1
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Saxena K, Inholz K, Basler M, Aichem A. FAT10 inhibits TRIM21 to down-regulate antiviral type-I interferon secretion. Life Sci Alliance 2024; 7:e202402786. [PMID: 38977311 PMCID: PMC11231494 DOI: 10.26508/lsa.202402786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/10/2024] Open
Abstract
The ubiquitin-like modifier FAT10 is upregulated under pro-inflammatory conditions, targets its substrates for proteasomal degradation and functions as a negative regulator of the type-I IFN response. Influenza A virus infection upregulates the production of type-I IFN and the expression of the E3 ligase TRIM21, which regulates type-I IFN production in a positive feedback manner. In this study, we show that FAT10 becomes covalently conjugated to TRIM21 and that this targets TRIM21 for proteasomal degradation. We further show that the coiled-coil and PRYSPRY domains of TRIM21 and the C-terminal diglycine motif of FAT10 are important for the TRIM21-FAT10 interaction. Moreover, upon influenza A virus infection and in the presence of FAT10 the total ubiquitination of TRIM21 is reduced and our data reveal that the FAT10-mediated degradation of TRIM21 diminishes IFNβ production. Overall, this study provides strong evidence that FAT10 down-regulates the antiviral type-I IFN production by modulating additional molecules of the RIG-I signaling pathway besides the already published OTUB1. In addition, we elucidate a novel mechanism of FAT10-mediated proteasomal degradation of TRIM21 that regulates its stability.
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Affiliation(s)
- Kritika Saxena
- https://ror.org/0546hnb39 Department of Biology, Division of Immunology, University of Konstanz, Konstanz, Germany
| | - Katharina Inholz
- https://ror.org/0546hnb39 Department of Biology, Division of Immunology, University of Konstanz, Konstanz, Germany
| | - Michael Basler
- https://ror.org/0546hnb39 Department of Biology, Division of Immunology, University of Konstanz, Konstanz, Germany
- https://ror.org/030dhdf69 Biotechnology Institute Thurgauhttps://ror.org/0546hnb39 at the University of Konstanz, Kreuzlingen, Switzerland
| | - Annette Aichem
- https://ror.org/0546hnb39 Department of Biology, Division of Immunology, University of Konstanz, Konstanz, Germany
- https://ror.org/030dhdf69 Biotechnology Institute Thurgauhttps://ror.org/0546hnb39 at the University of Konstanz, Kreuzlingen, Switzerland
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2
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Negi H, Ravichandran A, Dasgupta P, Reddy S, Das R. Plasticity of the proteasome-targeting signal Fat10 enhances substrate degradation. eLife 2024; 13:e91122. [PMID: 38984715 PMCID: PMC11299979 DOI: 10.7554/elife.91122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 07/09/2024] [Indexed: 07/11/2024] Open
Abstract
The proteasome controls levels of most cellular proteins, and its activity is regulated under stress, quiescence, and inflammation. However, factors determining the proteasomal degradation rate remain poorly understood. Proteasome substrates are conjugated with small proteins (tags) like ubiquitin and Fat10 to target them to the proteasome. It is unclear if the structural plasticity of proteasome-targeting tags can influence substrate degradation. Fat10 is upregulated during inflammation, and its substrates undergo rapid proteasomal degradation. We report that the degradation rate of Fat10 substrates critically depends on the structural plasticity of Fat10. While the ubiquitin tag is recycled at the proteasome, Fat10 is degraded with the substrate. Our results suggest significantly lower thermodynamic stability and faster mechanical unfolding in Fat10 compared to ubiquitin. Long-range salt bridges are absent in the Fat10 structure, creating a plastic protein with partially unstructured regions suitable for proteasome engagement. Fat10 plasticity destabilizes substrates significantly and creates partially unstructured regions in the substrate to enhance degradation. NMR-relaxation-derived order parameters and temperature dependence of chemical shifts identify the Fat10-induced partially unstructured regions in the substrate, which correlated excellently to Fat10-substrate contacts, suggesting that the tag-substrate collision destabilizes the substrate. These results highlight a strong dependence of proteasomal degradation on the structural plasticity and thermodynamic properties of the proteasome-targeting tags.
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Affiliation(s)
- Hitendra Negi
- National Center for Biological Sciences, Tata Institute of Fundamental ResearchBangaloreIndia
- SASTRA University, ThirumalaisamudramThanjavurIndia
| | - Aravind Ravichandran
- National Center for Biological Sciences, Tata Institute of Fundamental ResearchBangaloreIndia
- SASTRA University, ThirumalaisamudramThanjavurIndia
| | - Pritha Dasgupta
- National Center for Biological Sciences, Tata Institute of Fundamental ResearchBangaloreIndia
| | - Shridivya Reddy
- National Center for Biological Sciences, Tata Institute of Fundamental ResearchBangaloreIndia
| | - Ranabir Das
- National Center for Biological Sciences, Tata Institute of Fundamental ResearchBangaloreIndia
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3
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Arkinson C, Dong KC, Gee CL, Costello SM, Marqusee S, Martin A. Nub1 traps unfolded FAT10 for ubiquitin-independent degradation by the 26S proteasome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598715. [PMID: 38915702 PMCID: PMC11195292 DOI: 10.1101/2024.06.12.598715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The ubiquitin-like modifier FAT10 targets hundreds of proteins in the mammalian immune system to the 26S proteasome for degradation. This degradation pathway requires the cofactor Nub1, yet the underlying mechanisms remain unknown. Here, we reconstituted a minimal in vitro system and revealed that Nub1 utilizes FAT10's intrinsic instability to trap its N-terminal ubiquitin-like domain in an unfolded state and deliver it to the 26S proteasome for engagement, allowing the degradation of FAT10-ylated substrates in a ubiquitin- and p97-independent manner. Through hydrogen-deuterium exchange, structural modeling, and site-directed mutagenesis, we identified the formation of a peculiar complex with FAT10 that activates Nub1 for docking to the 26S proteasome, and our cryo-EM studies visualized the highly dynamic Nub1 complex bound to the proteasomal Rpn1 subunit during FAT10 delivery and the early stages of ATP-dependent degradation. These studies thus identified a novel mode of cofactor-mediated, ubiquitin-independent substrate delivery to the 26S proteasome that relies on trapping partially unfolded states for engagement by the proteasomal ATPase motor.
