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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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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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3
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Nambiar A, Manjithaya R. Driving autophagy - the role of molecular motors. J Cell Sci 2024; 137:jcs260481. [PMID: 38329417 DOI: 10.1242/jcs.260481] [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] [Indexed: 02/09/2024] Open
Abstract
Most of the vesicular transport pathways inside the cell are facilitated by molecular motors that move along cytoskeletal networks. Autophagy is a well-explored catabolic pathway that is initiated by the formation of an isolation membrane known as the phagophore, which expands to form a double-membraned structure that captures its cargo and eventually moves towards the lysosomes for fusion. Molecular motors and cytoskeletal elements have been suggested to participate at different stages of the process as the autophagic vesicles move along cytoskeletal tracks. Dynein and kinesins govern autophagosome trafficking on microtubules through the sequential recruitment of their effector proteins, post-translational modifications and interactions with LC3-interacting regions (LIRs). In contrast, myosins are actin-based motors that participate in various stages of the autophagic flux, as well as in selective autophagy pathways. However, several outstanding questions remain with regard to how the dominance of a particular motor protein over another is controlled, and to the molecular mechanisms that underlie specific disease variants in motor proteins. In this Review, we aim to provide an overview of the role of molecular motors in autophagic flux, as well as highlight their dysregulation in diseases, such as neurodegenerative disorders and pathogenic infections, and ageing.
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Affiliation(s)
- Akshaya Nambiar
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Ravi Manjithaya
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
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4
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Stein RA, Mchaourab HS. Rosetta Energy Analysis of AlphaFold2 models: Point Mutations and Conformational Ensembles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.05.556364. [PMID: 37732281 PMCID: PMC10508732 DOI: 10.1101/2023.09.05.556364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
There has been an explosive growth in the applications of AlphaFold2, and other structure prediction platforms, to accurately predict protein structures from a multiple sequence alignment (MSA) for downstream structural analysis. However, two outstanding questions persist in the field regarding the robustness of AlphaFold2 predictions of the consequences of point mutations and the completeness of its prediction of protein conformational ensembles. We combined our previously developed method SPEACH_AF with model relaxation and energetic analysis with Rosetta to address these questions. SPEACH_AF introduces residue substitutions across the MSA and not just within the input sequence. With respect to conformational ensembles, we combined SPEACH_AF and a new MSA subsampling method, AF_cluster, and for a benchmarked set of proteins, we found that the energetics of the conformational ensembles generated by AlphaFold2 correspond to those of experimental structures and explored by standard molecular dynamic methods. With respect to point mutations, we compared the structural and energetic consequences of having the mutation(s) in the input sequence versus in the whole MSA (SPEACH_AF). Both methods yielded models different from the wild-type sequence, with more robust changes when the mutation(s) were in the whole MSA. While our findings demonstrate the robustness of AlphaFold2 in analyzing point mutations and exploring conformational ensembles, they highlight the need for multi parameter structural and energetic analyses of these models to generate experimentally testable hypotheses.
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Affiliation(s)
- Richard A Stein
- Department of Molecular Physiology and Biophysics and Center for Applied AI in Protein Dynamics Vanderbilt University
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics and Center for Applied AI in Protein Dynamics Vanderbilt University
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5
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Artcibasova A, Wang L, Anchisi S, Yamauchi Y, Schmolke M, Matthias P, Stelling J. A quantitative model for virus uncoating predicts influenza A infectivity. Cell Rep 2023; 42:113558. [PMID: 38103200 DOI: 10.1016/j.celrep.2023.113558] [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: 06/30/2022] [Revised: 10/13/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
For virus infection of new host cells, the disassembly of the protective outer protein shell (capsid) is a critical step, but the mechanisms and host-virus interactions underlying the dynamic, active, and regulated uncoating process are largely unknown. Here, we develop an experimentally supported, multiscale kinetics model that elucidates mechanisms of influenza A virus (IAV) uncoating in cells. Biophysical modeling demonstrates that interactions between capsid M1 proteins, host histone deacetylase 6 (HDAC6), and molecular motors can physically break the capsid in a tug-of-war mechanism. Biochemical analysis and biochemical-biophysical modeling identify unanchored ubiquitin chains as essential and allow robust prediction of uncoating efficiency in cells. Remarkably, the different infectivity of two clinical strains can be ascribed to a single amino acid variation in M1 that affects binding to HDAC6. By identifying crucial modules of viral infection kinetics, the mechanisms and models presented here could help formulate novel strategies for broad-range antiviral treatment.
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Affiliation(s)
- Alina Artcibasova
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland
| | - Longlong Wang
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4031 Basel, Switzerland
| | - Stephanie Anchisi
- Department of Microbiology and Molecular Medicine and Geneva Center of Inflammation Research, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Yohei Yamauchi
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Mirco Schmolke
- Department of Microbiology and Molecular Medicine and Geneva Center of Inflammation Research, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Patrick Matthias
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4031 Basel, Switzerland.
| | - Jörg Stelling
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland.
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6
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Canon L, Kikuti C, Planelles-Herrero VJ, Lin T, Mayeux F, Sirkia H, Lee YI, Heidsieck L, Velikovsky L, David A, Liu X, Moussaoui D, Forest E, Höök P, Petersen KJ, Morgan TE, Di Cicco A, Sirés-Campos J, Derivery E, Lévy D, Delevoye C, Sweeney HL, Houdusse A. How myosin VI traps its off-state, is activated and dimerizes. Nat Commun 2023; 14:6732. [PMID: 37872146 PMCID: PMC10593786 DOI: 10.1038/s41467-023-42376-2] [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: 01/05/2023] [Accepted: 10/10/2023] [Indexed: 10/25/2023] Open
Abstract
Myosin VI (Myo6) is the only minus-end directed nanomotor on actin, allowing it to uniquely contribute to numerous cellular functions. As for other nanomotors, the proper functioning of Myo6 relies on precise spatiotemporal control of motor activity via a poorly defined off-state and interactions with partners. Our structural, functional, and cellular studies reveal key features of myosin regulation and indicate that not all partners can activate Myo6. TOM1 and Dab2 cannot bind the off-state, while GIPC1 binds Myo6, releases its auto-inhibition and triggers proximal dimerization. Myo6 partners thus differentially recruit Myo6. We solved a crystal structure of the proximal dimerization domain, and show that its disruption compromises endocytosis in HeLa cells, emphasizing the importance of Myo6 dimerization. Finally, we show that the L926Q deafness mutation disrupts Myo6 auto-inhibition and indirectly impairs proximal dimerization. Our study thus demonstrates the importance of partners in the control of Myo6 auto-inhibition, localization, and activation.
