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Breuer T, Tibbe C, Troost T, Klein T. Structural Analysis of the ESCRT-III Regulator Lethal(2) Giant Discs/Coiled-Coil and C2 Domain-Containing Protein 1 (Lgd/CC2D1). Cells 2024; 13:1174. [PMID: 39056756 PMCID: PMC11275157 DOI: 10.3390/cells13141174] [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: 06/03/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
Members of the LGD/CC2D1 protein family contain repeats of the family-defining DM14 domains. Via this domain, they interact with members of the CHMP family, which are essential for the ESCRT machinery-mediated formation of intraluminal vesicles during endosome maturation. Here, we investigate the requirement of the DM14 domains for the function of Lgd in detail. We found that although both odd-numbered DM14s can act in a functionally redundant manner, the redundancy is not complete and both contribute to the full function of Lgd. Our analysis indicates that some of the AAs that form the KARRxxR motif of the onDM14s are not exchangeable by similarly charged AAs without loss of function, indicating that they not only provide charge, but also fulfil structural roles. Furthermore, we show that the region of Lgd between DM14-4 and the C2 domain as well as its C-terminal region to the C2 domain are important for protein stability/function. Moreover, we analysed the importance of AAs that are conserved in all DM14 domains. Finally, our analysis of the C. elegans ortholog of Lgd revealed that it has only one DM14 domain that is functionally equivalent to the onDM14s. Altogether, the results further the understanding of how Lgd family members regulate the ESCRT machinery.
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Affiliation(s)
| | | | | | - Thomas Klein
- Institute of Genetics, Heinrich-Heine-Universitaet Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany; (T.B.); (C.T.); (T.T.)
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Bhattacharya A, Parlanti P, Cavallo L, Farrow E, Spivey T, Renieri A, Mari F, Manzini MC. A novel framework for functional annotation of variants of uncertain significance in ID/ASD risk gene CC2D1A. Hum Mol Genet 2024; 33:1229-1240. [PMID: 38652285 DOI: 10.1093/hmg/ddae070] [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: 11/30/2023] [Revised: 03/07/2024] [Accepted: 04/11/2024] [Indexed: 04/25/2024] Open
Abstract
Intellectual disability (ID) and autism spectrum disorder (ASD) are genetically heterogeneous with hundreds of identified risk genes, most affecting only a few patients. Novel missense variants in these genes are being discovered as clinical exome sequencing is now routinely integrated into diagnosis, yet most of them are annotated as variants of uncertain significance (VUS). VUSs are a major roadblock in using patient genetics to inform clinical action. We developed a framework to characterize VUSs in Coiled-coil and C2 domain containing 1A (CC2D1A), a gene causing autosomal recessive ID with comorbid ASD in 40% of cases. We analyzed seven VUSs (p.Pro319Leu, p.Ser327Leu, p.Gly441Val, p.Val449Met, p.Thr580Ile, p.Arg886His and p.Glu910Lys) from four cases of individuals with ID and ASD. Variants were cloned and overexpressed in HEK293 individually and in their respective heterozygous combination. CC2D1A is a signaling scaffold that positively regulates PKA-CREB signaling by repressing phosphodiesterase 4D (PDE4D) to prevent cAMP degradation. After testing multiple parameters including direct interaction between PDE4D and CC2D1A, cAMP levels and CREB activation, we found that the most sensitive readout was CREB transcriptional activity using a luciferase assay. Compared to WT CC2D1A, five VUSs (p.Pro319Leu, p.Gly441Val, p.Val449Met, p.Thr580Ile, and p.Arg886His) led to significantly blunted response to forskolin induced CREB activation. This luciferase assay approach can be scaled up to annotate ~150 CC2D1A VUSs that are currently listed in ClinVar. Since CREB activation is a common denominator for multiple ASD/ID genes, our paradigm can also be adapted for their VUSs.
