1
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Behbehani R, Johnson C, Holmes AJ, Gratian MJ, Mulvihill DP, Buss F. The two C. elegans class VI myosins, SPE-15/HUM-3 and HUM-8, share similar motor properties, but have distinct developmental and tissue expression patterns. Front Physiol 2024; 15:1368054. [PMID: 38660538 PMCID: PMC11040104 DOI: 10.3389/fphys.2024.1368054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/22/2024] [Indexed: 04/26/2024] Open
Abstract
Myosins of class VI move toward the minus-end of actin filaments and play vital roles in cellular processes such as endocytosis, autophagy, protein secretion, and the regulation of actin filament dynamics. In contrast to the majority of metazoan organisms examined to date which contain a single MYO6 gene, C. elegans, possesses two MYO6 homologues, SPE-15/HUM-3 and HUM-8. Through a combination of in vitro biochemical/biophysical analysis and cellular assays, we confirmed that both SPE-15/HUM-3 and HUM-8 exhibit reverse directionality, velocities, and ATPase activity similar to human MYO6. Our characterization also revealed that unlike SPE-15/HUM-3, HUM-8 is expressed as two distinct splice isoforms, one with an additional unique 14 amino acid insert in the cargo-binding domain. While lipid and adaptor binding sites are conserved in SPE-15/HUM-3 and HUM-8, this conservation does not enable recruitment to endosomes in mammalian cells. Finally, we performed super-resolution confocal imaging on transgenic worms expressing either mNeonGreen SPE-15/HUM-3 or wrmScarlet HUM-8. Our results show a clear distinction in tissue distribution between SPE-15/HUM-3 and HUM-8. While SPE-15/HUM-3 exhibited specific expression in the gonads and neuronal tissue in the head, HUM-8 was exclusively localized in the intestinal epithelium. Overall, these findings align with the established tissue distributions and localizations of human MYO6.
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Affiliation(s)
- Ranya Behbehani
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Chloe Johnson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Alexander J. Holmes
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Matthew J. Gratian
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | | | - Folma Buss
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
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2
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Chen D, Chen Y, Feng J, Huang W, Han Z, Liu Y, Lin Q, Li L, Lin Y. Guanine nucleotide exchange factor RABGEF1 facilitates TNF-induced necroptosis by targeting cIAP1. Biochem Biophys Res Commun 2024; 703:149669. [PMID: 38377943 DOI: 10.1016/j.bbrc.2024.149669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 02/04/2024] [Accepted: 02/09/2024] [Indexed: 02/22/2024]
Abstract
Necroptosis is a form of regulated cell death that depends on the receptor-interacting serine-threonine kinase 3 (RIPK3) and mixed lineage kinase domain-like (MLKL). The molecular mechanisms underlying distinct instances of necroptosis have only recently begun to emerge. In the present study, we characterized RABGEF1 as a positive regulator of RIPK1/RIPK3 activation in vitro. Based on the overexpression and knockdown experiments, we determined that RABGEF1 accelerated the phosphorylation of RIPK1 and promoted necrosome formation in L929 cells. The pro-necrotic effect of RABGEF1 is associated with its E3 ubiquitin ligase activity and guanine nucleotide exchange factor (GEF) activity. We further confirmed that RABGEF1 interacts with cIAP1 protein by inhibiting its function and plays a regulatory role in necroptosis, which can be abolished by treatment with the antagonist Smac mimetic (SM)-164. In conclusion, our study highlights a potential and novel role of RABGEF1 in promoting TNF-induced cell necrosis.
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Affiliation(s)
- Danni Chen
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Yushi Chen
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Jianting Feng
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Wenyang Huang
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Zeteng Han
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Yuanyuan Liu
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Qiaofa Lin
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Lisheng Li
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China; Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, 1 Xueyuan Road, Minhou, Fuzhou, China.
| | - Yingying Lin
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.
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3
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Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G. Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Mol Cell 2024; 84:839-853.e12. [PMID: 38242129 PMCID: PMC10939898 DOI: 10.1016/j.molcel.2023.12.036] [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: 09/12/2023] [Revised: 12/06/2023] [Accepted: 12/21/2023] [Indexed: 01/21/2024]
Abstract
RNF168 plays a central role in the DNA damage response (DDR) by ubiquitylating histone H2A at K13 and K15. These modifications direct BRCA1-BARD1 and 53BP1 foci formation in chromatin, essential for cell-cycle-dependent DNA double-strand break (DSB) repair pathway selection. The mechanism by which RNF168 catalyzes the targeted accumulation of H2A ubiquitin conjugates to form repair foci around DSBs remains unclear. Here, using cryoelectron microscopy (cryo-EM), nuclear magnetic resonance (NMR) spectroscopy, and functional assays, we provide a molecular description of the reaction cycle and dynamics of RNF168 as it modifies the nucleosome and recognizes its ubiquitylation products. We demonstrate an interaction of a canonical ubiquitin-binding domain within full-length RNF168, which not only engages ubiquitin but also the nucleosome surface, clarifying how such site-specific ubiquitin recognition propels a signal amplification loop. Beyond offering mechanistic insights into a key DDR protein, our study aids in understanding site specificity in both generating and interpreting chromatin ubiquitylation.
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Affiliation(s)
- Qi Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Debiao Zhao
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | | | | | - Maria Victoria Botuyan
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA.
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; Department of Cancer Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA.
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4
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Niu F, Li L, Wang L, Xiao J, Xu S, Liu Y, Lin L, Yu C, Wei Z. Autoinhibition and activation of myosin VI revealed by its cryo-EM structure. Nat Commun 2024; 15:1187. [PMID: 38331992 PMCID: PMC10853514 DOI: 10.1038/s41467-024-45424-7] [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: 09/15/2023] [Accepted: 01/23/2024] [Indexed: 02/10/2024] Open
Abstract
Myosin VI is the only molecular motor that moves towards the minus end along actin filaments. Numerous cellular processes require myosin VI and tight regulations of the motor's activity. Defects in myosin VI activity are known to cause genetic diseases such as deafness and cardiomyopathy. However, the molecular mechanisms underlying the activity regulation of myosin VI remain elusive. Here, we determined the high-resolution cryo-electron microscopic structure of myosin VI in its autoinhibited state. Our structure reveals that autoinhibited myosin VI adopts a compact, monomeric conformation via extensive interactions between the head and tail domains, orchestrated by an elongated single-α-helix region resembling a "spine". This autoinhibited structure effectively blocks cargo binding sites and represses the motor's ATPase activity. Certain cargo adaptors such as GIPC can release multiple inhibitory interactions and promote motor activity, pointing to a cargo-mediated activation of the processive motor. Moreover, our structural findings allow rationalization of disease-associated mutations in myosin VI. Beyond the activity regulation mechanisms of myosin VI, our study also sheds lights on how activities of other myosin motors such as myosin VII and X might be regulated.
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Affiliation(s)
- Fengfeng Niu
- Department of Neuroscience and Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, Shenzhen, Guangdong, China
| | - Lingxuan Li
- Department of Neuroscience and Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Lei Wang
- Department of Neuroscience and Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Jinman Xiao
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, and Shenzhen Key Laboratory of Cell Microenvironment, Shenzhen, Guangdong, China
| | - Shun Xu
- Department of Neuroscience and Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yong Liu
- Department of Neuroscience and Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Leishu Lin
- Department of Neuroscience and Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Cong Yu
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China.
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, and Shenzhen Key Laboratory of Cell Microenvironment, Shenzhen, Guangdong, China.
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong, China.
| | - Zhiyi Wei
- Department of Neuroscience and Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China.
- Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, Shenzhen, Guangdong, China.
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong, China.
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5
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Yakoub G, Choi YS, Wong RP, Strauch T, Ann KJ, Cohen RE, Ulrich HD. Avidity-based biosensors for ubiquitylated PCNA reveal choreography of DNA damage bypass. SCIENCE ADVANCES 2023; 9:eadf3041. [PMID: 37672592 PMCID: PMC10482348 DOI: 10.1126/sciadv.adf3041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 08/03/2023] [Indexed: 09/08/2023]
Abstract
In eukaryotes, the posttranslational modifier ubiquitin is used to regulate the amounts, interactions, or activities of proteins in diverse pathways and signaling networks. Its effects are mediated by monoubiquitin or polyubiquitin chains of varying geometries. We describe the design, validation, and application of a series of avidity-based probes against the ubiquitylated forms of the DNA replication clamp, proliferating cell nuclear antigen (PCNA), in budding yeast. Directed against total ubiquitylated PCNA or specifically K63-polyubiquitylated PCNA, the probes are tunable in their activities and can be used either as biosensors or as inhibitors of the PCNA-dependent DNA damage bypass pathway. Used in live cells, the probes revealed the timing of PCNA ubiquitylation during damage bypass and a particular susceptibility of the ribosomal DNA locus to the activation of the pathway. Our approach is applicable to a wide range of ubiquitin-conjugated proteins, thus representing a generalizable strategy for the design of biosensors for specific (poly)ubiquitylated forms of individual substrates.
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Affiliation(s)
- George Yakoub
- Institute of Molecular Biology gGmbH, Ackermannweg 4, D-55128 Mainz, Germany
| | - Yun-Seok Choi
- Department of Biochemistry and Molecular Biology, Colorado State University, 273 MRB, 1870 Campus Delivery, Fort Collins, CO 80523-1870, USA
| | - Ronald P. Wong
- Institute of Molecular Biology gGmbH, Ackermannweg 4, D-55128 Mainz, Germany
| | - Tina Strauch
- Institute of Molecular Biology gGmbH, Ackermannweg 4, D-55128 Mainz, Germany
| | - Kezia J. Ann
- Institute of Molecular Biology gGmbH, Ackermannweg 4, D-55128 Mainz, Germany
| | - Robert E. Cohen
- Department of Biochemistry and Molecular Biology, Colorado State University, 273 MRB, 1870 Campus Delivery, Fort Collins, CO 80523-1870, USA
| | - Helle D. Ulrich
- Institute of Molecular Biology gGmbH, Ackermannweg 4, D-55128 Mainz, Germany
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6
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Wilmes S, Kümmel D. Insights into the role of the membranes in Rab GTPase regulation. Curr Opin Cell Biol 2023; 83:102177. [PMID: 37327649 DOI: 10.1016/j.ceb.2023.102177] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/18/2023]
Abstract
Rab GTPases are molecular switches with essential roles in mediating vesicular trafficking and establishing organelle identity. The conversion from the inactive, cytosolic to the membrane-bound, active species and back is tightly controlled by regulatory proteins. Recently, the roles of membrane properties and lipid composition of different target organelles in determining the activity state of Rabs have come to light. The investigation of several Rab guanine nucleotide exchange factors (GEFs) has revealed principles of how the recruitment via lipid interactions and the spatial confinement on the membrane surface contribute to spatiotemporal specificity in the Rab GTPase network. This paints an intricate picture of the control mechanisms in Rab activation and highlights the importance of the membrane lipid code in the organization of the endomembrane system.
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Affiliation(s)
- Stephan Wilmes
- University of Münster, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany
| | - Daniel Kümmel
- University of Münster, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany.
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7
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Lachgar-Ruiz M, Morín M, Martelletti E, Ingham NJ, Preite L, Lewis MA, Serrão de Castro LS, Steel KP, Moreno-Pelayo MÁ. Insights into the pathophysiology of DFNA44 hearing loss associated with CCDC50 frameshift variants. Dis Model Mech 2023; 16:dmm049757. [PMID: 37165931 PMCID: PMC10445743 DOI: 10.1242/dmm.049757] [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: 07/12/2022] [Accepted: 05/02/2023] [Indexed: 05/12/2023] Open
Abstract
Non-syndromic sensorineural hearing loss (SNHL) is the most common sensory disorder, and it presents a high genetic heterogeneity. As part of our clinical genetic studies, we ascertained a previously unreported mutation in CCDC50 [c.828_858del, p.(Asp276Glufs*40)] segregating with hearing impairment in a Spanish family with SNHL associated with the autosomal dominant deafness locus DFNA44, which is predicted to disrupt protein function. To gain insight into the mechanism behind DFNA44 mutations, we analysed two Ccdc50 presumed loss-of-function mouse mutants, which showed normal hearing thresholds up to 6 months of age, indicating that haploinsufficiency is unlikely to be the pathogenic mechanism. We then carried out in vitro studies on a set of artificial mutants and on the p.(Asp276Glufs*40) and p.(Phe292Hisfs*37) human mutations, and determined that only the mutants containing the six-amino-acid sequence CLENGL as part of their aberrant protein tail showed an abnormal distribution consisting of perinuclear aggregates of the CCDC50 protein (also known as Ymer). Therefore, we conclude that the CLENGL sequence is necessary to form these aggregates. Taken together, the in vivo and in vitro results obtained in this study suggest that the two identified mutations in CCDC50 exert their effect through a dominant-negative or gain-of-function mechanism rather than by haploinsufficiency.
