References
- Caughey B, Lansbury PT. Protofibrils, pores, fibrils, and neurodegeneration: separating the responsible protein aggregates from the innocent bystanders. Annu Rev Neurosci. 2003;26:267–298.
- Chiti F, Dobson CM. Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem. 2006;75:333–366.
- Chin LS, Olzmann JA, Li L. Parkin-mediated ubiquitin signalling in aggresome formation and autophagy. Biochem Soc Trans. 2010;38:144–149.
- Richter-Landsberg C, Leyk J. Inclusion body formation, macroautophagy, and the role of HDAC6 in neurodegeneration. Acta Neuropathol. 2013;126:793–807.
- Takalo M, Salminen A, Soininen H, et al. Protein aggregation and degradation mechanisms in neurodegenerative diseases. Am J Neurodegener Dis. 2013;2:1–14.
- Yan J. Interplay between HDAC6 and its interacting partners: essential roles in the aggresome-autophagy pathway and neurodegenerative diseases. DNA Cell Biol. 2014;33:567–580.
- Lilienbaum A. Relationship between the proteasomal system and autophagy. Int J Biochem Mol Biol. 2013;4:1–26.
- Kopito RR. Aggresomes, inclusion bodies and protein aggregation. Trends Cell Biol. 2000;10:524–530.
- Johnston JA, Ward CL, Kopito RR. Aggresomes: a cellular response to misfolded proteins. J Cell Biol. 1998;143:1883–1898.
- Lamark T, Johansen T. Aggrephagy: selective disposal of protein aggregates by macroautophagy. Int J Cell Biol. 2012;2012:736905.
- Kawaguchi Y, Kovacs JJ, McLaurin A, et al. The deacetylase HDAC6 regulates aggresome formation and cell viability in response to misfolded protein stress. Cell. 2003;115:727–738.
- Gamerdinger M, Kaya AM, Wolfrum U, et al. BAG3 mediates chaperone-based aggresome-targeting and selective autophagy of misfolded proteins. EMBO Rep. 2011;12:149–156.
- Park Y, Park J, Kim YK. Crosstalk between translation and the aggresome-autophagy pathway. Autophagy. 2018;14:1079–1081.
- Park Y, Park J, Hwang HJ, et al. Nonsense-mediated mRNA decay factor UPF1 promotes aggresome formation. Nat Commun. 2020;11:3106.
- Park J, Park Y, Ryu I, et al. Misfolded polypeptides are selectively recognized and transported toward aggresomes by a CED complex. Nat Commun. 2017;8:15730.
- Meriin AB, Zaarur N, Sherman MY. Association of translation factor eEF1A with defective ribosomal products generates a signal for aggresome formation. J Cell Sci. 2012;125:2665–2674.
- Eschbach J, Dupuis L. Cytoplasmic dynein in neurodegeneration. Pharmacol Ther. 2011;130:348–363.
- Urnavicius L, Zhang K, Diamant AG, et al. The structure of the dynactin complex and its interaction with dynein. Science (New York, NY). 2015;347:1441–1446.
- Benzinger TL, Gregory DM, Burkoth TS, et al. Propagating structure of Alzheimer’s beta-amyloid(10-35) is parallel beta-sheet with residues in exact register. Proc Natl Acad Sci U S A. 1998;95:13407–13412.
- Der-Sarkissian A, Jao CC, Chen J, et al. Structural organization of alpha-synuclein fibrils studied by site-directed spin labeling. J Biol Chem. 2003;278:37530–37535.
- McNaught KS, Shashidharan P, Perl DP, et al. Aggresome-related biogenesis of Lewy bodies. Eur J Neurosci. 2002;16:2136–2148.
- Ross CA, Poirier MA. Protein aggregation and neurodegenerative disease. Nat Med. 2004;10(Suppl):S10–17.
- Wileman T. Aggresomes and autophagy generate sites for virus replication. Science (New York, NY). 2006;312:875–878.
