1
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Wolfram M, Greif A, Baidukova O, Voll H, Tauber S, Lindacher J, Hegemann P, Kreimer G. Insights into degradation and targeting of the photoreceptor channelrhodopsin-1. PLANT, CELL & ENVIRONMENT 2024; 47:4188-4211. [PMID: 38935876 DOI: 10.1111/pce.15017] [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: 03/20/2024] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 06/29/2024]
Abstract
In Chlamydomonas, the directly light-gated, plasma membrane-localized cation channels channelrhodopsins ChR1 and ChR2 are the primary photoreceptors for phototaxis. Their targeting and abundance is essential for optimal movement responses. However, our knowledge how Chlamydomonas achieves this is still at its infancy. Here we show that ChR1 internalization occurs via light-stimulated endocytosis. Prior or during endocytosis ChR1 is modified and forms high molecular mass complexes. These are the solely detectable ChR1 forms in extracellular vesicles and their abundance therein dynamically changes upon illumination. The ChR1-containing extracellular vesicles are secreted via the plasma membrane and/or the ciliary base. In line with this, ciliogenesis mutants exhibit increased ChR1 degradation rates. Further, we establish involvement of the cysteine protease CEP1, a member of the papain-type C1A subfamily. ΔCEP1-knockout strains lack light-induced ChR1 degradation, whereas ChR2 degradation was unaffected. Low light stimulates CEP1 expression, which is regulated via phototropin, a SPA1 E3 ubiquitin ligase and cyclic AMP. Further, mutant and inhibitor analyses revealed involvement of the small GTPase ARL11 and SUMOylation in ChR1 targeting to the eyespot and cilia. Our study thus defines the degradation pathway of this central photoreceptor of Chlamydomonas and identifies novel elements involved in its homoeostasis and targeting.
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Affiliation(s)
- Michaela Wolfram
- Department of Biology, Cell Biology, Friedrich-Alexander Universität, Erlangen-Nürnberg, Germany
| | - Arne Greif
- Department of Biology, Cell Biology, Friedrich-Alexander Universität, Erlangen-Nürnberg, Germany
| | - Olga Baidukova
- Institute of Biology, Experimental Biophysics, Humboldt Universität, Berlin, Germany
| | - Hildegard Voll
- Department of Biology, Cell Biology, Friedrich-Alexander Universität, Erlangen-Nürnberg, Germany
| | - Sandra Tauber
- Department of Biology, Cell Biology, Friedrich-Alexander Universität, Erlangen-Nürnberg, Germany
| | - Jana Lindacher
- Department of Biology, Cell Biology, Friedrich-Alexander Universität, Erlangen-Nürnberg, Germany
| | - Peter Hegemann
- Institute of Biology, Experimental Biophysics, Humboldt Universität, Berlin, Germany
| | - Georg Kreimer
- Department of Biology, Cell Biology, Friedrich-Alexander Universität, Erlangen-Nürnberg, Germany
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2
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Ishii H, Yamagishi M, Yajima J. Two Tetrahymena kinesin-9 family members exhibit slow plus-end-directed motility in vitro. Sci Rep 2024; 14:20993. [PMID: 39251704 PMCID: PMC11385561 DOI: 10.1038/s41598-024-71280-y] [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: 03/26/2024] [Accepted: 08/27/2024] [Indexed: 09/11/2024] Open
Abstract
The kinesin-9 family comprises two subfamilies specific to ciliated eukaryotic cells, and has recently attracted considerable attention because of its importance in ciliary bending and formation. However, only scattered data are available on the motor properties of kinesin-9 family members; these properties have not been compared under identical experimental conditions using kinesin-9 motors from the same species. Here, we report the comprehensive motor properties of two kinesin-9 molecules of Tetrahymena thermophila, TtK9A (Kif9/Klp1 ortholog) and TtK9B1 (Kif6 ortholog), using microtubule-based in vitro assays, including single-motor and multi-motor assays and microtubule-stimulated ATPase assays. Both subfamilies exhibit microtubule plus-end-directed, extremely slow motor activity, both in single and multiple molecules. TtK9A shows lower processivity than TtK9B1. Our findings indicate that the considerable slow movement of kinesin-9 that corresponds to low ATP hydrolysis rates is a common feature of the ciliary kinesin-9 family.