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Affiliation(s)
- Connor Arkinson
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA94720, USA
| | - Ken C. Dong
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA94720, USA
| | - Christine L. Gee
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA94720, USA
| | - Shawn M. Costello
- Biophysics Graduate Program, University of California, Berkeley, CA, USA
| | - Susan Marqusee
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Andreas Martin
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA94720, USA
- Lead contact
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4
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Bonacci T, Bolhuis DL, Brown NG, Emanuele MJ. Mechanisms of USP18 deISGylation revealed by comparative analysis with its human paralog USP41. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596309. [PMID: 38853827 PMCID: PMC11160589 DOI: 10.1101/2024.05.28.596309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The ubiquitin-like protein ISG15 (interferon-stimulated gene 15) regulates the host response to bacterial and viral infections through its conjugation to proteins (ISGylation) following interferon production. ISGylation is antagonized by the highly specific cysteine protease USP18, which is the major deISGylating enzyme. However, mechanisms underlying USP18's extraordinary specificity towards ISG15 remains elusive. Here, we show that USP18 interacts with its paralog USP41, whose catalytic domain shares 97% identity with USP18. However, USP41 does not act as a deISGylase, which led us to perform a comparative analysis to decipher the basis for this difference, revealing molecular determinants of USP18's specificity towards ISG15. We found that USP18 C-terminus, as well as a conserved Leucine at position 198, are essential for its enzymatic activity and likely act as functional surfaces based on AlphaFold predictions. Finally, we propose that USP41 antagonizes conjugation of the understudied ubiquitin-like protein FAT10 (HLA-F adjacent transcript 10) from substrates in a catalytic-independent manner. Altogether, our results offer new insights into USP18's specificity towards ISG15, while identifying USP41 as a negative regulator of FAT10 conjugation.
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Affiliation(s)
- Thomas Bonacci
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Derek L Bolhuis
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael J Emanuele
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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5
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Ravichandran A, Das R. The Thermodynamic Properties of Fat10ylated Proteins Are Regulated by the Fat10ylation Site. ACS OMEGA 2024; 9:22265-22276. [PMID: 38799324 PMCID: PMC11112694 DOI: 10.1021/acsomega.4c01396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024]
Abstract
Degradation of proteins by the proteasome is crucial in regulating their levels in the cell. Post-translational modifications, such as ubiquitylation and Fat10ylation, trigger proteasomal degradation of the substrate proteins. While ubiquitylation regulates multiple cellular pathways, Fat10ylation functions explicitly in the inflammatory response pathway. At the proteasome, ubiquitin is recycled after being cleaved from the substrate, while Fat10 is degraded simultaneously with its substrate. Although the thermodynamic properties of the substrate are critical for effective proteasomal degradation, they remain poorly understood for the Fat10-proteasome pathway. We studied the thermodynamic properties of the Fat10∼substrate conjugate to uncover mechanistic details of the pathway. First, the mechanical unfolding of Fat10∼substrate was studied by molecular dynamics simulations, which suggested that the unfolding pathway and unfolding energy of the substrate depend on the site of Fat10 modification. We also investigated different pathways for the entry of the Fat10∼substrate into the proteasome core. Our analysis supports a model where the entry of Fat10, followed by the substrate, is the energetically preferred pathway. Further, we studied Fat10's effect on the thermodynamic properties of distinct substrates, considering their size, flexibility, and surface properties. The results uncovered significant entropic destabilization of substrates due to Fat10ylation, particularly in smaller substrates. For larger substrates, multi-monoFat10ylation is necessary to induce destabilization. Our study further reveals that Fat10 modification at negative patches on substrate surfaces is essential for optimal destabilization and subsequent degradation. These findings provide atomistic insights into the degradation mechanisms in the Fat10 proteasome pathway with potential implications for therapeutic interventions.
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Affiliation(s)
- Aravind Ravichandran
- National
Center for Biological Sciences, Tata Institute
of Fundamental Research, Bangalore 560065, India
- SASTRA
University, Thirumalaisamudram, Thanjavur 613401, India
| | - Ranabir Das
- National
Center for Biological Sciences, Tata Institute
of Fundamental Research, Bangalore 560065, India
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6
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Saxena K, Roverato ND, Reithmann M, Mah MM, Schregle R, Schmidtke G, Silbern I, Urlaub H, Aichem A. FAT10 is phosphorylated by IKKβ to inhibit the antiviral type-I interferon response. Life Sci Alliance 2024; 7:e202101282. [PMID: 37940187 PMCID: PMC10631552 DOI: 10.26508/lsa.202101282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023] Open
Abstract
IFN-I secretion provides a rapid host defense against infection with RNA viruses. Within the host cell, viral RNA triggers the activation of the RIG-I signaling pathway, leading to the production of IFN-I. Because an exaggerated IFN-I response causes severe tissue damage, RIG-I signaling is tightly regulated. One of the factors that control the IFN-I response is the ubiquitin-like modifier FAT10, which is induced by TNF and IFNγ and targets covalently FAT10-linked proteins for proteasomal degradation. However, the mechanism of how FAT10 modulates IFN-I secretion remains to be fully elucidated. Here, we provide strong evidence that FAT10 is phosphorylated by IκB kinase β (IKKβ) upon TNF stimulation and during influenza A virus infection on several serine and threonine residues. FAT10 phosphorylation increases the binding of FAT10 to the TRAF3-deubiquitylase OTUB1 and its FAT10-mediated activation. Consequently, FAT10 phosphorylation results in a low ubiquitylation state of TRAF3, which is unable to maintain interferon regulatory factor 3 phosphorylation and downstream induction of IFN-I. Taken together, we reveal a mechanism of how phosphorylation of FAT10 limits the production of tissue-destructive IFN-I in inflammation.
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Affiliation(s)
- Kritika Saxena
- https://ror.org/0546hnb39 Department of Biology, Division of Immunology, University of Konstanz, Konstanz, Germany
| | - Nicola Domenico Roverato
- https://ror.org/0546hnb39 Department of Biology, Division of Immunology, University of Konstanz, Konstanz, Germany
| | - Melody Reithmann
- https://ror.org/0546hnb39 Department of Biology, Division of Immunology, University of Konstanz, Konstanz, Germany
| | - Mei Min Mah
- https://ror.org/0546hnb39 Department of Biology, Division of Immunology, University of Konstanz, Konstanz, Germany
| | - Richard Schregle
- https://ror.org/0546hnb39 Department of Biology, Division of Immunology, University of Konstanz, Konstanz, Germany
- https://ror.org/030dhdf69 Biotechnology Institute Thurgauhttps://ror.org/0546hnb39 at The University of Konstanz, Kreuzlingen, Switzerland
| | - Gunter Schmidtke
- https://ror.org/0546hnb39 Department of Biology, Division of Immunology, University of Konstanz, Konstanz, Germany
| | - Ivan Silbern
- https://ror.org/03av75f26 Bioanalytical Mass Spectrometry Research Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Henning Urlaub
- https://ror.org/03av75f26 Bioanalytical Mass Spectrometry Research Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Annette Aichem
- https://ror.org/0546hnb39 Department of Biology, Division of Immunology, University of Konstanz, Konstanz, Germany
- https://ror.org/030dhdf69 Biotechnology Institute Thurgauhttps://ror.org/0546hnb39 at The University of Konstanz, Kreuzlingen, Switzerland
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7
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Hunt LC, Pagala V, Stephan A, Xie B, Kodali K, Kavdia K, Wang YD, Shirinifard A, Curley M, Graca FA, Fu Y, Poudel S, Li Y, Wang X, Tan H, Peng J, Demontis F. An adaptive stress response that confers cellular resilience to decreased ubiquitination. Nat Commun 2023; 14:7348. [PMID: 37963875 PMCID: PMC10646096 DOI: 10.1038/s41467-023-43262-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 11/02/2023] [Indexed: 11/16/2023] Open
Abstract
Ubiquitination is a post-translational modification initiated by the E1 enzyme UBA1, which transfers ubiquitin to ~35 E2 ubiquitin-conjugating enzymes. While UBA1 loss is cell lethal, it remains unknown how partial reduction in UBA1 activity is endured. Here, we utilize deep-coverage mass spectrometry to define the E1-E2 interactome and to determine the proteins that are modulated by knockdown of UBA1 and of each E2 in human cells. These analyses define the UBA1/E2-sensitive proteome and the E2 specificity in protein modulation. Interestingly, profound adaptations in peroxisomes and other organelles are triggered by decreased ubiquitination. While the cargo receptor PEX5 depends on its mono-ubiquitination for binding to peroxisomal proteins and importing them into peroxisomes, we find that UBA1/E2 knockdown induces the compensatory upregulation of other PEX proteins necessary for PEX5 docking to the peroxisomal membrane. Altogether, this study defines a homeostatic mechanism that sustains peroxisomal protein import in cells with decreased ubiquitination capacity.
