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Chen H, Wu Z, Yan Z, Chen C, Zhang Y, Wang Q, Gao Y, Ling K, Hu J, Wei Q. The ARPKD Protein DZIP1L Regulates Ciliary Protein Entry by Modulating the Architecture and Function of Ciliary Transition Fibers. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308820. [PMID: 38634253 PMCID: PMC11200010 DOI: 10.1002/advs.202308820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/13/2024] [Indexed: 04/19/2024]
Abstract
Serving as the cell's sensory antennae, primary cilia are linked to numerous human genetic diseases when they malfunction. DZIP1L, identified as one of the genetic causes of human autosomal recessive polycystic kidney disease (ARPKD), is an evolutionarily conserved ciliary basal body protein. Although it has been reported that DZIP1L is involved in the ciliary entry of PKD proteins, the underlying mechanism remains elusive. Here, an uncharacterized role of DZIP1L is reported in modulating the architecture and function of transition fibers (TFs), striking ciliary base structures essential for selective cilia gating. Using C. elegans as a model, C01G5.7 (hereafter termed DZIP-1) is identified as the sole homolog of DZIP1L, which specifically localizes to TFs. While DZIP-1 or ANKR-26 (the ortholog of ANKRD26) deficiency shows subtle impact on TFs, co-depletion of DZIP-1 and ANKR-26 disrupts TF assembly and cilia gating for soluble and membrane proteins, including the ortholog of ADPKD protein polycystin-2. Notably, the synergistic role for DZIP1L and ANKRD26 in the formation and function of TFs is highly conserved in mammalian cilia. Hence, the findings illuminate an evolutionarily conserved role of DZIP1L in TFs architecture and function, highlighting TFs as a vital part of the ciliary gate implicated in ciliopathies ARPKD.
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Affiliation(s)
- Huicheng Chen
- CAS Key Laboratory of Insect Developmental and Evolutionary BiologyCAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai200032China
- University of Chinese Academy of SciencesBeijing100039China
- Center for Energy Metabolism and ReproductionInstitute of Biomedicine and BiotechnologyShenzhen Institutes of Advanced TechnologyChinese Academy of Sciences (CAS)Shenzhen518055China
| | - Zhimao Wu
- Center for Energy Metabolism and ReproductionInstitute of Biomedicine and BiotechnologyShenzhen Institutes of Advanced TechnologyChinese Academy of Sciences (CAS)Shenzhen518055China
| | - Ziwei Yan
- CAS Key Laboratory of Insect Developmental and Evolutionary BiologyCAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai200032China
- University of Chinese Academy of SciencesBeijing100039China
| | - Chuan Chen
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMN55905USA
| | - Yingying Zhang
- Center for Energy Metabolism and ReproductionInstitute of Biomedicine and BiotechnologyShenzhen Institutes of Advanced TechnologyChinese Academy of Sciences (CAS)Shenzhen518055China
| | - Qiaoling Wang
- Institute of Medicine and Pharmaceutical SciencesZhengzhou UniversityZhengzhou430000China
| | - Yuqing Gao
- Center for Energy Metabolism and ReproductionInstitute of Biomedicine and BiotechnologyShenzhen Institutes of Advanced TechnologyChinese Academy of Sciences (CAS)Shenzhen518055China
| | - Kun Ling
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMN55905USA
| | - Jinghua Hu
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMN55905USA
| | - Qing Wei
- Center for Energy Metabolism and ReproductionInstitute of Biomedicine and BiotechnologyShenzhen Institutes of Advanced TechnologyChinese Academy of Sciences (CAS)Shenzhen518055China
- School of Synthetic BiologyShanxi Key Laboratory of Nucleic Acid BiopesticidesShanxi UniversityTaiyuan030006China
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Bergeron JJM. Proteomics Impact on Cell Biology to Resolve Cell Structure and Function. Mol Cell Proteomics 2024; 23:100758. [PMID: 38574860 PMCID: PMC11070594 DOI: 10.1016/j.mcpro.2024.100758] [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: 02/07/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
The acceleration of advances in proteomics has enabled integration with imaging at the EM and light microscopy levels, cryo-EM of protein structures, and artificial intelligence with proteins comprehensively and accurately resolved for cell structures at nanometer to subnanometer resolution. Proteomics continues to outpace experimentally based structural imaging, but their ultimate integration is a path toward the goal of a compendium of all proteins to understand mechanistically cell structure and function.
