity on persistent viral infection A role for neutrophils in viral respiratory disease.


id: cord-131093-osukknqr
author: Suzen, Neslihan
title: Informational Space of Meaning for Scientific Texts
date: 2020-04-28
extension: .txt
mime: text/plain
words: 30701
sentence: 809
flesch: 57
cache: cache/cord-131093-osukknqr.txt
txt: txt/cord-131093-osukknqr.txt
summary:
  numer 3.7 × 10 −2 54 age 1 × 10 −2 5 turbul 3.7 × 10 −2 55 magnetohydrodynam 1 × 10 −2 6 veloc 3.6 × 10 −2 56 steadi 9.7 × 10 −3 7 reynold 2.8 × 10 −2 57 cyclotron 9.6 × 10 −3 8 equat 2.8 × 10 −2 58 motion 9.6 × 10 −3 9 particl 2.7 × 10 −2 59 energi 9.4 × 10 −3 10 wave 2.6 × 10 −2 60 analyt 9.2 × 10 −3 11 tokamak 2.6 × 10 −2 61 navier 9.2 × 10 −3 12 instabl 2.5 × 10 −2 62 forc 9.2 × 10 −3 13 simul 2.3 × 10 −2 63 transit 9 × 10 −3 14 field 2.1 × 10 −2 64 divertor 9 × 10 −3 15 regim 2 × 10 −2 65 convect 8.9 × 10 −3 16 vortic 2 × 10 −2 66 propag 8.9 × 10 −3 17 discharg 2 × 10 −2 67 activ 8.7 × 10 −3 18 patient 1. collis 4 × 10 −2 59 spin 1 × 10 −2 10 gev 3.9 × 10 −2 scalar 7.3 × 10 −2 51 collis 1.9 × 10 −2 2 quark 6.4 × 10 −2 52 conclus 1.9 × 10 −2 3 higg 5.9 × 10 −2 53 increas 1.9 × 10 −2 4 gaug 5.9 × 10 −2 54 string 1.9 × 10 −2 5 lhc 5.9 × 10 −2 55 black 1.9 × 10 −2 6 cosmolog 5.3 × 10 −2 56 proton 1.8 × 10 −2 7 gev 5.2 × 10 −2 57 nucleon 1.8 × 10 −2 8 boson 5.2 × 10 −2 induc 3.7 × 10 −2 53 pathway 1.1 × 10 −2 4 rat 3.6 × 10 −2 54 studi 1 × 10 −2 5 express 3 × 10 −2 55 base 1 × 10 −2 6 increas 3 × 10 −2 56 inhibitor 1 × 10 −2 7 paper 2.7 × 10 −2 57 signal 1 × 10 −2 8 receptor 2.5 × 10 −2 58 kinas 1 × 10 −2 9 regul 2.4 × 10 −2 59 glucos 9.9 × 10 −3 10 respons 2.4 × 10 −2 60 propos 9.7 × 10 −3 11 physiolog 2.4 × 10 −2 61 mechan 9.5 × 10 −3 12 protein 2.4 × 10 −2 articl 3.4 × 10 −2 56 temperatur 1 × 10 −2 7 social 3.4 × 10 −2 57 trade 1 × 10 −2 8 polit 3.3 × 10 −2 58 labour 9.9 × 10 −3 9 urban 3.1 × 10 −2 59 hous 9.8 × 10 −3 10 economi 2.1 × 10 −2 72 pollin 1 × 10 −2 23 patient 2 × 10 −2 73 auxin 1 × 10 −2 24 breed 1.9 × 10 −2 74 model 1 × 10 −2 25 isol 1.9 × 10 −2 75 biomass 9.9 × 10 −3 −3 99 provid 6 × 10 −3 50 queri 9 × 10 −3 100 featur 5.9 × 10 −3 propos 6.7 × 10 −2 52 surfac 9.7 × 10 −3 3 algorithm 5.7 × 10 −2 53 diseas 9.6 × 10 −3 4 user 3.4 × 10 −2 54 introduc 9.6 × 10 −3 5 comput 3.3 × 10 −2 55 queri 9.5 × 10 −3 6 problem 3 × 10 −2 56 indic 9.5 × 10 −3 7 conclus 2.7 × 10 −2 57 web 9.3 × 10 −3 8 network 2.5 × 10 −2 58 materi 9.3 × 10 −3 9 studi 2.5 × 10 −2 59 solv 9 × 10 −3 10 base 2.2 × 10 −2 60 effici 8.9 × 10 −3 11 patient 1.9 × 10 −2 61 gene 8.9 × 10 −3 12 secur 1. 1 × 10 −2 95 exist 6.9 × 10 −3 46 node 1 × 10 −2 96 mass 6.7 × 10 −3 47 automat 1 × 10 −2 97 platform 6.7 × 10 −3 48 framework 9.9 × 10 −3 98 messag 6.7 × 10 −3 49 speci 9.9 × 10 −3 99 prepar 6.7 × 10


id: cord-343963-99rd3o79
author: Wong, Mun-Teng
date: 2014-12-29
extension: .txt
mime: text/plain
words: 17306
sentence: 707
flesch: 34
cache: cache/cord-343963-99rd3o79.txt
txt: txt/cord-343963-99rd3o79.txt
title:
  Emerging roles of interferon-stimulated genes in the innate immune response to hepatitis C virus infection

summary:
  RIG-I-mediated type I interferon-dependent innate immunity Phosphorylation of hepatitis C virus-encoded nonstructural protein NS5A Phosphorylation of the hepatitis C virus NS5A protein in vitro and in vivo: properties of the NS5A-associated kinase Phosphorylation of hepatitis C virus NS5A nonstructural protein: a new paradigm for phosphorylation-dependent viral RNA replication? Reduction of hepatitis C virus NS5A hyperphosphorylation by selective inhibition of cellular kinases activates viral RNA replication in cell culture Hepatitis C virus NS5A: tales of a promiscuous protein Hepatitis C virus nonstructural protein 5A modulates the Toll-like receptor-MyD88-dependent signaling pathway in macrophage cell lines Evidence that hepatitis C virus resistance to interferon is mediated