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Affiliation(s)
- María Lachgar-Ruiz
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London SE1 1UL, UK
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS and Biomedical Network Research Centre on Rare Diseases (CIBERER), km 9.100, 28034 Madrid, Spain
| | - Matías Morín
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS and Biomedical Network Research Centre on Rare Diseases (CIBERER), km 9.100, 28034 Madrid, Spain
| | - Elisa Martelletti
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Neil J. Ingham
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Lorenzo Preite
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Morag A. Lewis
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Luciana Santos Serrão de Castro
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS and Biomedical Network Research Centre on Rare Diseases (CIBERER), km 9.100, 28034 Madrid, Spain
| | - Karen P. Steel
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Miguel Ángel Moreno-Pelayo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS and Biomedical Network Research Centre on Rare Diseases (CIBERER), km 9.100, 28034 Madrid, Spain
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8
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Shi J, Hauschulte K, Mikicic I, Maharjan S, Arz V, Strauch T, Heidelberger JB, Schaefer JV, Dreier B, Plückthun A, Beli P, Ulrich HD, Wollscheid HP. Nuclear myosin VI maintains replication fork stability. Nat Commun 2023; 14:3787. [PMID: 37355687 PMCID: PMC10290672 DOI: 10.1038/s41467-023-39517-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 06/09/2023] [Indexed: 06/26/2023] Open
Abstract
The actin cytoskeleton is of fundamental importance for cellular structure and plasticity. However, abundance and function of filamentous actin in the nucleus are still controversial. Here we show that the actin-based molecular motor myosin VI contributes to the stabilization of stalled or reversed replication forks. In response to DNA replication stress, myosin VI associates with stalled replication intermediates and cooperates with the AAA ATPase Werner helicase interacting protein 1 (WRNIP1) in protecting these structures from DNA2-mediated nucleolytic attack. Using functionalized affinity probes to manipulate myosin VI levels in a compartment-specific manner, we provide evidence for the direct involvement of myosin VI in the nucleus and against a contribution of the abundant cytoplasmic pool during the replication stress response.
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Affiliation(s)
- Jie Shi
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Kristine Hauschulte
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Ivan Mikicic
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Srijana Maharjan
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
- Mainz Biomed N.V., Robert-Koch-Str. 50, D - 55129, Mainz, Germany
| | - Valerie Arz
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Tina Strauch
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Jan B Heidelberger
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
- Max Planck School Matter to Life, Jahnstr. 29, D - 69120, Heidelberg, Germany
| | - Jonas V Schaefer
- University of Zurich, Department of Biochemistry, Winterthurerstr. 190, CH - 8057, Zurich, Switzerland
| | - Birgit Dreier
- University of Zurich, Department of Biochemistry, Winterthurerstr. 190, CH - 8057, Zurich, Switzerland
| | - Andreas Plückthun
- University of Zurich, Department of Biochemistry, Winterthurerstr. 190, CH - 8057, Zurich, Switzerland
| | - Petra Beli
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University, Hanns-Dieter-Hüsch-Weg 15, D - 55128, Mainz, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany.
| | - Hans-Peter Wollscheid
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany.
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9
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Shinde SR, Mick DU, Aoki E, Rodrigues RB, Gygi SP, Nachury MV. The ancestral ESCRT protein TOM1L2 selects ubiquitinated cargoes for retrieval from cilia. Dev Cell 2023; 58:677-693.e9. [PMID: 37019113 PMCID: PMC10133032 DOI: 10.1016/j.devcel.2023.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/19/2022] [Accepted: 03/07/2023] [Indexed: 04/07/2023]
Abstract
Many G protein-coupled receptors (GPCRs) reside within cilia of mammalian cells and must undergo regulated exit from cilia for the appropriate transduction of signals such as hedgehog morphogens. Lysine 63-linked ubiquitin (UbK63) chains mark GPCRs for regulated removal from cilia, but the molecular basis of UbK63 recognition inside cilia remains elusive. Here, we show that the BBSome-the trafficking complex in charge of retrieving GPCRs from cilia-engages the ancestral endosomal sorting factor target of Myb1-like 2 (TOM1L2) to recognize UbK63 chains within cilia of human and mouse cells. TOM1L2 directly binds to UbK63 chains and the BBSome, and targeted disruption of the TOM1L2/BBSome interaction results in the accumulation of TOM1L2, ubiquitin, and the GPCRs SSTR3, Smoothened, and GPR161 inside cilia. Furthermore, the single-cell alga Chlamydomonas also requires its TOM1L2 ortholog in order to clear ubiquitinated proteins from cilia. We conclude that TOM1L2 broadly enables the retrieval of UbK63-tagged proteins by the ciliary trafficking machinery.
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Affiliation(s)
- Swapnil Rohidas Shinde
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David U Mick
- Center of Human and Molecular Biology and Center for Molecular Signaling, Department of Medical Biochemistry and Molecular Biology, Saarland University School of Medicine, Homburg, Germany
| | - Erika Aoki
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Rachel B Rodrigues
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Maxence V Nachury
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA 94143, USA.
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10
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Wang J, Chen H, Deng Q, Chen Y, Wang Z, Yan Z, Wang Y, Tang H, Liang H, Jiang Y. High expression of RNF169 is associated with poor prognosis in pancreatic adenocarcinoma by regulating tumour immune infiltration. Front Genet 2023; 13:1022626. [PMID: 36685833 PMCID: PMC9849556 DOI: 10.3389/fgene.2022.1022626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
Background: Pancreatic adenocarcinoma (PAAD) is a highly deadly and aggressive tumour with a poor prognosis. However, the prognostic value of RNF169 and its related mechanisms in PAAD have not been elucidated. In this study, we aimed to explore prognosis-related genes, especially RNF169 in PAAD and to identify novel potential prognostic predictors of PAAD. Methods: The GEPIA and UALCAN databases were used to investigate the expression and prognostic value of RNF169 in PAAD. The correlation between RNF169 expression and immune infiltration was determined by using TIMER and TISIDB. Correlation analysis with starBase was performed to identify a potential regulatory axis of lncRNA-miRNA-RNF169. Results: The data showed that the level of RNF169 mRNA expression in PAAD tissues was higher than that in normal tissues. High RNF169 expression was correlated with poor prognosis in PAAD. In addition, analysis with the TISIDB and TIMER databases revealed that RNF169 expression was positively correlated with tumour immune infiltration in PAAD. Correlation analysis suggested that the long non-coding RNA (lncRNA) AL049555.1 and the microRNA (miRNA) hsa-miR-324-5p were involved in the expression of RNF169, composing a potential regulatory axis to control the progression of PAAD. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that RNF169 plays a role in PAAD through pathways such as TNF, Hippo, JAK-STAT and Toll-like receptor signaling. Conclusion: In summary, the upregulation of RNF169 expression mediated by ncRNAs might influence immune cell infiltration in the microenvironment; thus, it can be used as a prognostic biomarker and a potential therapeutic target in PAAD.
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Affiliation(s)
- Jieyan Wang
- Department of Urology, The People’s Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzhen, Guangdong, China
| | - Hanghang Chen
- Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Qiong Deng
- Department of Urology, The People’s Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzhen, Guangdong, China
| | - Yeda Chen
- Department of Urology, The People’s Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzhen, Guangdong, China
| | - Zhu Wang
- Department of Urology, The People’s Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzhen, Guangdong, China
| | - Zhengzheng Yan
- Dongguan Key Laboratory of Respiratory and Critical Care Medicine, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, China
| | - Yinglin Wang
- Department of Pediatrics, The Second Hospital of Zhuzhou, Zhuzhou, Hunan, China
| | - Haoxuan Tang
- Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Hui Liang
- Department of Urology, The People’s Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzhen, Guangdong, China,*Correspondence: Hui Liang, ; Yong Jiang,
| | - Yong Jiang
- Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China,Dongguan Key Laboratory of Respiratory and Critical Care Medicine, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, China,*Correspondence: Hui Liang, ; Yong Jiang,
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11
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Kümmel D, Herrmann E, Langemeyer L, Ungermann C. Molecular insights into endolysosomal microcompartment formation and maintenance. Biol Chem 2022; 404:441-454. [PMID: 36503831 DOI: 10.1515/hsz-2022-0294] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022]
Abstract
Abstract
The endolysosomal system of eukaryotic cells has a key role in the homeostasis of the plasma membrane, in signaling and nutrient uptake, and is abused by viruses and pathogens for entry. Endocytosis of plasma membrane proteins results in vesicles, which fuse with the early endosome. If destined for lysosomal degradation, these proteins are packaged into intraluminal vesicles, converting an early endosome to a late endosome, which finally fuses with the lysosome. Each of these organelles has a unique membrane surface composition, which can form segmented membrane microcompartments by membrane contact sites or fission proteins. Furthermore, these organelles are in continuous exchange due to fission and fusion events. The underlying machinery, which maintains organelle identity along the pathway, is regulated by signaling processes. Here, we will focus on the Rab5 and Rab7 GTPases of early and late endosomes. As molecular switches, Rabs depend on activating guanine nucleotide exchange factors (GEFs). Over the last years, we characterized the Rab7 GEF, the Mon1-Ccz1 (MC1) complex, and key Rab7 effectors, the HOPS complex and retromer. Structural and functional analyses of these complexes lead to a molecular understanding of their function in the context of organelle biogenesis.
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Affiliation(s)
- Daniel Kümmel
- Institute of Biochemistry, University of Münster , Corrensstraße 36 , D-48149 Münster , Germany
| | - Eric Herrmann
- Institute of Biochemistry, University of Münster , Corrensstraße 36 , D-48149 Münster , Germany
| | - Lars Langemeyer
- Department of Biology/Chemistry, Biochemistry section , Osnabrück University , Barbarastraße 13 , D-49076 Osnabrück , Germany
- Center of Cellular Nanoanalytics (CellNanOs) , Osnabrück University , Barbarastraße 11 , D-49076 Osnabrück , Germany
| | - Christian Ungermann
- Department of Biology/Chemistry, Biochemistry section , Osnabrück University , Barbarastraße 13 , D-49076 Osnabrück , Germany
- Center of Cellular Nanoanalytics (CellNanOs) , Osnabrück University , Barbarastraße 11 , D-49076 Osnabrück , Germany
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12
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Yin X, Liu Q, Liu F, Tian X, Yan T, Han J, Jiang S. Emerging Roles of Non-proteolytic Ubiquitination in Tumorigenesis. Front Cell Dev Biol 2022; 10:944460. [PMID: 35874839 PMCID: PMC9298949 DOI: 10.3389/fcell.2022.944460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/15/2022] [Indexed: 12/13/2022] Open
Abstract
Ubiquitination is a critical type of protein post-translational modification playing an essential role in many cellular processes. To date, more than eight types of ubiquitination exist, all of which are involved in distinct cellular processes based on their structural differences. Studies have indicated that activation of the ubiquitination pathway is tightly connected with inflammation-related diseases as well as cancer, especially in the non-proteolytic canonical pathway, highlighting the vital roles of ubiquitination in metabolic programming. Studies relating degradable ubiquitination through lys48 or lys11-linked pathways to cellular signaling have been well-characterized. However, emerging evidence shows that non-degradable ubiquitination (linked to lys6, lys27, lys29, lys33, lys63, and Met1) remains to be defined. In this review, we summarize the non-proteolytic ubiquitination involved in tumorigenesis and related signaling pathways, with the aim of providing a reference for future exploration of ubiquitination and the potential targets for cancer therapies.
