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Title: Structural basis for concerted recruitment and activation of IRF-3 by innate immune adaptor proteins

Abstract

Type I IFNs are key cytokines mediating innate antiviral immunity. cGMP-AMP synthase, ritinoic acid-inducible protein 1 (RIG-I)–like receptors, and Toll-like receptors recognize microbial double-stranded (ds)DNA, dsRNA, and LPS to induce the expression of type I IFNs. These signaling pathways converge at the recruitment and activation of the transcription factor IRF-3 (IFN regulatory factor 3). The adaptor proteins STING (stimulator of IFN genes), MAVS (mitochondrial antiviral signaling), and TRIF (TIR domain-containing adaptor inducing IFN-β) mediate the recruitment of IRF-3 through a conserved pLxIS motif. Here in this paper, we show that the pLxIS motif of phosphorylated STING, MAVS, and TRIF binds to IRF-3 in a similar manner, whereas residues upstream of the motif confer specificity. The structure of the IRF-3 phosphomimetic mutant S386/396E bound to the cAMP response element binding protein (CREB)-binding protein reveals that the pLxIS motif also mediates IRF-3 dimerization and activation. Moreover, rotavirus NSP1 (nonstructural protein 1) employs a pLxIS motif to target IRF-3 for degradation, but phosphorylation of NSP1 is not required for its activity. These results suggest a concerted mechanism for the recruitment and activation of IRF-3 that can be subverted by viral proteins to evade innate immune responses.

Authors:
 [1];  [1];  [2];  [3];  [1];  [4];  [5];  [2];  [1]
  1. Texas A & M Univ., College Station, TX (United States). Dept. of Biochemistry and Biophysics
  2. Texas A & M Univ., College Station, TX (United States). College of Medicine, Dept. of Molecular and Cellular Medicine
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Berkeley Center for Structural Biology, Physical Biosciences Division
  4. Cincinnati Children's Hospital Medical Center, Cincinnati, OH (United States). Center for Systems Immunology, Division of Immunobiology; Cincinnati Children's Hospital Medical Center, Cincinnati, OH (United States). Division of Infectious Diseases
  5. Cincinnati Children's Hospital Medical Center, Cincinnati, OH (United States). Center for Systems Immunology, Division of Immunobiology; Cincinnati Children's Hospital Medical Center, Cincinnati, OH (United States). Division of Infectious Diseases
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1379399
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 113; Journal Issue: 24; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences, Washington, DC (United States)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; innate immunity; signaling; type I interferon; transcription factor; crystal structure

Citation Formats

Zhao, Baoyu, Shu, Chang, Gao, Xinsheng, Sankaran, Banumathi, Du, Fenglei, Shelton, Catherine L., Herr, Andrew B., Ji, Jun-Yuan, and Li, Pingwei. Structural basis for concerted recruitment and activation of IRF-3 by innate immune adaptor proteins. United States: N. p., 2016. Web. doi:10.1073/pnas.1603269113.
Zhao, Baoyu, Shu, Chang, Gao, Xinsheng, Sankaran, Banumathi, Du, Fenglei, Shelton, Catherine L., Herr, Andrew B., Ji, Jun-Yuan, & Li, Pingwei. Structural basis for concerted recruitment and activation of IRF-3 by innate immune adaptor proteins. United States. doi:https://doi.org/10.1073/pnas.1603269113
Zhao, Baoyu, Shu, Chang, Gao, Xinsheng, Sankaran, Banumathi, Du, Fenglei, Shelton, Catherine L., Herr, Andrew B., Ji, Jun-Yuan, and Li, Pingwei. Thu . "Structural basis for concerted recruitment and activation of IRF-3 by innate immune adaptor proteins". United States. doi:https://doi.org/10.1073/pnas.1603269113. https://www.osti.gov/servlets/purl/1379399.
@article{osti_1379399,
title = {Structural basis for concerted recruitment and activation of IRF-3 by innate immune adaptor proteins},
author = {Zhao, Baoyu and Shu, Chang and Gao, Xinsheng and Sankaran, Banumathi and Du, Fenglei and Shelton, Catherine L. and Herr, Andrew B. and Ji, Jun-Yuan and Li, Pingwei},
abstractNote = {Type I IFNs are key cytokines mediating innate antiviral immunity. cGMP-AMP synthase, ritinoic acid-inducible protein 1 (RIG-I)–like receptors, and Toll-like receptors recognize microbial double-stranded (ds)DNA, dsRNA, and LPS to induce the expression of type I IFNs. These signaling pathways converge at the recruitment and activation of the transcription factor IRF-3 (IFN regulatory factor 3). The adaptor proteins STING (stimulator of IFN genes), MAVS (mitochondrial antiviral signaling), and TRIF (TIR domain-containing adaptor inducing IFN-β) mediate the recruitment of IRF-3 through a conserved pLxIS motif. Here in this paper, we show that the pLxIS motif of phosphorylated STING, MAVS, and TRIF binds to IRF-3 in a similar manner, whereas residues upstream of the motif confer specificity. The structure of the IRF-3 phosphomimetic mutant S386/396E bound to the cAMP response element binding protein (CREB)-binding protein reveals that the pLxIS motif also mediates IRF-3 dimerization and activation. Moreover, rotavirus NSP1 (nonstructural protein 1) employs a pLxIS motif to target IRF-3 for degradation, but phosphorylation of NSP1 is not required for its activity. These results suggest a concerted mechanism for the recruitment and activation of IRF-3 that can be subverted by viral proteins to evade innate immune responses.},
doi = {10.1073/pnas.1603269113},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 24,
volume = 113,
place = {United States},
year = {2016},
month = {6}
}