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Affiliation(s)
- Aniket Bhattacharya
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers - Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Paola Parlanti
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers - Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Luca Cavallo
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers - Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Edward Farrow
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, George Washington University, 2121 I St NW, Washington, DC 20052, United States
| | - Tyler Spivey
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, George Washington University, 2121 I St NW, Washington, DC 20052, United States
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Viale Bracci 2, 53100 Siena, Italy
| | - Francesca Mari
- Medical Genetics, University of Siena, Viale Bracci 2, 53100 Siena, Italy
| | - M Chiara Manzini
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers - Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
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Shimizu H, Hosseini-Alghaderi S, Woodcock SA, Baron M. Alternative mechanisms of Notch activation by partitioning into distinct endosomal domains. J Cell Biol 2024; 223:e202211041. [PMID: 38358349 PMCID: PMC10868400 DOI: 10.1083/jcb.202211041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 11/17/2023] [Accepted: 01/30/2024] [Indexed: 02/16/2024] Open
Abstract
Different membrane microdomain compositions provide unique environments that can regulate signaling receptor function. We identify microdomains on the endosome membrane of Drosophila endosomes, enriched in lipid-raft or clathrin/ESCRT-0, which are associated with Notch activation by distinct, ligand-independent mechanisms. Transfer of Notch between microdomains is regulated by Deltex and Suppressor of deltex ubiquitin ligases and is limited by a gate-keeper role for ESCRT complexes. Ubiquitination of Notch by Deltex recruits it to the clathrin/ESCRT-0 microdomain and enhances Notch activation by an ADAM10-independent/TRPML-dependent mechanism. This requirement for Deltex is bypassed by the downregulation of ESCRT-III. In contrast, while ESCRT-I depletion also activates Notch, it does so by an ADAM10-dependent/TRPML-independent mechanism and Notch is retained in the lipid raft-like microdomain. In the absence of such endosomal perturbation, different activating Notch mutations also localize to different microdomains and are activated by different mechanisms. Our findings demonstrate the interplay between Notch regulators, endosomal trafficking components, and Notch genetics, which defines membrane locations and activation mechanisms.
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Affiliation(s)
- Hideyuki Shimizu
- School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Samira Hosseini-Alghaderi
- School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Simon A. Woodcock
- School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Martin Baron
- School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
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Clarke AL, Lettman MM, Audhya A. Lgd regulates ESCRT-III complex accumulation at multivesicular endosomes to control intralumenal vesicle formation. Mol Biol Cell 2022; 33:ar144. [PMID: 36287829 PMCID: PMC9727795 DOI: 10.1091/mbc.e22-08-0342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/13/2022] [Accepted: 10/18/2022] [Indexed: 02/04/2023] Open
Abstract
Membrane remodeling mediated by heteropolymeric filaments composed of ESCRT-III subunits is an essential process that occurs at a variety of organelles to maintain cellular homeostasis. Members of the evolutionarily conserved Lgd/CC2D1 protein family have been suggested to regulate ESCRT-III polymer assembly, although their specific roles, particularly in vivo, remain unclear. Using the Caenorhabditis elegans early embryo as a model system, we show that Lgd/CC2D1 localizes to endosomal membranes, and its loss impairs endolysosomal cargo sorting and degradation. At the ultrastructural level, the absence of Lgd/CC2D1 results in the accumulation of enlarged endosomal compartments that contain a reduced number of intralumenal vesicles (ILVs). However, unlike aberrant endosome morphology caused by depletion of other ESCRT components, ILV size is only modestly altered in embryos lacking Lgd/CC2D1. Instead, loss of Lgd/CC2D1 impairs normal accumulation of ESCRT-III on endosomal membranes, likely slowing the kinetics of ILV formation. Together, our findings suggest a role for Lgd/CC2D1 in the recruitment and/or stable assembly of ESCRT-III subunits on endosomal membranes to facilitate efficient ILV biogenesis.
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Affiliation(s)
- Aryel L. Clarke
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705
| | - Molly M. Lettman
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705
| | - Anjon Audhya
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705
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Baeumers M, Schulz K, Klein T. Using Drosophila melanogaster to Analyse the Human Paralogs of the ESCRT-III Core Component Shrub/CHMP4/Snf7 and Its Interactions with Members of the LGD/CC2D1 Family. Int J Mol Sci 2022; 23:7507. [PMID: 35886850 PMCID: PMC9320689 DOI: 10.3390/ijms23147507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 11/17/2022] Open
Abstract
The evolutionary conserved ESCRT-III complex is a device for membrane remodelling in various cellular processes, such as the formation of intraluminal vesicles (ILVs), cytokinesis, and membrane repair. The common theme of all these processes is the abscission of membrane away from the cytosol. At its heart in Drosophila is Shrub, CHMP4 in humans, which dynamically polymerises into filaments through electrostatic interactions among the protomers. For the full activity, Shrub/CHMP4 requires physical interaction with members of the Lgd protein family. This interaction is mediated by the odd-numbered DM14 domains of Lgd, which bind to the negative interaction surface of Shrub. While only one Lgd and one Shrub exist in the genome of Drosophila, mammals have two Lgd orthologs, LGD1/CC2D1B and LGD2/CC2D1A, as well as three CHMP4s in their genomes, CHMP4A, CHMP4B, and CHMP4C. The rationale for the diversification of the ESCRT components is not understood. We here use Drosophila as a model system to analyse the activity of the human orthologs of Shrub and Lgd at an organismal level. This enabled us to use the plethora of available techniques available for Drosophila. We present evidence that CHMP4B is the true ortholog of Shrub, while CHMP4A and CHMP4C have diverging activities. Nevertheless, CHMP4A and CHMP4C can enhance the activity of CHMP4B, raising the possibility that they can form heteropolymers in vivo. Our structure-function analysis of the LGD1 and LGD2 indicates that the C2 domain of the LGD proteins has a specific function beyond protein stability and subcellular localisation. Moreover, our data specify that CHMP4B interacts more efficiently with LGD1 than with LGD2.