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Affiliation(s)
- Xiu Yin
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Qingbin Liu
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Fen Liu
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Xinchen Tian
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China.,Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Tinghao Yan
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China.,Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jie Han
- Department of Thyroid and Breast Surgery, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Shulong Jiang
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
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13
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Sato Y. Structural basis for the linkage specificity of ubiquitin-binding domain and deubiquitinase. J Biochem 2022; 172:1-7. [PMID: 35394523 DOI: 10.1093/jb/mvac031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/06/2022] [Indexed: 11/14/2022] Open
Abstract
Ubiquitination is a post-translational modification system essential for regulating a wide variety of biological processes in eukaryotes. Ubiquitin (Ub) itself undergoes post-translational modifications, including ubiquitination. All seven lysine residues and one N-terminal amino group of Ub can act as acceptors for further ubiquitination, producing eight types of Ub chains. Ub chains of different linkage types have different cellular functions and are referred to as the 'ubiquitin code'. Decoder molecules that contain linkage-specific Ub-binding domains (UBDs) recognize the Ub chains to regulate different cellular functions. On the other hand, deubiquitinases (DUBs) cleave Ub chains to reverse ubiquitin signals. This review discusses the molecular mechanisms of linkage-specific recognitions of Ub chains by UBDs and DUBs, which have been revealed by structural studies.
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Affiliation(s)
- Yusuke Sato
- Center for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan.,Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
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14
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Cotton TR, Cobbold SA, Bernardini JP, Richardson LW, Wang XS, Lechtenberg BC. Structural basis of K63-ubiquitin chain formation by the Gordon-Holmes syndrome RBR E3 ubiquitin ligase RNF216. Mol Cell 2021; 82:598-615.e8. [PMID: 34998453 DOI: 10.1016/j.molcel.2021.12.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 10/11/2021] [Accepted: 12/08/2021] [Indexed: 12/13/2022]
Abstract
An increasing number of genetic diseases are linked to deregulation of E3 ubiquitin ligases. Loss-of-function mutations in the RING-between-RING (RBR) family E3 ligase RNF216 (TRIAD3) cause Gordon-Holmes syndrome (GHS) and related neurodegenerative diseases. Functionally, RNF216 assembles K63-linked ubiquitin chains and has been implicated in regulation of innate immunity signaling pathways and synaptic plasticity. Here, we report crystal structures of key RNF216 reaction states including RNF216 in complex with ubiquitin and its reaction product, K63 di-ubiquitin. Our data provide a molecular explanation for chain-type specificity and reveal the molecular basis for disruption of RNF216 function by pathogenic GHS mutations. Furthermore, we demonstrate how RNF216 activity and chain-type specificity are regulated by phosphorylation and that RNF216 is allosterically activated by K63-linked di-ubiquitin. These molecular insights expand our understanding of RNF216 function and its role in disease and further define the mechanistic diversity of the RBR E3 ligase family.
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Affiliation(s)
- Thomas R Cotton
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Simon A Cobbold
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jonathan P Bernardini
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Lachlan W Richardson
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Xiangyi S Wang
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Bernhard C Lechtenberg
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia.
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15
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Beyerle ER, Guenza MG. Identifying the leading dynamics of ubiquitin: A comparison between the tICA and the LE4PD slow fluctuations in amino acids' position. J Chem Phys 2021; 155:244108. [PMID: 34972386 DOI: 10.1063/5.0059688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Molecular Dynamics (MD) simulations of proteins implicitly contain the information connecting the atomistic molecular structure and proteins' biologically relevant motion, where large-scale fluctuations are deemed to guide folding and function. In the complex multiscale processes described by MD trajectories, it is difficult to identify, separate, and study those large-scale fluctuations. This problem can be formulated as the need to identify a small number of collective variables that guide the slow kinetic processes. The most promising method among the ones used to study the slow leading processes in proteins' dynamics is the time-structure based on time-lagged independent component analysis (tICA), which identifies the dominant components in a noisy signal. Recently, we developed an anisotropic Langevin approach for the dynamics of proteins, called the anisotropic Langevin Equation for Protein Dynamics or LE4PD-XYZ. This approach partitions the protein's MD dynamics into mostly uncorrelated, wavelength-dependent, diffusive modes. It associates with each mode a free-energy map, where one measures the spatial extension and the time evolution of the mode-dependent, slow dynamical fluctuations. Here, we compare the tICA modes' predictions with the collective LE4PD-XYZ modes. We observe that the two methods consistently identify the nature and extension of the slowest fluctuation processes. The tICA separates the leading processes in a smaller number of slow modes than the LE4PD does. The LE4PD provides time-dependent information at short times and a formal connection to the physics of the kinetic processes that are missing in the pure statistical analysis of tICA.
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Affiliation(s)
- E R Beyerle
- Institute for Fundamental Science and Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, USA
| | - M G Guenza
- Institute for Fundamental Science and Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, USA
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16
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Magistrati E, Maestrini G, Niño CA, Lince-Faria M, Beznoussenko G, Mironov A, Maspero E, Bettencourt-Dias M, Polo S. Myosin VI regulates ciliogenesis by promoting the turnover of the centrosomal/satellite protein OFD1. EMBO Rep 2021; 23:e54160. [PMID: 34957672 PMCID: PMC8892233 DOI: 10.15252/embr.202154160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/01/2021] [Accepted: 12/08/2021] [Indexed: 11/11/2022] Open
Abstract
The actin motor protein myosin VI is a multivalent protein with diverse functions. Here, we identified and characterised a myosin VI ubiquitous interactor, the oral‐facial‐digital syndrome 1 (OFD1) protein, whose mutations cause malformations of the face, oral cavity, digits and polycystic kidney disease. We found that myosin VI regulates the localisation of OFD1 at the centrioles and, as a consequence, the recruitment of the distal appendage protein Cep164. Myosin VI depletion in non‐tumoural cell lines causes an aberrant localisation of OFD1 along the centriolar walls, which is due to a reduction in the OFD1 mobile fraction. Finally, loss of myosin VI triggers a severe defect in ciliogenesis that could be, at least partially, ascribed to an impairment in the autophagic removal of OFD1 from satellites. Altogether, our results highlight an unprecedent layer of regulation of OFD1 and a pivotal role of myosin VI in coordinating the formation of the distal appendages and primary cilium with important implications for the genetic disorders known as ciliopathies.
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Affiliation(s)
- Elisa Magistrati
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Giorgia Maestrini
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Carlos A Niño
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | | | | | - Alexandre Mironov
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Elena Maspero
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | | | - Simona Polo
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy.,Dipartimento di Oncologia ed Emato-oncologia, Università degli Studi di Milano, Milan, Italy
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17
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Parkinson G, Roboti P, Zhang L, Taylor S, Woodman P. His domain protein tyrosine phosphatase and Rabaptin-5 couple endo-lysosomal sorting of EGFR with endosomal maturation. J Cell Sci 2021; 134:272512. [PMID: 34657963 PMCID: PMC8627557 DOI: 10.1242/jcs.259192] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/13/2021] [Indexed: 01/20/2023] Open
Abstract
His domain protein tyrosine phosphatase (HD-PTP; also known as PTPN23) collaborates with endosomal sorting complexes required for transport (ESCRTs) to sort endosomal cargo into intralumenal vesicles, forming the multivesicular body (MVB). Completion of MVB sorting is accompanied by maturation of the endosome into a late endosome, an event that requires inactivation of the early endosomal GTPase Rab5 (herein referring to generically to all isoforms). Here, we show that HD-PTP links ESCRT function with endosomal maturation. HD-PTP depletion prevents MVB sorting, while also blocking cargo from exiting Rab5-rich endosomes. HD-PTP-depleted cells contain hyperphosphorylated Rabaptin-5 (also known as RABEP1), a cofactor for the Rab5 guanine nucleotide exchange factor Rabex-5 (also known as RABGEF1), although HD-PTP is unlikely to directly dephosphorylate Rabaptin-5. In addition, HD-PTP-depleted cells exhibit Rabaptin-5-dependent hyperactivation of Rab5. HD-PTP binds directly to Rabaptin-5, between its Rabex-5- and Rab5-binding domains. This binding reaction involves the ESCRT-0/ESCRT-III binding site in HD-PTP, which is competed for by an ESCRT-III peptide. Jointly, these findings indicate that HD-PTP may alternatively scaffold ESCRTs and modulate Rabex-5–Rabaptin-5 activity, thereby helping to coordinate the completion of MVB sorting with endosomal maturation. Summary: Sorting of endocytic cargo to the multivesicular body is accompanied by endosomal maturation. Here, we provide a potential mechanism by which these two processes are linked.
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Affiliation(s)
- Gabrielle Parkinson
- Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Peristera Roboti
- Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Ling Zhang
- Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Sandra Taylor
- Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Philip Woodman
- Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
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18
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Hou P, Lin Y, Li Z, Lu R, Wang Y, Tian T, Jia P, Zhang X, Cao L, Zhou Z, Li C, Gu J, Guo D. Autophagy receptor CCDC50 tunes the STING-mediated interferon response in viral infections and autoimmune diseases. Cell Mol Immunol 2021; 18:2358-2371. [PMID: 34453126 PMCID: PMC8484562 DOI: 10.1038/s41423-021-00758-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/04/2021] [Indexed: 02/07/2023] Open
Abstract
DNA sensing and timely activation of interferon (IFN)-mediated innate immunity are crucial for the defense against DNA virus infections and the clearance of abnormal cells. However, overactivation of immune responses may lead to tissue damage and autoimmune diseases; therefore, these processes must be intricately regulated. STING is the key adaptor protein, which is activated by cyclic GMP-AMP, the second messenger derived from cGAS-mediated DNA sensing. Here, we report that CCDC50, a newly identified autophagy receptor, tunes STING-directed type I IFN signaling activity by delivering K63-polyubiquitinated STING to autolysosomes for degradation. Knockout of CCDC50 significantly increases herpes simplex virus 1 (HSV-1)- or DNA ligand-induced production of type I IFN and proinflammatory cytokines. Ccdc50-deficient mice show increased production of IFN, decreased viral replication, reduced cell infiltration, and improved survival rates compared with their wild-type littermates when challenged with HSV-1. Remarkably, the expression of CCDC50 is downregulated in systemic lupus erythematosus (SLE), a chronic autoimmune disease. CCDC50 levels are negatively correlated with IFN signaling pathway activation and disease severity in human SLE patients. CCDC50 deficiency potentiates the cGAS-STING-mediated immune response triggered by SLE serum. Thus, our findings reveal the critical role of CCDC50 in the immune regulation of viral infections and autoimmune diseases and provide insights into the therapeutic implications of CCDC50 manipulation.
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Affiliation(s)
- Panpan Hou
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Study (CIIS), School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Yuxin Lin
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Study (CIIS), School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Zibo Li
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Study (CIIS), School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Ruiqing Lu
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Study (CIIS), School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Yicheng Wang
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Study (CIIS), School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Tian Tian
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Abramson Research Center, The Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Penghui Jia
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Study (CIIS), School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Xi Zhang
- grid.412558.f0000 0004 1762 1794Division of Rheumatology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Liu Cao
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Study (CIIS), School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Zhongwei Zhou
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Study (CIIS), School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Chunmei Li
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Study (CIIS), School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Jieruo Gu
- grid.412558.f0000 0004 1762 1794Division of Rheumatology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Deyin Guo
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Study (CIIS), School of Medicine, Sun Yat-sen University, Shenzhen, China
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19
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Hepowit NL, Kolbe CC, Zelle SR, Latz E, MacGurn JA. Regulation of ubiquitin and ubiquitin-like modifiers by phosphorylation. FEBS J 2021; 289:4797-4810. [PMID: 34214249 PMCID: PMC9271371 DOI: 10.1111/febs.16101] [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: 04/19/2021] [Revised: 05/28/2021] [Accepted: 07/01/2021] [Indexed: 12/31/2022]
Abstract
The regulatory influence of ubiquitin is vast, encompassing all cellular processes, by virtue of its central roles in protein degradation, membrane trafficking, and cell signaling. But how does ubiquitin, a 76 amino acid peptide, carry out such diverse, complex functions in eukaryotic cells? Part of the answer is rooted in the high degree of complexity associated with ubiquitin polymers, which can be 'read' and processed differently depending on topology and cellular context. However, recent evidence indicates that post-translational modifications on ubiquitin itself enhance the complexity of the ubiquitin code. Here, we review recent discoveries related to the regulation of the ubiquitin code by phosphorylation. We summarize what is currently known about phosphorylation of ubiquitin at Ser65, Ser57, and Thr12, and we discuss the potential for phosphoregulation of ubiquitin at other sites. We also discuss accumulating evidence that ubiquitin-like modifiers, such as SUMO, are likewise regulated by phosphorylation. A complete understanding of these regulatory codes and their complex lexicon will require dissection of mechanisms that govern phosphorylation of ubiquitin and ubiquitin-like proteins, particularly in the context of cellular stress and disease.