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Affiliation(s)
- Hiroto Ishii
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-Ku, Tokyo, 153-8902, Japan
| | - Masahiko Yamagishi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-Ku, Tokyo, 153-8902, Japan
- Komaba Institute for Science, The University of Tokyo, 3-8-1 Komaba, Meguro-Ku, Tokyo, 153-8902, Japan
| | - Junichiro Yajima
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-Ku, Tokyo, 153-8902, Japan.
- Komaba Institute for Science, The University of Tokyo, 3-8-1 Komaba, Meguro-Ku, Tokyo, 153-8902, Japan.
- Research Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, 3-8-1 Komaba, Meguro-Ku, Tokyo, 153-8902, Japan.
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3
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Morikawa M, Yamaguchi H, Kikkawa M. Calaxin is a key factor for calcium-dependent waveform control in zebrafish sperm. Life Sci Alliance 2024; 7:e202402632. [PMID: 38876797 PMCID: PMC11178939 DOI: 10.26508/lsa.202402632] [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: 01/30/2024] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/16/2024] Open
Abstract
Calcium is critical for regulating the waveform of motile cilia and flagella. Calaxin is currently the only known molecule involved in the calcium-dependent regulation in ascidians. We have recently shown that Calaxin stabilizes outer arm dynein (OAD), and the knockout of Calaxin results in primary ciliary dyskinesia phenotypes in vertebrates. However, from the knockout experiments, it was not clear which functions depend on calcium and how Calaxin regulates the waveform. To address this question, here, we generated transgenic zebrafish expressing a mutant E130A-Calaxin deficient in calcium binding. E130A-Calaxin restored the OAD reduction of calaxin -/- sperm and the abnormal movement of calaxin -/- left-right organizer cilia, showing that Calaxin's stabilization of OADs is calcium-independent. In contrast, our quantitative analysis of E130A-Calaxin sperms showed that the calcium-induced asymmetric beating was not restored, linking Calaxin's calcium-binding ability with an asymmetric flagellar beating for the first time. Our data show that Calaxin is a calcium-dependent regulator of the ciliary beating and a calcium-independent OAD stabilizer.
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Affiliation(s)
- Motohiro Morikawa
- https://ror.org/057zh3y96 Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Yamaguchi
- https://ror.org/057zh3y96 Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masahide Kikkawa
- https://ror.org/057zh3y96 Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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4
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Boegholm N, Petriman NA, Tanvir NM, Lorentzen E. Architecture of RabL2-associated complexes at the ciliary base: A structural modeling perspective: Deciphering the structural organization of ciliary RabL2 complexes. Bioessays 2024; 46:e2300222. [PMID: 38991980 DOI: 10.1002/bies.202300222] [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: 11/24/2023] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024]
Abstract
Cilia are slender, micrometer-long organelles present on the surface of eukaryotic cells. They function in signaling and locomotion and are constructed by intraflagellar transport (IFT). The assembly of IFT complexes into so-called IFT trains to initiate ciliary entry at the base of the cilium remains a matter of debate. Here, we use structural modeling to provide an architectural framework for how RabL2 is anchored at the ciliary base via CEP19 before being handed over to IFT trains for ciliary entry. Our models suggest that the N-terminal domain of CEP43 forms a homo-dimer to anchor at the subdistal appendages of cilia through a direct interaction with CEP350. A long linker region separates the N-terminal domain of CEP43 from the C-terminal domain, which captures CEP19 above the subdistal appendages and close to the distal appendages. Furthermore, we present a structural model for how RabL2-CEP19 associates with the IFT-B complex, providing insight into how RabL2 is handed over from CEP19 to the IFT complex. Interestingly, RabL2 association with the IFT-B complex appears to induce a significant conformational change in the IFT complex via a kink in the coiled-coils of the IFT81/74 proteins, which may prime the IFT machinery for entry into cilia.
