TRIM25 predominately associates with anti-viral stress granules.
Humans
Poly-ADP-Ribose Binding Proteins
/ metabolism
Tripartite Motif Proteins
/ metabolism
RNA Recognition Motif Proteins
/ metabolism
Ubiquitin-Protein Ligases
/ metabolism
Stress Granules
/ metabolism
RNA Helicases
/ metabolism
Ubiquitination
DNA Helicases
/ metabolism
Signal Transduction
DEAD Box Protein 58
/ metabolism
Transcription Factors
/ metabolism
Immunity, Innate
RNA, Double-Stranded
/ metabolism
HEK293 Cells
HeLa Cells
Cytoplasmic Granules
/ metabolism
RNA Virus Infections
/ virology
Receptors, Immunologic
/ metabolism
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
15 May 2024
15 May 2024
Historique:
received:
02
07
2023
accepted:
07
05
2024
medline:
16
5
2024
pubmed:
16
5
2024
entrez:
15
5
2024
Statut:
epublish
Résumé
Stress granules (SGs) are induced by various environmental stressors, resulting in their compositional and functional heterogeneity. SGs play a crucial role in the antiviral process, owing to their potent translational repressive effects and ability to trigger signal transduction; however, it is poorly understood how these antiviral SGs differ from SGs induced by other environmental stressors. Here we identify that TRIM25, a known driver of the ubiquitination-dependent antiviral innate immune response, is a potent and critical marker of the antiviral SGs. TRIM25 undergoes liquid-liquid phase separation (LLPS) and co-condenses with the SG core protein G3BP1 in a dsRNA-dependent manner. The co-condensation of TRIM25 and G3BP1 results in a significant enhancement of TRIM25's ubiquitination activity towards multiple antiviral proteins, which are mainly located in SGs. This co-condensation is critical in activating the RIG-I signaling pathway, thus restraining RNA virus infection. Our studies provide a conceptual framework for better understanding the heterogeneity of stress granule components and their response to distinct environmental stressors.
Identifiants
pubmed: 38750080
doi: 10.1038/s41467-024-48596-4
pii: 10.1038/s41467-024-48596-4
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
4127Informations de copyright
© 2024. The Author(s).
Références
Anderson, P. & Kedersha, N. RNA granules: post-transcriptional and epigenetic modulators of gene expression. Nat. Rev. Mol. Cell Biol. 10, 430–436 (2009).
pubmed: 19461665
doi: 10.1038/nrm2694
Guillen-Boixet, J. et al. RNA-induced conformational switching and clustering of G3BP drive stress granule assembly by condensation. Cell 181, 346–361.e17 (2020).
pubmed: 32302572
pmcid: 7181197
doi: 10.1016/j.cell.2020.03.049
Yang, P. et al. G3BP1 is a tunable switch that triggers phase separation to assemble stress granules. Cell 181, 325–345.e8 (2020).
pubmed: 32302571
pmcid: 7448383
doi: 10.1016/j.cell.2020.03.046
Eiermann, N., Haneke, K., Sun, Z., Stoecklin, G. & Ruggieri, A. Dance with the devil: stress granules and signaling in antiviral responses. Viruses 12, 984 (2020).
pubmed: 32899736
pmcid: 7552005
doi: 10.3390/v12090984
McCormick, C. & Khaperskyy, D. A. Translation inhibition and stress granules in the antiviral immune response. Nat. Rev. Immunol. 17, 647–660 (2017).
pubmed: 28669985
doi: 10.1038/nri.2017.63
Poblete-Duran, N., Prades-Perez, Y., Vera-Otarola, J., Soto-Rifo, R. & Valiente-Echeverria, F. Who regulates whom? An overview of RNA granules and viral infections. Viruses 8, 180 (2016).
pubmed: 27367717
pmcid: 4974515
doi: 10.3390/v8070180
Guan, Y. et al. Multiple functions of stress granules in viral infection at a glance. Front. Microbiol. 14, 1138864 (2023).