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Affiliation(s)
- Nathaniel L Hepowit
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Carl-Christian Kolbe
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, Germany
| | - Sarah R Zelle
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Eicke Latz
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, Germany.,German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Department of Infectious Diseases & Immunology, UMass Medical School, Worcester, MA, USA.,Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jason A MacGurn
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
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20
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Hou P, Yang K, Jia P, Liu L, Lin Y, Li Z, Li J, Chen S, Guo S, Pan J, Wu J, Peng H, Zeng W, Li C, Liu Y, Guo D. A novel selective autophagy receptor, CCDC50, delivers K63 polyubiquitination-activated RIG-I/MDA5 for degradation during viral infection. Cell Res 2021; 31:62-79. [PMID: 32612200 PMCID: PMC7852694 DOI: 10.1038/s41422-020-0362-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 06/11/2020] [Indexed: 02/07/2023] Open
Abstract
Autophagy is a conserved process that delivers cytosolic substances to the lysosome for degradation, but its direct role in the regulation of antiviral innate immunity remains poorly understood. Here, through high-throughput screening, we discovered that CCDC50 functions as a previously unknown autophagy receptor that negatively regulates the type I interferon (IFN) signaling pathway initiated by RIG-I-like receptors (RLRs), the sensors for RNA viruses. The expression of CCDC50 is enhanced by viral infection, and CCDC50 specifically recognizes K63-polyubiquitinated RLRs, thus delivering the activated RIG-I/MDA5 for autophagic degradation. The association of CCDC50 with phagophore membrane protein LC3 is confirmed by crystal structure analysis. In contrast to other known autophagic cargo receptors that associate with either the LIR-docking site (LDS) or the UIM-docking site (UDS) of LC3, CCDC50 can bind to both LDS and UDS, representing a new type of cargo receptor. In mouse models with RNA virus infection, CCDC50 deficiency reduces the autophagic degradation of RIG-I/MDA5 and promotes type I IFN responses, resulting in enhanced viral resistance and improved survival rates. These results reveal a new link between autophagy and antiviral innate immune responses and provide additional insights into the regulatory mechanisms of RLR-mediated antiviral signaling.
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Affiliation(s)
- Panpan Hou
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies (CIIS), Seventh Affiliated Hospital, School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Kongxiang Yang
- Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Penghui Jia
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies (CIIS), Seventh Affiliated Hospital, School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Lan Liu
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies (CIIS), Seventh Affiliated Hospital, School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Yuxin Lin
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies (CIIS), Seventh Affiliated Hospital, School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Zibo Li
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies (CIIS), Seventh Affiliated Hospital, School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Jun Li
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies (CIIS), Seventh Affiliated Hospital, School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Shuliang Chen
- School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Shuting Guo
- School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Ji'An Pan
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies (CIIS), Seventh Affiliated Hospital, School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Junyu Wu
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies (CIIS), Seventh Affiliated Hospital, School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Hong Peng
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies (CIIS), Seventh Affiliated Hospital, School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Weijie Zeng
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies (CIIS), Seventh Affiliated Hospital, School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Chunmei Li
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies (CIIS), Seventh Affiliated Hospital, School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Yingfang Liu
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies (CIIS), Seventh Affiliated Hospital, School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Deyin Guo
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies (CIIS), Seventh Affiliated Hospital, School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China.
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21
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Myomics: myosin VI structural and functional plasticity. Curr Opin Struct Biol 2020; 67:33-40. [PMID: 33053464 DOI: 10.1016/j.sbi.2020.09.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 11/21/2022]
Abstract
Myosin VI is a minus end-directed actin motor protein that fulfils several roles in the cell. The interaction of myosin VI with its cellular cargoes is dictated by the presence of binding domains at the C-terminus of the protein. In this review, we describe how alternative splicing and structural and conformational changes modulate the plasticity of the myosin VI interactome. Recent findings highlight how the various partners can cooperate or compete for binding to allow a precise temporal and spatial regulation of myosin VI recruitment to different cellular compartments, where its motor or anchor function is needed.
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22
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Walser F, Mulder MPC, Bragantini B, Burger S, Gubser T, Gatti M, Botuyan MV, Villa A, Altmeyer M, Neri D, Ovaa H, Mer G, Penengo L. Ubiquitin Phosphorylation at Thr12 Modulates the DNA Damage Response. Mol Cell 2020; 80:423-436.e9. [PMID: 33022275 DOI: 10.1016/j.molcel.2020.09.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 04/14/2020] [Accepted: 09/12/2020] [Indexed: 11/26/2022]
Abstract
The ubiquitin system regulates the DNA damage response (DDR) by modifying histone H2A at Lys15 (H2AK15ub) and triggering downstream signaling events. Here, we find that phosphorylation of ubiquitin at Thr12 (pUbT12) controls the DDR by inhibiting the function of 53BP1, a key factor for DNA double-strand break repair by non-homologous end joining (NHEJ). Detectable as a chromatin modification on H2AK15ub, pUbT12 accumulates in nuclear foci and is increased upon DNA damage. Mutating Thr12 prevents the removal of ubiquitin from H2AK15ub by USP51 deubiquitinating enzyme, leading to a pronounced accumulation of ubiquitinated chromatin. Chromatin modified by pUbT12 is inaccessible to 53BP1 but permissive to the homologous recombination (HR) proteins RNF169, RAD51, and the BRCA1/BARD1 complex. Phosphorylation of ubiquitin at Thr12 in the chromatin context is a new histone mark, H2AK15pUbT12, that regulates the DDR by hampering the activity of 53BP1 at damaged chromosomes.
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Affiliation(s)
- Franziska Walser
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Monique P C Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands; Oncode Institute and Department of Cell and Chemical Biology, Chemical Immunology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Benoît Bragantini
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Sibylle Burger
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Tatiana Gubser
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Marco Gatti
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
| | | | - Alessandra Villa
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), 8093 Zurich, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), 8093 Zurich, Switzerland
| | - Huib Ovaa
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands; Oncode Institute and Department of Cell and Chemical Biology, Chemical Immunology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Lorenza Penengo
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland.
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23
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Pascolutti R, Algisi V, Conte A, Raimondi A, Pasham M, Upadhyayula S, Gaudin R, Maritzen T, Barbieri E, Caldieri G, Tordonato C, Confalonieri S, Freddi S, Malabarba MG, Maspero E, Polo S, Tacchetti C, Haucke V, Kirchhausen T, Di Fiore PP, Sigismund S. Molecularly Distinct Clathrin-Coated Pits Differentially Impact EGFR Fate and Signaling. Cell Rep 2020; 27:3049-3061.e6. [PMID: 31167147 PMCID: PMC6581797 DOI: 10.1016/j.celrep.2019.05.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/04/2019] [Accepted: 05/02/2019] [Indexed: 12/22/2022] Open
Abstract
Adaptor protein 2 (AP2) is a major constituent of clathrin-coated pits (CCPs). Whether it is essential for all forms of clathrin-mediated endocytosis (CME) in mammalian cells is an open issue. Here, we demonstrate, by live TIRF microscopy, the existence of a subclass of relatively short-lived CCPs lacking AP2 under physiological, unperturbed conditions. This subclass is retained in AP2-knockout cells and is able to support the internalization of epidermal growth factor receptor (EGFR) but not of transferrin receptor (TfR). The AP2-independent internalization mechanism relies on the endocytic adaptors eps15, eps15L1, and epsin1. The absence of AP2 impairs the recycling of the EGFR to the cell surface, thereby augmenting its degradation. Accordingly, under conditions of AP2 ablation, we detected dampening of EGFR-dependent AKT signaling and cell migration, arguing that distinct classes of CCPs could provide specialized functions in regulating EGFR recycling and signaling. Distinct classes of CCPs exist, molecularly defined by the presence or lack of AP2 The AP2-negative CCPs support the internalization of EGFR but not of TfR The AP2-negative CCPs rely on the endocytic adaptors eps15/eps15L1 and epsin1 The two classes of CCPs determine distinct EGFR fates and signaling outputs
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Affiliation(s)
- Roberta Pascolutti
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy
| | - Veronica Algisi
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy
| | - Alexia Conte
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy; Istituto Europeo di Oncologia IRCCS, Via Ripamonti 435, 20141 Milan, Italy
| | - Andrea Raimondi
- Experimental Imaging Centre, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy
| | - Mithun Pasham
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Srigokul Upadhyayula
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Raphael Gaudin
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Institut de Recherche en Infectiologie de Montpellier, UMR 9004, CNRS/UM, 1919 route de Mende, 34293 Montpellier cedex 5, France
| | - Tanja Maritzen
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Elisa Barbieri
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy; Istituto Europeo di Oncologia IRCCS, Via Ripamonti 435, 20141 Milan, Italy
| | - Giusi Caldieri
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy; Istituto Europeo di Oncologia IRCCS, Via Ripamonti 435, 20141 Milan, Italy; Università degli Studi di Milano, Dipartimento di Oncologia ed Emato-oncologia, Via Santa Sofia 9/1, 20122 Milan, Italy
| | - Chiara Tordonato
- Istituto Europeo di Oncologia IRCCS, Via Ripamonti 435, 20141 Milan, Italy
| | - Stefano Confalonieri
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy; Istituto Europeo di Oncologia IRCCS, Via Ripamonti 435, 20141 Milan, Italy
| | - Stefano Freddi
- Istituto Europeo di Oncologia IRCCS, Via Ripamonti 435, 20141 Milan, Italy
| | - Maria Grazia Malabarba
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy; Istituto Europeo di Oncologia IRCCS, Via Ripamonti 435, 20141 Milan, Italy; Università degli Studi di Milano, Dipartimento di Oncologia ed Emato-oncologia, Via Santa Sofia 9/1, 20122 Milan, Italy
| | - Elena Maspero
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy
| | - Simona Polo
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy; Università degli Studi di Milano, Dipartimento di Oncologia ed Emato-oncologia, Via Santa Sofia 9/1, 20122 Milan, Italy
| | - Carlo Tacchetti
- Experimental Imaging Centre, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy; Università Vita-Salute San Raffaele, Milan, Italy
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Tom Kirchhausen
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Pier Paolo Di Fiore
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy; Istituto Europeo di Oncologia IRCCS, Via Ripamonti 435, 20141 Milan, Italy; Università degli Studi di Milano, Dipartimento di Oncologia ed Emato-oncologia, Via Santa Sofia 9/1, 20122 Milan, Italy
| | - Sara Sigismund
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy; Istituto Europeo di Oncologia IRCCS, Via Ripamonti 435, 20141 Milan, Italy; Università degli Studi di Milano, Dipartimento di Oncologia ed Emato-oncologia, Via Santa Sofia 9/1, 20122 Milan, Italy.
