2
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Petriman NA, Loureiro‐López M, Taschner M, Zacharia NK, Georgieva MM, Boegholm N, Wang J, Mourão A, Russell RB, Andersen JS, Lorentzen E. Biochemically validated structural model of the 15-subunit intraflagellar transport complex IFT-B. EMBO J 2022; 41:e112440. [PMID: 36354106 PMCID: PMC9753473 DOI: 10.15252/embj.2022112440] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022] Open
Abstract
Cilia are ubiquitous eukaryotic organelles impotant for cellular motility, signaling, and sensory reception. Cilium formation requires intraflagellar transport of structural and signaling components and involves 22 different proteins organized into intraflagellar transport (IFT) complexes IFT-A and IFT-B that are transported by molecular motors. The IFT-B complex constitutes the backbone of polymeric IFT trains carrying cargo between the cilium and the cell body. Currently, high-resolution structures are only available for smaller IFT-B subcomplexes leaving > 50% structurally uncharacterized. Here, we used Alphafold to structurally model the 15-subunit IFT-B complex. The model was validated using cross-linking/mass-spectrometry data on reconstituted IFT-B complexes, X-ray scattering in solution, diffraction from crystals as well as site-directed mutagenesis and protein-binding assays. The IFT-B structure reveals an elongated and highly flexible complex consistent with cryo-electron tomographic reconstructions of IFT trains. The IFT-B complex organizes into IFT-B1 and IFT-B2 parts with binding sites for ciliary cargo and the inactive IFT dynein motor, respectively. Interestingly, our results are consistent with two different binding sites for IFT81/74 on IFT88/70/52/46 suggesting the possibility of different structural architectures for the IFT-B1 complex. Our data present a structural framework to understand IFT-B complex assembly, function, and ciliopathy variants.
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Affiliation(s)
- Narcis A Petriman
- Department of Molecular Biology and GeneticsAarhus UniversityAarhus CDenmark
| | - Marta Loureiro‐López
- Department for Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark
| | - Michael Taschner
- Department of Fundamental MicrobiologyUniversity of LausanneLausanneSwitzerland
| | - Nevin K Zacharia
- Department of Molecular Biology and GeneticsAarhus UniversityAarhus CDenmark
| | | | - Niels Boegholm
- Department of Molecular Biology and GeneticsAarhus UniversityAarhus CDenmark
| | - Jiaolong Wang
- Department of Molecular Biology and GeneticsAarhus UniversityAarhus CDenmark
| | - André Mourão
- Institute of Structural BiologyHelmholtz Zentrum MünchenNeuherbergGermany
| | | | - Jens S Andersen
- Department for Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark
| | - Esben Lorentzen
- Department of Molecular Biology and GeneticsAarhus UniversityAarhus CDenmark
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4
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Guleria VS, Parit R, Quadri N, Das R, Upadhyai P. The intraflagellar transport protein IFT52 associated with short-rib thoracic dysplasia is essential for ciliary function in osteogenic differentiation in vitro and for sensory perception in Drosophila. Exp Cell Res 2022; 418:113273. [PMID: 35839863 DOI: 10.1016/j.yexcr.2022.113273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/30/2022] [Accepted: 07/02/2022] [Indexed: 11/04/2022]
Abstract
Primary cilia are non-motile sensory cell-organelle that are essential for organismal development, differentiation, and postnatal homeostasis. Their biogenesis and function are mediated by the intraflagellar transport (IFT) system. Pathogenic variants in IFT52, a central component of the IFT-B complex is associated with short-rib thoracic dysplasia with or without polydactyly 16 (SRTD16), with major skeletal manifestations, in addition to other features. Here we sought to examine the role of IFT52 in osteoblast differentiation. Using lentiviral shRNA interference Ift52 was depleted in C3H10T1/2 mouse mesenchymal stem cells. This led to the disruption of the IFT-B anterograde trafficking machinery that impaired primary ciliogenesis and blocked osteogenic differentiation. In Ift52 silenced cells, Hedgehog (Hh) pathway upregulation during osteogenesis was attenuated and despite Smoothened Agonist (SAG) based Hh activation, osteogenic differentiation was incompletely restored. Further we investigated IFT52 activity in Drosophila, wherein the only ciliated somatic cells are the bipolar sensory neurons of the peripheral nervous system. Knockdown of IFT52 in Drosophila neuronal tissues reduced lifespan with the loss of embryonic chordotonal cilia, and produced severe locomotion, auditory and proprioceptive defects in larva and adults. Together these findings improve our knowledge of the role of IFT52 in various physiological contexts and its associated human disorder.