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Affiliation(s)
- Louise Canon
- Structural Motility, UMR 144 CNRS/Curie Institute, PSL Research University, 26 rue d'Ulm, 75258, Paris cedex 05, France
| | - Carlos Kikuti
- Structural Motility, UMR 144 CNRS/Curie Institute, PSL Research University, 26 rue d'Ulm, 75258, Paris cedex 05, France
| | - Vicente J Planelles-Herrero
- Structural Motility, UMR 144 CNRS/Curie Institute, PSL Research University, 26 rue d'Ulm, 75258, Paris cedex 05, France
| | - Tianming Lin
- Department of Pharmacology & Therapeutics and the Myology Institute, University of Florida College of Medicine, PO Box 100267, Gainesville, Florida, 32610-0267, USA
| | - Franck Mayeux
- Structural Motility, UMR 144 CNRS/Curie Institute, PSL Research University, 26 rue d'Ulm, 75258, Paris cedex 05, France
| | - Helena Sirkia
- Structural Motility, UMR 144 CNRS/Curie Institute, PSL Research University, 26 rue d'Ulm, 75258, Paris cedex 05, France
| | - Young Il Lee
- Department of Pharmacology & Therapeutics and the Myology Institute, University of Florida College of Medicine, PO Box 100267, Gainesville, Florida, 32610-0267, USA
| | - Leila Heidsieck
- Structural Motility, UMR 144 CNRS/Curie Institute, PSL Research University, 26 rue d'Ulm, 75258, Paris cedex 05, France
| | - Léonid Velikovsky
- Structural Motility, UMR 144 CNRS/Curie Institute, PSL Research University, 26 rue d'Ulm, 75258, Paris cedex 05, France
| | - Amandine David
- Structural Motility, UMR 144 CNRS/Curie Institute, PSL Research University, 26 rue d'Ulm, 75258, Paris cedex 05, France
| | - Xiaoyan Liu
- Department of Pharmacology & Therapeutics and the Myology Institute, University of Florida College of Medicine, PO Box 100267, Gainesville, Florida, 32610-0267, USA
| | - Dihia Moussaoui
- Structural Motility, UMR 144 CNRS/Curie Institute, PSL Research University, 26 rue d'Ulm, 75258, Paris cedex 05, France
| | - Emma Forest
- Structural Motility, UMR 144 CNRS/Curie Institute, PSL Research University, 26 rue d'Ulm, 75258, Paris cedex 05, France
- École Nationale Supérieure de Chimie de Montpellier, 240 Avenue du Professeur Emile Jeanbrau, 34090, Montpellier, France
| | - Peter Höök
- Department of Pharmacology & Therapeutics and the Myology Institute, University of Florida College of Medicine, PO Box 100267, Gainesville, Florida, 32610-0267, USA
| | - Karl J Petersen
- Structural Motility, UMR 144 CNRS/Curie Institute, PSL Research University, 26 rue d'Ulm, 75258, Paris cedex 05, France
| | | | - Aurélie Di Cicco
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico-Chimie Curie, 75005, Paris, France
| | - Julia Sirés-Campos
- Structure et Compartimentation Membranaire, UMR 144 CNRS/Curie Institute, PSL Research University, 26 rue d'Ulm, 75258, Paris cedex 05, France
| | | | - Daniel Lévy
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico-Chimie Curie, 75005, Paris, France
| | - Cédric Delevoye
- Structure et Compartimentation Membranaire, UMR 144 CNRS/Curie Institute, PSL Research University, 26 rue d'Ulm, 75258, Paris cedex 05, France
| | - H Lee Sweeney
- Department of Pharmacology & Therapeutics and the Myology Institute, University of Florida College of Medicine, PO Box 100267, Gainesville, Florida, 32610-0267, USA.
| | - Anne Houdusse
- Structural Motility, UMR 144 CNRS/Curie Institute, PSL Research University, 26 rue d'Ulm, 75258, Paris cedex 05, France.
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7
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Tan LX, Germer CJ, Thamban T, La Cunza N, Lakkaraju A. Optineurin tunes outside-in signaling to regulate lysosome biogenesis and phagocytic clearance in the retina. Curr Biol 2023; 33:3805-3820.e7. [PMID: 37586372 PMCID: PMC10529777 DOI: 10.1016/j.cub.2023.07.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/16/2023] [Accepted: 07/19/2023] [Indexed: 08/18/2023]
Abstract
Balancing the competing demands of phagolysosomal degradation and autophagy is a significant challenge for phagocytic tissues. Yet how this plasticity is accomplished in health and disease is poorly understood. In the retina, circadian phagocytosis and degradation of photoreceptor outer segments by the postmitotic retinal pigment epithelium (RPE) are essential for healthy vision. Disrupted autophagy due to mechanistic target of rapamycin (mTOR) overactivation in the RPE is associated with blinding macular degenerations; however, outer segment degradation is unaffected in these diseases, indicating that distinct mechanisms regulate these clearance mechanisms. Here, using advanced imaging and mouse models, we identify optineurin as a key regulator that tunes phagocytosis and lysosomal capacity to meet circadian demands and helps prioritize outer segment clearance by the RPE in macular degenerations. High-resolution live-cell imaging implicates optineurin in scissioning outer segment tips prior to engulfment, analogous to microglial trogocytosis of neuronal processes. Optineurin is essential for recruiting light chain 3 (LC3), which anchors outer segment phagosomes to microtubules and facilitates phagosome maturation and fusion with lysosomes. This dynamically activates transcription factor EB (TFEB) to induce lysosome biogenesis in an mTOR-independent, transient receptor potential-mucolipin 1 (TRPML1)-dependent manner. RNA-seq analyses show that expression of TFEB target genes temporally tracks with optineurin recruitment and that lysosomal and autophagy genes are controlled by distinct transcriptional programs in the RPE. The unconventional plasma membrane-to-nucleus signaling mediated by optineurin ensures outer segment degradation under conditions of impaired autophagy in macular degeneration models. Independent regulation of these critical clearance mechanisms would help safeguard the metabolic fitness of the RPE throughout the organismal lifespan.
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Affiliation(s)
- Li Xuan Tan
- Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Colin J Germer
- Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Thushara Thamban
- Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nilsa La Cunza
- Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Aparna Lakkaraju
- Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
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8
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Menin L, Weber J, Villa S, Martini E, Maspero E, Niño CA, Cancila V, Poli A, Maiuri P, Palamidessi A, Frittoli E, Bianchi F, Tripodo C, Walters KJ, Giavazzi F, Scita G, Polo S. A planar polarized MYO6-DOCK7-RAC1 axis promotes tissue fluidification in mammary epithelia. Cell Rep 2023; 42:113001. [PMID: 37590133 PMCID: PMC10530600 DOI: 10.1016/j.celrep.2023.113001] [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: 03/17/2023] [Revised: 04/24/2023] [Accepted: 08/01/2023] [Indexed: 08/19/2023] Open
Abstract
Tissue fluidification and collective motility are pivotal in regulating embryonic morphogenesis, wound healing, and tumor metastasis. These processes frequently require that each cell constituent of a tissue coordinates its migration activity and directed motion through the oriented extension of lamellipodium cell protrusions, promoted by RAC1 activity. While the upstream RAC1 regulators in individual migratory cells or leader cells during invasion or wound healing are well characterized, how RAC1 is controlled in follower cells remains unknown. Here, we identify a MYO6-DOCK7 axis essential for spatially restricting RAC1 activity in a planar polarized fashion in model tissue monolayers. The MYO6-DOCK7 axis specifically controls the extension of cryptic lamellipodia required to drive tissue fluidification and cooperative-mode motion in otherwise solid and static carcinoma cell collectives.
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Affiliation(s)
- Luca Menin
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Janine Weber
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Stefano Villa
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Segrate, Italy
| | - Emanuele Martini
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Elena Maspero
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Carlos A Niño
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Valeria Cancila
- Human Pathology Section, Department of Health Sciences, University of Palermo School of Medicine, Palermo, Italy
| | - Alessandro Poli
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Paolo Maiuri
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | | | | | - Fabrizio Bianchi
- Unit of Cancer Biomarkers, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Claudio Tripodo
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy; Human Pathology Section, Department of Health Sciences, University of Palermo School of Medicine, Palermo, Italy
| | - Kylie J Walters
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Fabio Giavazzi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Segrate, Italy
| | - Giorgio Scita
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy; Dipartimento di Oncologia ed Emato-oncologia, Università degli Studi di Milano, Milan, Italy.
| | - Simona Polo
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy; Dipartimento di Oncologia ed Emato-oncologia, Università degli Studi di Milano, Milan, Italy.