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Works referenced in this record:

The mechanism of double-stranded DNA sensing through the cGAS-STING pathway
journal, December 2014


STING Specifies IRF3 Phosphorylation by TBK1 in the Cytosolic DNA Signaling Pathway
journal, March 2012


Cyclic GMP-AMP Containing Mixed Phosphodiester Linkages Is An Endogenous High-Affinity Ligand for STING
journal, July 2013


Type I Inteferon Gene Induction by the Interferon Regulatory Factor Family of Transcription Factors
journal, September 2006


Structural Insights into the Functions of TBK1 in Innate Antimicrobial Immunity
journal, July 2013


Insights into interferon regulatory factor activation from the crystal structure of dimeric IRF5
journal, October 2008

  • Chen, Weijun; Lam, Suvana S.; Srinath, Hema
  • Nature Structural & Molecular Biology, Vol. 15, Issue 11
  • DOI: 10.1038/nsmb.1496

Overview of the CCP 4 suite and current developments
journal, March 2011

  • Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910045749

Type I Interferons in Host Defense
journal, September 2006


Identification and Characterization of MAVS, a Mitochondrial Antiviral Signaling Protein that Activates NF-κB and IRF3
journal, September 2005


Role of Adaptor TRIF in the MyD88-Independent Toll-Like Receptor Signaling Pathway
journal, August 2003


Crystal Structure of IRF-3 in Complex with CBP
journal, September 2005


RIG-I-like receptors: cytoplasmic sensors for non-self RNA: RIG-I-like receptors
journal, August 2011


Cyclic GMP-AMP Synthase Is Activated by Double-Stranded DNA-Induced Oligomerization
journal, December 2013


Features and development of Coot
journal, March 2010

  • Emsley, P.; Lohkamp, B.; Scott, W. G.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444910007493

Cyclic GMP-AMP Synthase Is a Cytosolic DNA Sensor That Activates the Type I Interferon Pathway
journal, December 2012


Rotavirus nonstructural protein 1 subverts innate immune response by inducing degradation of IFN regulatory factor 3
journal, March 2005

  • Barro, M.; Patton, J. T.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 11
  • DOI: 10.1073/pnas.0408376102

Pattern Recognition Receptors and Inflammation
journal, March 2010


Structure of IRF-3 Bound to the PRDIII-I Regulatory Element of the Human Interferon-β Enhancer
journal, June 2007


The family of five: TIR-domain-containing adaptors in Toll-like receptor signalling
journal, May 2007

  • O'Neill, Luke A. J.; Bowie, Andrew G.
  • Nature Reviews Immunology, Vol. 7, Issue 5
  • DOI: 10.1038/nri2079

Functional IRF3 deficiency in a patient with herpes simplex encephalitis
journal, July 2015

  • Andersen, Line Lykke; Mørk, Nanna; Reinert, Line S.
  • The Journal of Experimental Medicine, Vol. 212, Issue 9
  • DOI: 10.1084/jem.20142274

Interferon-Stimulated Genes: A Complex Web of Host Defenses
journal, March 2014


PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

Innate Immune Sensing and Signaling of Cytosolic Nucleic Acids
journal, March 2014