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Affiliation(s)
- Liam C Hunt
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Department of Biology, Rhodes College, 2000 North Pkwy, Memphis, TN, 38112, USA
| | - Vishwajeeth Pagala
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Anna Stephan
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Boer Xie
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kiran Kodali
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kanisha Kavdia
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yong-Dong Wang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Abbas Shirinifard
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Michelle Curley
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Flavia A Graca
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yingxue Fu
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Suresh Poudel
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yuxin Li
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Haiyan Tan
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Junmin Peng
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Fabio Demontis
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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8
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Schnell L, Zubrod A, Catone N, Bialas J, Aichem A. Tumor necrosis factor mediates USE1-independent FAT10ylation under inflammatory conditions. Life Sci Alliance 2023; 6:e202301985. [PMID: 37604583 PMCID: PMC10442930 DOI: 10.26508/lsa.202301985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 08/11/2023] [Accepted: 08/11/2023] [Indexed: 08/23/2023] Open
Abstract
The ubiquitin-like modifier FAT10 is up-regulated in many different cell types by IFNγ and TNFα (TNF) and directly targets proteins for proteasomal degradation. FAT10 gets covalently conjugated to its conjugation substrates by the E1 activating enzyme UBA6, the E2 conjugating enzyme USE1, and E3 ligases including Parkin. To date, USE1 was supposed to be the only E2 enzyme for FAT10ylation, and we show here that a knockout of USE1 strongly diminished FAT10 conjugation. Remarkably, under inflammatory conditions in the presence of TNF, FAT10 conjugation appears to be independent of USE1. We report on the identification of additional E2 conjugating enzymes, which were previously not associated with FAT10. We confirm their capacity to be charged with FAT10 onto their active site cysteine, and to rescue FAT10 conjugation in the absence of USE1. This finding strongly widens the field of FAT10 research by pointing to multiple, so far unknown pathways for the conjugation of FAT10, disclosing novel possibilities for pharmacological interventions to regulate FAT10 conjugation under inflammatory conditions and/or viral infections.
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Affiliation(s)
- Leonie Schnell
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland
- https://ror.org/0546hnb39 Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Alina Zubrod
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland
- https://ror.org/0546hnb39 Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Nicola Catone
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland
- https://ror.org/0546hnb39 Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Johanna Bialas
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland
- https://ror.org/0546hnb39 Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Annette Aichem
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland
- https://ror.org/0546hnb39 Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany
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9
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Mueller S, Bialas J, Ryu S, Catone N, Aichem A. The ubiquitin-like modifier FAT10 covalently modifies HUWE1 and strengthens the interaction of AMBRA1 and HUWE1. PLoS One 2023; 18:e0290002. [PMID: 37578983 PMCID: PMC10424871 DOI: 10.1371/journal.pone.0290002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/31/2023] [Indexed: 08/16/2023] Open
Abstract
The ubiquitin-like modifier FAT10 is highly upregulated under inflammatory conditions and targets its conjugation substrates to the degradation by the 26S proteasome. This process termed FAT10ylation is mediated by an enzymatic cascade and includes the E1 activating enzyme ubiquitin-like modifier activating enzyme 6 (UBA6), the E2 conjugating enzyme UBA6-specific E2 enzyme 1 (USE1) and E3 ligases, such as Parkin. In this study, the function of the HECT-type ubiquitin E3 ligase HUWE1 was investigated as a putative E3 ligase and/or conjugation substrate of FAT10. Our data provide strong evidence that HUWE1 is FAT10ylated in a UBA6 and FAT10 diglycine-dependent manner in vitro and in cellulo and that the HUWE1-FAT10 conjugate is targeted to proteasomal degradation. Since the mutation of all relevant cysteine residues within the HUWE1 HECT domain did not abolish FAT10 conjugation, a role of HUWE1 as E3 ligase for FAT10ylation is rather unlikely. Moreover, we have identified the autophagy-related protein AMBRA1 as a new FAT10 interaction partner. We show that the HUWE1-FAT10 conjugate formation is diminished in presence of AMBRA1, while the interaction between AMBRA1 and HUWE1 is strengthened in presence of FAT10. This implies a putative interplay of all three proteins in cellular processes such as mitophagy.
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Affiliation(s)
- Stefanie Mueller
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland
- Division of Immunology, Department of Biology, University of Konstanz, Kontstanz, Germany
| | - Johanna Bialas
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland
- Division of Immunology, Department of Biology, University of Konstanz, Kontstanz, Germany
| | - Stella Ryu
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland
- Division of Immunology, Department of Biology, University of Konstanz, Kontstanz, Germany
| | - Nicola Catone
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland
| | - Annette Aichem
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland
- Division of Immunology, Department of Biology, University of Konstanz, Kontstanz, Germany
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10
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Brockmann F, Catone N, Wünsch C, Offensperger F, Scheffner M, Schmidtke G, Aichem A. FAT10 and NUB1L cooperate to activate the 26S proteasome. Life Sci Alliance 2023; 6:e202201463. [PMID: 37188463 PMCID: PMC10185811 DOI: 10.26508/lsa.202201463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 05/17/2023] Open
Abstract
The interaction of the 19S regulatory particle of the 26S proteasome with ubiquitylated proteins leads to gate opening of the 20S core particle and increases its proteolytic activity by binding of the ubiquitin chain to the inhibitory deubiquitylation enzyme USP14 on the 19S regulatory subunit RPN1. Covalent modification of proteins with the cytokine inducible ubiquitin-like modifier FAT10 is an alternative signal for proteasomal degradation. Here, we report that FAT10 and its interaction partner NUB1L facilitate the gate opening of the 20S proteasome in an ubiquitin- and USP14-independent manner. We also show that FAT10 is capable to activate all peptidolytic activities of the 26S proteasome, however only together with NUB1L, by binding to the UBA domains of NUB1L and thereby interfering with NUB1L dimerization. The binding of FAT10 to NUB1L leads to an increased affinity of NUB1L for the subunit RPN1. In conclusion, the herein described cooperation of FAT10 and NUB1L is a substrate-induced mechanism to activate the 26S proteasome.