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9
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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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10
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Taibi V, Polo S, Maspero E. Monitoring HECT Ubiquitination Activity In Vitro. Methods Mol Biol 2023; 2602:81-92. [PMID: 36446968 DOI: 10.1007/978-1-0716-2859-1_6] [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] [Indexed: 06/16/2023]
Abstract
In vitro ubiquitination tools have been employed to mechanistically study the ubiquitin enzymatic cascade. Here, we describe an assay capable to monitor ubiquitin conjugation in real time using the Time-Resolved Fluorescence Resonance Energy Transfer (TR-FRET) system. The assay requires purified E1 and E2 enzymes, the HECT E3 ligase of choice and two fluorophore-labeled ubiquitins. This single step technique represents an excellent tool to study the enzymatic activity during chain elongation, to compare ligase activity in the presence or absence of the substrate, and to set-up high-throughput screenings for enzymatic activity modulators (i.e., activators or inhibitors).
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Affiliation(s)
- Vincenzo Taibi
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Simona Polo
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy.
- Dipartimento di oncologia ed emato-oncologia, Università degli Studi di Milano, Milan, Italy.
| | - Elena Maspero
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy.
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11
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Lombardi PM, Haile S, Rusanov T, Rodell R, Anoh R, Baer JG, Burke KA, Gray LN, Hacker AR, Kebreau KR, Ngandu CK, Orland HA, Osei-Asante E, Schmelyun DP, Shorb DE, Syed SH, Veilleux JM, Majumdar A, Mosammaparast N, Wolberger C. The ASCC2 CUE domain in the ALKBH3-ASCC DNA repair complex recognizes adjacent ubiquitins in K63-linked polyubiquitin. J Biol Chem 2022; 298:101545. [PMID: 34971705 PMCID: PMC8800115 DOI: 10.1016/j.jbc.2021.101545] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 11/28/2022] Open
Abstract
Alkylation of DNA and RNA is a potentially toxic lesion that can result in mutations and even cell death. In response to alkylation damage, K63-linked polyubiquitin chains are assembled that localize the Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3-Activating Signal Cointegrator 1 Complex Subunit (ASCC) repair complex to damage sites in the nucleus. The protein ASCC2, a subunit of the ASCC complex, selectively binds K63-linked polyubiquitin chains via its coupling of ubiquitin conjugation to ER degradation (CUE) domain. The basis for polyubiquitin-binding specificity was unclear, because CUE domains in other proteins typically bind a single ubiquitin and do not discriminate among different polyubiquitin linkage types. We report here that the ASCC2 CUE domain selectively binds K63-linked diubiquitin by contacting both the distal and proximal ubiquitin. The ASCC2 CUE domain binds the distal ubiquitin in a manner similar to that reported for other CUE domains bound to a single ubiquitin, whereas the contacts with the proximal ubiquitin are unique to ASCC2. Residues in the N-terminal portion of the ASCC2 α1 helix contribute to the binding interaction with the proximal ubiquitin of K63-linked diubiquitin. Mutation of residues within the N-terminal portion of the ASCC2 α1 helix decreases ASCC2 recruitment in response to DNA alkylation, supporting the functional significance of these interactions during the alkylation damage response. Our study reveals the versatility of CUE domains in ubiquitin recognition.
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Affiliation(s)
- Patrick M Lombardi
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Department of Science, Mount St. Mary's University, Emmitsburg, Maryland, USA.
| | - Sara Haile
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Timur Rusanov
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Rebecca Rodell
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Rita Anoh
- Department of Science, Mount St. Mary's University, Emmitsburg, Maryland, USA
| | - Julia G Baer
- Department of Science, Mount St. Mary's University, Emmitsburg, Maryland, USA
| | - Kate A Burke
- Department of Science, Mount St. Mary's University, Emmitsburg, Maryland, USA
| | - Lauren N Gray
- Department of Science, Mount St. Mary's University, Emmitsburg, Maryland, USA
| | - Abigail R Hacker
- Department of Science, Mount St. Mary's University, Emmitsburg, Maryland, USA
| | - Kayla R Kebreau
- Department of Science, Mount St. Mary's University, Emmitsburg, Maryland, USA
| | - Christine K Ngandu
- Department of Science, Mount St. Mary's University, Emmitsburg, Maryland, USA
| | - Hannah A Orland
- Department of Science, Mount St. Mary's University, Emmitsburg, Maryland, USA
| | | | - Dhane P Schmelyun
- Department of Science, Mount St. Mary's University, Emmitsburg, Maryland, USA
| | - Devin E Shorb
- Department of Science, Mount St. Mary's University, Emmitsburg, Maryland, USA
| | - Shaheer H Syed
- Department of Science, Mount St. Mary's University, Emmitsburg, Maryland, USA
| | - Julianna M Veilleux
- Department of Science, Mount St. Mary's University, Emmitsburg, Maryland, USA
| | - Ananya Majumdar
- Biomolecular NMR Center, The Johns Hopkins University, Baltimore, Maryland, USA
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
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12
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Affiliation(s)
- Gwen R Buel
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Kylie J Walters
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
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13
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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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14
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Giangreco G, Malabarba MG, Sigismund S. Specialised endocytic proteins regulate diverse internalisation mechanisms and signalling outputs in physiology and cancer. Biol Cell 2020; 113:165-182. [PMID: 33617023 DOI: 10.1111/boc.202000129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/20/2022]
Abstract
Although endocytosis was first described as the process mediating macromolecule or nutrient uptake through the plasma membrane, it is now recognised as a critical component of the cellular infrastructure involved in numerous processes, ranging from receptor signalling, proliferation and migration to polarity and stem cell regulation. To realise these varying roles, endocytosis needs to be finely regulated. Accordingly, multiple endocytic mechanisms exist that require specialised molecular machineries and an array of endocytic adaptor proteins with cell-specific functions. This review provides some examples of specialised functions of endocytic adaptors and other components of the endocytic machinery in different cell physiological processes, and how the alteration of these functions is linked to cancer. In particular, we focus on: (i) cargo selection and endocytic mechanisms linked to different adaptors; (ii) specialised functions in clathrin-mediated versus non-clathrin endocytosis; (iii) differential regulation of endocytic mechanisms by post-translational modification of endocytic proteins; (iv) cell context-dependent expression and function of endocytic proteins. As cases in point, we describe two endocytic protein families, dynamins and epsins. Finally, we discuss how dysregulation of the physiological role of these specialised endocytic proteins is exploited by cancer cells to increase cell proliferation, migration and invasion, leading to anti-apoptotic or pro-metastatic behaviours.