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Affiliation(s)
- Niels Boegholm
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Narcis A Petriman
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Niaj M Tanvir
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Esben Lorentzen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
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5
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Dai X, Xu R, Li N. The Interplay between Airway Cilia and Coronavirus Infection, Implications for Prevention and Control of Airway Viral Infections. Cells 2024; 13:1353. [PMID: 39195243 DOI: 10.3390/cells13161353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 08/10/2024] [Accepted: 08/12/2024] [Indexed: 08/29/2024] Open
Abstract
Coronaviruses (CoVs) are a class of respiratory viruses with the potential to cause severe respiratory diseases by infecting cells of the upper respiratory tract, bronchial epithelium, and lung. The airway cilia are distributed on the surface of respiratory epithelial cells, forming the first point of contact between the host and the inhaled coronaviruses. The function of the airway cilia is to oscillate and sense, thereby defending against and removing pathogens to maintain the cleanliness and patency of the respiratory tract. Following infection of the respiratory tract, coronaviruses exploit the cilia to invade and replicate in epithelial cells while also damaging the cilia to facilitate the spread and exacerbation of respiratory diseases. It is therefore imperative to investigate the interactions between coronaviruses and respiratory cilia, as well as to elucidate the functional mechanism of respiratory cilia following coronavirus invasion, in order to develop effective strategies for the prevention and treatment of respiratory viral infections. This review commences with an overview of the fundamental characteristics of airway cilia, and then, based on the interplay between airway cilia and coronavirus infection, we propose that ciliary protection and restoration may represent potential therapeutic approaches in emerging and re-emerging coronavirus pandemics.
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Affiliation(s)
- Xuyao Dai
- Department of Biomedical Engineering and Technology, Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Ruodan Xu
- Department of Biomedical Engineering and Technology, Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Ning Li
- Department of Biomedical Engineering and Technology, Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
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6
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Pir MS, Begar E, Yenisert F, Demirci HC, Korkmaz ME, Karaman A, Tsiropoulou S, Firat-Karalar EN, Blacque OE, Oner SS, Doluca O, Cevik S, Kaplan OI. CilioGenics: an integrated method and database for predicting novel ciliary genes. Nucleic Acids Res 2024; 52:8127-8145. [PMID: 38989623 DOI: 10.1093/nar/gkae554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/21/2024] [Accepted: 07/09/2024] [Indexed: 07/12/2024] Open
Abstract
Uncovering the full list of human ciliary genes holds enormous promise for the diagnosis of cilia-related human diseases, collectively known as ciliopathies. Currently, genetic diagnoses of many ciliopathies remain incomplete (1-3). While various independent approaches theoretically have the potential to reveal the entire list of ciliary genes, approximately 30% of the genes on the ciliary gene list still stand as ciliary candidates (4,5). These methods, however, have mainly relied on a single strategy to uncover ciliary candidate genes, making the categorization challenging due to variations in quality and distinct capabilities demonstrated by different methodologies. Here, we develop a method called CilioGenics that combines several methodologies (single-cell RNA sequencing, protein-protein interactions (PPIs), comparative genomics, transcription factor (TF) network analysis, and text mining) to predict the ciliary capacity of each human gene. Our combined approach provides a CilioGenics score for every human gene that represents the probability that it will become a ciliary gene. Compared to methods that rely on a single method, CilioGenics performs better in its capacity to predict ciliary genes. Our top 500 gene list includes 258 new ciliary candidates, with 31 validated experimentally by us and others. Users may explore the whole list of human genes and CilioGenics scores on the CilioGenics database (https://ciliogenics.com/).
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Affiliation(s)
- Mustafa S Pir
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Efe Begar
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkiye
| | - Ferhan Yenisert
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Hasan C Demirci
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Mustafa E Korkmaz
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Asli Karaman
- Istanbul Medeniyet University, Science and Advanced Technologies Research Center (BILTAM), 34700 Istanbul, Turkiye
| | - Sofia Tsiropoulou
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Elif Nur Firat-Karalar
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkiye
- School of Medicine, Koç University, Istanbul 34450, Turkiye
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Sukru S Oner
- Istanbul Medeniyet University, Science and Advanced Technologies Research Center (BILTAM), 34700 Istanbul, Turkiye
- Goztepe Prof. Dr. Suleyman Yalcin City Hospital, Istanbul, Turkiye
| | - Osman Doluca
- Izmir University of Economics, Faculty of Engineering, Department of Biomedical Engineering, Izmir, Turkiye
| | - Sebiha Cevik
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Oktay I Kaplan
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
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7
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Gao J, Tong M, Lee C, Gaertig J, Legal T, Bui KH. DomainFit: Identification of protein domains in cryo-EM maps at intermediate resolution using AlphaFold2-predicted models. Structure 2024; 32:1248-1259.e5. [PMID: 38754431 PMCID: PMC11316655 DOI: 10.1016/j.str.2024.04.017] [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: 11/28/2023] [Revised: 03/18/2024] [Accepted: 04/19/2024] [Indexed: 05/18/2024]
Abstract
Cryoelectron microscopy (cryo-EM) has revolutionized the structural determination of macromolecular complexes. With the paradigm shift to structure determination of highly complex endogenous macromolecular complexes ex vivo and in situ structural biology, there are an increasing number of structures of native complexes. These complexes often contain unidentified proteins, related to different cellular states or processes. Identifying proteins at resolutions lower than 4 Å remains challenging because side chains cannot be visualized reliably. Here, we present DomainFit, a program for semi-automated domain-level protein identification from cryo-EM maps, particularly at resolutions lower than 4 Å. By fitting domains from AlphaFold2-predicted models into cryo-EM maps, the program performs statistical analyses and attempts to identify the domains and protein candidates forming the density. Using DomainFit, we identified two microtubule inner proteins, one of which contains a CCDC81 domain and is exclusively localized in the proximal region of the doublet microtubule in Tetrahymena thermophila.
