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Recently, RIG-I and MDA5 have been identified as essential cytosolic receptors for intracellular viral RNAs and synthetic dsRNAs, mediating the TLR-independent induction of type I IFN genes</csml:comment>
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Recently, RIG-I and MDA5 have been identified as essential cytosolic receptors for intracellular viral RNAs and synthetic dsRNAs, mediating the TLR-independent induction of type I IFN genes</csml:comment>
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This CARD mediates CARD-CARD interactions with RIG-I and MDA5 and transmits downstream signaling </csml:comment>
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This CARD mediates CARD-CARD interactions with RIG-I and MDA5 and transmits downstream signaling </csml:comment>
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IPS-1 has been shown to interact with several signaling proteins, such as tumor necrosis factor receptor-associated factor 2 (TRAF2), TRAF6, Fas-associated protein with the death domain (FADD), and receptor interacting protein-1 (RIP1)</csml:comment>
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IPS-1 has been shown to interact with several signaling proteins, such as tumor necrosis factor receptor-associated factor 2 (TRAF2), TRAF6, Fas-associated protein with the death domain (FADD), and receptor interacting protein-1 (RIP1)</csml:comment>
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The conformational change promotes the interaction between the RIG-I and MDA5 CARDs and the CARD-containing adaptor protein IPS-1, which is located on the mitochondrial membrane, resulting in the activation of TBK1 via TRAF3 as well as IKK complex via FADD, RIP1 (not depicted), and TRAF6.T
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The conformational change promotes the interaction between the RIG-I and MDA5 CARDs and the CARD-containing adaptor protein IPS-1, which is located on the mitochondrial membrane, resulting in the activation of TBK1 via TRAF3 as well as IKK complex via FADD, RIP1 (not depicted), and TRAF6.T
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<csml:comment type="text">PMID: 16979567,16858409
Considering the fact that TRAF3 interacts with IPS-1 , TRAF3 probably provides a link between IPS-1 and TBK1 (Figure 2).

PMID: 16979567
The conformational change promotes the interaction between the RIG-I and MDA5 CARDs and the CARD-containing adaptor protein IPS-1, which is located on the mitochondrial membrane, resulting in the activation of TBK1 via TRAF3 as well as IKK complex via FADD, RIP1 (not depicted), and TRAF6.</csml:comment>
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<csml:comment type="text">PMID: 16979567,16858409
Considering the fact that TRAF3 interacts with IPS-1 , TRAF3 probably provides a link between IPS-1 and TBK1 (Figure 2).

PMID: 16979567
The conformational change promotes the interaction between the RIG-I and MDA5 CARDs and the CARD-containing adaptor protein IPS-1, which is located on the mitochondrial membrane, resulting in the activation of TBK1 via TRAF3 as well as IKK complex via FADD, RIP1 (not depicted), and TRAF6.</csml:comment>
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The conformational change promotes the interaction between the RIG-I and MDA5 CARDs and the CARD-containing adaptor protein IPS-1, which is located on the mitochondrial membrane, resulting in the activation of TBK1 via TRAF3 as well as IKK complex via FADD, RIP1 (not depicted), and TRAF6.</csml:comment>
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The conformational change promotes the interaction between the RIG-I and MDA5 CARDs and the CARD-containing adaptor protein IPS-1, which is located on the mitochondrial membrane, resulting in the activation of TBK1 via TRAF3 as well as IKK complex via FADD, RIP1 (not depicted), and TRAF6.</csml:comment>
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Inducible IκB kinase (IKKi; also known as IKKε), which is structurally related to TBK1, was also shown to phosphorylate IRF3 and IRF7 in vitro; however, gene-targeting studies revealed that the contribution of IKKi to the cytosolic pathway is minor</csml:comment>
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Activated TBK1 induces the phosphorylation (P−) of IRF3 and IRF7, resulting in their homo- or heterodimerization.</csml:comment>
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Inducible IκB kinase (IKKi; also known as IKKε), which is structurally related to TBK1, was also shown to phosphorylate IRF3 and IRF7 in vitro; however, gene-targeting studies revealed that the contribution of IKKi to the cytosolic pathway is minor</csml:comment>
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<csml:comment type="text">PMID: 16979567
Activated TBK1 induces the phosphorylation (P−) of IRF3 and IRF7, resulting in their homo- or heterodimerization.