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Affiliation(s)
| | - Maria Grazia Malabarba
- IEO, Istituto Europeo di Oncologia IRCCS, Milan, Italy.,Università degli Studi di Milano, Dipartimento di Oncologia ed Emato-oncologia, , Milan, Italy
| | - Sara Sigismund
- IEO, Istituto Europeo di Oncologia IRCCS, Milan, Italy.,Università degli Studi di Milano, Dipartimento di Oncologia ed Emato-oncologia, , Milan, Italy
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15
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USP25 Regulates EGFR Fate by Modulating EGF-Induced Ubiquitylation Dynamics. Biomolecules 2020; 10:biom10111548. [PMID: 33202887 PMCID: PMC7696865 DOI: 10.3390/biom10111548] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 11/28/2022] Open
Abstract
Deregulated epidermal growth factor receptor (EGFR) signaling is a key feature in different stages of oncogenesis. One important mechanism whereby cancer cells achieve increased and uncontrolled EGFR signaling is escaping down-modulation of the receptor. Ubiquitylation of the EGFR plays a decisive role in this process, as it regulates receptor internalization, trafficking and degradation. Deubiquitinating enzymes (DUBs) may oppose the ubiquitylation process, antagonizing or even promoting receptor degradation. Here, we use qualitative and quantitative assays to measure EGFR internalization and degradation after Ubiquitin Specific Peptidase 25 (USP25) depletion. We show that, by acting at the early steps of EGFR internalization, USP25 restrains the degradation of the EGFR by assisting in the association of the E3 ubiquitin ligase c-Cbl with EGFR, thereby modulating the amplitude of ubiquitylation on the receptor. This study establishes USP25 as a negative regulator of the EGFR down-modulation process and suggests that it is a promising target for pharmacological intervention to hamper oncogenic growth signals in tumors that depend on the EGFR.
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16
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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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17
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The Functional Characterization of TcMyoF Implicates a Family of Cytostome-Cytopharynx Targeted Myosins as Integral to the Endocytic Machinery of Trypanosoma cruzi. mSphere 2020; 5:5/3/e00313-20. [PMID: 32554712 PMCID: PMC7300353 DOI: 10.1128/msphere.00313-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The parasite Trypanosoma cruzi is the etiological agent of Chagas disease and chronically infects upwards of 7 million people in the Americas. Current diagnostics and treatments remain grossly inadequate due, in part, to our general lack of understanding of this parasite’s basic biology. One aspect that has resisted detailed scrutiny is the mechanism employed by this parasite to extract nutrient resources from the radically different environments that it encounters as it transitions between its invertebrate and mammalian hosts. These parasites engulf food via a tubular invagination of its membrane, a strategy used by many protozoan species, but how this structure is formed or functions mechanistically remains a complete mystery. The significance of our research is in the identification of the mechanistic underpinnings of this feeding organelle that may bring to light new potential therapeutic targets to impede parasite feeding and thus halt the spread of this deadly human pathogen. Of the pathogenic trypanosomatids, Trypanosoma cruzi alone retains an ancient feeding apparatus known as the cytostome-cytopharynx complex (SPC) that it uses as its primary mode of endocytosis in a manner akin to its free-living kinetoplastid relatives who capture and eat bacterial prey via this endocytic organelle. In a recent report, we began the process of dissecting how this organelle functions by identifying the first SPC-specific proteins in T. cruzi. Here, we continued these studies and report on the identification of the first enzymatic component of the SPC, a previously identified orphan myosin motor (MyoF) specifically targeted to the SPC. We overexpressed MyoF as a dominant-negative mutant, resulting in parasites that, although viable, were completely deficient in measurable endocytosis in vitro. To our surprise, however, a full deletion of MyoF demonstrated only a decrease in the overall rate of endocytosis, potentially indicative of redundant myosin motors at work. Thereupon, we identified three additional orphan myosin motors, two of which (MyoB and MyoE) were targeted to the preoral ridge region adjacent to the cytostome entrance and another (MyoC) which was targeted to the cytopharynx tubular structure similar to that of MyoF. Additionally, we show that the C-terminal tails of each myosin are sufficient for targeting a fluorescent reporter to SPC subregions. This work highlights a potential mechanism used by the SPC to drive the inward flow of material for digestion and unveils a new level of overlapping complexity in this system with four distinct myosin isoforms targeted to this feeding structure. IMPORTANCE The parasite Trypanosoma cruzi is the etiological agent of Chagas disease and chronically infects upwards of 7 million people in the Americas. Current diagnostics and treatments remain grossly inadequate due, in part, to our general lack of understanding of this parasite’s basic biology. One aspect that has resisted detailed scrutiny is the mechanism employed by this parasite to extract nutrient resources from the radically different environments that it encounters as it transitions between its invertebrate and mammalian hosts. These parasites engulf food via a tubular invagination of its membrane, a strategy used by many protozoan species, but how this structure is formed or functions mechanistically remains a complete mystery. The significance of our research is in the identification of the mechanistic underpinnings of this feeding organelle that may bring to light new potential therapeutic targets to impede parasite feeding and thus halt the spread of this deadly human pathogen.
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18
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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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19
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Shahul Hameed D, van Tilburg GBA, Merkx R, Flierman D, Wienk H, El Oualid F, Hofmann K, Boelens R, Ovaa H. Diubiquitin-Based NMR Analysis: Interactions Between Lys6-Linked diUb and UBA Domain of UBXN1. Front Chem 2020; 7:921. [PMID: 32039147 PMCID: PMC6987245 DOI: 10.3389/fchem.2019.00921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/18/2019] [Indexed: 12/03/2022] Open
Abstract
Ubiquitination is a process in which a protein is modified by the covalent attachment of the C-terminal carboxylic acid of ubiquitin (Ub) to the ε-amine of lysine or N-terminal methionine residue of a substrate protein or another Ub molecule. Each of the seven internal lysine residues and the N-terminal methionine residue of Ub can be linked to the C-terminus of another Ub moiety to form 8 distinct Ub linkages and the resulting differences in linkage types elicit different Ub signaling pathways. Cellular responses are triggered when proteins containing ubiquitin-binding domains (UBDs) recognize and bind to specific polyUb linkage types. To get more insight into the differences between polyUb chains, all of the seven lysine-linked di-ubiquitin molecules (diUbs) were prepared and used as a model to study their structural conformations in solution using NMR spectroscopy. We report the synthesis of diUb molecules, fully 15N-labeled on the distal (N-terminal) Ub moiety and revealed their structural orientation with respect to the proximal Ub. As expected, the diUb molecules exist in different conformations in solution, with multiple conformations known to exist for K6-, K48-, and K63-linked diUb molecules. These multiple conformations allow structural flexibility in binding with UBDs thereby inducing unique responses. One of the well-known but poorly understood UBD-Ub interaction is the recognition of K6 polyubiquitin by the ubiquitin-associated (UBA) domain of UBXN1 in the BRCA-mediated DNA repair pathway. Using our synthetic 15N-labeled diUbs, we establish here how a C-terminally extended UBA domain of UBXN1 confers specificity to K6 diUb while the non-extended version of the domain does not show any linkage preference. We show that the two distinct conformations of K6 diUb that exist in solution converge into a single conformation upon binding to this extended form of the UBA domain of the UBXN1 protein. It is likely that more of such extended UBA domains exist in nature and can contribute to linkage-specificity in Ub signaling. The isotopically labeled diUb compounds described here and the use of NMR to study their interactions with relevant partner molecules will help accelerate our understanding of Ub signaling pathways.