pubmed: 36937261
pmcid: 10014870
doi: 10.3389/fmicb.2023.1138864
Manjunath, L. et al. APOBEC3B drives PKR-mediated translation shutdown and protects stress granules in response to viral infection. Nat. Commun. 14, 820 (2023).
pubmed: 36781883
pmcid: 9925369
doi: 10.1038/s41467-023-36445-9
Wolozin, B. & Ivanov, P. Stress granules and neurodegeneration. Nat. Rev. Neurosci. 20, 649–666 (2019).
pubmed: 31582840
pmcid: 6986315
doi: 10.1038/s41583-019-0222-5
Marmor-Kollet, H. et al. Spatiotemporal proteomic analysis of stress granule disassembly using APEX reveals regulation by SUMOylation and links to ALS pathogenesis. Mol. Cell 80, 876–891.e6 (2020).
pubmed: 33217318
pmcid: 7816607
doi: 10.1016/j.molcel.2020.10.032
Markmiller, S. et al. Context-dependent and disease-specific diversity in protein interactions within stress granules. Cell 172, 590–604.e13 (2018).
pubmed: 29373831
pmcid: 5969999
doi: 10.1016/j.cell.2017.12.032
Asadi, M. R. et al. Stress granules involved in formation, progression and metastasis of cancer: a scoping review. Front. Cell Dev. Biol. 9, 745394 (2021).
pubmed: 34604242
pmcid: 8485071
doi: 10.3389/fcell.2021.745394
Lee, J. I. & Namkoong, S. Stress granules dynamics: benefits in cancer. BMB Rep. 55, 577–586 (2022).
pubmed: 36330685
pmcid: 9813431
doi: 10.5483/BMBRep.2022.55.12.141
Advani, V. M. & Ivanov, P. Stress granule subtypes: an emerging link to neurodegeneration. Cell Mol. Life Sci. 77, 4827–4845 (2020).
pubmed: 32500266
pmcid: 7668291
doi: 10.1007/s00018-020-03565-0
Aulas, A. et al. Stress-specific differences in assembly and composition of stress granules and related foci. J. Cell Sci. 130, 927–937 (2017).
pubmed: 28096475
pmcid: 5358336
Reineke, L. C. & Neilson, J. R. Differences between acute and chronic stress granules, and how these differences may impact function in human disease. Biochem. Pharmacol. 162, 123–131 (2019).
pubmed: 30326201
doi: 10.1016/j.bcp.2018.10.009
Zeng, W. J. et al. Initiation of stress granule assembly by rapid clustering of IGF2BP proteins upon osmotic shock. Biochim. Biophys. Acta Mol. Cell Res. 1867, 118795 (2020).
pubmed: 32668274
doi: 10.1016/j.bbamcr.2020.118795
Liu, Y. et al. Hypoxia-induced FUS-circTBC1D14 stress granules promote autophagy in TNBC. Adv. Sci. 10, e2204988 (2023).
doi: 10.1002/advs.202204988
Cabral, A. J., Costello, D. C. & Farny, N. G. The enigma of ultraviolet radiation stress granules: research challenges and new perspectives. Front. Mol. Biosci. 9, 1066650 (2022).
pubmed: 36533077
pmcid: 9751325
doi: 10.3389/fmolb.2022.1066650
Rozman, B., Fisher, T. & Stern-Ginossar, N. Translation—a tug of war during viral infection. Mol. Cell 83, 481–495 (2023).
pubmed: 36334591
doi: 10.1016/j.molcel.2022.10.012
Kim, S. S., Sze, L., Liu, C. & Lam, K. P. The stress granule protein G3BP1 binds viral dsRNA and RIG-I to enhance interferon-beta response. J. Biol. Chem. 294, 6430–6438 (2019).
pubmed: 30804210
pmcid: 6484135
doi: 10.1074/jbc.RA118.005868
Liu, Z. S. et al. G3BP1 promotes DNA binding and activation of cGAS. Nat. Immunol. 20, 18–28 (2019).