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Affiliation(s)
- Florian Brockmann
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Nicola Catone
- Biotechnology Institute Thurgauhttps://ror.org/0546hnb39 at the University of Konstanz, Kreuzlingen, Switzerland
| | - Christine Wünsch
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Fabian Offensperger
- Division of Biochemistry, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Martin Scheffner
- Division of Biochemistry, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Gunter Schmidtke
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Annette Aichem
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany
- Biotechnology Institute Thurgauhttps://ror.org/0546hnb39 at the University of Konstanz, Kreuzlingen, Switzerland
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11
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Oliveri F, Keller SJ, Goebel H, Alvarez Salinas GO, Basler M. The ubiquitin-like modifier FAT10 is degraded by the 20S proteasome in vitro but not in cellulo. Life Sci Alliance 2023; 6:e202201760. [PMID: 37012049 PMCID: PMC10070814 DOI: 10.26508/lsa.202201760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 03/23/2023] [Accepted: 03/23/2023] [Indexed: 04/05/2023] Open
Abstract
Ubiquitin-independent protein degradation via the 20S proteasome without the 19S regulatory particle has gained increasing attention over the last years. The degradation of the ubiquitin-like modifier FAT10 by the 20S proteasome was investigated in this study. We found that FAT10 was rapidly degraded by purified 20S proteasomes in vitro, which was attributed to the weak folding of FAT10 and the N-terminally disordered tail. To confirm our results in cellulo, we established an inducible RNA interference system in which the AAA-ATPase Rpt2 of the 19S regulatory particle is knocked down to impair the function of the 26S proteasome. Using this system, degradation of FAT10 in cellulo was strongly dependent on functional 26S proteasome. Our data indicate that in vitro degradation studies with purified proteins do not necessarily reflect biological degradation mechanisms occurring in cells and, therefore, cautious data interpretation is required when 20S proteasome function is studied in vitro.
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Affiliation(s)
- Franziska Oliveri
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany
| | | | - Heike Goebel
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany
| | | | - Michael Basler
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany;
- Biotechnology Institute Thurgau https://ror.org/0546hnb39 at the University of Konstanz, Kreuzlingen, Switzerland
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12
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Franke L, Peter C. Visualizing the Residue Interaction Landscape of Proteins by Temporal Network Embedding. J Chem Theory Comput 2023; 19:2985-2995. [PMID: 37122117 DOI: 10.1021/acs.jctc.2c01228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Characterizing the structural dynamics of proteins with heterogeneous conformational landscapes is crucial to understanding complex biomolecular processes. To this end, dimensionality reduction algorithms are used to produce low-dimensional embeddings of the high-dimensional conformational phase space. However, identifying a compact and informative set of input features for the embedding remains an ongoing challenge. Here, we propose to harness the power of Residue Interaction Networks (RINs) and their centrality measures, established tools to provide a graph theoretical view on molecular structure. Specifically, we combine the closeness centrality, which captures global features of the protein conformation at residue-wise resolution, with EncoderMap, a hybrid neural-network autoencoder/multidimensional-scaling like dimensionality reduction algorithm. We find that the resulting low-dimensional embedding is a meaningful visualization of the residue interaction landscape that resolves structural details of the protein behavior while retaining global interpretability. This feature-based graph embedding of temporal protein graphs makes it possible to apply the general descriptive power of RIN formalisms to the analysis of protein simulations of complex processes such as protein folding and multidomain interactions requiring no protein-specific input. We demonstrate this on simulations of the fast folding protein Trp-Cage and the multidomain signaling protein FAT10. Due to its generality and modularity, the presented approach can easily be transferred to other protein systems.
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Affiliation(s)
- Leon Franke
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, Konstanz 78457, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, Konstanz 78457, Germany
| | - Christine Peter
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, Konstanz 78457, Germany
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13
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Wimalarathne MM, Wilkerson-Vidal QC, Hunt EC, Love-Rutledge ST. The case for FAT10 as a novel target in fatty liver diseases. Front Pharmacol 2022; 13:972320. [PMID: 36386217 PMCID: PMC9665838 DOI: 10.3389/fphar.2022.972320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 10/12/2022] [Indexed: 12/13/2022] Open
Abstract
Human leukocyte antigen F locus adjacent transcript 10 (FAT10) is a ubiquitin-like protein that targets proteins for degradation. TNFα and IFNγ upregulate FAT10, which increases susceptibility to inflammation-driven diseases like nonalcoholic fatty liver disease (NAFLD), non-alcoholic steatohepatitis (NASH), and hepatocellular carcinoma (HCC). It is well established that inflammation contributes to fatty liver disease, but how inflammation contributes to upregulation and what genes are involved is still poorly understood. New evidence shows that FAT10 plays a role in mitophagy, autophagy, insulin signaling, insulin resistance, and inflammation which may be directly associated with fatty liver disease development. This review will summarize the current literature regarding FAT10 role in developing liver diseases and potential therapeutic targets for nonalcoholic/alcoholic fatty liver disease and hepatocellular carcinoma.
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14
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Yuan L, Gao F, Lv Z, Nayak D, Nayak A, Santos Bury PD, Cano KE, Jia L, Oleinik N, Atilgan FC, Ogretmen B, Williams KM, Davies C, El Oualid F, Wasmuth EV, Olsen SK. Crystal structures reveal catalytic and regulatory mechanisms of the dual-specificity ubiquitin/FAT10 E1 enzyme Uba6. Nat Commun 2022; 13:4880. [PMID: 35986001 PMCID: PMC9391358 DOI: 10.1038/s41467-022-32613-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 08/08/2022] [Indexed: 11/11/2022] Open
Abstract
The E1 enzyme Uba6 initiates signal transduction by activating ubiquitin and the ubiquitin-like protein FAT10 in a two-step process involving sequential catalysis of adenylation and thioester bond formation. To gain mechanistic insights into these processes, we determined the crystal structure of a human Uba6/ubiquitin complex. Two distinct architectures of the complex are observed: one in which Uba6 adopts an open conformation with the active site configured for catalysis of adenylation, and a second drastically different closed conformation in which the adenylation active site is disassembled and reconfigured for catalysis of thioester bond formation. Surprisingly, an inositol hexakisphosphate (InsP6) molecule binds to a previously unidentified allosteric site on Uba6. Our structural, biochemical, and biophysical data indicate that InsP6 allosterically inhibits Uba6 activity by altering interconversion of the open and closed conformations of Uba6 while also enhancing its stability. In addition to revealing the molecular mechanisms of catalysis by Uba6 and allosteric regulation of its activities, our structures provide a framework for developing Uba6-specific inhibitors and raise the possibility of allosteric regulation of other E1s by naturally occurring cellular metabolites.