18)	PMID: 16979567
 Phosphorylated IRF3 forms homodimers and induces IFN-β and Cxcl10 genes
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Activated TBK1 induces the phosphorylation (P−) of IRF3 and IRF7, resulting in their homo- or heterodimerization.</csml:comment>
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Activated TBK1 induces the phosphorylation (P−) of IRF3 and IRF7, resulting in their homo- or heterodimerization.</csml:comment>
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These dimers then translocate to the nucleus and induce chemokines (including CXCL10) as well as small amounts of IFN-beta.</csml:comment>
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These dimers then translocate to the nucleus and induce chemokines (including CXCL10) as well as small amounts of IFN-beta.</csml:comment>
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<csml:comment type="text">PMID: 16979567
These dimers then translocate to the nucleus and induce chemokines (including CXCL10) as well as small amounts of IFN-beta.

PMID: 16979567
The activated TBK1 mediates phosphorylation of serine residues in IRF3, rather than those in IRF7, inducing its dimerization and entry into the nucleus where it induces the transcription of the IFN-β gene.</csml:comment>
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<csml:comment type="text">PMID: 16979567
These dimers then translocate to the nucleus and induce chemokines (including CXCL10) as well as small amounts of IFN-β</csml:comment>
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<csml:comment type="text">PMID: 16979567
These dimers then translocate to the nucleus and induce chemokines (including CXCL10) as well as small amounts of IFN-β</csml:comment>
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These dimers then translocate to the nucleus and induce chemokines (including CXCL10) as well as small amounts of IFN-β

18)	PMID: 16979567
 Phosphorylated IRF3 forms homodimers and induces IFN-β and Cxcl10 genes
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These dimers then translocate to the nucleus and induce chemokines (including CXCL10) as well as small amounts of IFN-β</csml:comment>
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These dimers then translocate to the nucleus and induce chemokines (including CXCL10) as well as small amounts of IFN-β</csml:comment>
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These dimers then translocate to the nucleus and induce chemokines (including CXCL10) as well as small amounts of IFN-β

PMID: 16979567
The activated TBK1 mediates phosphorylation of serine residues in IRF3, rather than those in IRF7, inducing its dimerization and entry into the nucleus where it induces the transcription of the IFN-β gene.