through repression of the PKR protein kinase by the nonstructural 5A protein How hepatitis C virus counteracts the interferon response: the jury is still out on NS5A Control of PKR protein kinase by hepatitis C virus nonstructural 5A protein: molecular mechanisms of kinase regulation Hepatitis C virus nonstructural 5A protein induces interleukin-8, leading to partial inhibition of the interferoninduced antiviral response Relationships between hepatitis C virus replication and CXCL-8 production in vitro Hepatitis C virus NS5A protein interacts with 29,59-oligoadenylate synthetase and inhibits antiviral activity of IFN in an IFN sensitivity-determining region-independent manner Activation and evasion of the antiviral 29-59 oligoadenylate synthetase/ribonuclease L pathway by hepatitis C virus mRNA Hepatitis C virus NS5A protein protects against TNF-alpha mediated apoptotic cell death Inhibition of intrahepatic gamma interferon production by hepatitis C virus nonstructural protein 5A in transgenic mice Hepatitis C virus nonstructural protein 5A inhibits tumor necrosis factor-a-mediated apoptosis in Huh7 cells Activation of endoplasmic reticulum stress response by hepatitis viruses upregulates protein phosphatase 2A Protein phosphatase 2A: a highly regulated family of serine/threonine phosphatases implicated in cell growth and signalling PP2A targeting by viral proteins: a widespread biological strategy from DNA/RNA tumor viruses to HIV-1 Hepatitis C virus inhibits interferon signaling through upregulation of protein phosphatase 2A Upregulation of protein phosphatase 2Ac by hepatitis C virus modulates NS3 helicase activity through inhibition of protein arginine methyltransferase 1 Transcriptional induction of two genes in human cells by b interferon Functional classification of interferon-stimulated genes identified using microarrays A central role for RNA in the induction and biological activities of type 1 interferons Targeted impairment of innate antiviral responses in the liver of chronic hepatitis C patients Negative feedback regulation of RIG-I-mediated antiviral signaling by interferoninduced ISG15 conjugation Immune signaling by RIG-I-like receptors Retinoic acid inducible gene-I (RIG-I) signaling of hepatic stellate cells inhibits hepatitis C virus replication in hepatocytes Interferon-b pretreatment of conventional and plasmacytoid human dendritic cells enhances their activation by influenza virus A structure-based model of RIG-I activation Emerging role of ubiquitination in antiviral RIG-I signaling DDX60, a DEXD/H box helicase, is a novel antiviral factor promoting RIG-I-like receptor-mediated signaling Hepatitis C virus induces interferon-and interferon-stimulated genes in primary liver cultures IRF family of transcription factors as regulators of host defense Regulation of PKR and IRF-1 during hepatitis C virus RNA replication Constitutive expression of an ISGF2/IRF1 transgene leads to interferon-independent activation of interferon-inducible genes and resistance to virus infection Regulation of hepatitis C virus replication by interferon regulatory factor 1 IRF-7 is the master regulator of type-I interferon-dependent immune responses Hepatitis C virus infection impairs IRF-7 translocation and Alpha interferon synthesis in immortalized human hepatocytes IRF-3, IRF-5, and IRF-7 coordinately regulate the type I IFN response in myeloid dendritic cells downstream of MAVS signaling Hepatitis C virus inhibits intracellular interferon alpha expression in human hepatic cell lines Serum-derived hepatitis C virus infectivity in interferon regulatory factor-7-suppressed human primary hepatocytes Interferon regulatory factor IRF-7 induces the antiviral alpha interferon response and protects against lethal West Nile virus infection Antiviral actions of interferons Impact of protein kinase PKR in cell biology: from antiviral to antiproliferative