pubmed: 30510222
doi: 10.1038/s41590-018-0262-4
Zhao, M. et al. The stress granule protein G3BP1 promotes pre-condensation of cGAS to allow rapid responses to DNA. EMBO Rep. 23, e53166 (2022).
pubmed: 34779554
doi: 10.15252/embr.202153166
Yoo, J. S. et al. DHX36 enhances RIG-I signaling by facilitating PKR-mediated antiviral stress granule formation. PLoS Pathog. 10, e1004012 (2014).
pubmed: 24651521
pmcid: 3961341
doi: 10.1371/journal.ppat.1004012
Huang, W. et al. Molecular determinants for regulation of G3BP1/2 phase separation by the SARS-CoV-2 nucleocapsid protein. Cell Discov. 7, 69 (2021).
pubmed: 34400613
pmcid: 8368218
doi: 10.1038/s41421-021-00306-w
Luo, L. et al. SARS-CoV-2 nucleocapsid protein phase separates with G3BPs to disassemble stress granules and facilitate viral production. Sci. Bull. 66, 1194–1204 (2021).
doi: 10.1016/j.scib.2021.01.013
Zheng, Z. Q., Wang, S. Y., Xu, Z. S., Fu, Y. Z. & Wang, Y. Y. SARS-CoV-2 nucleocapsid protein impairs stress granule formation to promote viral replication. Cell Discov. 7, 38 (2021).
pubmed: 34035218
pmcid: 8147577
doi: 10.1038/s41421-021-00275-0
Bao, M., Hofsink, N. & Plosch, T. LPS versus Poly I:C model: comparison of long-term effects of bacterial and viral maternal immune activation on the offspring. Am. J. Physiol. Regul. Integr. Comp. Physiol. 322, R99–R111 (2022).
pubmed: 34874190
doi: 10.1152/ajpregu.00087.2021
Roux, K. J., Kim, D. I., Raida, M. & Burke, B. A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells. J. Cell Biol. 196, 801–810 (2012).
pubmed: 22412018
pmcid: 3308701
doi: 10.1083/jcb.201112098
Burke, J. M., Lester, E. T., Tauber, D. & Parker, R. RNase L promotes the formation of unique ribonucleoprotein granules distinct from stress granules. J. Biol. Chem. 295, 1426–1438 (2020).
pubmed: 31896577
pmcid: 7008361
doi: 10.1074/jbc.RA119.011638
Burke, J. M., Moon, S. L., Matheny, T. & Parker, R. RNase L reprograms translation by widespread mRNA turnover escaped by antiviral mRNAs. Mol. Cell 75, 1203–1217.e5 (2019).
pubmed: 31494035
pmcid: 6754297
doi: 10.1016/j.molcel.2019.07.029
Sanchez, J. G. et al. TRIM25 binds RNA to modulate cellular anti-viral defense. J. Mol. Biol. 430, 5280–5293 (2018).
pubmed: 30342007
pmcid: 6289755
doi: 10.1016/j.jmb.2018.10.003
Haubrich, K. et al. Mechanistic insights into RNA binding and RNA-regulated RIG-I ubiquitination by TRIM25. bioRxiv https://doi.org/10.1101/2020.05.04.070177 (2021).
Álvarez, L. et al. The molecular dissection of TRIM25‘s RNA-binding mechanism provides key insights into its antiviral activity. Res. Sq. https://doi.org/10.21203/rs.3.rs-3692619/v1 (2023).