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24
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Cezanne A, Lauer J, Solomatina A, Sbalzarini IF, Zerial M. A non-linear system patterns Rab5 GTPase on the membrane. eLife 2020; 9:e54434. [PMID: 32510320 PMCID: PMC7279886 DOI: 10.7554/elife.54434] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 05/21/2020] [Indexed: 12/21/2022] Open
Abstract
Proteins can self-organize into spatial patterns via non-linear dynamic interactions on cellular membranes. Modelling and simulations have shown that small GTPases can generate patterns by coupling guanine nucleotide exchange factors (GEF) to effectors, generating a positive feedback of GTPase activation and membrane recruitment. Here, we reconstituted the patterning of the small GTPase Rab5 and its GEF/effector complex Rabex5/Rabaptin5 on supported lipid bilayers. We demonstrate a 'handover' of Rab5 from Rabex5 to Rabaptin5 upon nucleotide exchange. A minimal system consisting of Rab5, RabGDI and a complex of full length Rabex5/Rabaptin5 was necessary to pattern Rab5 into membrane domains. Rab5 patterning required a lipid membrane composition mimicking that of early endosomes, with PI(3)P enhancing membrane recruitment of Rab5 and acyl chain packing being critical for domain formation. The prevalence of GEF/effector coupling in nature suggests a possible universal system for small GTPase patterning involving both protein and lipid interactions.
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Affiliation(s)
- Alice Cezanne
- Max-Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Janelle Lauer
- Max-Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Anastasia Solomatina
- Max-Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Chair of Scientific Computing for Systems Biology, Faculty of Computer ScienceDresdenGermany
- MOSAIC Group, Center for Systems Biology DresdenDresdenGermany
| | - Ivo F Sbalzarini
- Max-Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Chair of Scientific Computing for Systems Biology, Faculty of Computer ScienceDresdenGermany
- MOSAIC Group, Center for Systems Biology DresdenDresdenGermany
| | - Marino Zerial
- Max-Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
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25
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Wang TS, Coppens I, Saorin A, Brady NR, Hamacher-Brady A. Endolysosomal Targeting of Mitochondria Is Integral to BAX-Mediated Mitochondrial Permeabilization during Apoptosis Signaling. Dev Cell 2020; 53:627-645.e7. [PMID: 32504557 DOI: 10.1016/j.devcel.2020.05.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 01/03/2020] [Accepted: 05/13/2020] [Indexed: 12/29/2022]
Abstract
Mitochondrial outer membrane permeabilization (MOMP) is a core event in apoptosis signaling. However, the underlying mechanism of BAX and BAK pore formation remains incompletely understood. We demonstrate that mitochondria are globally and dynamically targeted by endolysosomes (ELs) during MOMP. In response to pro-apoptotic BH3-only protein signaling and pharmacological MOMP induction, ELs increasingly form transient contacts with mitochondria. Subsequently, ELs rapidly accumulate within the entire mitochondrial compartment. This switch-like accumulation period temporally coincides with mitochondrial BAX clustering and cytochrome c release. Remarkably, interactions of ELs with mitochondria control BAX recruitment and pore formation. Knockdown of Rab5A, Rab5C, or USP15 interferes with EL targeting of mitochondria and functionally uncouples BAX clustering from cytochrome c release, while knockdown of the Rab5 exchange factor Rabex-5 impairs both BAX clustering and cytochrome c release. Together, these data reveal that EL-mitochondrial inter-organelle communication is an integral regulatory component of functional MOMP execution during cellular apoptosis signaling.
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Affiliation(s)
- Tim Sen Wang
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA; Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Isabelle Coppens
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Anna Saorin
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Nathan Ryan Brady
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA.
| | - Anne Hamacher-Brady
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA; Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA.
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26
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Berk JM, Lim C, Ronau JA, Chaudhuri A, Chen H, Beckmann JF, Loria JP, Xiong Y, Hochstrasser M. A deubiquitylase with an unusually high-affinity ubiquitin-binding domain from the scrub typhus pathogen Orientia tsutsugamushi. Nat Commun 2020; 11:2343. [PMID: 32393759 PMCID: PMC7214410 DOI: 10.1038/s41467-020-15985-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 04/02/2020] [Indexed: 01/07/2023] Open
Abstract
Ubiquitin mediated signaling contributes critically to host cell defenses during pathogen infection. Many pathogens manipulate the ubiquitin system to evade these defenses. Here we characterize a likely effector protein bearing a deubiquitylase (DUB) domain from the obligate intracellular bacterium Orientia tsutsugamushi, the causative agent of scrub typhus. The Ulp1-like DUB prefers ubiquitin substrates over ubiquitin-like proteins and efficiently cleaves polyubiquitin chains of three or more ubiquitins. The co-crystal structure of the DUB (OtDUB) domain with ubiquitin revealed three bound ubiquitins: one engages the S1 site, the second binds an S2 site contributing to chain specificity and the third binds a unique ubiquitin-binding domain (UBD). The UBD modulates OtDUB activity, undergoes a pronounced structural transition upon binding ubiquitin, and binds monoubiquitin with an unprecedented ~5 nM dissociation constant. The characterization and high-resolution structure determination of this enzyme should aid in its development as a drug target to counter Orientia infections.
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Affiliation(s)
- Jason M Berk
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Christopher Lim
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Judith A Ronau
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Discovery, Research and Development, AbbVie, Inc., North Chicago, IL, 60064, USA
| | - Apala Chaudhuri
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Hongli Chen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - John F Beckmann
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36830, USA
| | - J Patrick Loria
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
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27
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The 'dark matter' of ubiquitin-mediated processes: opportunities and challenges in the identification of ubiquitin-binding domains. Biochem Soc Trans 2020; 47:1949-1962. [PMID: 31829417 DOI: 10.1042/bst20190869] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/05/2019] [Accepted: 11/28/2019] [Indexed: 12/19/2022]
Abstract
Ubiquitin modifications of target proteins act to localise, direct and specify a diverse range of cellular processes, many of which are biomedically relevant. To allow this diversity, ubiquitin modifications exhibit remarkable complexity, determined by a combination of polyubiquitin chain length, linkage type, numbers of ubiquitin chains per target, and decoration of ubiquitin with other small modifiers. However, many questions remain about how different ubiquitin signals are specifically recognised and transduced by the decoding ubiquitin-binding domains (UBDs) within ubiquitin-binding proteins. This review briefly outlines our current knowledge surrounding the diversity of UBDs, identifies key challenges in their discovery and considers recent structural studies with implications for the increasing complexity of UBD function and identification. Given the comparatively low numbers of functionally characterised polyubiquitin-selective UBDs relative to the ever-expanding variety of polyubiquitin modifications, it is possible that many UBDs have been overlooked, in part due to limitations of current approaches used to predict their presence within the proteome. Potential experimental approaches for UBD discovery are considered; web-based informatic analyses, Next-Generation Phage Display, deubiquitinase-resistant diubiquitin, proximity-dependent biotinylation and Ubiquitin-Phototrap, including possible advantages and limitations. The concepts discussed here work towards identifying new UBDs which may represent the 'dark matter' of the ubiquitin system.
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28
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O'Loughlin T, Kendrick-Jones J, Buss F. Approaches to Identify and Characterise MYO6-Cargo Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1239:355-380. [PMID: 32451866 DOI: 10.1007/978-3-030-38062-5_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Given the prevalence and importance of the actin cytoskeleton and the host of associated myosin motors, it comes as no surprise to find that they are linked to a plethora of cellular functions and pathologies. Although our understanding of the biophysical properties of myosin motors has been aided by the high levels of conservation in their motor domains and the extensive work on myosin in skeletal muscle contraction, our understanding of how the nonmuscle myosins participate in such a wide variety of cellular processes is less clear. It is now well established that the highly variable myosin tails are responsible for targeting these myosins to distinct cellular sites for specific functions, and although a number of adaptor proteins have been identified, our current understanding of the cellular processes involved is rather limited. Furthermore, as more adaptor proteins, cargoes and complexes are identified, the importance of elucidating the regulatory mechanisms involved is essential. Ca2+, and now phosphorylation and ubiquitination, are emerging as important regulators of cargo binding, and it is likely that other post-translational modifications are also involved. In the case of myosin VI (MYO6), a number of immediate binding partners have been identified using traditional approaches such as yeast two-hybrid screens and affinity-based pull-downs. However, these methods have only been successful in identifying the cargo adaptors, but not the cargoes themselves, which may often comprise multi-protein complexes. Furthermore, motor-adaptor-cargo interactions are dynamic by nature and often weak, transient and highly regulated and therefore difficult to capture using traditional affinity-based methods. In this chapter we will discuss the various approaches including functional proteomics that have been used to uncover and characterise novel MYO6-associated proteins and complexes and how this work contributes to a fuller understanding of the targeting and function(s) of this unique myosin motor.
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Affiliation(s)
- Thomas O'Loughlin
- Cambridge Institute for Medical Research, University of Cambridge, The Keith Peters Building, Cambridge, UK
| | | | - Folma Buss
- Cambridge Institute for Medical Research, University of Cambridge, The Keith Peters Building, Cambridge, UK.
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29
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Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4. Nat Commun 2019; 10:5708. [PMID: 31836717 PMCID: PMC6910952 DOI: 10.1038/s41467-019-13697-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 11/21/2019] [Indexed: 01/07/2023] Open
Abstract
Npl4 is likely to be the most upstream factor recognizing Lys48-linked polyubiquitylated substrates in the proteasomal degradation pathway in yeast. Along with Ufd1, Npl4 forms a heterodimer (UN), and functions as a cofactor for the Cdc48 ATPase. Here, we report the crystal structures of yeast Npl4 in complex with Lys48-linked diubiquitin and with the Npl4-binding motif of Ufd1. The distal and proximal ubiquitin moieties of Lys48-linked diubiquitin primarily interact with the C-terminal helix and N-terminal loop of the Npl4 C-terminal domain (CTD), respectively. Mutational analysis suggests that the CTD contributes to linkage selectivity and initial binding of ubiquitin chains. Ufd1 occupies a hydrophobic groove of the Mpr1/Pad1 N-terminal (MPN) domain of Npl4, which corresponds to the catalytic groove of the MPN domain of JAB1/MPN/Mov34 metalloenzyme (JAMM)-family deubiquitylating enzyme. This study provides important structural insights into the polyubiquitin chain recognition by the Cdc48-UN complex and its assembly.
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30
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Choi YS, Lian S, Cohen RE. Fluorescent Sensors That Enable a General Method To Quantify Affinities of Receptor Proteins for Polyubiquitin Ligands. ACS Sens 2019; 4:2908-2914. [PMID: 31599572 DOI: 10.1021/acssensors.9b01240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In all eukaryotic cells, modifications of proteins by polymers of ubiquitin (polyUb) are signals used in diverse biological processes. To better understand how polyUb signals are read and promote their different functions, quantitative measurements of their interactions with receptor proteins are needed. However, affinities and selectivities of different forms of polyUb with various receptors have been difficult to determine because the availability of well-defined polyUb chains can be limiting and there is a lack of general, sensitive methods to assay their interactions. We have addressed this challenge by developing a series of fluorescent protein sensors for polyUb; by competition of the sensors against receptor proteins in vitro for limiting amounts of polyUb, receptor·polyUb affinities can be quantified. Due to the high affinities of the polyUb sensors (Kd ∼ 10-9 M), binding assays using this competition format require much less polyUb (<0.1%) than would be needed in direct titrations of the polyUb ligands. Furthermore, the high sensitivity and large dynamic range of the sensor fluorescence readout allow for precise measurements even for very tight interactions (i.e., nanomolar Kd). Importantly, as demonstrated here with Ub2 and Ub3 ligands, the assay does not require labeling of either the receptor protein or the polyUb, and it can be used with polyUb ligands composed of virtually any Ub-Ub linkage type.