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Affiliation(s)
- Jerry Gao
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Montréal, QC H3A 0C7, Canada; Centre de recherche en biologie structurale, McGill University, Montréal, QC H3G 0B1, Canada
| | - Maxwell Tong
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Montréal, QC H3A 0C7, Canada; Centre de recherche en biologie structurale, McGill University, Montréal, QC H3G 0B1, Canada
| | - Chinkyu Lee
- Department of Cellular Biology, University of Georgia, Athens 30602-2607, GA, USA
| | - Jacek Gaertig
- Department of Cellular Biology, University of Georgia, Athens 30602-2607, GA, USA
| | - Thibault Legal
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Montréal, QC H3A 0C7, Canada; Centre de recherche en biologie structurale, McGill University, Montréal, QC H3G 0B1, Canada.
| | - Khanh Huy Bui
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Montréal, QC H3A 0C7, Canada; Centre de recherche en biologie structurale, McGill University, Montréal, QC H3G 0B1, Canada.
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8
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Koenitzer JR, Gupta DK, Twan WK, Xu H, Hadas N, Hawkins FJ, Beermann ML, Penny GM, Wamsley NT, Berical A, Major MB, Dutcher SK, Brody SL, Horani A. Transcriptional analysis of primary ciliary dyskinesia airway cells reveals a dedicated cilia glutathione pathway. JCI Insight 2024; 9:e180198. [PMID: 39042459 PMCID: PMC11385084 DOI: 10.1172/jci.insight.180198] [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: 03/01/2024] [Accepted: 07/18/2024] [Indexed: 07/25/2024] Open
Abstract
Primary ciliary dyskinesia (PCD) is a genetic condition that results in dysmotile cilia. The repercussions of cilia dysmotility and gene variants on the multiciliated cell remain poorly understood. We used single-cell RNA-Seq, proteomics, and advanced microscopy to compare primary culture epithelial cells from patients with PCD, their heterozygous mothers, and healthy individuals, and we induced pluripotent stem cells (iPScs) generated from a patient with PCD. Transcriptomic analysis revealed unique signatures in PCD airway cells compared with their mothers' cells and the cells of healthy individuals. Gene expression in heterozygous mothers' cells diverged from both control and PCD cells, marked by increased inflammatory and cellular stress signatures. Primary and iPS-derived PCD multiciliated cells had increased expression of glutathione-S-transferases GSTA2 and GSTA1, as well as NRF2 target genes, accompanied by elevated levels of reactive oxygen species (ROS). Immunogold labeling in human cilia and proteomic analysis of the ciliated organism Chlamydomonas reinhardtii demonstrated that GSTA2 localizes to motile cilia. Loss of human GSTA2 and C. reinhardtii GSTA resulted in slowed cilia motility, pointing to local cilia regulatory roles. Our findings identify cellular responses unique to PCD variants and independent of environmental stress and uncover a dedicated ciliary GSTA2 pathway essential for normal motility that may be a therapeutic target.