Panas, M. D. et al. Viral and cellular proteins containing FGDF motifs bind G3BP to block stress granule formation. PLoS Pathog. 11, e1004659 (2015).
pubmed: 25658430
pmcid: 4450067
doi: 10.1371/journal.ppat.1004659
Yang, E. et al. Elucidation of TRIM25 ubiquitination targets involved in diverse cellular and antiviral processes. PLoS Pathog. 18, e1010743 (2022).
pubmed: 36067236
pmcid: 9481182
doi: 10.1371/journal.ppat.1010743
Schulte, T. et al. Combined structural, biochemical and cellular evidence demonstrates that both FGDF motifs in alphavirus nsP3 are required for efficient replication. Open Biol. 6, 160078 (2016).
pubmed: 27383630
pmcid: 4967826
doi: 10.1098/rsob.160078
Kruse, T. et al. Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities. Nat. Commun. 12, 6761 (2021).
pubmed: 34799561
pmcid: 8605023
doi: 10.1038/s41467-021-26498-z
Choudhury, N. R. et al. RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination. BMC Biol. 15, 105 (2017).
pubmed: 29117863
pmcid: 5678581
doi: 10.1186/s12915-017-0444-9
Koliopoulos, M. G. et al. Molecular mechanism of influenza A NS1-mediated TRIM25 recognition and inhibition. Nat. Commun. 9, 1820 (2018).
pubmed: 29739942
pmcid: 5940772
doi: 10.1038/s41467-018-04214-8
Lian, H. et al. The zinc-finger protein ZCCHC3 binds RNA and facilitates viral RNA sensing and activation of the RIG-I-like receptors. Immunity 49, 438–448.e5 (2018).
pubmed: 30193849
doi: 10.1016/j.immuni.2018.08.014
Lian, H. et al. ZCCHC3 is a co-sensor of cGAS for dsDNA recognition in innate immune response. Nat. Commun. 9, 3349 (2018).
pubmed: 30135424
pmcid: 6105683
doi: 10.1038/s41467-018-05559-w
Li, B. et al. circNDUFB2 inhibits non-small cell lung cancer progression via destabilizing IGF2BPs and activating anti-tumor immunity. Nat. Commun. 12, 295 (2021).
pubmed: 33436560
pmcid: 7804955
doi: 10.1038/s41467-020-20527-z
Galao, R. P. et al. TRIM25 and ZAP target the Ebola virus ribonucleoprotein complex to mediate interferon-induced restriction. PLoS Pathog. 18, e1010530 (2022).
pubmed: 35533151
pmcid: 9119685
doi: 10.1371/journal.ppat.1010530
Yang, E., Nguyen, L. P., Wisherop, C. A., Kan, R. L. & Li, M. M. H. The role of ZAP and TRIM25 RNA binding in restricting viral translation. Front. Cell Infect. Microbiol. 12, 886929 (2022).
pubmed: 35800389
pmcid: 9253567
doi: 10.3389/fcimb.2022.886929
Law, L. M. J. et al. ZAP’s stress granule localization is correlated with its antiviral activity and induced by virus replication. PLoS Pathog. 15, e1007798 (2019).
pubmed: 31116799
pmcid: 6548403
doi: 10.1371/journal.ppat.1007798
Li, M. M. et al. TRIM25 enhances the antiviral action of zinc-finger antiviral protein (ZAP). PLoS Pathog. 13, e1006145 (2017).
pubmed: 28060952
pmcid: 5245905
doi: 10.1371/journal.ppat.1006145
Schwerk, J. et al. RNA-binding protein isoforms ZAP-S and ZAP-L have distinct antiviral and immune resolution functions. Nat. Immunol. 20, 1610–1620 (2019).
pubmed: 31740798
pmcid: 7240801
doi: 10.1038/s41590-019-0527-6
Sanchez-Aparicio, M. T., Ayllon, J., Leo-Macias, A., Wolff, T. & Garcia-Sastre, A. Subcellular localizations of RIG-I, TRIM25, and MAVS complexes. J. Virol. 91, e01155-16 (2017).
pubmed: 27807226
pmcid: 5215348
doi: 10.1128/JVI.01155-16
Loo, Y. M. & Gale, M. Jr. Immune signaling by RIG-I-like receptors. Immunity 34, 680–692 (2011).
pubmed: 21616437
pmcid: 3177755
doi: 10.1016/j.immuni.2011.05.003
Hou, F. et al. MAVS forms functional prion-like aggregates to activate and propagate antiviral innate immune response. Cell 146, 448–461 (2011).