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Affiliation(s)
- Lingmin Yuan
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Fei Gao
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Department of Research & Development, Beijing IPE Center for Clinical Laboratory CO, Beijing, 100176, China
| | - Zongyang Lv
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Digant Nayak
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Anindita Nayak
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Priscila Dos Santos Bury
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Kristin E Cano
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Lijia Jia
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Natalia Oleinik
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Firdevs Cansu Atilgan
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Besim Ogretmen
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Katelyn M Williams
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Christopher Davies
- Department of Biochemistry & Molecular Biology, University of South Alabama, Mobile, AL, 36688, USA
| | - Farid El Oualid
- UbiQ Bio B.V., Science Park 408, 1098 XH, Amsterdam, The Netherlands
| | - Elizabeth V Wasmuth
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Shaun K Olsen
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
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15
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Structures of UBA6 explain its dual specificity for ubiquitin and FAT10. Nat Commun 2022; 13:4789. [PMID: 35970836 PMCID: PMC9378703 DOI: 10.1038/s41467-022-32040-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/13/2022] [Indexed: 12/02/2022] Open
Abstract
The covalent modification of target proteins with ubiquitin or ubiquitin-like modifiers is initiated by E1 activating enzymes, which typically transfer a single modifier onto cognate conjugating enzymes. UBA6 is an unusual E1 since it activates two highly distinct modifiers, ubiquitin and FAT10. Here, we report crystal structures of UBA6 in complex with either ATP or FAT10. In the UBA6-FAT10 complex, the C-terminal domain of FAT10 binds to where ubiquitin resides in the UBA1-ubiquitin complex, however, a switch element ensures the alternate recruitment of either modifier. Simultaneously, the N-terminal domain of FAT10 interacts with the 3-helix bundle of UBA6. Site-directed mutagenesis identifies residues permitting the selective activation of either ubiquitin or FAT10. These results pave the way for studies investigating the activation of either modifier by UBA6 in physiological and pathophysiological settings. UBA6 is an E1 enzyme that can activate both ubiquitin and FAT10. Here, the authors employ X-ray crystallography and biochemical techniques to explain this dual specificity, and identify UBA6 variants that are selectively impaired in the activation of either ubiquitin or FAT10.
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16
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Zhu T, Cui Y, Geng W, Liu G, Jiang H, Li R, Wu B. Creating an Unusual Glycine-Rich Motif in a Peptide Amidase Leads to Versatile Protein C-Terminal Traceless Functionalization. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tong Zhu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yinglu Cui
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenchao Geng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Guoxia Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Ruifeng Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bian Wu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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17
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Zhu J, Zhao J, Luo C, Zhu Z, Peng X, Zhu X, Lin K, Bu F, Zhang W, Li Q, Wang K, Hu Z, Yu X, Chen L, Yuan R. FAT10 promotes chemotherapeutic resistance in pancreatic cancer by inducing epithelial-mesenchymal transition via stabilization of FOXM1 expression. Cell Death Dis 2022; 13:497. [PMID: 35614040 PMCID: PMC9132907 DOI: 10.1038/s41419-022-04960-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 12/14/2022]
Abstract
Pancreatic cancer (PC) is one of the deadliest malignant tumors, and its resistance to gemcitabine chemotherapy is the primary reason for poor prognosis in patients. Ubiquitin-like protein FAT10 has recently been reported to promote tumor chemotherapy resistance. In this study, the expression of FAT10 in PC was significantly higher than that in adjacent noncancerous tissues. Increased expression of FAT10 in PC was related to a late TNM stage and decreased overall survival. Functional experiments revealed that downregulating the expression of FAT10 inhibits the proliferation and epithelial-mesenchymal transition (EMT) of PC cells, promotes the apoptosis of PC cells, and enhances sensitivity to gemcitabine chemotherapy. In addition, upregulation of FAT10 increased the expression of FOXM1 protein. The effect of downregulating FAT10 was reversed by FOXM1 overexpression, and FOXM1 knockdown inhibited EMT driven by FAT10 overexpression. Mechanistically, FAT10 stabilized the expression of FOXM1 by competing with ubiquitin to bind FOXM1 and inhibiting the ubiquitination-mediated degradation of FOXM1. In conclusion, the FAT10-FOXM1 axis is a pivotal driver of PC proliferation and gemcitabine resistance, and the results provide novel insights into chemotherapy resistance in PC.
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Affiliation(s)
- Jinfeng Zhu
- Department of General Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China
| | - Jiefeng Zhao
- Department of General Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China
| | - Chen Luo
- Department of General Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China
| | - Zhengming Zhu
- Department of General Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China
| | - Xingyu Peng
- Department of General Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China
| | - Xiaojian Zhu
- Department of General Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China
| | - Kang Lin
- Department of General Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China
| | - Fanqin Bu
- Department of General Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China
| | - Wenjun Zhang
- Department of General Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China
| | - Qing Li
- Department of Pathology, the Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China
| | - Kai Wang
- Department of General Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China
- Jiangxi Provincial Clinical Research Center for General Surgery Disease, Nanchang, 330006, Jiangxi Province, China
| | - Zhigang Hu
- Department of General Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China
| | - Xin Yu
- Department of General Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China
- Jiangxi Provincial Clinical Research Center for General Surgery Disease, Nanchang, 330006, Jiangxi Province, China
| | - Leifeng Chen
- Department of General Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China.
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China.
| | - Rongfa Yuan
- Department of General Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China.
- Jiangxi Provincial Clinical Research Center for General Surgery Disease, Nanchang, 330006, Jiangxi Province, China.
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18
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Arshad M, Abdul Hamid N, Chan MC, Ismail F, Tan GC, Pezzella F, Tan KL. NUB1 and FAT10 Proteins as Potential Novel Biomarkers in Cancer: A Translational Perspective. Cells 2021; 10:cells10092176. [PMID: 34571823 PMCID: PMC8468723 DOI: 10.3390/cells10092176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 12/30/2022] Open
Abstract
Cancer increases the global disease burden substantially, but it remains a challenge to manage it. The search for novel biomarkers is essential for risk assessment, diagnosis, prognosis, prediction of treatment response, and cancer monitoring. This paper examined NEDD8 ultimate buster-1 (NUB1) and F-adjacent transcript 10 (FAT10) proteins as novel biomarkers in cancer. This literature review is based on the search of the electronic database, PubMed. NUB1 is an interferon-inducible protein that mediates apoptotic and anti-proliferative actions in cancer, while FAT10 is a ubiquitin-like modifier that promotes cancer. The upregulated expression of both NUB1 and FAT10 has been observed in various cancers. NUB1 protein binds to FAT10 non-covalently to promote FAT10 degradation. An overexpressed FAT10 stimulates nuclear factor-kappa β, activates the inflammatory pathways, and induces the proliferation of cancer. The FAT10 protein interacts with the mitotic arrest deficient 2 protein, causing chromosomal instability and breast tumourigenesis. FAT10 binds to the proliferating cell nuclear antigen protein and inhibits the DNA damage repair response. In addition, FAT10 involves epithelial–mesenchymal transition, invasion, apoptosis, and multiplication in hepatocellular carcinoma. Our knowledge about them is still limited. There is a need to further develop NUB1 and FAT10 as novel biomarkers.