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Affiliation(s)
- Dharjath Shahul Hameed
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
| | - Gabrielle B A van Tilburg
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
| | - Remco Merkx
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Dennis Flierman
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Farid El Oualid
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,UbiQ Bio BV, Amsterdam, Netherlands
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Rolf Boelens
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Huib Ovaa
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
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20
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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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21
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Biancospino M, Buel GR, Niño CA, Maspero E, Scotto di Perrotolo R, Raimondi A, Redlingshöfer L, Weber J, Brodsky FM, Walters KJ, Polo S. Clathrin light chain A drives selective myosin VI recruitment to clathrin-coated pits under membrane tension. Nat Commun 2019; 10:4974. [PMID: 31672988 PMCID: PMC6823378 DOI: 10.1038/s41467-019-12855-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/27/2019] [Indexed: 11/17/2022] Open
Abstract
Clathrin light chains (CLCa and CLCb) are major constituents of clathrin-coated vesicles. Unique functions for these evolutionary conserved paralogs remain elusive, and their role in clathrin-mediated endocytosis in mammalian cells is debated. Here, we find and structurally characterize a direct and selective interaction between CLCa and the long isoform of the actin motor protein myosin VI, which is expressed exclusively in highly polarized tissues. Using genetically-reconstituted Caco-2 cysts as proxy for polarized epithelia, we provide evidence for coordinated action of myosin VI and CLCa at the apical surface where these proteins are essential for fission of clathrin-coated pits. We further find that myosin VI and Huntingtin-interacting protein 1-related protein (Hip1R) are mutually exclusive interactors with CLCa, and suggest a model for the sequential function of myosin VI and Hip1R in actin-mediated clathrin-coated vesicle budding.
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Affiliation(s)
- Matteo Biancospino
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, 20139, Milan, Italy
| | - Gwen R Buel
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Carlos A Niño
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, 20139, Milan, Italy
| | - Elena Maspero
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, 20139, Milan, Italy
| | | | - Andrea Raimondi
- Experimental Imaging Center, San Raffaele Scientific Institute, Milan, Italy
| | - Lisa Redlingshöfer
- Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Janine Weber
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, 20139, Milan, Italy
| | - Frances M Brodsky
- Division of Biosciences, University College London, London, WC1E 6BT, UK.
| | - Kylie J Walters
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
| | - Simona Polo
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, 20139, Milan, Italy.
- Dipartimento di Oncologia ed Emato-oncologia, Universita' degli Studi di Milano, 20122, Milan, Italy.
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22
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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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23
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Hu S, Guo Y, Wang Y, Li Y, Fu T, Zhou Z, Wang Y, Liu J, Pan L. Structure of Myosin VI/Tom1 complex reveals a cargo recognition mode of Myosin VI for tethering. Nat Commun 2019; 10:3459. [PMID: 31371777 PMCID: PMC6673701 DOI: 10.1038/s41467-019-11481-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 07/16/2019] [Indexed: 12/31/2022] Open
Abstract
Myosin VI plays crucial roles in diverse cellular processes. In autophagy, Myosin VI can facilitate the maturation of autophagosomes through interactions with Tom1 and the autophagy receptors, Optineurin, NDP52 and TAX1BP1. Here, we report the high-resolution crystal structure of the C-terminal cargo-binding domain (CBD) of Myosin VI in complex with Tom1, which elucidates the mechanistic basis underpinning the specific interaction between Myosin VI and Tom1, and uncovers that the C-terminal CBD of Myosin VI adopts a unique cargo recognition mode to interact with Tom1 for tethering. Furthermore, we show that Myosin VI can serve as a bridging adaptor to simultaneously interact with Tom1 and autophagy receptors through two distinct interfaces. In all, our findings provide mechanistic insights into the interactions of Myosin VI with Tom1 and relevant autophagy receptors, and are valuable for further understanding the functions of these proteins in autophagy and the cargo recognition modes of Myosin VI. Myosin VI can facilitate the maturation of autophagosomes in autophagy through interactions with Tom1 and autophagy receptors. Here authors report the structure of the cargobinding domain of Myosin VI in complex with Tom1, which provides insights into Myosin IV’s cargo recognition modes.
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Affiliation(s)
- Shichen Hu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Yujiao Guo
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Yingli Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Ying Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Tao Fu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Zixuan Zhou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Yaru Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Jianping Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Lifeng Pan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200032, Shanghai, China.
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24
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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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25
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Carretero-Ortega J, Chhangawala Z, Hunt S, Narvaez C, Menéndez-González J, Gay CM, Zygmunt T, Li X, Torres-Vázquez J. GIPC proteins negatively modulate Plexind1 signaling during vascular development. eLife 2019; 8:e30454. [PMID: 31050647 PMCID: PMC6499541 DOI: 10.7554/elife.30454] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 04/15/2019] [Indexed: 12/18/2022] Open
Abstract
Semaphorins (SEMAs) and their Plexin (PLXN) receptors are central regulators of metazoan cellular communication. SEMA-PLXND1 signaling plays important roles in cardiovascular, nervous, and immune system development, and cancer biology. However, little is known about the molecular mechanisms that modulate SEMA-PLXND1 signaling. As PLXND1 associates with GIPC family endocytic adaptors, we evaluated the requirement for the molecular determinants of their association and PLXND1's vascular role. Zebrafish that endogenously express a Plxnd1 receptor with a predicted impairment in GIPC binding exhibit low penetrance angiogenesis deficits and antiangiogenic drug hypersensitivity. Moreover, gipc mutant fish show angiogenic impairments that are ameliorated by reducing Plxnd1 signaling. Finally, GIPC depletion potentiates SEMA-PLXND1 signaling in cultured endothelial cells. These findings expand the vascular roles of GIPCs beyond those of the Vascular Endothelial Growth Factor (VEGF)-dependent, proangiogenic GIPC1-Neuropilin 1 complex, recasting GIPCs as negative modulators of antiangiogenic PLXND1 signaling and suggest that PLXND1 trafficking shapes vascular development.
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Affiliation(s)
- Jorge Carretero-Ortega
- Department of Cell Biology, Skirball Institute of Biomolecular MedicineNew York University Langone Medical CenterNew YorkUnited States
| | - Zinal Chhangawala
- Department of Cell Biology, Skirball Institute of Biomolecular MedicineNew York University Langone Medical CenterNew YorkUnited States
| | - Shane Hunt
- Department of Cell Biology, Skirball Institute of Biomolecular MedicineNew York University Langone Medical CenterNew YorkUnited States
| | - Carlos Narvaez
- Department of Cell Biology, Skirball Institute of Biomolecular MedicineNew York University Langone Medical CenterNew YorkUnited States
| | - Javier Menéndez-González
- Department of Cell Biology, Skirball Institute of Biomolecular MedicineNew York University Langone Medical CenterNew YorkUnited States
| | - Carl M Gay
- Department of Cell Biology, Skirball Institute of Biomolecular MedicineNew York University Langone Medical CenterNew YorkUnited States
| | - Tomasz Zygmunt
- Department of Cell Biology, Skirball Institute of Biomolecular MedicineNew York University Langone Medical CenterNew YorkUnited States
| | - Xiaochun Li
- Department of Population HealthNew York University School of MedicineNew YorkUnited States
| | - Jesús Torres-Vázquez
- Department of Cell Biology, Skirball Institute of Biomolecular MedicineNew York University Langone Medical CenterNew YorkUnited States
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26
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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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27
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Hu S, Wang Y, Gong Y, Liu J, Li Y, Pan L. Mechanistic Insights into Recognitions of Ubiquitin and Myosin VI by Autophagy Receptor TAX1BP1. J Mol Biol 2018; 430:3283-3296. [DOI: 10.1016/j.jmb.2018.06.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/01/2018] [Accepted: 06/18/2018] [Indexed: 12/29/2022]
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28
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Dash B, Dib-Hajj SD, Waxman SG. Multiple myosin motors interact with sodium/potassium-ATPase alpha 1 subunits. Mol Brain 2018; 11:45. [PMID: 30086768 PMCID: PMC6081954 DOI: 10.1186/s13041-018-0388-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/20/2018] [Indexed: 11/10/2022] Open
Abstract
The alpha1 (α1) subunit of the sodium/potassium ATPase (i.e., Na+/K+-ATPase α1), the prototypical sodium pump, is expressed in each eukaryotic cell. They pump out three sodium ions in exchange for two extracellular potassium ions to establish a cellular electrochemical gradient important for firing of neuronal and cardiac action potentials. We hypothesized that myosin (myo or myh) motor proteins might interact with Na+/K+-ATPase α1 subunits in order for them to play an important role in the transport and trafficking of sodium pump. To this end immunoassays were performed to determine whether class II non-muscle myosins (i.e., NMHC-IIA/myh9, NMHC-IIB/myh10 or NMHC-IIC/myh14), myosin Va (myoVa) and myosin VI (myoVI) would interact with Na+/K+-ATPase α1 subunits. Immunoprecipitation of myh9, myh10, myh14, myoVa and myoVI from rat brain tissues led to the co-immunoprecipitation of Na+/K+-ATPase α1 subunits expressed there. Heterologous expression studies using HEK293 cells indicated that recombinant myh9, myh10, myh14 and myoVI interact with Na+/K+-ATPase α1 subunits expressed in HEK293 cells. Additional results indicated that loss of tail regions in recombinant myh9, myh10, myh14 and myoVI did not affect their interaction with Na+/K+-ATPase α1 subunits. However, recombinant myh9, myh10 and myh14 mutants having reduced or no actin binding ability, as a result of loss of their actin binding sites, displayed greatly reduced or null interaction with Na+/K+-ATPase α1 subunits. These results suggested the involvement of the actin binding site, but not tail regions, of NMHC-IIs in their interaction with Na+/K+-ATPase α1 subunits. Overall these results suggest a role for these diverse myosins in the trafficking and transport of sodium pump in neuronal and non-neuronal tissues.