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Affiliation(s)
- Miriam Baeumers
- Institute of Genetics, Heinrich-Heine-Universitaet Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany;
| | - Katharina Schulz
- Institut für Angewandte Bewegungswissenschaften, Professur für Sportmedizin/-Biologie, Technische Universität Chemnitz, Thüringer Weg 11, 09126 Chemnitz, Germany;
| | - Thomas Klein
- Institute of Genetics, Heinrich-Heine-Universitaet Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany;
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Acheta J, Hong J, Jeanette H, Brar S, Yalamanchili A, Feltri ML, Manzini MC, Belin S, Poitelon Y. Cc2d1b Contributes to the Regulation of Developmental Myelination in the Central Nervous System. Front Mol Neurosci 2022; 15:881571. [PMID: 35592111 PMCID: PMC9113218 DOI: 10.3389/fnmol.2022.881571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundNumerous studies have indicated that myelination is the result of the interplay between extracellular signals and an intricate network of transcription factors. Yet, the identification and characterization of the full repertoire of transcription factors that modulate myelination are still incomplete. CC2D1B is a member of the Lgd/CC2D1 family of proteins highly expressed in myelinating cells in the central and peripheral nervous systems. In addition, the absence of CC2D1B limits myelin formation in vitro. Here we propose to delineate the function of CC2D1B in myelinating cells during developmental myelination in vivo in the central and peripheral nervous systems.MethodsWe used a Cc2d1b constitutive knockout mouse model and then performed morphological analyses on semithin sections of sciatic nerves and electron micrographs of optic nerves. We also performed immunohistological studies on coronal brain sections. All analyses were performed at 30 days of age.ResultsIn the peripheral nervous system, animals ablated for Cc2d1b did not show any myelin thickness difference compared to control animals. In the central nervous system, immunohistological studies did not show any difference in the number of oligodendrocytes or the level of myelin proteins in the cortex, corpus callosum, and striatum. However, optic nerves showed a hypomyelination (0.844 ± 0.022) compared to control animals (0.832 ± 0.016) of large diameter myelinated fibers.ConclusionsWe found that CC2D1B plays a role in developmental myelination in the central nervous system. These results suggest that CC2D1B could contribute to gene regulation during oligodendrocytes myelination in optic nerves.
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Affiliation(s)
- Jenica Acheta
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY, United States
| | - Jiayue Hong
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY, United States
| | - Haley Jeanette
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY, United States
| | - Simrandeep Brar
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY, United States
| | - Anish Yalamanchili
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY, United States
| | - M. Laura Feltri
- Departments of Biochemistry and Neurology, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States
| | - M. Chiara Manzini
- Department of Neuroscience and Cell Biology, Rutgers-Robert Wood Johnson Medical School, Child Health Institute of New Jersey, New Brunswick, NJ, United States
| | - Sophie Belin
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY, United States
- *Correspondence: Sophie Belin ; Yannick Poitelon
| | - Yannick Poitelon
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY, United States
- *Correspondence: Sophie Belin ; Yannick Poitelon
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Schnute B, Shimizu H, Lyga M, Baron M, Klein T. Ubiquitylation is required for the incorporation of the Notch receptor into intraluminal vesicles to prevent prolonged and ligand-independent activation of the pathway. BMC Biol 2022; 20:65. [PMID: 35264151 PMCID: PMC8908686 DOI: 10.1186/s12915-022-01245-y] [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: 10/07/2021] [Accepted: 02/01/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ubiquitylation of the ligands and the receptor plays an important part in the regulation of the activity of the evolutionary conserved Notch signalling pathway. However, its function for activation of Notch is not completely understood, despite the identification of several E3 ligases devoted to the receptor. RESULTS Here we analysed a variant of the Notch receptor where all lysines in its intracellular domain are replaced by arginines. Our analysis of this variant revealed that ubiquitylation of Notch is not essential for its endocytosis. We identified two functions for ubiquitylation of lysines in the Notch receptor. First, it is required for the degradation of free Notch intracellular domain (NICD) in the nucleus, which prevents a prolonged activation of the pathway. More importantly, it is also required for the incorporation of Notch into intraluminal vesicles of maturing endosomes to prevent ligand-independent activation of the pathway from late endosomal compartments. CONCLUSIONS The findings clarify the role of lysine-dependent ubiquitylation of the Notch receptor and indicate that Notch is endocytosed by several independent operating mechanisms.
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Affiliation(s)
- Björn Schnute
- Institute of Genetics, Heinrich-Heine-University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany
| | - Hideyuki Shimizu
- School of Biological Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Marvin Lyga
- Institute of Genetics, Heinrich-Heine-University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany
| | - Martin Baron
- School of Biological Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Thomas Klein
- Institute of Genetics, Heinrich-Heine-University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany.
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