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Affiliation(s)
- Maria Arshad
- Faculty of Medicine & Health Sciences, Universiti Sains Islam Malaysia (USIM), Persiaran Ilmu, Putra Nilai, Nilai 71800, Malaysia; (M.A.); (N.A.H.)
| | - Nazefah Abdul Hamid
- Faculty of Medicine & Health Sciences, Universiti Sains Islam Malaysia (USIM), Persiaran Ilmu, Putra Nilai, Nilai 71800, Malaysia; (M.A.); (N.A.H.)
| | - Mun Chiang Chan
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia;
| | - Fuad Ismail
- Department of Radiotherapy & Oncology, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, Kuala Lumpur 56000, Malaysia;
| | - Geok Chin Tan
- Department of Pathology, Faculty of Medicine, Hospital Canselor Tuanku Muhriz, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Bandar Tun Razak, Kuala Lumpur 56000, Malaysia;
| | - Francesco Pezzella
- Tumour Pathology Laboratory, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK;
| | - Ka-Liong Tan
- Faculty of Medicine & Health Sciences, Universiti Sains Islam Malaysia (USIM), Persiaran Ilmu, Putra Nilai, Nilai 71800, Malaysia; (M.A.); (N.A.H.)
- Correspondence: or ; Tel.: +60-6798-2309; Fax: +60-6758-0404
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19
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Su H, Qin M, Liu Q, Jin B, Shi X, Xiang Z. Ubiquitin-Like Protein UBD Promotes Cell Proliferation in Colorectal Cancer by Facilitating p53 Degradation. Front Oncol 2021; 11:691347. [PMID: 34350116 PMCID: PMC8327751 DOI: 10.3389/fonc.2021.691347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/30/2021] [Indexed: 11/25/2022] Open
Abstract
Purpose Ubiquitin D (UBD) is a member of the ubiquitin-like modifier (UBL) family and is highly expressed in a variety of cancers including colorectal cancer (CRC). However, the mechanisms of its regulatory roles in CRC are largely elusive. In this study, we revealed the effect of UBD on the proliferation of CRC. Methods The expression of UBD in clinical tissue samples of CRC and seven CRC cell lines was detected using qRT-PCR, immunohistochemistry (IHC) and Western blotting. CCK-8, colony formation, EdU and flow cytometry assays were used to detect the functional changes of CRC cells transfected with UBD stable expression plasmids in vitro. A xenograft model was constructed to assess the effect of UBD on the growth of CRC cells in vivo. The connection between UBD and p53 was analyzed using Western blotting, immunoprecipitation, proteasome inhibition assay and Cycloheximide (CHX) chase assay. Results UBD was overexpressed in CRC tumor tissues compared with nontumor tissues, and its overexpression was positively associated with the tumor size and TNM stage of CRC patients. Functionally, UBD significantly accelerated CRC cell viability and proliferation in vitro and promoted tumorigenesis in vivo. Mechanistically, UBD interacted with p53 in CRC cells, downregulated the expression of p53 by regulating its degradation, shortened the p53 half-life, thereby further affecting the decrease in p21 and the increase in Cyclin D1, Cyclin E, CDK2, CDK4 and CDK6. Moreover, in vivo experiments showed that UBD-induced tumor growth in nude mice was dependent on a decrease in p53. Conclusions Our study proved that UBD mediates the degradation of p53, thereby facilitating the growth of CRC cells and ultimately promoting the progression of CRC. Therefore, UBD may be a potential therapeutic target and a promising prognostic biomarker for CRC.
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Affiliation(s)
- Hongbin Su
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Department of General Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Mengdi Qin
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Department of General Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qiang Liu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Department of General Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Bo Jin
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xianjun Shi
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zheng Xiang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Department of General Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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20
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Xiang S, Shao X, Cao J, Yang B, He Q, Ying M. FAT10: Function and Relationship with Cancer. Curr Mol Pharmacol 2021; 13:182-191. [PMID: 31729307 DOI: 10.2174/1874467212666191113130312] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/20/2019] [Accepted: 10/22/2019] [Indexed: 11/22/2022]
Abstract
Posttranslational protein modifications are known to be extensively involved in cancer, and a growing number of studies have revealed that the ubiquitin-like modifier FAT10 is directly involved in cancer development. FAT10 was found to be highly upregulated in various cancer types, such as glioma, hepatocellular carcinoma, breast cancer and gastrointestinal cancer. Protein FAT10ylation and interactions with FAT10 lead to the functional change of proteins, including proteasomal degradation, subcellular delocalization and stabilization, eventually having significant effects on cancer cell proliferation, invasion, metastasis and even tumorigenesis. In this review, we summarized the current knowledge on FAT10 and discussed its biological functions in cancer, as well as potential therapeutic strategies based on the FAT10 pathway.
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Affiliation(s)
- Senfeng Xiang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xuejing Shao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ji Cao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Bo Yang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qiaojun He
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Meidan Ying
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
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21
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Roverato ND, Sailer C, Catone N, Aichem A, Stengel F, Groettrup M. Parkin is an E3 ligase for the ubiquitin-like modifier FAT10, which inhibits Parkin activation and mitophagy. Cell Rep 2021; 34:108857. [PMID: 33730565 DOI: 10.1016/j.celrep.2021.108857] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 01/11/2021] [Accepted: 02/19/2021] [Indexed: 12/14/2022] Open
Abstract
Parkin is an E3 ubiquitin ligase belonging to the RING-between-RING family. Mutations in the Parkin-encoding gene PARK2 are associated with familial Parkinson's disease. Here, we investigate the interplay between Parkin and the inflammatory cytokine-induced ubiquitin-like modifier FAT10. FAT10 targets hundreds of proteins for degradation by the 26S proteasome. We show that FAT10 gets conjugated to Parkin and mediates its degradation in a proteasome-dependent manner. Parkin binds to the E2 enzyme of FAT10 (USE1), auto-FAT10ylates itself, and facilitates FAT10ylation of the Parkin substrate Mitofusin2 in vitro and in cells, thus identifying Parkin as a FAT10 E3 ligase. On mitochondrial depolarization, FAT10ylation of Parkin inhibits its activation and ubiquitin-ligase activity causing impairment of mitophagy progression and aggravation of rotenone-mediated death of dopaminergic neuronal cells. In conclusion, FAT10ylation inhibits Parkin and mitophagy rendering FAT10 a likely inflammation-induced exacerbating factor and potential drug target for Parkinson's disease.