pubmed: 21782231
pmcid: 3179916
doi: 10.1016/j.cell.2011.06.041
Gack, M. U. et al. TRIM25 RING-finger E3 ubiquitin ligase is essential for RIG-I-mediated antiviral activity. Nature 446, 916–920 (2007).
pubmed: 17392790
doi: 10.1038/nature05732
Cadena, C. et al. Ubiquitin-dependent and -independent roles of E3 ligase RIPLET in innate immunity. Cell 177, 1187–1200.e16 (2019).
pubmed: 31006531
pmcid: 6525047
doi: 10.1016/j.cell.2019.03.017
Heikel, G., Choudhury, N. R. & Michlewski, G. The role of Trim25 in development, disease and RNA metabolism. Biochem. Soc. Trans. 44, 1045–1050 (2016).
pubmed: 27528750
doi: 10.1042/BST20160077
Kato, K. et al. Structural analysis of RIG-I-like receptors reveals ancient rules of engagement between diverse RNA helicases and TRIM ubiquitin ligases. Mol. Cell 81, 599–613.e8 (2021).
pubmed: 33373584
doi: 10.1016/j.molcel.2020.11.047
Sanchez, J. G. et al. Mechanism of TRIM25 catalytic activation in the antiviral RIG-I pathway. Cell Rep. 16, 1315–1325 (2016).
pubmed: 27425606
pmcid: 5076470
doi: 10.1016/j.celrep.2016.06.070
Lin, H. et al. The long noncoding RNA Lnczc3h7a promotes a TRIM25-mediated RIG-I antiviral innate immune response. Nat. Immunol. 20, 812–823 (2019).
pubmed: 31036902
doi: 10.1038/s41590-019-0379-0
Zeng, W. et al. Reconstitution of the RIG-I pathway reveals a signaling role of unanchored polyubiquitin chains in innate immunity. Cell 141, 315–330 (2010).
pubmed: 20403326
pmcid: 2919214
doi: 10.1016/j.cell.2010.03.029
Gack, M. U. et al. Roles of RIG-I N-terminal tandem CARD and splice variant in TRIM25-mediated antiviral signal transduction. Proc. Natl Acad. Sci. USA 105, 16743–16748 (2008).
pubmed: 18948594
pmcid: 2575490
doi: 10.1073/pnas.0804947105
Song, D. et al. Yin and yang regulation of stress granules by Caprin-1. Proc. Natl Acad. Sci. USA 119, e2207975119 (2022).
pubmed: 36279435
pmcid: 9636964
doi: 10.1073/pnas.2207975119
Yang, Y. et al. TRIM25-mediated ubiquitination of G3BP1 regulates the proliferation and migration of human neuroblastoma cells. Biochim. Biophys. Acta Gene Regul. Mech. 1866, 194954 (2023).
Goncalves-Carneiro, D., Takata, M. A., Ong, H., Shilton, A. & Bieniasz, P. D. Origin and evolution of the zinc finger antiviral protein. PLoS Pathog. 17, e1009545 (2021).
pubmed: 33901262
pmcid: 8102003
doi: 10.1371/journal.ppat.1009545
Portz, B., Lee, B. L. & Shorter, J. FUS and TDP-43 phases in health and disease. Trends Biochem. Sci. 46, 550–563 (2021).
pubmed: 33446423
pmcid: 8195841
doi: 10.1016/j.tibs.2020.12.005
Li, Z., Liu, X. & Liu, M. Stress granule homeostasis, aberrant phase transition, and amyotrophic lateral sclerosis. ACS Chem. Neurosci. 13, 2356–2370 (2022).
pubmed: 35905138
doi: 10.1021/acschemneuro.2c00262
Wang, L., Yang, W., Li, B., Yuan, S. & Wang, F. Response to stress in biological disorders: implications of stress granule assembly and function. Cell Prolif. 54, e13086 (2021).
