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:
-
- Texas A & M Univ., College Station, TX (United States). Dept. of Biochemistry and Biophysics
- Texas A & M Univ., College Station, TX (United States). College of Medicine, Dept. of Molecular and Cellular Medicine
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Berkeley Center for Structural Biology, Physical Biosciences Division
- 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
- 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 Laboratory (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:
- Journal Article: 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. 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. 2016.
"Structural basis for concerted recruitment and activation of IRF-3 by innate immune adaptor proteins". United States. 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},
url = {https://www.osti.gov/biblio/1379399},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
issn = {0027-8424},
number = 24,
volume = 113,
place = {United States},
year = {Thu Jun 02 00:00:00 EDT 2016},
month = {Thu Jun 02 00:00:00 EDT 2016}
}
Web of Science
Works referenced in this record:
The mechanism of double-stranded DNA sensing through the cGAS-STING pathway
journal, December 2014
- Shu, Chang; Li, Xin; Li, Pingwei
- Cytokine & Growth Factor Reviews, Vol. 25, Issue 6
STING Specifies IRF3 Phosphorylation by TBK1 in the Cytosolic DNA Signaling Pathway
journal, March 2012
- Tanaka, Y.; Chen, Z. J.
- Science Signaling, Vol. 5, Issue 214
Cyclic GMP-AMP Containing Mixed Phosphodiester Linkages Is An Endogenous High-Affinity Ligand for STING
journal, July 2013
- Zhang, Xu; Shi, Heping; Wu, Jiaxi
- Molecular Cell, Vol. 51, Issue 2
Type I Inteferon Gene Induction by the Interferon Regulatory Factor Family of Transcription Factors
journal, September 2006
- Honda, Kenya; Takaoka, Akinori; Taniguchi, Tadatsugu
- Immunity, Vol. 25, Issue 3
Structural Insights into the Functions of TBK1 in Innate Antimicrobial Immunity
journal, July 2013
- Shu, Chang; Sankaran, Banumathi; Chaton, Catherine T.
- Structure, Vol. 21, Issue 7
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
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
Type I Interferons in Host Defense
journal, September 2006
- Stetson, Daniel B.; Medzhitov, Ruslan
- Immunity, Vol. 25, Issue 3
Identification and Characterization of MAVS, a Mitochondrial Antiviral Signaling Protein that Activates NF-κB and IRF3
journal, September 2005
- Seth, Rashu B.; Sun, Lijun; Ea, Chee-Kwee
- Cell, Vol. 122, Issue 5
Role of Adaptor TRIF in the MyD88-Independent Toll-Like Receptor Signaling Pathway
journal, August 2003
- Yamamoto, M.
- Science, Vol. 301, Issue 5633
Crystal Structure of IRF-3 in Complex with CBP
journal, September 2005
- Qin, Bin Y.; Liu, Cheng; Srinath, Hema
- Structure, Vol. 13, Issue 9
RIG-I-like receptors: cytoplasmic sensors for non-self RNA: RIG-I-like receptors
journal, August 2011
- Kato, Hiroki; Takahasi, Kiyohiro; Fujita, Takashi
- Immunological Reviews, Vol. 243, Issue 1
Cyclic GMP-AMP Synthase Is Activated by Double-Stranded DNA-Induced Oligomerization
journal, December 2013
- Li, Xin; Shu, Chang; Yi, Guanghui
- Immunity, Vol. 39, Issue 6
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
Cyclic GMP-AMP Synthase Is a Cytosolic DNA Sensor That Activates the Type I Interferon Pathway
journal, December 2012
- Sun, L.; Wu, J.; Du, F.
- Science, Vol. 339, Issue 6121
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
Pattern Recognition Receptors and Inflammation
journal, March 2010
- Takeuchi, Osamu; Akira, Shizuo
- Cell, Vol. 140, Issue 6
Structure of IRF-3 Bound to the PRDIII-I Regulatory Element of the Human Interferon-β Enhancer
journal, June 2007
- Escalante, Carlos R.; Nistal-Villán, Estanislao; Shen, Leyi
- Molecular Cell, Vol. 26, Issue 5
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
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
Interferon-Stimulated Genes: A Complex Web of Host Defenses
journal, March 2014
- Schneider, William M.; Chevillotte, Meike Dittmann; Rice, Charles M.
- Annual Review of Immunology, Vol. 32, Issue 1
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
Innate Immune Sensing and Signaling of Cytosolic Nucleic Acids
journal, March 2014
- Wu, Jiaxi; Chen, Zhijian J.
- Annual Review of Immunology, Vol. 32, Issue 1
STING-dependent cytosolic DNA sensing pathways
journal, February 2014
- Barber, Glen N.
- Trends in Immunology, Vol. 35, Issue 2
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
Cyclic [G(2′,5′)pA(3′,5′)p] Is the Metazoan Second Messenger Produced by DNA-Activated Cyclic GMP-AMP Synthase
journal, May 2013
- Gao, Pu; Ascano, Manuel; Wu, Yang
- Cell, Vol. 153, Issue 5
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
- Yamamoto, Masahiro; Sato, Shintaro; Mori, Kiyotoshi
- The Journal of Immunology, Vol. 169, Issue 12
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
Ser386 phosphorylation of transcription factor IRF-3 induces dimerization and association with CBP/p300 without overall conformational change: IRF-3 activation by S386 phosphorylation
journal, July 2010
- Takahasi, Kiyohiro; Horiuchi, Masataka; Fujii, Kiyonaga
- Genes to Cells
Contribution of Ser386 and Ser396 to Activation of Interferon Regulatory Factor 3
journal, May 2008
- Chen, Weijun; Srinath, Hema; Lam, Suvana S.