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Affiliation(s)
- Vishal Singh Guleria
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Rahul Parit
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Neha Quadri
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Ranajit Das
- Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, India
| | - Priyanka Upadhyai
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
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5
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Hwang T, Parker SS, Hill SM, Grant RA, Ilunga MW, Sivaraman V, Mouneimne G, Keating AE. Native proline-rich motifs exploit sequence context to target actin-remodeling Ena/VASP protein ENAH. eLife 2022; 11:70680. [PMID: 35076015 PMCID: PMC8789275 DOI: 10.7554/elife.70680] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 01/06/2022] [Indexed: 12/13/2022] Open
Abstract
The human proteome is replete with short linear motifs (SLiMs) of four to six residues that are critical for protein-protein interactions, yet the importance of the sequence surrounding such motifs is underexplored. We devised a proteomic screen to examine the influence of SLiM sequence context on protein-protein interactions. Focusing on the EVH1 domain of human ENAH, an actin regulator that is highly expressed in invasive cancers, we screened 36-residue proteome-derived peptides and discovered new interaction partners of ENAH and diverse mechanisms by which context influences binding. A pocket on the ENAH EVH1 domain that has diverged from other Ena/VASP paralogs recognizes extended SLiMs and favors motif-flanking proline residues. Many high-affinity ENAH binders that contain two proline-rich SLiMs use a noncanonical site on the EVH1 domain for binding and display a thermodynamic signature consistent with the two-motif chain engaging a single domain. We also found that photoreceptor cilium actin regulator (PCARE) uses an extended 23-residue region to obtain a higher affinity than any known ENAH EVH1-binding motif. Our screen provides a way to uncover the effects of proteomic context on motif-mediated binding, revealing diverse mechanisms of control over EVH1 interactions and establishing that SLiMs can’t be fully understood outside of their native context.
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Affiliation(s)
- Theresa Hwang
- Department of Biology, Massachusetts Institute of Technology
| | - Sara S Parker
- Department of Cellular & Molecular Medicine, University of Arizona
| | - Samantha M Hill
- Department of Cellular & Molecular Medicine, University of Arizona
| | - Robert A Grant
- Department of Biology, Massachusetts Institute of Technology
| | - Meucci W Ilunga
- Department of Biology, Massachusetts Institute of Technology
| | | | | | - Amy E Keating
- Department of Biology, Massachusetts Institute of Technology
- Department of Biological Engineering and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology
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6
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Sánchez-Bellver L, Toulis V, Marfany G. On the Wrong Track: Alterations of Ciliary Transport in Inherited Retinal Dystrophies. Front Cell Dev Biol 2021; 9:623734. [PMID: 33748110 PMCID: PMC7973215 DOI: 10.3389/fcell.2021.623734] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/09/2021] [Indexed: 01/14/2023] Open
Abstract
Ciliopathies are a group of heterogeneous inherited disorders associated with dysfunction of the cilium, a ubiquitous microtubule-based organelle involved in a broad range of cellular functions. Most ciliopathies are syndromic, since several organs whose cells produce a cilium, such as the retina, cochlea or kidney, are affected by mutations in ciliary-related genes. In the retina, photoreceptor cells present a highly specialized neurosensory cilium, the outer segment, stacked with membranous disks where photoreception and phototransduction occurs. The daily renewal of the more distal disks is a unique characteristic of photoreceptor outer segments, resulting in an elevated protein demand. All components necessary for outer segment formation, maintenance and function have to be transported from the photoreceptor inner segment, where synthesis occurs, to the cilium. Therefore, efficient transport of selected proteins is critical for photoreceptor ciliogenesis and function, and any alteration in either cargo delivery to the cilium or intraciliary trafficking compromises photoreceptor survival and leads to retinal degeneration. To date, mutations in more than 100 ciliary genes have been associated with retinal dystrophies, accounting for almost 25% of these inherited rare diseases. Interestingly, not all mutations in ciliary genes that cause retinal degeneration are also involved in pleiotropic pathologies in other ciliated organs. Depending on the mutation, the same gene can cause syndromic or non-syndromic retinopathies, thus emphasizing the highly refined specialization of the photoreceptor neurosensory cilia, and raising the possibility of photoreceptor-specific molecular mechanisms underlying common ciliary functions such as ciliary transport. In this review, we will focus on ciliary transport in photoreceptor cells and discuss the molecular complexity underpinning retinal ciliopathies, with a special emphasis on ciliary genes that, when mutated, cause either syndromic or non-syndromic retinal ciliopathies.