- Gaete-Argel A, Márquez CL, Barriga GP, et al. Strategies for success. Viral infections and membraneless organelles. Front Cell Infect Microbiol. 2019;9:336.
- Olasunkanmi OI, Chen S, Mageto J, et al. Virus-induced cytoplasmic aggregates and inclusions are critical cellular regulatory and antiviral factors. Viruses. 2020:12. doi: https://doi.org/10.3390/v12040399.
- Zheng K, Jiang Y, He Z, et al. Cellular defence or viral assist: the dilemma of HDAC6. J Gen Virol. 2017;98:322–337.
- Banerjee I, Miyake Y, Nobs SP, et al. Influenza A virus uses the aggresome processing machinery for host cell entry. Science (New York, NY). 2014;346:473–477.
- Liu Y, Shevchenko A, Shevchenko A, et al. Adenovirus exploits the cellular aggresome response to accelerate inactivation of the MRN complex. J Virol. 2005;79:14004–14016.
- Nozawa N, Yamauchi Y, Ohtsuka K, et al. Formation of aggresome-like structures in herpes simplex virus type 2-infected cells and a potential role in virus assembly. Exp Cell Res. 2004;299:486–497.
- Heath CM, Windsor M, Wileman T. Aggresomes resemble sites specialized for virus assembly. J Cell Biol. 2001;153:449–455.
- Friedman JR, Fredericks WJ, Jensen DE, et al. KAP-1, a novel corepressor for the highly conserved KRAB repression domain. Genes Dev. 1996;10:2067–2078.
- Hatakeyama S. TRIM family proteins: roles in autophagy, immunity, and carcinogenesis. Trends Biochem Sci. 2017;42:297–311.
- Yang Y, Fiskus W, Yong B, et al. Acetylated hsp70 and KAP1-mediated Vps34 SUMOylation is required for autophagosome creation in autophagy. Proc Natl Acad Sci U S A. 2013;110:6841–6846.
- van Gent M, Sparrer KMJ, Gack MU, et al. Their roles in antiviral host defenses. Annu Rev Virol. 2018;5:385–405.
- Jaworska AM, Wlodarczyk NA, Mackiewicz A, et al. The role of TRIM family proteins in the regulation of cancer stem cell self-renewal: concise review. Stem Cells. 2019. DOI: https://doi.org/10.1002/stem.3109.
- Hage A, Rajsbaum R. To TRIM or not to TRIM: the balance of host-virus interactions mediated by the ubiquitin system. J Gen Virol. 2019. DOI:https://doi.org/10.1099/jgv.0.001341
- Patil G, Li S. Tripartite motif proteins: an emerging antiviral protein family. Future Virol. 2019;14:107–122.
- Czerwinska P, Mazurek S, Wiznerowicz M. The complexity of TRIM28 contribution to cancer. J Biomed Sci. 2017;24:63.
- Krischuns T, Günl F, Henschel L, et al. Phosphorylation of TRIM28 enhances the expression of IFN-β and proinflammatory cytokines during HPAIV infection of human lung epithelial cells. Front Immunol. 2018;9:2229.
- Peng Y, Zhang M, Jiang Z, et al. TRIM28 activates autophagy and promotes cell proliferation in glioblastoma. Onco Targets Ther. 2019;12:397–404.
- Pineda CT, Ramanathan S, Fon Tacer K, et al. Degradation of AMPK by a cancer-specific ubiquitin ligase. Cell. 2015;160:715–728.
- Lelouard H, Ferrand V, Marguet D, et al. Dendritic cell aggresome-like induced structures are dedicated areas for ubiquitination and storage of newly synthesized defective proteins. J Cell Biol. 2004;164:667–675.
- Szeto J, Kaniuk NA, Canadien V, et al. ALIS are stress-induced protein storage compartments for substrates of the proteasome and autophagy. Autophagy. 2006;2:189–199.
- Zaarur N, Meriin AB, Gabai VL, et al. Triggering aggresome formation. Dissecting aggresome-targeting and aggregation signals in synphilin 1. J Biol Chem. 2008;283:27575–27584.