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Affiliation(s)
- John J M Bergeron
- Department of Medicine, McGill University Hospital Research Institute, Montreal, Quebec, Canada.
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Ganga AK, Sweeney LK, Ramos AR, Bishop CS, Hamel V, Guichard P, Breslow DK. A disease-associated PPP2R3C-MAP3K1 phospho-regulatory module controls centrosome function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587836. [PMID: 38617270 PMCID: PMC11014585 DOI: 10.1101/2024.04.02.587836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Centrosomes have critical roles in microtubule organization and in cell signaling.1-8 However, the mechanisms that regulate centrosome function are not fully defined, and thus how defects in centrosomal regulation contribute to disease is incompletely understood. From functional genomic analyses, we find here that PPP2R3C, a PP2A phosphatase subunit, is a distal centriole protein and functional partner of centriolar proteins CEP350 and FOP. We further show that a key function of PPP2R3C is to counteract the kinase activity of MAP3K1. In support of this model, MAP3K1 knockout suppresses growth defects caused by PPP2R3C inactivation, and MAP3K1 and PPP2R3C have opposing effects on basal and microtubule stress-induced JNK signaling. Illustrating the importance of balanced MAP3K1 and PPP2R3C activities, acute overexpression of MAP3K1 severely inhibits centrosome function and triggers rapid centriole disintegration. Additionally, inactivating PPP2R3C mutations and activating MAP3K1 mutations both cause congenital syndromes characterized by gonadal dysgenesis.9-15 As a syndromic PPP2R3C variant is defective in centriolar localization and binding to centriolar protein FOP, we propose that imbalanced activity of this centrosomal kinase-phosphatase pair is the shared cause of these disorders. Thus, our findings reveal a new centrosomal phospho-regulatory module, shed light on disorders of gonadal development, and illustrate the power of systems genetics to identify previously unrecognized gene functions.
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Affiliation(s)
- Anil Kumar Ganga
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Lauren K. Sweeney
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Armando Rubio Ramos
- Department of Molecular and Cellular Biology, University of Geneva, Faculty of Sciences, Geneva, Switzerland
| | - Cassandra S. Bishop
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Virginie Hamel
- Department of Molecular and Cellular Biology, University of Geneva, Faculty of Sciences, Geneva, Switzerland
| | - Paul Guichard
- Department of Molecular and Cellular Biology, University of Geneva, Faculty of Sciences, Geneva, Switzerland
| | - David K. Breslow
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
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Fang J, Tian W, Quintanilla MA, Beach JR, Lerit DA. The PCM scaffold enables RNA localization to centrosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.13.575509. [PMID: 38469150 PMCID: PMC10926663 DOI: 10.1101/2024.01.13.575509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
As microtubule-organizing centers, centrosomes direct assembly of the bipolar mitotic spindle required for chromosome segregation and genome stability. Centrosome activity requires the dynamic assembly of pericentriolar material (PCM), the composition and organization of which changes throughout the cell cycle. Recent studies highlight the conserved localization of several mRNAs encoded from centrosome-associated genes enriched at centrosomes, including Pericentrin-like protein (Plp) mRNA. However, relatively little is known about how RNAs localize to centrosomes and influence centrosome function. Here, we examine mechanisms underlying the subcellular localization of Plp mRNA. We find that Plp mRNA localization is puromycin-sensitive, and the Plp coding sequence is both necessary and sufficient for RNA localization, consistent with a co-translational transport mechanism. We identify regions within the Plp coding sequence that regulate Plp mRNA localization. Finally, we show that protein-protein interactions critical for elaboration of the PCM scaffold permit RNA localization to centrosomes. Taken together, these findings inform the mechanistic basis of Plp mRNA localization and lend insight into the oscillatory enrichment of RNA at centrosomes.