PMID: 16979567
In a similar way to the TLR4 signaling, TLR3 activates the Trif- (TRAM is not involved), TBK1-, and IRF3-dependent pathway to induce IFN-β gene</csml:comment>
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Secreted IFN-β then stimulates type I IFN receptor (heterodimer of IFNAR1 and IFNAR2) in an autocrine and a paracrine fashion, leading to activation of ISGF3 (heterotrimer of STAT1, STAT2, and IRF9) and the transcription of IRF7 gene.</csml:comment>
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Secreted IFN-β then stimulates type I IFN receptor (heterodimer of IFNAR1 and IFNAR2) in an autocrine and a paracrine fashion, leading to activation of ISGF3 (heterotrimer of STAT1, STAT2, and IRF9) and the transcription of IRF7 gene.</csml:comment>
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Secreted IFN-β then stimulates type I IFN receptor (heterodimer of IFNAR1 and IFNAR2) in an autocrine and a paracrine fashion, leading to activation of ISGF3 (heterotrimer of STAT1, STAT2, and IRF9) and the transcription of IRF7 gene.</csml:comment>
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Secreted IFN-β then stimulates type I IFN receptor (heterodimer of IFNAR1 and IFNAR2) in an autocrine and a paracrine fashion, leading to activation of ISGF3 (heterotrimer of STAT1, STAT2, and IRF9) and the transcription of IRF7 gene.</csml:comment>
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In addition, other viruses produce proteins that can interact with CBP/p300 and alter their interaction with IRFs, such as the vIRF-1 protein of human herpesvirus 8</csml:comment>
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Some viruses produce a protein that directly binds to and prevents the transactivation ability of IRF3 or IRF7, including the E6 oncoprotein of the human papillomavirus, the NSP1 of the rotavirus , and the RTA protein of Kaposi's sarcoma-associated herpesvirus</csml:comment>
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Some viruses produce a protein that directly binds to and prevents the transactivation ability of IRF3 or IRF7, including the E6 oncoprotein of the human papillomavirus, the NSP1 of the rotavirus , and the RTA protein of Kaposi's sarcoma-associated herpesvirus</csml:comment>
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Interestingly, it has been shown that hepatitis C virus (HCV) nonstructural proteins 3 and 4A (NS3/4A) cleave IPS-1, thereby inhibiting the RIG-I- and MDA5-mediated activation of IRF3 and/or IRF7 during HCV infection</csml:comment>
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TLR4 is the only receptor that can induce type I IFN (IFN-β, not IFN-α) gene by recognizing nonnucleic acid ligands, such as lipopolysaccharide (LPS)</csml:comment>
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TLR4 is expressed on the plasma membrane, and the extracellular portion of TLR4 associates with MD-2, which is prerequisite for TLR4 oligomerization and downstream signaling upon the recognition of LPS</csml:comment>
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<csml:comment type="text">14)  PMID: 16979567, 10359581
TLR4 is expressed on the plasma membrane, and the extracellular portion of TLR4 associates with MD-2, which is prerequisite for TLR4 oligomerization and downstream signaling upon the recognition of LPS
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The receptor complex composed of CD14, TLR4, and MD-2 stimulates the signaling pathway through the adaptor proteins TRAM and Trif, which leads to the activation of TBK1</csml:comment>
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The receptor complex composed of CD14, TLR4, and MD-2 stimulates the signaling pathway through the adaptor proteins TRAM and Trif, which leads to the activation of TBK1</csml:comment>
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Trif associates with TBK1 through TRAF3 and NAP1, which mediates the phosphorylation of IRF3. Phosphorylated IRF3 forms homodimers and induces IFN-β and Cxcl10 genes</csml:comment>
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Trif associates with TBK1 through TRAF3 and NAP1, which mediates the phosphorylation of IRF3. Phosphorylated IRF3 forms homodimers and induces IFN-β and Cxcl10 genes
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TLR3 recognizes poly(I:C) and probably viral dsRNAs derived from dsRNA viruses such as reovirus, or ssRNA viruses such as West Nile virus, respiratory syncytial virus, and EMCV
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TLR3 recognizes poly(I:C) and probably viral dsRNAs derived from dsRNA viruses such as reovirus, or ssRNA viruses such as West Nile virus, respiratory syncytial virus, and EMCV

PMID: 16979567, 15961631
Crystallographic studies have shown that TLR3 directly binds to dsRNA and forms a dimer to activate downstream signaling </csml:comment>
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Crystallographic studies have shown that TLR3 directly binds to dsRNA and forms a dimer to activate downstream signaling

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The recognition of dsRNA by TLR3 results in the phosphorylation of two specific tyrosines (Tyr759 and Tyr858) within the cytoplasmic tail of TLR3 and the recruitment of phosphatidylinositol 3-kinase (PI3K) to the receptor</csml:comment>
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The recognition of dsRNA by TLR3 results in the phosphorylation of two specific tyrosines (Tyr759 and Tyr858) within the cytoplasmic tail of TLR3 and the recruitment of phosphatidylinositol 3-kinase (PI3K) to the receptor