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Affiliation(s)
- Nicola D Roverato
- Department of Biology, Division of Immunology, University of Konstanz, 78457 Konstanz, Germany
| | - Carolin Sailer
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Nicola Catone
- Biotechnology Institute Thurgau at the University of Konstanz, 8280 Kreuzlingen, Switzerland
| | - Annette Aichem
- Department of Biology, Division of Immunology, University of Konstanz, 78457 Konstanz, Germany; Biotechnology Institute Thurgau at the University of Konstanz, 8280 Kreuzlingen, Switzerland
| | - Florian Stengel
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Marcus Groettrup
- Department of Biology, Division of Immunology, University of Konstanz, 78457 Konstanz, Germany; Biotechnology Institute Thurgau at the University of Konstanz, 8280 Kreuzlingen, Switzerland.
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22
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Vaughan RM, Kupai A, Rothbart SB. Chromatin Regulation through Ubiquitin and Ubiquitin-like Histone Modifications. Trends Biochem Sci 2020; 46:258-269. [PMID: 33308996 DOI: 10.1016/j.tibs.2020.11.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/27/2020] [Accepted: 11/09/2020] [Indexed: 02/07/2023]
Abstract
Chromatin functions are influenced by the addition, removal, and recognition of histone post-translational modifications (PTMs). Ubiquitin and ubiquitin-like (UBL) PTMs on histone proteins can function as signaling molecules by mediating protein-protein interactions. Fueled by the identification of novel ubiquitin and UBL sites and the characterization of the writers, erasers, and readers, the breadth of chromatin functions associated with ubiquitin signaling is emerging. Here, we highlight recently appreciated roles for histone ubiquitination in DNA methylation control, PTM crosstalk, nucleosome structure, and phase separation. We also discuss the expanding diversity and functions associated with histone UBL modifications. We conclude with a look toward the future and pose key questions that will drive continued discovery at the interface of epigenetics and ubiquitin signaling.
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Affiliation(s)
- Robert M Vaughan
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ariana Kupai
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Scott B Rothbart
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
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23
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Zhang K, Chen L, Zhang Z, Cao J, He L, Li L. Ubiquitin-like protein FAT10: A potential cardioprotective factor and novel therapeutic target in cancer. Clin Chim Acta 2020; 510:802-811. [DOI: 10.1016/j.cca.2020.09.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 12/12/2022]
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24
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Aichem A, Groettrup M. The ubiquitin-like modifier FAT10 - much more than a proteasome-targeting signal. J Cell Sci 2020; 133:133/14/jcs246041. [PMID: 32719056 DOI: 10.1242/jcs.246041] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Human leukocyte antigen (HLA)-F adjacent transcript 10 (FAT10) also called ubiquitin D (UBD) is a member of the ubiquitin-like modifier (ULM) family. The FAT10 gene is localized in the MHC class I locus and FAT10 protein expression is mainly restricted to cells and organs of the immune system. In all other cell types and tissues, FAT10 expression is highly inducible by the pro-inflammatory cytokines interferon (IFN)-γ and tumor necrosis factor (TNF). Besides ubiquitin, FAT10 is the only ULM which directly targets its substrates for degradation by the 26S proteasome. This poses the question as to why two ULMs sharing the proteasome-targeting function have evolved and how they differ from each other. This Review summarizes the current knowledge of the special structure of FAT10 and highlights its differences from ubiquitin. We discuss how these differences might result in differential outcomes concerning proteasomal degradation mechanisms and non-covalent target interactions. Moreover, recent insights about the structural and functional impact of FAT10 interacting with specific non-covalent interaction partners are reviewed.
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Affiliation(s)
- Annette Aichem
- Biotechnology Institute Thurgau at the University of Konstanz, CH-8280 Kreuzlingen, Switzerland.,Division of Immunology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Marcus Groettrup
- Biotechnology Institute Thurgau at the University of Konstanz, CH-8280 Kreuzlingen, Switzerland .,Division of Immunology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
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25
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Regulation of Interferon Induction by the Ubiquitin-Like Modifier FAT10. Biomolecules 2020; 10:biom10060951. [PMID: 32586037 PMCID: PMC7356809 DOI: 10.3390/biom10060951] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/19/2020] [Accepted: 06/21/2020] [Indexed: 12/28/2022] Open
Abstract
The revelation that the human major histocompatibility complex (MHC) class I locus encodes a ubiquitin-like protein designated HLA-F adjacent transcript 10 (FAT10) or ubiquitin D (UBD) has attracted increasing attention to the function of this protein. Interestingly, the pro-inflammatory cytokines interferon (IFN)-γ and tumor necrosis factor (TNF) α synergize to strongly induce FAT10 expression, thereby suggesting a role of FAT10 in the immune response. Recent reports that FAT10 downregulates type I interferon production while it upregulates IFN-γ pose mechanistic questions on how FAT10 differentially regulates interferon induction. Several covalent and non-covalent binding partners of FAT10 involved in signal transduction pathways leading to IFN synthesis have been identified. After introducing FAT10, we review here recent insights into how FAT10 affects proteins in the interferon pathways, like the virus-responsive pattern recognition receptor RIG-I, the ubiquitin ligase ZNF598, and the deubiquitylating enzyme OTUB1. Moreover, we outline the consequences of FAT10 deficiency on interferon synthesis and viral expansion in mice and human cells. We discuss the need for covalent isopeptide linkage of FAT10 to the involved target proteins and the concomitant targeting for proteasomal degradation. After years of investigating the elusive biological functions of this fascinating ubiquitin-like modifier, we review the emerging evidence for a novel role of FAT10 in interferon regulation.
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26
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Kandel-Kfir M, Garcia-Milan R, Gueta I, Lubitz I, Ben-Zvi I, Shaish A, Shir L, Harats D, Mahajan M, Canaan A, Kamari Y. IFNγ potentiates TNFα/TNFR1 signaling to induce FAT10 expression in macrophages. Mol Immunol 2020; 117:101-109. [DOI: 10.1016/j.molimm.2019.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/11/2019] [Accepted: 11/13/2019] [Indexed: 01/22/2023]
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27
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Aichem A, Sailer C, Ryu S, Catone N, Stankovic-Valentin N, Schmidtke G, Melchior F, Stengel F, Groettrup M. The ubiquitin-like modifier FAT10 interferes with SUMO activation. Nat Commun 2019; 10:4452. [PMID: 31575873 PMCID: PMC6773726 DOI: 10.1038/s41467-019-12430-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/10/2019] [Indexed: 12/25/2022] Open
Abstract
The covalent attachment of the cytokine-inducible ubiquitin-like modifier HLA-F adjacent transcript 10 (FAT10) to hundreds of substrate proteins leads to their rapid degradation by the 26 S proteasome independently of ubiquitylation. Here, we identify another function of FAT10, showing that it interferes with the activation of SUMO1/2/3 in vitro and down-regulates SUMO conjugation and the SUMO-dependent formation of promyelocytic leukemia protein (PML) bodies in cells. Mechanistically, we show that FAT10 directly binds to and impedes the activity of the heterodimeric SUMO E1 activating enzyme AOS1/UBA2 by competing very efficiently with SUMO for activation and thioester formation. Nevertheless, activation of FAT10 by AOS1/UBA2 does not lead to covalent conjugation of FAT10 with substrate proteins which relies on its cognate E1 enzyme UBA6. Hence, we report that one ubiquitin-like modifier (FAT10) inhibits the conjugation and function of another ubiquitin-like modifier (SUMO) by impairing its activation. FAT10 is an ubiquitin-like modifier that targets proteins to proteasomal degradation. Here, the authors show that FAT10 also regulates SUMO activation in vitro and in cells, providing evidence for functional crosstalk between two ubiquitin-like modifiers.