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Affiliation(s)
- Bhagirathi Dash
- Department of Neurology, Yale University Schoolof Medicine, New Haven, CT, 06510, USA.,Center for Neuroscience & Regeneration Research, Yale University School of Medicine, New Haven, CT, 06510, USA.,Rehabilitation Research center, VA Connecticut Healthcare System, 950 Campbell Avenue, Bldg. 34, West Haven, CT, 06516, USA
| | - Sulayman D Dib-Hajj
- Department of Neurology, Yale University Schoolof Medicine, New Haven, CT, 06510, USA.,Center for Neuroscience & Regeneration Research, Yale University School of Medicine, New Haven, CT, 06510, USA.,Rehabilitation Research center, VA Connecticut Healthcare System, 950 Campbell Avenue, Bldg. 34, West Haven, CT, 06516, USA
| | - Stephen G Waxman
- Department of Neurology, Yale University Schoolof Medicine, New Haven, CT, 06510, USA. .,Center for Neuroscience & Regeneration Research, Yale University School of Medicine, New Haven, CT, 06510, USA. .,Rehabilitation Research center, VA Connecticut Healthcare System, 950 Campbell Avenue, Bldg. 34, West Haven, CT, 06516, USA.
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29
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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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30
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The Superimposed Deubiquitination Effect of OTULIN and Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Nsp11 Promotes Multiplication of PRRSV. J Virol 2018; 92:JVI.00175-18. [PMID: 29444948 DOI: 10.1128/jvi.00175-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 02/12/2018] [Indexed: 02/06/2023] Open
Abstract
Linear ubiquitination plays an important role in the regulation of the immune response by regulating nuclear factor κB (NF-κB). The linear ubiquitination-specific deubiquitinase ovarian tumor domain deubiquitinase with linear linkage specificity (OTULIN) can control the immune signaling transduction pathway by restricting the Met1-linked ubiquitination process. In our study, the porcine OTLLIN gene was cloned and deubiquitin functions were detected in a porcine reproductive and respiratory syndrome virus (PRRSV)-infected-cell model. PRRSV infection promotes the expression of the OTULIN gene; in turn, overexpression of OTULIN contributes to PRRSV proliferation. There is negative regulation of innate immunity with OTULIN during viral infection. The cooperative effects of swine OTULIN and PRRSV Nsp11 potentiate the ability to reduce levels of cellular protein ubiquitin associated with innate immunity. Importantly, PRRSV Nsp11 recruits OTULIN through a nonenzymatic combination to enhance its ability to remove linear ubiquitination targeting NEMO, resulting in a superimposed effect that inhibits the production of type I interferons (IFNs). Our report presents a new model of virus utilization of the ubiquitin-protease system in vivo from the perspective of the viral proteins that interact with cell deubiquitination enzymes, providing new ideas for prevention and control of PRRSV.IMPORTANCE Deubiquitination effects of swine OTULIN were identified. The interaction between porcine OTULIN and PRRSV Nsp11 is dependent on the OTU domain. PRRSV Nsp11 recruits OTULIN through a nonenzymatic combination to promote removal of linear ubiquitination targeting NEMO, resulting in a superimposed effect that inhibits the production of type I IFNs.
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31
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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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32
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Kruppa AJ, Kishi-Itakura C, Masters TA, Rorbach JE, Grice GL, Kendrick-Jones J, Nathan JA, Minczuk M, Buss F. Myosin VI-Dependent Actin Cages Encapsulate Parkin-Positive Damaged Mitochondria. Dev Cell 2018; 44:484-499.e6. [PMID: 29398621 PMCID: PMC5932465 DOI: 10.1016/j.devcel.2018.01.007] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 10/30/2017] [Accepted: 01/08/2018] [Indexed: 01/08/2023]
Abstract
Mitochondrial quality control is essential to maintain cellular homeostasis and is achieved by removing damaged, ubiquitinated mitochondria via Parkin-mediated mitophagy. Here, we demonstrate that MYO6 (myosin VI), a unique myosin that moves toward the minus end of actin filaments, forms a complex with Parkin and is selectively recruited to damaged mitochondria via its ubiquitin-binding domain. This myosin motor initiates the assembly of F-actin cages to encapsulate damaged mitochondria by forming a physical barrier that prevents refusion with neighboring populations. Loss of MYO6 results in an accumulation of mitophagosomes and an increase in mitochondrial mass. In addition, we observe downstream mitochondrial dysfunction manifesting as reduced respiratory capacity and decreased ability to rely on oxidative phosphorylation for energy production. Our work uncovers a crucial step in mitochondrial quality control: the formation of MYO6-dependent actin cages that ensure isolation of damaged mitochondria from the network.
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Affiliation(s)
- Antonina J Kruppa
- Cambridge Institute for Medical Research, Department of Clinical Biochemistry, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK.
| | - Chieko Kishi-Itakura
- Cambridge Institute for Medical Research, Department of Clinical Biochemistry, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - Thomas A Masters
- Cambridge Institute for Medical Research, Department of Clinical Biochemistry, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - Joanna E Rorbach
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - Guinevere L Grice
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - John Kendrick-Jones
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - James A Nathan
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - Folma Buss
- Cambridge Institute for Medical Research, Department of Clinical Biochemistry, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK.