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In a similar way to the TLR4 signaling, TLR3 activates the Trif- (TRAM is not involved), TBK1-, and IRF3-dependent pathway to induce IFN-β gene</csml:comment>
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In a similar way to the TLR4 signaling, TLR3 activates the Trif- (TRAM is not involved), TBK1-, and IRF3-dependent pathway to induce IFN-β gene</csml:comment>
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In a similar way to the TLR4 signaling, TLR3 activates the Trif- (TRAM is not involved), TBK1-, and IRF3-dependent pathway to induce IFN-β gene</csml:comment>
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It was also reported that the tyrosine kinase c-Src is activated by poly(I:C), associates with TLR3, and is essential for dsRNA-induced IRF3 activation</csml:comment>
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RIP1 interacts with Trif through the C-terminal RIP homotypic interaction motif (RHIM) of Trif
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DNA viruses such as herpes simplex virus (HSV) contain many unmethylated CpG motifs in their genome, which are recognized by TLR9 and induce robust type I IFN production in pDCs

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Likewise, TLR7 signaling is essential for type I IFN induction in response to influenza virus or VSV infection by recognizing viral genomic ssRNA</csml:comment>
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In contrast to TLR3- or TLR4-mediated Trif-dependent IFN gene induction, the TLR9 subfamily members exclusively utilize MyD88 as the signaling adaptor.</csml:comment>
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MyD88 directly interacts with IRF7 (not with IRF3) through its death domain</csml:comment>
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IRF7 also interacts with TRAF6, another adaptor molecule functioning downstream of MyD88, and the overexpression of TRAF6 induces type I IFN genes through the activation of IRF7</csml:comment>
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<csml:comment type="text">PMID: 16979567,15492225, 15361868
IRF7 also interacts with TRAF6, another adaptor molecule functioning downstream of MyD88, and the overexpression of TRAF6 induces type I IFN genes through the activation of IRF7</csml:comment>
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Similarly to IRF7, IRF1 directly interacts with MyD88

PMID: 16979567
Thus, the IRF1 induced by IFN-γ binds to MyD88 and is modified by unidentified signaling molecule(s) to migrate into the nucleus and activate gene induction</csml:comment>
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<csml:comment type="text">PMID: 16979567
As opposed to IRF7, which is induced by type I IFN, IRF1 is strongly induced by IFN-γ signaling. </csml:comment>
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Thus, the IRF1 induced by IFN-γ binds to MyD88 and is modified by unidentified signaling molecule(s) to migrate into the nucleus and activate gene induction</csml:comment>
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Thus, the IRF1 induced by IFN-γ binds to MyD88 and is modified by unidentified signaling molecule(s) to migrate into the nucleus and activate gene induction</csml:comment>
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<csml:comment type="text">PMID: 16979567,11961557
Furthermore, IFN-beta gene is induced by several nonviral agents such as the receptor activator of NF-κB ligand (RANKL), which activates NF-κB, c-JUN, and c-Fos, but not IRFs</csml:comment>
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<csml:comment type="text">PMID: 16979567,11961557
Furthermore, IFN-beta gene is induced by several nonviral agents such as the receptor activator of NF-κB ligand (RANKL), which activates NF-κB, c-JUN, and c-Fos, but not IRFs</csml:comment>
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Furthermore, IFN-beta gene is induced by several nonviral agents such as the receptor activator of NF-κB ligand (RANKL), which activates NF-κB, c-JUN, and c-Fos, but not IRFs</csml:comment>
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Furthermore, IFN-beta gene is induced by several nonviral agents such as the receptor activator of NF-κB ligand (RANKL), which activates NF-κB, c-JUN, and c-Fos, but not IRFs</csml:comment>
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Upon TLR7 or TLR9 (expressed in endosomes) stimulation, IRF7 interacting with MyD88 is activated by the IRAK4-IRAK1-IKKalpha kinase cascade.</csml:comment>
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