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Affiliation(s)
- Annette Aichem
- Biotechnology Institute Thurgau at the University of Konstanz, CH-8280, Kreuzlingen, Switzerland. .,Department of Biology, Division of Immunology, University of Konstanz, D-78457, Konstanz, Germany.
| | - Carolin Sailer
- Department of Biology, University of Konstanz, D-78457, Konstanz, Germany
| | - Stella Ryu
- Biotechnology Institute Thurgau at the University of Konstanz, CH-8280, Kreuzlingen, Switzerland.,Department of Biology, Division of Immunology, University of Konstanz, D-78457, Konstanz, Germany
| | - Nicola Catone
- Biotechnology Institute Thurgau at the University of Konstanz, CH-8280, Kreuzlingen, Switzerland
| | - Nicolas Stankovic-Valentin
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, D-69120, Heidelberg, Germany
| | - Gunter Schmidtke
- Department of Biology, Division of Immunology, University of Konstanz, D-78457, Konstanz, Germany
| | - Frauke Melchior
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, D-69120, Heidelberg, Germany
| | - Florian Stengel
- Department of Biology, University of Konstanz, D-78457, Konstanz, Germany
| | - Marcus Groettrup
- Biotechnology Institute Thurgau at the University of Konstanz, CH-8280, Kreuzlingen, Switzerland.,Department of Biology, Division of Immunology, University of Konstanz, D-78457, Konstanz, Germany
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28
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Wang F, Zhao B. UBA6 and Its Bispecific Pathways for Ubiquitin and FAT10. Int J Mol Sci 2019; 20:ijms20092250. [PMID: 31067743 PMCID: PMC6539292 DOI: 10.3390/ijms20092250] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/26/2019] [Accepted: 04/28/2019] [Indexed: 12/25/2022] Open
Abstract
Questions have been raised since the discovery of UBA6 and its significant coexistence with UBE1 in the ubiquitin–proteasome system (UPS). The facts that UBA6 has the dedicated E2 enzyme USE1 and the E1–E2 cascade can activate and transfer both ubiquitin and ubiquitin-like protein FAT10 have attracted a great deal of attention to the regulational mechanisms of the UBA6–USE1 cascade and to how FAT10 and ubiquitin differentiate with each other. This review recapitulates the latest advances in UBA6 and its bispecific UBA6–USE1 pathways for both ubiquitin and FAT10. The intricate networks of UBA6 and its interplays with ubiquitin and FAT10 are briefly reviewed, as are their individual and collective functions in diverse physiological conditions.
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Affiliation(s)
- Fengting Wang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Bo Zhao
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China.
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29
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Aichem A, Boehm AN, Catone N, Schmidtke G, Groettrup M. Analysis of modification and proteolytic targeting by the ubiquitin-like modifier FAT10. Methods Enzymol 2019; 618:229-256. [PMID: 30850054 DOI: 10.1016/bs.mie.2018.12.040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The ubiquitin-like modifier FAT10 (also called ubiquitin D (UBD)) interacts noncovalently with a substantial number of proteins and also gets covalently conjugated to many substrate proteins, leading to their degradation by the 26S proteasome. FAT10 comprises two loosely folded ubiquitin-like domains that are connected by a flexible linker, and this unusual structure makes it highly prone to aggregation. Here, we report methods to purify high amounts of soluble recombinant FAT10 for various uses, such as in vitro FAT10ylation assays. In addition, we describe how to generate and handle overexpressed as well as endogenous FAT10 in cellulo for use in immunoprecipitations, Western blot analyses, and FAT10 degradation studies.
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Affiliation(s)
- Annette Aichem
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland; Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Annika N Boehm
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland; Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Nicola Catone
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland
| | - Gunter Schmidtke
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Marcus Groettrup
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland; Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany.
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30
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Bialas J, Boehm AN, Catone N, Aichem A, Groettrup M. The ubiquitin-like modifier FAT10 stimulates the activity of deubiquitylating enzyme OTUB1. J Biol Chem 2019; 294:4315-4330. [PMID: 30718280 DOI: 10.1074/jbc.ra118.005406] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 01/16/2019] [Indexed: 11/06/2022] Open
Abstract
The deubiquitylation of target proteins is mediated by deubiquitylating enzymes (DUB) such as OTUB1, which plays an important role in immune response, cell cycle progression, and DNA repair. Within these processes, OTUB1 reduces the ubiquitylation of target proteins in two distinct ways, either by using its catalytic DUB activity or in a noncatalytic manner by inhibiting the E2-conjugating enzyme. Here, we show that the ubiquitin-like modifier FAT10 regulates OTUB1 stability and functionality in different ways. Covalent FAT10ylation of OTUB1 resulted in its proteasomal degradation, whereas a noncovalent interaction stabilized OTUB1. We provide evidence that OTUB1 interacts directly with FAT10 and the E2-conjugating enzyme USE1. This interaction strongly stimulated OTUB1 DUB activity toward Lys-48-linked diubiquitin. Furthermore, the noncovalent interaction between FAT10 and OTUB1 not only enhanced its isopeptidase activity toward Lys-48-linked ubiquitin moieties but also strengthened its noncatalytic activity in reducing Lys-63 polyubiquitylation of its target protein TRAF3 (TNF receptor-associated factor 3). Additionally, the cellular clearance of overall polyubiquitylation by OTUB1 was strongly stimulated through the presence of FAT10. The addition of FAT10 also led to an increased interaction between OTUB1 and its cognate E2 UbcH5B, implying a function of FAT10 in the inhibition of polyubiquitylation. Overall, these data indicate that FAT10 not only plays a role in covalent modification, leading its substrates to proteasomal degradation, but also regulates the stability and functionality of target proteins by interacting in a noncovalent manner. FAT10 is thereby able to exert a major influence on ubiquitylation processes.
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Affiliation(s)
- Johanna Bialas
- From the Division of Immunology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany and.,the Biotechnology Institute Thurgau at the University of Konstanz, 8280 Kreuzlingen, Switzerland
| | - Annika N Boehm
- From the Division of Immunology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany and.,the Biotechnology Institute Thurgau at the University of Konstanz, 8280 Kreuzlingen, Switzerland
| | - Nicola Catone
- the Biotechnology Institute Thurgau at the University of Konstanz, 8280 Kreuzlingen, Switzerland
| | - Annette Aichem
- From the Division of Immunology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany and .,the Biotechnology Institute Thurgau at the University of Konstanz, 8280 Kreuzlingen, Switzerland
| | - Marcus Groettrup
- From the Division of Immunology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany and.,the Biotechnology Institute Thurgau at the University of Konstanz, 8280 Kreuzlingen, Switzerland
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