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Affiliation(s)
- Yun-Seok Choi
- Department of Biochemistry and Molecular Biology, Colorado State University, 1870 Campus Delivery, Fort Collins, Colorado 80523, United States
- School of Natural Sciences, Black Hills State University, Spearfish, South Dakota 57799, United States
| | - Sharon Lian
- Department of Biochemistry and Molecular Biology, Colorado State University, 1870 Campus Delivery, Fort Collins, Colorado 80523, United States
| | - Robert E. Cohen
- Department of Biochemistry and Molecular Biology, Colorado State University, 1870 Campus Delivery, Fort Collins, Colorado 80523, United States
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31
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Lauer J, Segeletz S, Cezanne A, Guaitoli G, Raimondi F, Gentzel M, Alva V, Habeck M, Kalaidzidis Y, Ueffing M, Lupas AN, Gloeckner CJ, Zerial M. Auto-regulation of Rab5 GEF activity in Rabex5 by allosteric structural changes, catalytic core dynamics and ubiquitin binding. eLife 2019; 8:46302. [PMID: 31718772 PMCID: PMC6855807 DOI: 10.7554/elife.46302] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 10/22/2019] [Indexed: 02/06/2023] Open
Abstract
Intracellular trafficking depends on the function of Rab GTPases, whose activation is regulated by guanine exchange factors (GEFs). The Rab5 GEF, Rabex5, was previously proposed to be auto-inhibited by its C-terminus. Here, we studied full-length Rabex5 and Rabaptin5 proteins as well as domain deletion Rabex5 mutants using hydrogen deuterium exchange mass spectrometry. We generated a structural model of Rabex5, using chemical cross-linking mass spectrometry and integrative modeling techniques. By correlating structural changes with nucleotide exchange activity for each construct, we uncovered new auto-regulatory roles for the ubiquitin binding domains and the Linker connecting those domains to the catalytic core of Rabex5. We further provide evidence that enhanced dynamics in the catalytic core are linked to catalysis. Our results suggest a more complex auto-regulation mechanism than previously thought and imply that ubiquitin binding serves not only to position Rabex5 but to also control its Rab5 GEF activity through allosteric structural alterations.
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Affiliation(s)
- Janelle Lauer
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Sandra Segeletz
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Alice Cezanne
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Francesco Raimondi
- Bioquant, Heidelberg University, Heidelberg, Germany.,Heidelberg University Biochemistry Centre (BZH), Heidelberg, Germany
| | - Marc Gentzel
- Molecular Analysis-Mass Spectrometry Center for Molecular and Cellular Bioengineering, Technical University Dresden, Dresden, Germany
| | - Vikram Alva
- Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Michael Habeck
- Statistical Inverse Problems in Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Felix Bernstein Institute for Mathematical Statistics in the Biosciences, University of Göttingen, Göttingen, Germany
| | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Marius Ueffing
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Andrei N Lupas
- Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Christian Johannes Gloeckner
- German Center for Neurodegenerative Diseases, Tübingen, Germany.,Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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32
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Beyerle ER, Guenza MG. Kinetics analysis of ubiquitin local fluctuations with Markov state modeling of the LE4PD normal modes. J Chem Phys 2019; 151:164119. [PMID: 31675886 DOI: 10.1063/1.5123513] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Local fluctuations are important for protein binding and molecular recognition because they provide conformational states that can be trapped through a selection mechanism of binding. Thus, an accurate characterization of local fluctuations may be important for modeling the kinetic mechanism that leads to the biological activity of a protein. In this paper, we study the fluctuation dynamics of the regulatory protein ubiquitin and propose a novel theoretical approach to model its fluctuations. A coarse-grained, diffusive, mode-dependent description of fluctuations is accomplished using the Langevin Equation for Protein Dynamics (LE4PD). This equation decomposes the dynamics of a protein, simulated by molecular dynamics, into dynamical pathways that explore mode-dependent free energy surfaces. We calculate the time scales of the slow, high-amplitude fluctuations by modeling the kinetics of barrier crossing in the two-dimensional free energy surfaces using Markov state modeling. We find that the LE4PD predicts slow fluctuations in three important binding regions in ubiquitin: the C-terminal tail, the Lys11 loop, and the 50 s loop. These results suggest that the LE4PD can provide useful information on the role of fluctuations in the process of molecular recognition regulating the biological activity of ubiquitin.
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Affiliation(s)
- Eric R Beyerle
- Department of Chemistry and Biochemistry and Institute of Theoretical Science, University of Oregon, Eugene, Oregon 97403, USA
| | - Marina G Guenza
- Department of Chemistry and Biochemistry and Institute of Theoretical Science, University of Oregon, Eugene, Oregon 97403, USA
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33
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Takahashi TS, Sato Y, Yamagata A, Goto-Ito S, Saijo M, Fukai S. Structural basis of ubiquitin recognition by the winged-helix domain of Cockayne syndrome group B protein. Nucleic Acids Res 2019; 47:3784-3794. [PMID: 30753618 PMCID: PMC6468306 DOI: 10.1093/nar/gkz081] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 01/25/2019] [Accepted: 02/01/2019] [Indexed: 12/18/2022] Open
Abstract
Cockayne syndrome group B (CSB, also known as ERCC6) protein is involved in many DNA repair processes and essential for transcription-coupled repair (TCR). The central region of CSB has the helicase motif, whereas the C-terminal region contains important regulatory elements for repair of UV- and oxidative stress-induced damages and double-strand breaks (DSBs). A previous study suggested that a small part (∼30 residues) within this region was responsible for binding to ubiquitin (Ub). Here, we show that the Ub-binding of CSB requires a larger part of CSB, which was previously identified as a winged-helix domain (WHD) and is involved in the recruitment of CSB to DSBs. We also present the crystal structure of CSB WHD in complex with Ub. CSB WHD folds as a single globular domain, defining a class of Ub-binding domains (UBDs) different from 23 UBD classes identified so far. The second α-helix and C-terminal extremity of CSB WHD interact with Ub. Together with structure-guided mutational analysis, we identified the residues critical for the binding to Ub. CSB mutants defective in the Ub binding reduced repair of UV-induced damage. This study supports the notion that DSB repair and TCR may be associated with the Ub-binding of CSB.
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Affiliation(s)
- Tomio S Takahashi
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo 113-0032, Japan
| | - Yusuke Sato
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo 113-0032, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Atsushi Yamagata
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo 113-0032, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Sakurako Goto-Ito
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo 113-0032, Japan
| | - Masafumi Saijo
- Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 1-3, Suita, Osaka 565-0871, Japan
| | - Shuya Fukai
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo 113-0032, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
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34
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High-affinity free ubiquitin sensors for quantifying ubiquitin homeostasis and deubiquitination. Nat Methods 2019; 16:771-777. [PMID: 31308549 PMCID: PMC6669086 DOI: 10.1038/s41592-019-0469-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 05/21/2019] [Indexed: 02/07/2023]
Abstract
Ubiquitin (Ub) conjugation is an essential post-translational modification that affects nearly all proteins in eukaryotes. The functions and mechanisms of ubiquitination are areas of extensive study, and yet the dynamics and regulation of even free (i.e., unconjugated) Ub are poorly understood. A major impediment has been the lack of simple and robust techniques to quantify Ub levels in cells and to monitor Ub release from conjugates. Here we describe avidity-based fluorescent sensors that address this need. The sensors bind specifically to free Ub, have Kd values down to 60 pM, and, in concert with a newly developed workflow, allow us to distinguish and quantify the pools of free, protein-conjugated, and thioesterified forms of Ub from cell lysates. Alternatively, free Ub in fixed cells can be visualized microscopically by staining with a sensor. Real-time assays using the sensors afford unprecedented flexibility and precision to measure deubiquitination of virtually any (poly)Ub conjugate.
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35
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de Jonge JJ, Batters C, O'Loughlin T, Arden SD, Buss F. The MYO6 interactome: selective motor-cargo complexes for diverse cellular processes. FEBS Lett 2019; 593:1494-1507. [PMID: 31206648 DOI: 10.1002/1873-3468.13486] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/07/2019] [Accepted: 06/10/2019] [Indexed: 12/16/2022]
Abstract
Myosins of class VI (MYO6) are unique actin-based motor proteins that move cargo towards the minus ends of actin filaments. As the sole myosin with this directionality, it is critically important in a number of biological processes. Indeed, loss or overexpression of MYO6 in humans is linked to a variety of pathologies including deafness, cardiomyopathy, neurodegenerative diseases as well as cancer. This myosin interacts with a wide variety of direct binding partners such as for example the selective autophagy receptors optineurin, TAX1BP1 and NDP52 and also Dab2, GIPC, TOM1 and LMTK2, which mediate distinct functions of different MYO6 isoforms along the endocytic pathway. Functional proteomics has recently been used to identify the wider MYO6 interactome including several large functionally distinct multi-protein complexes, which highlight the importance of this myosin in regulating the actin and septin cytoskeleton. Interestingly, adaptor-binding not only triggers cargo attachment, but also controls the inactive folded conformation and dimerisation of MYO6. Thus, the C-terminal tail domain mediates cargo recognition and binding, but is also crucial for modulating motor activity and regulating cytoskeletal track dynamics.
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Affiliation(s)
| | | | - Thomas O'Loughlin
- Cambridge Institute for Medical Research, University of Cambridge, UK
| | - Susan D Arden
- Cambridge Institute for Medical Research, University of Cambridge, UK
| | - Folma Buss
- Cambridge Institute for Medical Research, University of Cambridge, UK
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36
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Rab7a and Mitophagosome Formation. Cells 2019; 8:cells8030224. [PMID: 30857122 PMCID: PMC6468461 DOI: 10.3390/cells8030224] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 02/27/2019] [Accepted: 03/01/2019] [Indexed: 12/14/2022] Open
Abstract
The small GTPase, Rab7a, and the regulators of its GDP/GTP-binding status were shown to have roles in both endocytic membrane traffic and autophagy. Classically known to regulate endosomal retrograde transport and late endosome-lysosome fusion, earlier work has indicated a role for Rab7a in autophagosome-lysosome fusion as well as autolysosome maturation. However, as suggested by recent findings on PTEN-induced kinase 1 (PINK1)-Parkin-mediated mitophagy, Rab7a and its regulators are critical for the correct targeting of Atg9a-bearing vesicles to effect autophagosome formation around damaged mitochondria. This mitophagosome formation role for Rab7a is dependent on an intact Rab cycling process mediated by the Rab7a-specific guanine nucleotide exchange factor (GEF) and GTPase activating proteins (GAPs). Rab7a activity in this regard is also dependent on the retromer complex, as well as phosphorylation by the TRAF family-associated NF-κB activator binding kinase 1 (TBK1). Here, we discuss these recent findings and broadened perspectives on the role of the Rab7a network in PINK1-Parkin mediated mitophagy.
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37
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Mattern M, Sutherland J, Kadimisetty K, Barrio R, Rodriguez MS. Using Ubiquitin Binders to Decipher the Ubiquitin Code. Trends Biochem Sci 2019; 44:599-615. [PMID: 30819414 DOI: 10.1016/j.tibs.2019.01.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 12/13/2022]
Abstract
Post-translational modifications (PTMs) by ubiquitin (Ub) are versatile, highly dynamic, and involved in nearly all aspects of eukaryote biological function. The reversibility and heterogeneity of Ub chains attached to protein substrates have complicated their isolation, quantification, and characterization. Strategies have emerged to isolate endogenous ubiquitylated targets, including technologies based on the use of Ub-binding peptides, such as tandem-repeated Ub-binding entities (TUBEs). TUBEs allow the identification and characterization of Ub chains, and novel substrates for deubiquitylases (DUBs) and Ub ligases (E3s). Here we review their impact on purification, analysis of pan or chain-selective polyubiquitylated proteins and underline the biological relevance of this information. Together with peptide aptamers and other Ub affinity-based approaches, TUBEs will contribute to unraveling the secrets of the Ub code.
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Affiliation(s)
- Michael Mattern
- Progenra Inc., 277 Great Valley Parkway, Malvern 19355, Pennsylvania, USA; These authors contributed equally
| | - James Sutherland
- CIC bioGUNE, Technology Park of Bizkaia, Bldg. 801A, 48160 Derio, Spain; These authors contributed equally
| | - Karteek Kadimisetty
- LifeSensors Inc., 271 Great Valley Parkway, Malvern 19355, Pennsylvania, USA
| | - Rosa Barrio
- CIC bioGUNE, Technology Park of Bizkaia, Bldg. 801A, 48160 Derio, Spain
| | - Manuel S Rodriguez
- ITAV-IPBS-UPS CNRS USR3505, 1 place Pierre Potier, Oncopole entrée B, 31106 Toulouse, France.