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33
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Takahashi TS, Hirade Y, Toma A, Sato Y, Yamagata A, Goto-Ito S, Tomita A, Nakada S, Fukai S. Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168. Nat Commun 2018; 9:170. [PMID: 29330428 PMCID: PMC5766498 DOI: 10.1038/s41467-017-02345-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 11/22/2017] [Indexed: 12/18/2022] Open
Abstract
The E3 ubiquitin (Ub) ligase RNF168 plays a critical role in the initiation of the DNA damage response to double-strand breaks (DSBs). The recruitment of RNF168 by ubiquitylated targets involves two distinct regions, Ub-dependent DSB recruitment module (UDM) 1 and UDM2. Here we report the crystal structures of the complex between UDM1 and Lys63-linked diUb (K63-Ub2) and that between the C-terminally truncated UDM2 (UDM2ΔC) and K63-Ub2. In both structures, UDM1 and UDM2ΔC fold as a single α-helix. Their simultaneous bindings to the distal and proximal Ub moieties provide specificity for Lys63-linked Ub chains. Structural and biochemical analyses of UDM1 elucidate an Ub-binding mechanism between UDM1 and polyubiquitylated targets. Mutations of Ub-interacting residues in UDM2 prevent the accumulation of RNF168 to DSB sites in U2OS cells, whereas those in UDM1 have little effect, suggesting that the interaction of UDM2 with ubiquitylated and polyubiquitylated targets mainly contributes to the RNF168 recruitment. E3 ubiquitin ligase RNF168 is important for the repair of DNA double-strand breaks and recognizes ubiquitylated targets through two Ub-dependent DSB recruitment modules UDM1 and UDM2. Here the authors combine crystallography, cell biology and biochemical experiments to reveal how UDM1 and UDM2 interact with polyubiquitin chains.
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Affiliation(s)
- Tomio S Takahashi
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Yoshihiro Hirade
- Department of Bioregulation and Cellular Response, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Aya Toma
- Institute of Molecular and Cellular 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, 277-8501, Japan
| | - Yusuke Sato
- Institute of Molecular and Cellular 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, 277-8501, Japan
| | - Atsushi Yamagata
- Institute of Molecular and Cellular 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, 277-8501, Japan
| | - Sakurako Goto-Ito
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Akiko Tomita
- Department of Bioregulation and Cellular Response, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Shinichiro Nakada
- Department of Bioregulation and Cellular Response, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan. .,Institute for Advanced Co-Creation Studies, Osaka University, Osaka, 565-0871, Japan.
| | - Shuya Fukai
- Institute of Molecular and Cellular 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, 277-8501, Japan.
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34
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Shang G, Brautigam CA, Chen R, Lu D, Torres-Vázquez J, Zhang X. Structure analyses reveal a regulated oligomerization mechanism of the PlexinD1/GIPC/myosin VI complex. eLife 2017; 6. [PMID: 28537552 PMCID: PMC5461112 DOI: 10.7554/elife.27322] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/23/2017] [Indexed: 12/22/2022] Open
Abstract
The GIPC family adaptor proteins mediate endocytosis by tethering cargo proteins to the myosin VI motor. The structural mechanisms for the GIPC/cargo and GIPC/myosin VI interactions remained unclear. PlexinD1, a transmembrane receptor that regulates neuronal and cardiovascular development, is a cargo of GIPCs. GIPC-mediated endocytic trafficking regulates PlexinD1 signaling. Here, we unravel the mechanisms of the interactions among PlexinD1, GIPCs and myosin VI by a series of crystal structures of these proteins in apo or bound states. GIPC1 forms a domain-swapped dimer in an autoinhibited conformation that hinders binding of both PlexinD1 and myosin VI. PlexinD1 binding to GIPC1 releases the autoinhibition, promoting its interaction with myosin VI. GIPCs and myosin VI interact through two distinct interfaces and form an open-ended alternating array. Our data support that this alternating array underlies the oligomerization of the GIPC/Myosin VI complexes in solution and cells. DOI:http://dx.doi.org/10.7554/eLife.27322.001
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Affiliation(s)
- Guijun Shang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Chad A Brautigam
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Rui Chen
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Defen Lu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Jesús Torres-Vázquez
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, New York, United States
| | - Xuewu Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
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35
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Investigations of human myosin VI targeting using optogenetically controlled cargo loading. Proc Natl Acad Sci U S A 2017; 114:E1607-E1616. [PMID: 28193860 DOI: 10.1073/pnas.1614716114] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Myosins play countless critical roles in the cell, each requiring it to be activated at a specific location and time. To control myosin VI with this specificity, we created an optogenetic tool for activating myosin VI by fusing the light-sensitive Avena sativa phototropin1 LOV2 domain to a peptide from Dab2 (LOVDab), a myosin VI cargo protein. Our approach harnesses the native targeting and activation mechanism of myosin VI, allowing direct inferences on myosin VI function. LOVDab robustly recruits human full-length myosin VI to various organelles in vivo and hinders peroxisome motion in a light-controllable manner. LOVDab also activates myosin VI in an in vitro gliding filament assay. Our data suggest that protein and lipid cargoes cooperate to activate myosin VI, allowing myosin VI to integrate Ca2+, lipid, and protein cargo signals in the cell to deploy in a site-specific manner.
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36
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Waxse BJ, Sengupta P, Hesketh GG, Lippincott-Schwartz J, Buss F. Myosin VI facilitates connexin 43 gap junction accretion. J Cell Sci 2017; 130:827-840. [PMID: 28096472 PMCID: PMC5358335 DOI: 10.1242/jcs.199083] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/04/2017] [Indexed: 12/19/2022] Open
Abstract
In this study, we demonstrate myosin VI enrichment at Cx43 (also known as GJA1)-containing gap junctions (GJs) in heart tissue, primary cardiomyocytes and cell culture models. In primary cardiac tissue and in fibroblasts from the myosin VI-null mouse as well as in tissue culture cells transfected with siRNA against myosin VI, we observe reduced GJ plaque size with a concomitant reduction in intercellular communication, as shown by fluorescence recovery after photobleaching (FRAP) and a new method of selective calcein administration. Analysis of the molecular role of myosin VI in Cx43 trafficking indicates that myosin VI is dispensable for the delivery of Cx43 to the cell surface and connexon movement in the plasma membrane. Furthermore, we cannot corroborate clathrin or Dab2 localization at gap junctions and we do not observe a function for the myosin-VI-Dab2 complex in clathrin-dependent endocytosis of annular gap junctions. Instead, we found that myosin VI was localized at the edge of Cx43 plaques by using total internal reflection fluorescence (TIRF) microscopy and use FRAP to identify a plaque accretion defect as the primary manifestation of myosin VI loss in Cx43 homeostasis. A fuller understanding of this derangement may explain the cardiomyopathy or gliosis associated with the loss of myosin VI.
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Affiliation(s)
- Bennett J Waxse
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland 20892, USA.,Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 2XY, UK
| | - Prabuddha Sengupta
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland 20892, USA
| | - Geoffrey G Hesketh
- Mount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario M5G 1X5, Canada
| | - Jennifer Lippincott-Schwartz
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland 20892, USA
| | - Folma Buss
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 2XY, UK
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37
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Kristariyanto YA, Abdul Rehman SA, Weidlich S, Knebel A, Kulathu Y. A single MIU motif of MINDY-1 recognizes K48-linked polyubiquitin chains. EMBO Rep 2017; 18:392-402. [PMID: 28082312 DOI: 10.15252/embr.201643205] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 12/13/2016] [Accepted: 12/16/2016] [Indexed: 11/09/2022] Open
Abstract
The eight different types of ubiquitin (Ub) chains that can be formed play important roles in diverse cellular processes. Linkage-selective recognition of Ub chains by Ub-binding domain (UBD)-containing proteins is central to coupling different Ub signals to specific cellular responses. The motif interacting with ubiquitin (MIU) is a small UBD that has been characterized for its binding to monoUb. The recently discovered deubiquitinase MINDY-1/FAM63A contains a tandem MIU repeat (tMIU) that is highly selective at binding to K48-linked polyUb. We here identify that this linkage-selective binding is mediated by a single MIU motif (MIU2) in MINDY-1. The crystal structure of MIU2 in complex with K48-linked polyubiquitin chains reveals that MIU2 on its own binds to all three Ub moieties in an open conformation that can only be accommodated by K48-linked triUb. The weak Ub binder MIU1 increases overall affinity of the tMIU for polyUb chains without affecting its linkage selectivity. Our analyses reveal new concepts for linkage selectivity and polyUb recognition by UBDs.