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Affiliation(s)
| | - Deepesh Kumar Gupta
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Wang Kyaw Twan
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Huihui Xu
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Nicholas Hadas
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Finn J Hawkins
- Center for Regenerative Medicine and
- The Pulmonary Center, Department of Medicine, Boston University and Boston Medical Center, Boston, Massachusetts, USA
| | | | | | - Nathan T Wamsley
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Andrew Berical
- Center for Regenerative Medicine and
- The Pulmonary Center, Department of Medicine, Boston University and Boston Medical Center, Boston, Massachusetts, USA
| | - Michael B Major
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Susan K Dutcher
- Department of Genetics and
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | | | - Amjad Horani
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri, USA
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9
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Vilarrasa-Blasi J, Vellosillo T, Jinkerson RE, Fauser F, Xiang T, Minkoff BB, Wang L, Kniazev K, Guzman M, Osaki J, Barrett-Wilt GA, Sussman MR, Jonikas MC, Dinneny JR. Multi-omics analysis of green lineage osmotic stress pathways unveils crucial roles of different cellular compartments. Nat Commun 2024; 15:5988. [PMID: 39013881 PMCID: PMC11252407 DOI: 10.1038/s41467-024-49844-3] [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: 10/19/2022] [Accepted: 06/21/2024] [Indexed: 07/18/2024] Open
Abstract
Maintenance of water homeostasis is a fundamental cellular process required by all living organisms. Here, we use the single-celled green alga Chlamydomonas reinhardtii to establish a foundational understanding of osmotic-stress signaling pathways through transcriptomics, phosphoproteomics, and functional genomics approaches. Comparison of pathways identified through these analyses with yeast and Arabidopsis allows us to infer their evolutionary conservation and divergence across these lineages. 76 genes, acting across diverse cellular compartments, were found to be important for osmotic-stress tolerance in Chlamydomonas through their functions in cytoskeletal organization, potassium transport, vesicle trafficking, mitogen-activated protein kinase and chloroplast signaling. We show that homologs for five of these genes have conserved functions in stress tolerance in Arabidopsis and reveal a novel PROFILIN-dependent stage of acclimation affecting the actin cytoskeleton that ensures tissue integrity upon osmotic stress. This study highlights the conservation of the stress response in algae and land plants, and establishes Chlamydomonas as a unicellular plant model system to dissect the osmotic stress signaling pathway.
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Affiliation(s)
- Josep Vilarrasa-Blasi
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA.
| | - Tamara Vellosillo
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
| | - Robert E Jinkerson
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Friedrich Fauser
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Tingting Xiang
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Benjamin B Minkoff
- Department of Biochemistry and Center for Genomics Science Innovation, University of Wisconsin, Madison, WI, 53706, USA
| | - Lianyong Wang
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Kiril Kniazev
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Michael Guzman
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
| | - Jacqueline Osaki
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
| | | | - Michael R Sussman
- Department of Biochemistry and Center for Genomics Science Innovation, University of Wisconsin, Madison, WI, 53706, USA
| | - Martin C Jonikas
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA.
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10
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Yao XJ, Chen Q, Yu HP, Ruan DD, Li SJ, Wu M, Liao LS, Lin XF, Fang ZT, Luo JW, Xie BS. A novel splicing mutation DNAH5 c.13,338 + 5G > C is involved in the pathogenesis of primary ciliary dyskinesia in a family with primary familial brain calcification. BMC Pulm Med 2024; 24:343. [PMID: 39014333 PMCID: PMC11251106 DOI: 10.1186/s12890-024-03164-w] [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: 11/02/2023] [Accepted: 07/11/2024] [Indexed: 07/18/2024] Open
Abstract
BACKGROUND Primary ciliary dyskinesia (PCD) is an autosomal recessive hereditary disease characterized by recurrent respiratory infections. In clinical manifestations, DNAH5 (NM_001361.3) is one of the recessive pathogenic genes. Primary familial brain calcification (PFBC) is a neurodegenerative disease characterized by bilateral calcification in the basal ganglia and other brain regions. PFBC can be inherited in an autosomal dominant or recessive manner. A family with PCD caused by a DNAH5 compound heterozygous variant and PFBC caused by a MYORG homozygous variant was analyzed. METHODS In this study, we recruited three generations of Han families with primary ciliary dyskinesia combined with primary familial brain calcification. Their clinical phenotype data were collected, next-generation sequencing was performed to screen suspected pathogenic mutations in the proband and segregation analysis of families was carried out by Sanger sequencing. The mutant and wild-type plasmids were constructed and transfected into HEK293T cells instantaneously, and splicing patterns were detected by Minigene splicing assay. The structure and function of mutations were analyzed by bioinformatics analysis. RESULTS The clinical phenotypes of the proband (II10) and his sister (II8) were bronchiectasis, recurrent pulmonary infection, multiple symmetric calcifications of bilateral globus pallidus and cerebellar dentate nucleus, paranasal sinusitis in the whole group, and electron microscopy of bronchial mucosa showed that the ciliary axoneme was defective. There was also total visceral inversion in II10 but not in II8. A novel splice variant C.13,338 + 5G > C and a frameshift variant C.4314delT (p. Asn1438lysfs *10) were found in the DNAH5 gene in proband (II10) and II8. c.347_348dupCTGGCCTTCCGC homozygous insertion variation was found in the MYORG of the proband. The two pathogenic genes were co-segregated in the family. Minigene showed that DNAH5 c.13,338 + 5G > C has two abnormal splicing modes: One is that part of the intron bases where the mutation site located is translated, resulting in early translation termination of DNAH5; The other is the mutation resulting in the deletion of exon76. CONCLUSIONS The newly identified DNAH5 splicing mutation c.13,338 + 5G > C is involved in the pathogenesis of PCD in the family, and forms a compound heterozygote with the pathogenic variant DNAH5 c.4314delT lead to the pathogenesis of PCD.