- Journal of Molecular Biology, Vol. 379, Issue 2
Rotavirus Antagonism of the Innate Immune Response
journal, November 2009
- Arnold, Michelle; Patton, John
- Viruses, Vol. 1, Issue 3
Innate Recognition of Viruses
journal, September 2007
- Pichlmair, Andreas; Reis e. Sousa, Caetano
- Immunity, Vol. 27, Issue 3
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
Viral RNA detection by RIG-I-like receptors
journal, February 2015
- Yoneyama, Mitsutoshi; Onomoto, Koji; Jogi, Michihiko
- Current Opinion in Immunology, Vol. 32
Phosphorylation of innate immune adaptor proteins MAVS, STING, and TRIF induces IRF3 activation
journal, January 2015
- Liu, S.; Cai, X.; Wu, J.
- Science, Vol. 347, Issue 6227
An Atomic Model of the Interferon-β Enhanceosome
journal, June 2007
- Panne, Daniel; Maniatis, Tom; Harrison, Stephen C.
- Cell, Vol. 129, Issue 6
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
Structure-Function Analysis of STING Activation by c[G(2′,5′)pA(3′,5′)p] and Targeting by Antiviral DMXAA
journal, August 2013
- Gao, Pu; Ascano, Manuel; Zillinger, Thomas
- Cell, Vol. 154, Issue 4
Cyclic GMP-AMP Is an Endogenous Second Messenger in Innate Immune Signaling by Cytosolic DNA
journal, December 2012
- Wu, J.; Sun, L.; Chen, X.
- Science, Vol. 339, Issue 6121
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
[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997
- Otwinowski, Zbyszek; Minor, Wladek
- Macromolecular Crystallography Part A, 307-326
Works referencing / citing this record:
SWI2/SNF2 ATPase CHR2 remodels pri-miRNAs via Serrate to impede miRNA production
journal, May 2018
- Wang, Zhiye; Ma, Zeyang; Castillo-González, Claudia
- Nature, Vol. 557, Issue 7706
Transcription factor dimerization activates the p300 acetyltransferase
journal, October 2018
- Ortega, Esther; Rengachari, Srinivasan; Ibrahim, Ziad
- Nature, Vol. 562, Issue 7728
Structural basis of STING binding with and phosphorylation by TBK1
journal, March 2019
- Zhang, Conggang; Shang, Guijun; Gui, Xiang
- Nature, Vol. 567, Issue 7748
A conserved PLPLRT/SD motif of STING mediates the recruitment and activation of TBK1
journal, May 2019
- Zhao, Baoyu; Du, Fenglei; Xu, Pengbiao
- Nature, Vol. 569, Issue 7758
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
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
The eukaryotic linear motif resource – 2018 update
journal, November 2017
- Gouw, Marc; Michael, Sushama; Sámano-Sánchez, Hugo
- Nucleic Acids Research, Vol. 46, Issue D1
Rotavirus NSP1 Requires Casein Kinase II-Mediated Phosphorylation for Hijacking of Cullin-RING Ligases
journal, August 2017
- Davis, Kaitlin A.; Morelli, Marco; Patton, John T.
- mBio, Vol. 8, Issue 4
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
Structural basis of STAT2 recognition by IRF9 reveals molecular insights into ISGF3 function
journal, April 2017
- Rengachari, Srinivasan; Groiss, Silvia; Devos, Juliette
- Proceedings of the National Academy of Sciences
Transcription factor dimerization activates the p300 acetyltransferase
journal, October 2018
- Ortega, Esther; Rengachari, Srinivasan; Ibrahim, Ziad
- Nature, Vol. 562, Issue 7728
A conserved PLPLRT/SD motif of STING mediates the recruitment and activation of TBK1
journal, May 2019
- Zhao, Baoyu; Du, Fenglei; Xu, Pengbiao
- Nature, Vol. 569, Issue 7758
The eukaryotic linear motif resource – 2018 update
journal, November 2017
- Gouw, Marc; Michael, Sushama; Sámano-Sánchez, Hugo
- Nucleic Acids Research, Vol. 46, Issue D1
Structural basis of STAT2 recognition by IRF9 reveals molecular insights into ISGF3 function
journal, April 2017
- Rengachari, Srinivasan; Groiss, Silvia; Devos, Juliette
- Proceedings of the National Academy of Sciences
Rotavirus NSP1 Requires Casein Kinase II-Mediated Phosphorylation for Hijacking of Cullin-RING Ligases
journal, August 2017
- Davis, Kaitlin A.; Morelli, Marco; Patton, John T.
- mBio, Vol. 8, Issue 4
The Significance of Type-I Interferons in the Pathogenesis and Therapy of Human Immunodeficiency Virus 1 Infection
journal, November 2017
- Wang, Bowen; Kang, Wen; Zuo, Jiahui
- Frontiers in Immunology, Vol. 8