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38
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Sakai R, Fukuda R, Unida S, Aki M, Ono Y, Endo A, Kusumi S, Koga D, Fukushima T, Komada M, Okiyoneda T. The integral function of the endocytic recycling compartment is regulated by RFFL-mediated ubiquitylation of Rab11 effectors. J Cell Sci 2019; 132:jcs.228007. [PMID: 30659120 DOI: 10.1242/jcs.228007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/03/2019] [Indexed: 12/11/2022] Open
Abstract
Endocytic trafficking is regulated by ubiquitylation (also known as ubiquitination) of cargoes and endocytic machineries. The role of ubiquitylation in lysosomal delivery has been well documented, but its role in the recycling pathway is largely unknown. Here, we report that the ubiquitin (Ub) ligase RFFL regulates ubiquitylation of endocytic recycling regulators. An RFFL dominant-negative (DN) mutant induced clustering of endocytic recycling compartments (ERCs) and delayed endocytic cargo recycling without affecting lysosomal traffic. A BioID RFFL interactome analysis revealed that RFFL interacts with the Rab11 effectors EHD1, MICALL1 and class I Rab11-FIPs. The RFFL DN mutant strongly captured these Rab11 effectors and inhibited their ubiquitylation. The prolonged interaction of RFFL with Rab11 effectors was sufficient to induce the clustered ERC phenotype and to delay cargo recycling. RFFL directly ubiquitylates these Rab11 effectors in vitro, but RFFL knockout (KO) only reduced the ubiquitylation of Rab11-FIP1. RFFL KO had a minimal effect on the ubiquitylation of EHD1, MICALL1, and Rab11-FIP2, and failed to delay transferrin recycling. These results suggest that multiple Ub ligases including RFFL regulate the ubiquitylation of Rab11 effectors, determining the integral function of the ERC.
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Affiliation(s)
- Ryohei Sakai
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, Hyogo 669-1337, Japan
| | - Ryosuke Fukuda
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, Hyogo 669-1337, Japan
| | - Shin Unida
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, Hyogo 669-1337, Japan
| | - Misaki Aki
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, Hyogo 669-1337, Japan
| | - Yuji Ono
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, Hyogo 669-1337, Japan
| | - Akinori Endo
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Satoshi Kusumi
- Division of Morphological Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima 890-8544, Japan
| | - Daisuke Koga
- Department of Microscopic Anatomy and Cell Biology, Asahikawa Medical University, Asahikawa 078-8510, Hokkaido, Japan
| | - Toshiaki Fukushima
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Masayuki Komada
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Tsukasa Okiyoneda
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, Hyogo 669-1337, Japan
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39
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Cdc48/VCP Promotes Chromosome Morphogenesis by Releasing Condensin from Self-Entrapment in Chromatin. Mol Cell 2019; 69:664-676.e5. [PMID: 29452641 DOI: 10.1016/j.molcel.2018.01.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 11/04/2017] [Accepted: 01/22/2018] [Indexed: 01/26/2023]
Abstract
The morphological transformation of amorphous chromatin into distinct chromosomes is a hallmark of mitosis. To achieve this, chromatin must be compacted and remodeled by a ring-shaped enzyme complex known as condensin. However, the mechanistic basis underpinning condensin's role in chromosome remodeling has remained elusive. Here we show that condensin has a strong tendency to trap itself in its own reaction product during chromatin compaction and yet is capable of interacting with chromatin in a highly dynamic manner in vivo. To resolve this apparent paradox, we identified specific chromatin remodelers and AAA-class ATPases that act in a coordinated manner to release condensin from chromatin entrapment. The Cdc48 segregase is the central linchpin of this regulatory mechanism and promotes ubiquitin-dependent cycling of condensin on mitotic chromatin as well as effective chromosome condensation. Collectively, our results show that condensin inhibition by its own reaction product is relieved by forceful enzyme extraction from chromatin.
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40
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Zamai M, Trullo A, Giordano M, Corti V, Arza Cuesta E, Francavilla C, Cavallaro U, Caiolfa VR. Number and brightness analysis reveals that NCAM and FGF2 elicit different assembly and dynamics of FGFR1 in live cells. J Cell Sci 2019; 132:jcs.220624. [PMID: 30478195 DOI: 10.1242/jcs.220624] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/15/2018] [Indexed: 12/31/2022] Open
Abstract
Both fibroblast growth factor-2 (FGF2) and neural cell adhesion molecule (NCAM) trigger FGF receptor 1 (FGFR1) signaling; however, they induce remarkably distinct receptor trafficking and cellular responses. The molecular basis of such a dichotomy and the role of distinct types of ligand-receptor interaction remain elusive. Number of molecules and brightness (N&B) analysis revealed that FGF2 and NCAM promote different FGFR1 assembly and dynamics at the plasma membrane. NCAM stimulation elicits long-lasting cycles of short-lived FGFR1 monomers and multimers, a behavior that might reflect a rapid FGFR1 internalization and recycling. FGF2, instead, induces stable dimerization at the dose that stimulates cell proliferation. Reducing the occupancy of FGFR1 in response to low FGF2 doses causes a switch towards cyclically exposed and unstable receptor dimers, consistently with previously reported biphasic response to FGF2 and with the divergent signaling elicited by different ligand concentrations. Similar instability was observed upon altering the endocytic pathway. Thus, FGF2 and NCAM induce differential FGFR1 clustering at the cell surface, which might account for the distinct intracellular fate of the receptor and, hence, for the different signaling cascades and cellular responses.
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Affiliation(s)
- Moreno Zamai
- Centro di Imaging Sperimentale (CIS), Ospedale San Raffaele, IRCCS, Milan 20132, Italy.,Microscopy and Dynamic Imaging Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Antonio Trullo
- Centro di Imaging Sperimentale (CIS), Ospedale San Raffaele, IRCCS, Milan 20132, Italy
| | - Marco Giordano
- Unit of Gynecological Oncology Research, European Institute of Oncology IRCCS, Milan 20141, Italy
| | - Valeria Corti
- Centro di Imaging Sperimentale (CIS), Ospedale San Raffaele, IRCCS, Milan 20132, Italy
| | - Elvira Arza Cuesta
- Microscopy and Dynamic Imaging Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Chiara Francavilla
- Division of Molecular and Cellular Functions, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Ugo Cavallaro
- Unit of Gynecological Oncology Research, European Institute of Oncology IRCCS, Milan 20141, Italy
| | - Valeria R Caiolfa
- Centro di Imaging Sperimentale (CIS), Ospedale San Raffaele, IRCCS, Milan 20132, Italy .,Microscopy and Dynamic Imaging Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
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41
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Veggiani G, Sidhu SS. Peptides meet ubiquitin: Simple interactions regulating complex cell signaling. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Gianluca Veggiani
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research; University of Toronto; Toronto Ontario Canada
- Department of Molecular Genetics; University of Toronto; Toronto Ontario Canada
| | - Sachdev S. Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research; University of Toronto; Toronto Ontario Canada
- Department of Molecular Genetics; University of Toronto; Toronto Ontario Canada
- Department of Biochemistry; University of Toronto; Toronto Ontario Canada
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42
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Schmid JA, Berti M, Walser F, Raso MC, Schmid F, Krietsch J, Stoy H, Zwicky K, Ursich S, Freire R, Lopes M, Penengo L. Histone Ubiquitination by the DNA Damage Response Is Required for Efficient DNA Replication in Unperturbed S Phase. Mol Cell 2018; 71:897-910.e8. [PMID: 30122534 DOI: 10.1016/j.molcel.2018.07.011] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 06/01/2018] [Accepted: 07/11/2018] [Indexed: 01/16/2023]
Abstract
Chromatin ubiquitination by the ubiquitin ligase RNF168 is critical to regulate the DNA damage response (DDR). DDR deficiencies lead to cancer-prone syndromes, but whether this reflects DNA repair defects is still elusive. We identified key factors of the RNF168 pathway as essential mediators of efficient DNA replication in unperturbed S phase. We found that loss of RNF168 leads to reduced replication fork progression and to reversed fork accumulation, particularly evident at repetitive sequences stalling replication. Slow fork progression depends on MRE11-dependent degradation of reversed forks, implicating RNF168 in reversed fork protection and restart. Consistent with regular nucleosomal organization of reversed forks, the replication function of RNF168 requires H2A ubiquitination. As this novel function is shared with the key DDR players ATM, γH2A.X, RNF8, and 53BP1, we propose that double-stranded ends at reversed forks engage classical DDR factors, suggesting an alternative function of this pathway in preventing genome instability and human disease.
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Affiliation(s)
- Jonas Andreas Schmid
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Matteo Berti
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Franziska Walser
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Maria Chiara Raso
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Fabian Schmid
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Jana Krietsch
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Henriette Stoy
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Katharina Zwicky
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Sebastian Ursich
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Raimundo Freire
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, Ofra s/n, La Cuesta, La Laguna, Tenerife 38320, Spain
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland.
| | - Lorenza Penengo
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland.
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43
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Mohammad A, Vanden Broek K, Wang C, Daryabeigi A, Jantsch V, Hansen D, Schedl T. Initiation of Meiotic Development Is Controlled by Three Post-transcriptional Pathways in Caenorhabditis elegans. Genetics 2018; 209:1197-1224. [PMID: 29941619 PMCID: PMC6063227 DOI: 10.1534/genetics.118.300985] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/20/2018] [Indexed: 11/18/2022] Open
Abstract
A major event in germline development is the transition from stem/progenitor cells to entry into meiosis and gametogenesis. This transition requires downregulation of mitotic cell cycle activity and upregulation of processes associated with meiosis. We identify the Caenorhabditis elegans SCFPROM-1 E3 ubiquitin-ligase complex as functioning to downregulate mitotic cell cycle protein levels including cyclin E, WAPL-1, and KNL-2 at meiotic entry and, independently, promoting homologous chromosome pairing as a positive regulator of the CHK-2 kinase. SCFPROM-1 is thus a novel regulator of meiotic entry, coordinating downregulation of mitotic cell cycle proteins and promoting homolog pairing. We further show that SCFPROM-1 functions redundantly, in parallel to the previously described GLD-1 and GLD-2 meiotic entry pathways, downstream of and inhibited by GLP-1 Notch signaling, which specifies the stem cell fate. Accordingly, C. elegans employs three post-transcriptional pathways, SCFPROM-1-mediated protein degradation, GLD-1-mediated translational repression, and GLD-2-mediated translational activation, to control and coordinate the initiation of meiotic development.
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Affiliation(s)
- Ariz Mohammad
- Department of Genetics, School of Medicine, Washington University in St. Louis, Missouri 63110
| | - Kara Vanden Broek
- Department of Biological Sciences, University of Calgary, T2N 1N4, Canada
| | - Christopher Wang
- Department of Biological Sciences, University of Calgary, T2N 1N4, Canada
| | - Anahita Daryabeigi
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, 1030, Austria
| | - Verena Jantsch
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, 1030, Austria
| | - Dave Hansen
- Department of Biological Sciences, University of Calgary, T2N 1N4, Canada
| | - Tim Schedl
- Department of Genetics, School of Medicine, Washington University in St. Louis, Missouri 63110
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44
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Saei A, Palafox M, Benoukraf T, Kumari N, Jaynes PW, Iyengar PV, Muñoz-Couselo E, Nuciforo P, Cortés J, Nötzel C, Kumarakulasinghe NB, Richard JLC, Bin Adam Isa ZF, Pang B, Guzman M, Siqin Z, Yang H, Tam WL, Serra V, Eichhorn PJA. Loss of USP28-mediated BRAF degradation drives resistance to RAF cancer therapies. J Exp Med 2018; 215:1913-1928. [PMID: 29880484 PMCID: PMC6028519 DOI: 10.1084/jem.20171960] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 03/09/2018] [Accepted: 05/09/2018] [Indexed: 11/04/2022] Open
Abstract
RAF kinase inhibitors are clinically active in patients with BRAF (V600E) mutant melanoma. However, rarely do tumors regress completely, with the majority of responses being short-lived. This is partially mediated through the loss of negative feedback loops after MAPK inhibition and reactivation of upstream signaling. Here, we demonstrate that the deubiquitinating enzyme USP28 functions through a feedback loop to destabilize RAF family members. Loss of USP28 stabilizes BRAF enhancing downstream MAPK activation and promotes resistance to RAF inhibitor therapy in culture and in vivo models. Importantly, we demonstrate that USP28 is deleted in a proportion of melanoma patients and may act as a biomarker for response to BRAF inhibitor therapy in patients. Furthermore, we identify Rigosertib as a possible therapeutic strategy for USP28-depleted tumors. Our results show that loss of USP28 enhances MAPK activity through the stabilization of RAF family members and is a key factor in BRAF inhibitor resistance.