STING-dependent cytosolic DNA sensing pathways
journal, February 2014


STING is a direct innate immune sensor of cyclic di-GMP
journal, September 2011

  • Burdette, Dara L.; Monroe, Kathryn M.; Sotelo-Troha, Katia
  • Nature, Vol. 478, Issue 7370
  • DOI: 10.1038/nature10429

Cutting Edge: A Novel Toll/IL-1 Receptor Domain-Containing Adapter That Preferentially Activates the IFN-β Promoter in the Toll-Like Receptor Signaling
journal, December 2002


cGAS produces a 2′-5′-linked cyclic dinucleotide second messenger that activates STING
journal, May 2013

  • Ablasser, Andrea; Goldeck, Marion; Cavlar, Taner
  • Nature, Vol. 498, Issue 7454
  • DOI: 10.1038/nature12306

Contribution of Ser386 and Ser396 to Activation of Interferon Regulatory Factor 3
journal, May 2008


Rotavirus Antagonism of the Innate Immune Response
journal, November 2009


Innate Recognition of Viruses
journal, September 2007


Crystal structure of IRF-3 reveals mechanism of autoinhibition and virus-induced phosphoactivation
journal, October 2003

  • Qin, Bin Y.; Liu, Cheng; Lam, Suvana S.
  • Nature Structural & Molecular Biology, Vol. 10, Issue 11
  • DOI: 10.1038/nsb1002

Viral RNA detection by RIG-I-like receptors
journal, February 2015


Phosphorylation of innate immune adaptor proteins MAVS, STING, and TRIF induces IRF3 activation
journal, January 2015


An Atomic Model of the Interferon-β Enhanceosome
journal, June 2007


Interferon Regulatory Factor 3 Is Regulated by a Dual Phosphorylation-dependent Switch
journal, May 2007

  • Panne, Daniel; McWhirter, Sarah M.; Maniatis, Tom
  • Journal of Biological Chemistry, Vol. 282, Issue 31
  • DOI: 10.1074/jbc.M703019200

Structure-Function Analysis of STING Activation by c[G(2′,5′)pA(3′,5′)p] and Targeting by Antiviral DMXAA
journal, August 2013


Cyclic GMP-AMP Is an Endogenous Second Messenger in Innate Immune Signaling by Cytosolic DNA
journal, December 2012


Rotavirus NSP1 Mediates Degradation of Interferon Regulatory Factors through Targeting of the Dimerization Domain
journal, July 2013

  • Arnold, M. M.; Barro, M.; Patton, J. T.
  • Journal of Virology, Vol. 87, Issue 17
  • DOI: 10.1128/JVI.01146-13

[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997


    Works referencing / citing this record:

    SWI2/SNF2 ATPase CHR2 remodels pri-miRNAs via Serrate to impede miRNA production
    journal, May 2018


    Transcription factor dimerization activates the p300 acetyltransferase
    journal, October 2018


    Structural basis of STING binding with and phosphorylation by TBK1
    journal, March 2019


    A conserved PLPLRT/SD motif of STING mediates the recruitment and activation of TBK1
    journal, May 2019


    Entirely plasmid-based reverse genetics system for rotaviruses
    journal, January 2017

    • Kanai, Yuta; Komoto, Satoshi; Kawagishi, Takahiro
    • Proceedings of the National Academy of Sciences, Vol. 114, Issue 9
    • DOI: 10.1073/pnas.1618424114

    Structural basis of STAT2 recognition by IRF9 reveals molecular insights into ISGF3 function
    journal, January 2018

    • Rengachari, Srinivasan; Groiss, Silvia; Devos, Juliette M.
    • Proceedings of the National Academy of Sciences, Vol. 115, Issue 4
    • DOI: 10.1073/pnas.1718426115

    The eukaryotic linear motif resource – 2018 update
    journal, November 2017

    • Gouw, Marc; Michael, Sushama; Sámano-Sánchez, Hugo
    • Nucleic Acids Research, Vol. 46, Issue D1
    • DOI: 10.1093/nar/gkx1077

    Rotavirus NSP1 Requires Casein Kinase II-Mediated Phosphorylation for Hijacking of Cullin-RING Ligases
    journal, August 2017


    Suramin potently inhibits cGAMP synthase, cGAS, in THP1 cells to modulate IFN-β levels
    journal, June 2018

    • Wang, Modi; Sooreshjani, Moloud A.; Mikek, Clinton
    • Future Medicinal Chemistry, Vol. 10, Issue 11
    • DOI: 10.4155/fmc-2017-0322