- Engelender S, Kaminsky Z, Guo X, et al. Synphilin-1 associates with alpha-synuclein and promotes the formation of cytosolic inclusions. Nat Genet. 1999;22:110–114.
- Doyle JM, Gao J, Wang J, et al. MAGE-RING protein complexes comprise a family of E3 ubiquitin ligases. Mol Cell. 2010;39:963–974.
- Ivanov AV, Peng H, Yurchenko V, et al. PHD domain-mediated E3 ligase activity directs intramolecular sumoylation of an adjacent bromodomain required for gene silencing. Mol Cell. 2007;28:823–837.
- Li S, Min JY, Krug RM, et al. Binding of the influenza A virus NS1 protein to PKR mediates the inhibition of its activation by either PACT or double-stranded RNA. Virology. 2006;349:13–21.
- Bergmann M, Garcia-Sastre A, Carnero E, et al. Influenza virus NS1 protein counteracts PKR-mediated inhibition of replication. J Virol. 2000;74:6203–6206.
- Kochs G, García-Sastre A, Martínez-Sobrido L. Multiple anti-interferon actions of the influenza A virus NS1 protein. J Virol. 2007;81:7011–7021.
- Sharma K, Tripathi S, Ranjan P, et al. Influenza A virus nucleoprotein exploits Hsp40 to inhibit PKR activation. PLoS One. 2011;6:e20215.
- García-Sastre A, Egorov A, Matassov D, et al. Influenza A virus lacking the NS1 gene replicates in interferon-deficient systems. Virology. 1998;252:324–330.
- Nenasheva VV, Tarantul VZ. Many faces of TRIM proteins on the road from pluripotency to neurogenesis. Stem Cells Dev. 2019. DOI:https://doi.org/10.1089/scd.2019.0152
- Rousseaux MW, Revelli JP, Vazquez-Velez GE, et al. Depleting Trim28 in adult mice is well tolerated and reduces levels of alpha-synuclein and tau. eLife. 2018:7. doi: https://doi.org/10.7554/eLife.36768.
- Watanabe M, Hatakeyama S. TRIM proteins and diseases. J Biochem. 2017;161:135–144.
- Rousseaux MW, De Haro M, Lasagna-Reeves CA, et al. TRIM28 regulates the nuclear accumulation and toxicity of both alpha-synuclein and tau. eLife. 2016:5. doi: https://doi.org/10.7554/eLife.19809.
- Kim KM, Cho H, Choi K, et al. A new MIF4G domain-containing protein, CTIF, directs nuclear cap-binding protein CBP80/20-dependent translation. Genes Dev. 2009;23:2033–2045.
- Kim YK, Furic L, Desgroseillers L, et al. Mammalian Staufen1 recruits Upf1 to specific mRNA 3ʹUTRs so as to elicit mRNA decay. Cell. 2005;120:195–208.
- Fenger-Gron M, Fillman C, Norrild B, et al. Multiple processing body factors and the ARE binding protein TTP activate mRNA decapping. Mol Cell. 2005;20:905–915.
- Ryu I, Won YS, Ha H, et al. eIF4A3 phosphorylation by CDKs affects NMD during the cell cycle. Cell Rep. 2019;26:2126–2139 e2129.
- Park OH, Ha H, Lee Y, et al. Endoribonucleolytic cleavage of m(6)A-containing RNAs by RNase P/MRP complex. Mol Cell. 2019;74:494–507 e498.
- Jeong K, Ryu I, Park J, et al. Staufen1 and UPF1 exert opposite actions on the replacement of the nuclear cap-binding complex by eIF4E at the 5ʹ end of mRNAs. Nucleic Acids Res. 2019;47:9313–9328.
- Tokunaga M, Imamoto N, Sakata-Sogawa K. Highly inclined thin illumination enables clear single-molecule imaging in cells. Nat Methods. 2008;5:159–161.