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Affiliation(s)
- Laura Sánchez-Bellver
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
- Institute of Biomedicine (IBUB-IRSJD), Universitat de Barcelona, Barcelona, Spain
| | - Vasileios Toulis
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
- CIBERER, ISCIII, Universitat de Barcelona, Barcelona, Spain
| | - Gemma Marfany
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
- Institute of Biomedicine (IBUB-IRSJD), Universitat de Barcelona, Barcelona, Spain
- CIBERER, ISCIII, Universitat de Barcelona, Barcelona, Spain
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7
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Dupont MA, Humbert C, Huber C, Siour Q, Guerrera IC, Jung V, Christensen A, Pouliet A, Garfa-Traoré M, Nitschké P, Injeyan M, Millar K, Chitayat D, Shannon P, Girisha KM, Shukla A, Mechler C, Lorentzen E, Benmerah A, Cormier-Daire V, Jeanpierre C, Saunier S, Delous M. Human IFT52 mutations uncover a novel role for the protein in microtubule dynamics and centrosome cohesion. Hum Mol Genet 2020; 28:2720-2737. [PMID: 31042281 DOI: 10.1093/hmg/ddz091] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 12/26/2022] Open
Abstract
Mutations in genes encoding components of the intraflagellar transport (IFT) complexes have previously been associated with a spectrum of diseases collectively termed ciliopathies. Ciliopathies relate to defects in the formation or function of the cilium, a sensory or motile organelle present on the surface of most cell types. IFT52 is a key component of the IFT-B complex and ensures the interaction of the two subcomplexes, IFT-B1 and IFT-B2. Here, we report novel IFT52 biallelic mutations in cases with a short-rib thoracic dysplasia (SRTD) or a congenital anomaly of kidney and urinary tract (CAKUT). Combining in vitro and in vivo studies in zebrafish, we showed that SRTD-associated missense mutation impairs IFT-B complex assembly and IFT-B2 ciliary localization, resulting in decreased cilia length. In comparison, CAKUT-associated missense mutation has a mild pathogenicity, thus explaining the lack of skeletal defects in CAKUT case. In parallel, we demonstrated that the previously reported homozygous nonsense IFT52 mutation associated with Sensenbrenner syndrome [Girisha et al. (2016) A homozygous nonsense variant in IFT52 is associated with a human skeletal ciliopathy. Clin. Genet., 90, 536-539] leads to exon skipping and results in a partially functional protein. Finally, our work uncovered a novel role for IFT52 in microtubule network regulation. We showed that IFT52 interacts and partially co-localized with centrin at the distal end of centrioles where it is involved in its recruitment and/or maintenance. Alteration of this function likely contributes to centriole splitting observed in Ift52-/- cells. Altogether, our findings allow a better comprehensive genotype-phenotype correlation among IFT52-related cases and revealed a novel, extra-ciliary role for IFT52, i.e. disruption may contribute to pathophysiological mechanisms.
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Affiliation(s)
- Marie Alice Dupont
- Laboratory of Hereditary Kidney Diseases, INSERM, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Camille Humbert
- Laboratory of Hereditary Kidney Diseases, INSERM, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Céline Huber
- Laboratory of Molecular and Physiopathological bases of osteochondrodysplasia, INSERM, Paris, France.,Department of Genetics, Reference Centre for Skeletal Dysplasia, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Quentin Siour
- Laboratory of Molecular and Physiopathological bases of osteochondrodysplasia, INSERM, Paris, France.,Department of Genetics, Reference Centre for Skeletal Dysplasia, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Ida Chiara Guerrera
- Proteomics Platform 3P5-Necker, Paris Descartes-Sorbonne Paris Cité University, Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Vincent Jung
- Proteomics Platform 3P5-Necker, Paris Descartes-Sorbonne Paris Cité University, Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Anni Christensen
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Aurore Pouliet
- Genomics Core Facility, Imagine Institute and Structure Fédérative de Recherche Necker, INSERM UMR1163 and INSERM US24/CNRS UMS3633, Paris Descartes-Sorbonne Paris Cité University, Paris, France
| | - Meriem Garfa-Traoré
- Cell Imaging Platform UMS 24, Structure Fédérative de Recherche Necker, Inserm US24/CNRS UMS3633, Paris, France
| | - Patrick Nitschké
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France.,Bioinformatics Core Facility, Paris Descartes-Sorbonne Paris Cité University, Paris, France
| | - Marie Injeyan
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Kathryn Millar
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - David Chitayat
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada.,Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Patrick Shannon
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Charlotte Mechler
- Assistance Publique - Hôpitaux de Paris, Louis Mourier Hospital, Colombes, France
| | - Esben Lorentzen
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Alexandre Benmerah
- Laboratory of Hereditary Kidney Diseases, INSERM, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Valérie Cormier-Daire
- Laboratory of Molecular and Physiopathological bases of osteochondrodysplasia, INSERM, Paris, France.,Department of Genetics, Reference Centre for Skeletal Dysplasia, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Cécile Jeanpierre
- Laboratory of Hereditary Kidney Diseases, INSERM, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Sophie Saunier
- Laboratory of Hereditary Kidney Diseases, INSERM, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Marion Delous
- Laboratory of Hereditary Kidney Diseases, INSERM, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
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