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Affiliation(s)
- Junnan Fang
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322
- Equal contributions
| | - Weiyi Tian
- Equal contributions
- Emory College of Arts and Sciences, Emory University, Atlanta, GA 30322
| | - Melissa A. Quintanilla
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Jordan R. Beach
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Dorothy A. Lerit
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322
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Woerz F, Hoffmann F, Antony S, Bolz S, Jarboui MA, Junger K, Klose F, Stehle IF, Boldt K, Ueffing M, Beyer T. Interactome Analysis Reveals a Link of the Novel ALMS1-CEP70 Complex to Centrosomal Clusters. Mol Cell Proteomics 2024; 23:100701. [PMID: 38122899 PMCID: PMC10820798 DOI: 10.1016/j.mcpro.2023.100701] [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: 06/02/2023] [Revised: 11/08/2023] [Accepted: 12/17/2023] [Indexed: 12/23/2023] Open
Abstract
Alström syndrome (ALMS) is a very rare autosomal-recessive disorder, causing a broad range of clinical defects most notably retinal degeneration, type 2 diabetes, and truncal obesity. The ALMS1 gene encodes a complex and huge ∼0.5 MDa protein, which has hampered analysis in the past. The ALMS1 protein is localized to the centrioles and the basal body of cilia and is involved in signaling processes, for example, TGF-β signaling. However, the exact molecular function of ALMS1 at the basal body remains elusive and controversial. We recently demonstrated that protein complex analysis utilizing endogenously tagged cells provides an excellent tool to investigate protein interactions of ciliary proteins. Here, CRISPR/Cas9-mediated endogenously tagged ALMS1 cells were used for affinity-based protein complex analysis. Centrosomal and microtubule-associated proteins were identified, which are potential regulators of ALMS1 function, such as the centrosomal protein 70 kDa (CEP70). Candidate proteins were further investigated in ALMS1-deficient hTERT-RPE1 cells. Loss of ALMS1 led to shortened cilia with no change in structural protein localization, for example, acetylated and ɣ-tubulin, Centrin-3, or the novel interactor CEP70. Conversely, reduction of CEP70 resulted in decreased ALMS1 at the ciliary basal body. Complex analysis of CEP70 revealed domain-specific ALMS1 interaction involving the TPR-containing C-terminal (TRP-CT) fragment of CEP70. In addition to ALMS1, several ciliary proteins, including CEP135, were found to specifically bind to the TPR-CT domain. Data are available via ProteomeXchange with the identifier PXD046401. Protein interactors identified in this study provide candidate lists that help to understand ALMS1 and CEP70 function in cilia-related protein modification, cell death, and disease-related mechanisms.
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Affiliation(s)
- Franziska Woerz
- Eberhard Karls University Tübingen, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany.
| | - Felix Hoffmann
- Eberhard Karls University Tübingen, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Shibu Antony
- Eberhard Karls University Tübingen, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Sylvia Bolz
- Eberhard Karls University Tübingen, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Mohamed Ali Jarboui
- Eberhard Karls University Tübingen, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Katrin Junger
- Eberhard Karls University Tübingen, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Franziska Klose
- Eberhard Karls University Tübingen, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Isabel F Stehle
- Eberhard Karls University Tübingen, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Karsten Boldt
- Eberhard Karls University Tübingen, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Marius Ueffing
- Eberhard Karls University Tübingen, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Tina Beyer
- Eberhard Karls University Tübingen, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany.
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