pubmed: 34170048
pmcid: 8349659
doi: 10.1111/cpr.13086
Cui, Q. et al. Diverse CMT2 neuropathies are linked to aberrant G3BP interactions in stress granules. Cell 186, 803–820.e5 (2023).
pubmed: 36738734
doi: 10.1016/j.cell.2022.12.046
Paget, M. et al. Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA. Mol. Cell 83, 1180–1196.e8 (2023).
pubmed: 37028415
pmcid: 10170497
doi: 10.1016/j.molcel.2023.03.010
Sears, R. M., May, D. G. & Roux, K. J. BioID as a tool for protein-proximity labeling in living cells. Methods Mol. Biol. 2012, 299–313 (2019).
pubmed: 31161514
pmcid: 6583792
doi: 10.1007/978-1-4939-9546-2_15
Lyu, H. et al. Proximity labeling reveals OTUD3 as a DNA-binding deubiquitinase of cGAS. Cell Rep. 42, 112309 (2023).
pubmed: 36966392
doi: 10.1016/j.celrep.2023.112309
Mao, L. et al. Phosphorylation of SNX27 by MAPK11/14 links cellular stress-signaling pathways with endocytic recycling. J. Cell Biol. 220, e202010048 (2021).
pubmed: 33605979
pmcid: 7901142
doi: 10.1083/jcb.202010048
Han, Z. et al. Model-based analysis uncovers mutations altering autophagy selectivity in human cancer. Nat. Commun. 12, 3258 (2021).
pubmed: 34059679
pmcid: 8166871
doi: 10.1038/s41467-021-23539-5
Gao, B. et al. Inhibition of anti-viral stress granule formation by coronavirus endoribonuclease nsp15 ensures efficient virus replication. PLoS Pathog. 17, e1008690 (2021).
pubmed: 33635931
pmcid: 7946191
doi: 10.1371/journal.ppat.1008690
Wang, S. et al. TRIM25 inhibits infectious bursal disease virus replication by targeting VP3 for ubiquitination and degradation. PLoS Pathog. 17, e1009900 (2021).
pubmed: 34516573
pmcid: 8459960
doi: 10.1371/journal.ppat.1009900
Shen, C. et al. Phase separation drives RNA virus-induced activation of the NLRP6 inflammasome. Cell 184, 5759–5774.e20 (2021).
pubmed: 34678144
pmcid: 8643277
doi: 10.1016/j.cell.2021.09.032
Liu, Z. et al. SCGN deficiency is a risk factor for autism spectrum disorder. Signal Transduct. Target. Ther. 8, 3 (2023).
pubmed: 36588101
pmcid: 9806109
doi: 10.1038/s41392-022-01225-2
Zhao, M. et al. A Golgi-resident GPR108 cooperates with E3 ubiquitin ligase Smurf1 to suppress antiviral innate immunity. Cell Rep. 42, 112655 (2023).
pubmed: 37330913
doi: 10.1016/j.celrep.2023.112655
Qin, Z. et al. Deactylation by SIRT1 enables liquid-liquid phase separation of IRF3/IRF7 in innate antiviral immunity. Nat. Immunol. 23, 1193–1207 (2022).
pubmed: 35879450
doi: 10.1038/s41590-022-01269-0
Gao, Y., Li, X., Li, P. & Lin, Y. A brief guideline for studies of phase-separated biomolecular condensates. Nat. Chem. Biol. 18, 1307–1318 (2022).
pubmed: 36400991
doi: 10.1038/s41589-022-01204-2
Yong, X. et al. SNX27-FERM-SNX1 complex structure rationalizes divergent trafficking pathways by SNX17 and SNX27. Proc. Natl Acad. Sci. USA 118, e2105510118 (2021).
pubmed: 34462354
pmcid: 8433557
doi: 10.1073/pnas.2105510118
Tu, Y. et al. TBC1D23 mediates Golgi-specific LKB1 signaling. Nat. Commun. 15, 1785 (2024).