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Affiliation(s)
- Azad Saei
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Marta Palafox
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Touati Benoukraf
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Nishi Kumari
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | | | | | | | - Paolo Nuciforo
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Javier Cortés
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Cancer Ramon y Cajal University Hospital, Madrid, Spain
- IOB Institute of Oncology, Quironsalud group, Madrid & Barcelona, Spain
| | - Christopher Nötzel
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Nesaretnam Barr Kumarakulasinghe
- Department of Hematology-Oncology, National University Cancer Institute, Singapore, National University Health System, Singapore, Singapore
| | | | | | - Brendan Pang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Marta Guzman
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Zhou Siqin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Wai Leong Tam
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Violeta Serra
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Pieter Johan Adam Eichhorn
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Australia
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45
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Herman EK, Ali M, Field MC, Dacks JB. Regulation of early endosomes across eukaryotes: Evolution and functional homology of Vps9 proteins. Traffic 2018; 19:546-563. [PMID: 29603841 PMCID: PMC6032885 DOI: 10.1111/tra.12570] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/21/2018] [Accepted: 03/27/2018] [Indexed: 12/11/2022]
Abstract
Endocytosis is a crucial process in eukaryotic cells. The GTPases Rab 5, 21 and 22 that mediate endocytosis are ancient eukaryotic features and all available evidence suggests retained conserved function. In animals and fungi, these GTPases are regulated in part by proteins possessing Vps9 domains. However, the diversity, evolution and functions of Vps9 proteins beyond animals or fungi are poorly explored. Here we report a comprehensive analysis of the Vps9 family of GTPase regulators, combining molecular evolutionary data with functional characterization in the non-opisthokont model organism Trypanosoma brucei. At least 3 subfamilies, Alsin, Varp and Rabex5 + GAPVD1, are found across eukaryotes, suggesting that all are ancient features of regulation of endocytic Rab protein function. There are examples of lineage-specific Vps9 subfamily member expansions and novel domain combinations, suggesting diversity in precise regulatory mechanisms between individual lineages. Characterization of the Rabex5 + GAPVD1 and Alsin orthologues in T. brucei demonstrates that both proteins are involved in endocytosis, and that simultaneous knockdown prevents membrane recruitment of Rab5 and Rab21, indicating conservation of function. These data demonstrate that, for the Vps9-domain family at least, modulation of Rab function is mediated by evolutionarily conserved protein-protein interactions.
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Affiliation(s)
- Emily K. Herman
- Department of Cell Biology, Faculty of Medicine and DentistryUniversity of AlbertaEdmontonCanada
| | - Moazzam Ali
- School of Life SciencesUniversity of DundeeDundeeUK
| | | | - Joel B. Dacks
- Department of Cell Biology, Faculty of Medicine and DentistryUniversity of AlbertaEdmontonCanada
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46
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Yadav U, Arya R, Kundu S, Sundd M. The “Recognition Helix” of the Type II Acyl Carrier Protein (ACP) Utilizes a “Ubiquitin Interacting Motif (UIM)”-like Surface To Bind Its Partners. Biochemistry 2018; 57:3690-3701. [DOI: 10.1021/acs.biochem.8b00220] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Usha Yadav
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Richa Arya
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Monica Sundd
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
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47
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Ryan TA, Tumbarello DA. Optineurin: A Coordinator of Membrane-Associated Cargo Trafficking and Autophagy. Front Immunol 2018; 9:1024. [PMID: 29867991 PMCID: PMC5962687 DOI: 10.3389/fimmu.2018.01024] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/24/2018] [Indexed: 12/13/2022] Open
Abstract
Optineurin is a multifunctional adaptor protein intimately involved in various vesicular trafficking pathways. Through interactions with an array of proteins, such as myosin VI, huntingtin, Rab8, and Tank-binding kinase 1, as well as via its oligomerisation, optineurin has the ability to act as an adaptor, scaffold, or signal regulator to coordinate many cellular processes associated with the trafficking of membrane-delivered cargo. Due to its diverse interactions and its distinct functions, optineurin is an essential component in a number of homeostatic pathways, such as protein trafficking and organelle maintenance. Through the binding of polyubiquitinated cargoes via its ubiquitin-binding domain, optineurin also serves as a selective autophagic receptor for the removal of a wide range of substrates. Alternatively, it can act in an ubiquitin-independent manner to mediate the clearance of protein aggregates. Regarding its disease associations, mutations in the optineurin gene are associated with glaucoma and have more recently been found to correlate with Paget’s disease of bone and amyotrophic lateral sclerosis (ALS). Indeed, ALS-associated mutations in optineurin result in defects in neuronal vesicular localisation, autophagosome–lysosome fusion, and secretory pathway function. More recent molecular and functional analysis has shown that it also plays a role in mitophagy, thus linking it to a number of other neurodegenerative conditions, such as Parkinson’s. Here, we review the role of optineurin in intracellular membrane trafficking, with a focus on autophagy, and describe how upstream signalling cascades are critical to its regulation. Current data and contradicting reports would suggest that optineurin is an important and selective autophagy receptor under specific conditions, whereby interplay, synergy, and functional redundancy with other receptors occurs. We will also discuss how dysfunction in optineurin-mediated pathways may lead to perturbation of critical cellular processes, which can drive the pathologies of number of diseases. Therefore, further understanding of optineurin function, its target specificity, and its mechanism of action will be critical in fully delineating its role in human disease.
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Affiliation(s)
- Thomas A Ryan
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - David A Tumbarello
- Biological Sciences, University of Southampton, Southampton, United Kingdom
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48
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Kwasna D, Abdul Rehman SA, Natarajan J, Matthews S, Madden R, De Cesare V, Weidlich S, Virdee S, Ahel I, Gibbs-Seymour I, Kulathu Y. Discovery and Characterization of ZUFSP/ZUP1, a Distinct Deubiquitinase Class Important for Genome Stability. Mol Cell 2018; 70:150-164.e6. [PMID: 29576527 PMCID: PMC5896202 DOI: 10.1016/j.molcel.2018.02.023] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/17/2018] [Accepted: 02/15/2018] [Indexed: 01/17/2023]
Abstract
Deubiquitinating enzymes (DUBs) are important regulators of ubiquitin signaling. Here, we report the discovery of deubiquitinating activity in ZUFSP/C6orf113. High-resolution crystal structures of ZUFSP in complex with ubiquitin reveal several distinctive features of ubiquitin recognition and catalysis. Our analyses reveal that ZUFSP is a novel DUB with no homology to any known DUBs, leading us to classify ZUFSP as the seventh DUB family. Intriguingly, the minimal catalytic domain does not cleave polyubiquitin. We identify two ubiquitin binding domains in ZUFSP: a ZHA (ZUFSP helical arm) that binds to the distal ubiquitin and an atypical UBZ domain in ZUFSP that binds to polyubiquitin. Importantly, both domains are essential for ZUFSP to selectively cleave K63-linked polyubiquitin. We show that ZUFSP localizes to DNA lesions, where it plays an important role in genome stability pathways, functioning to prevent spontaneous DNA damage and also promote cellular survival in response to exogenous DNA damage.
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Affiliation(s)
- Dominika Kwasna
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Syed Arif Abdul Rehman
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Jayaprakash Natarajan
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Stephen Matthews
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Ross Madden
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Virginia De Cesare
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Simone Weidlich
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Satpal Virdee
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Ivan Ahel
- DNA Damage Response Laboratory, Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Ian Gibbs-Seymour
- DNA Damage Response Laboratory, Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK.
| | - Yogesh Kulathu
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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49
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Nowsheen S, Aziz K, Aziz A, Deng M, Qin B, Luo K, Jeganathan KB, Zhang H, Liu T, Yu J, Deng Y, Yuan J, Ding W, van Deursen JM, Lou Z. L3MBTL2 orchestrates ubiquitin signalling by dictating the sequential recruitment of RNF8 and RNF168 after DNA damage. Nat Cell Biol 2018; 20:455-464. [PMID: 29581593 PMCID: PMC6083879 DOI: 10.1038/s41556-018-0071-x] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 02/22/2018] [Indexed: 12/12/2022]
Abstract
Cells respond to cytotoxic DNA double-strand breaks (DSBs) by recruiting DNA repair proteins to the damaged site. This recruitment is dependent on ubiquitylation of adjacent chromatin areas by E3 ubiquitin ligases such as RNF8 and RNF168, which are recruited sequentially to the DSBs. However, it is unclear what dictates the sequential order and recruits RNF168 to the DNA lesion. Here, we reveal that L3MBTL2 (lethal(3)malignant brain tumour-like protein 2) is the missing link between RNF8 and RNF168. We found that L3MBTL2 is recruited by MDC1 and subsequently ubiquitylated by RNF8. Ubiquitylated L3MBTL2, in turn, facilitates recruitment of RNF168 to the DNA lesion and promotes DNA DSB repair. These results identify L3MBTL2 as a key target of RNF8 following DNA damage and demonstrates how the DNA damage response pathway is orchestrated by ubiquitin signalling.
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Affiliation(s)
- Somaira Nowsheen
- Mayo Medical Scientist Training Program, Mayo Clinic School of Medicine and Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, USA
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Khaled Aziz
- Mayo Medical Scientist Training Program, Mayo Clinic School of Medicine and Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, USA
| | - Asef Aziz
- Department of Pediatrics and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Min Deng
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Bo Qin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Kuntian Luo
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Karthik B Jeganathan
- Department of Pediatrics and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Henan Zhang
- Department of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Tongzheng Liu
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Institute of Tumor Pharmacology, Jinan University, Guangzhou, China
| | - Jia Yu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Yibin Deng
- Laboratory of Cancer Genetics, The University of Minnesota Hormel Institute, Austin, MN, USA
| | - Jian Yuan
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wei Ding
- Department of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Jan M van Deursen
- Department of Pediatrics and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, USA.
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China.
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50
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O'Loughlin T, Masters TA, Buss F. The MYO6 interactome reveals adaptor complexes coordinating early endosome and cytoskeletal dynamics. EMBO Rep 2018; 19:e44884. [PMID: 29467281 PMCID: PMC5891429 DOI: 10.15252/embr.201744884] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 01/17/2018] [Accepted: 01/30/2018] [Indexed: 12/15/2022] Open
Abstract
The intracellular functions of myosin motors requires a number of adaptor molecules, which control cargo attachment, but also fine-tune motor activity in time and space. These motor-adaptor-cargo interactions are often weak, transient or highly regulated. To overcome these problems, we use a proximity labelling-based proteomics strategy to map the interactome of the unique minus end-directed actin motor MYO6. Detailed biochemical and functional analysis identified several distinct MYO6-adaptor modules including two complexes containing RhoGEFs: the LIFT (LARG-Induced F-actin for Tethering) complex that controls endosome positioning and motility through RHO-driven actin polymerisation; and the DISP (DOCK7-Induced Septin disPlacement) complex, a novel regulator of the septin cytoskeleton. These complexes emphasise the role of MYO6 in coordinating endosome dynamics and cytoskeletal architecture. This study provides the first in vivo interactome of a myosin motor protein and highlights the power of this approach in uncovering dynamic and functionally diverse myosin motor complexes.
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Affiliation(s)
- Thomas O'Loughlin
- Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge, UK
| | - Thomas A Masters
- Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge, UK
| | - Folma Buss
- Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge, UK
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