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Affiliation(s)
- Yosua Adi Kristariyanto
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Syed Arif Abdul Rehman
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Simone Weidlich
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Yogesh Kulathu
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
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38
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Rao T, Gao R, Takada S, Al Abo M, Chen X, Walters KJ, Pommier Y, Aihara H. Novel TDP2-ubiquitin interactions and their importance for the repair of topoisomerase II-mediated DNA damage. Nucleic Acids Res 2016; 44:10201-10215. [PMID: 27543075 PMCID: PMC5137425 DOI: 10.1093/nar/gkw719] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 07/30/2016] [Accepted: 08/08/2016] [Indexed: 12/22/2022] Open
Abstract
Tyrosyl DNA phosphodiesterase 2 (TDP2) is a multifunctional protein implicated in DNA repair, signal transduction and transcriptional regulation. In its DNA repair role, TDP2 safeguards genome integrity by hydrolyzing 5′-tyrosyl DNA adducts formed by abortive topoisomerase II (Top2) cleavage complexes to allow error-free repair of DNA double-strand breaks, thereby conferring cellular resistance against Top2 poisons. TDP2 consists of a C-terminal catalytic domain responsible for its phosphodiesterase activity, and a functionally uncharacterized N-terminal region. Here, we demonstrate that this N-terminal region contains a ubiquitin (Ub)-associated (UBA) domain capable of binding multiple forms of Ub with distinct modes of interactions and preference for either K48- or K63-linked polyUbs over monoUb. The structure of TDP2 UBA bound to monoUb shows a canonical mode of UBA-Ub interaction. However, the absence of the highly conserved MGF motif and the presence of a fourth α-helix make TDP2 UBA distinct from other known UBAs. Mutations in the TDP2 UBA-Ub binding interface do not affect nuclear import of TDP2, but severely compromise its ability to repair Top2-mediated DNA damage, thus establishing the importance of the TDP2 UBA–Ub interaction in DNA repair. The differential binding to multiple Ub forms could be important for responding to DNA damage signals under different contexts or to support the multi-functionality of TDP2.
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Affiliation(s)
- Timsi Rao
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rui Gao
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Saeko Takada
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Muthana Al Abo
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiang Chen
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Kylie J Walters
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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39
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Slowicka K, Vereecke L, van Loo G. Cellular Functions of Optineurin in Health and Disease. Trends Immunol 2016; 37:621-633. [PMID: 27480243 DOI: 10.1016/j.it.2016.07.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 07/07/2016] [Accepted: 07/12/2016] [Indexed: 12/21/2022]
Abstract
Optineurin (OPTN) was initially identified as a regulator of NF-κB and interferon signaling, but attracted most attention because of its association with various human disorders such as glaucoma, Paget disease of bone, and amyotrophic lateral sclerosis. Importantly, OPTN has recently been identified as an autophagy receptor important for the autophagic removal of pathogens, damaged mitochondria, and protein aggregates. This activity is most likely compromised in patients carrying OPTN mutations, and contributes to the observed phenotypes. In this review we summarize recent studies describing the molecular mechanisms by which OPTN controls immunity and autophagy, and discuss these findings in the context of several diseases that have been associated with OPTN (mal)function.
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Affiliation(s)
- Karolina Slowicka
- Inflammation Research Center, Unit of Cellular and Molecular (Patho)Physiology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
| | - Lars Vereecke
- Inflammation Research Center, Unit of Cellular and Molecular (Patho)Physiology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
| | - Geert van Loo
- Inflammation Research Center, Unit of Cellular and Molecular (Patho)Physiology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.
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40
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Pesiri V, Di Muzio E, Polticelli F, Acconcia F. Selective binding of estrogen receptor α to ubiquitin chains. IUBMB Life 2016; 68:569-77. [DOI: 10.1002/iub.1514] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 04/28/2016] [Indexed: 01/02/2023]
Affiliation(s)
- Valeria Pesiri
- Department of Sciences, Section Biomedical Sciences and Technology; University Roma Tre; Rome Italy
| | - Elena Di Muzio
- Department of Sciences, Section Biomedical Sciences and Technology; University Roma Tre; Rome Italy
| | - Fabio Polticelli
- Department of Sciences, Section Biomedical Sciences and Technology; University Roma Tre; Rome Italy
- National Institute of Nuclear Physics; Roma Tre Section Rome Italy
| | - Filippo Acconcia
- Department of Sciences, Section Biomedical Sciences and Technology; University Roma Tre; Rome Italy
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41
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Wollscheid HP, Biancospino M, He F, Magistrati E, Molteni E, Lupia M, Soffientini P, Rottner K, Cavallaro U, Pozzoli U, Mapelli M, Walters KJ, Polo S. Diverse functions of myosin VI elucidated by an isoform-specific α-helix domain. Nat Struct Mol Biol 2016; 23:300-308. [PMID: 26950368 PMCID: PMC4964928 DOI: 10.1038/nsmb.3187] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 02/09/2016] [Indexed: 01/01/2023]
Abstract
Myosin VI functions in endocytosis and cell motility. Alternative splicing of myosin VI mRNA generates two distinct isoform types, myosin VIshort and myosin VIlong, which differ in the C-terminal region. Their physiological and pathological role remains unknown. Here we identified an isoform-specific regulatory helix, named α2-linker that defines specific conformations and hence determines the target selectivity of human myosin VI. The presence of the α2-linker structurally defines a novel clathrin-binding domain that is unique to myosin VIlong and masks the known RRL interaction motif. This finding is relevant to ovarian cancer, where alternative myosin VI splicing is aberrantly regulated, and exon skipping dictates cell addiction to myosin VIshort for tumor cell migration. The RRL interactor optineurin contributes to this process by selectively binding myosin VIshort. Thus the α2-linker acts like a molecular switch that assigns myosin VI to distinct endocytic (myosin VIlong) or migratory (myosin VIshort) functional roles.
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Affiliation(s)
| | - Matteo Biancospino
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Milan 20139, Italy
| | - Fahu He
- Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Elisa Magistrati
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Milan 20139, Italy
| | - Erika Molteni
- Computational Biology, Scientific Institute IRCCS E.MEDEA, Bosisio Parini 23842, Italy
| | - Michela Lupia
- Molecular Medicine Program, European Institute of Oncology, Milan 20141, Italy
| | - Paolo Soffientini
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Milan 20139, Italy
| | - Klemens Rottner
- Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany.,Braunschweig University of Technology, 38106 Braunschweig, Germany
| | - Ugo Cavallaro
- Molecular Medicine Program, European Institute of Oncology, Milan 20141, Italy
| | - Uberto Pozzoli
- Computational Biology, Scientific Institute IRCCS E.MEDEA, Bosisio Parini 23842, Italy
| | - Marina Mapelli
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Kylie J Walters
- Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Simona Polo
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Milan 20139, Italy.,Dipartimento di oncologia ed emato-oncologia (DIPO), Universita' degli Studi di Milano, Milan 20122, Italy
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