action dsRNA-dependent protein kinase PKR and its role in stress, signaling and HCV infection PKR protein kinase is activated by hepatitis C virus and inhibits viral replication through translational control PKR-dependent mechanisms of gene expression from a subgenomic hepatitis C virus clone Identification of three interferon-inducible cellular enzymes that inhibit the replication of hepatitis C virus Alpha interferon induces distinct translational control programs to suppress hepatitis C virus RNA replication New antiviral pathway that mediates hepatitis C virus replicon interferon sensitivity through ADAR1 Hepatitis C virus controls interferon production through PKR activation Translational resistance of late alphavirus mRNA to eIF2a phosphorylation: a strategy to overcome the antiviral effect of protein kinase PKR Initiation of protein synthesis by hepatitis C virus is refractory to reduced eIF2.GTP.Met-tRNA(i)(Met) ternary complex availability Translational insensitivity to potent activation of PKR by HCV IRES RNA HCV NS5A co-operates with PKR in modulating HCV IRES-dependent translation Eukaryotic translation initiation machinery can operate in a bacterial-like mode without eIF2 Hepatitis C virus blocks interferon effector function by inducing protein kinase R phosphorylation Hepatitis C virus (HCV) induces formation of stress granules whose proteins regulate HCV RNA replication and virus assembly and egress P bodies, stress granules, and viral life cycles Stress granules: sites of mRNA triage that regulate mRNA stability and translatability Stress granules Eukaryotic stress granules: the ins and outs of translation Regulation of stress granules and P-bodies during RNA virus infection Diversion of stress granules and P-bodies during viral infection Dynamic oscillation of translation and stress granule formation mark the cellular response to virus infection Hepatitis C virus hijacks P-body and stress granule components around lipid droplets Hepatitis C virus coopts Ras-GTPase-activating protein-binding protein 1 for its genome replication Viral encounters with 29,59-oligoadenylate synthetase and RNase L during the interferon antiviral response New insights into the role of RNase L in innate immunity The oligoadenylate synthetase family: an ancient protein family with multiple antiviral activities The ribonuclease Ldependent antiviral roles of human 29,59-oligoadenylate synthetase family members against hepatitis C virus 59-Oligoadenylate synthetaselike gene highly induced by hepatitis C virus infection in human liver is inhibitory to viral replication in vitro Antiviral activities of ISG20 in positive-strand RNA virus infections ISG20, an actor of the innate immune response Adenosine deaminases acting on RNA (ADARs) are both antiviral and proviral Adenosine deaminases acting on RNA, RNA editing, and interferon action RNA-specific adenosine deaminase ADAR1 suppresses measles virus-induced apoptosis and activation of protein kinase PKR Expression of interferoninducible RNA adenosine deaminase ADAR1 during pathogen infection and mouse embryo development involves tissueselective promoter utilization and alternative splicing RNA editing of hepatitis delta virus antigenome by dsRNA-adenosine deaminase A specific base transition occurs on replicating hepatitis delta virus RNA RNA editing in hepatitis delta virus HCV-induced ER stress HCV protein expression can induce an ER stress response and lead to calcium release from the ER, which in turn activates the cyclic AMP responsive element-binding protein that binds to the cyclic AMP responsive element in the promoter of protein phosphatase 2A (PP2A), resulting in upregulation of PP2A. 114 Expressed in essentially all cell types, PP2A is a serine/threonine phosphatase that is involved in multiple cellular processes, such as the cell cycle, signal transduction and stress response.