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Grants
- 2021J02053, 2023J011159, 2022J01996 Natural Science Foundation of Fujian Province
- 2020-822, 2021-157, 2021-848, 2021-917, 2022-840) Fujian Provincial Finance Department
- 2020-822, 2021-157, 2021-848, 2021-917, 2022-840) Fujian Provincial Finance Department
- 2022CXA001, 2021CXB001, 2022CXB002 Medical Innovation Project of Fujian Province
- National famous and old Chinese medicine experts (Xuemei Zhang, Xiaohua Yan) inheritance studio construction project
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Affiliation(s)
- Xiu-Juan Yao
- Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, no. 134 East Street, Fuzhou, 350001, China
- Respiratory department, Fujian Provincial Hospital, Fuzhou, China
| | - Qian Chen
- Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, no. 134 East Street, Fuzhou, 350001, China
| | - Hong-Ping Yu
- Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, no. 134 East Street, Fuzhou, 350001, China
| | - Dan-Dan Ruan
- Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, no. 134 East Street, Fuzhou, 350001, China
| | - Shi-Jie Li
- Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, no. 134 East Street, Fuzhou, 350001, China
| | - Min Wu
- Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, no. 134 East Street, Fuzhou, 350001, China
| | - Li-Sheng Liao
- Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, no. 134 East Street, Fuzhou, 350001, China
- Department of Hematology, Fujian Provincial Hospital, Fuzhou, China
| | - Xin-Fu Lin
- Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, no. 134 East Street, Fuzhou, 350001, China
- Pediatrics department, Fujian Provincial Hospital, Fuzhou, China
| | - Zhu-Ting Fang
- Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, no. 134 East Street, Fuzhou, 350001, China.
- Interventional Department, Fujian Provincial Hospital, Fuzhou, China.
| | - Jie-Wei Luo
- Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, no. 134 East Street, Fuzhou, 350001, China.
- Department of Traditional Chinese Medicine, Fujian Provincial Hospital, Fuzhou, China.
| | - Bao-Song Xie
- Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, no. 134 East Street, Fuzhou, 350001, China.
- Respiratory department, Fujian Provincial Hospital, Fuzhou, China.
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11
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King SM, Sakato-Antoku M, Patel-King RS, Balsbaugh JL. The methylome of motile cilia. Mol Biol Cell 2024; 35:ar89. [PMID: 38696262 PMCID: PMC11244166 DOI: 10.1091/mbc.e24-03-0130] [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: 03/25/2024] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 05/04/2024] Open
Abstract
Cilia are highly complex motile, sensory, and secretory organelles that contain perhaps 1000 or more distinct protein components, many of which are subject to various posttranslational modifications such as phosphorylation, N-terminal acetylation, and proteolytic processing. Another common modification is the addition of one or more methyl groups to the side chains of arginine and lysine residues. These tunable additions delocalize the side-chain charge, decrease hydrogen bond capacity, and increase both bulk and hydrophobicity. Methylation is usually mediated by S-adenosylmethionine (SAM)-dependent methyltransferases and reversed by demethylases. Previous studies have identified several ciliary proteins that are subject to methylation including axonemal dynein heavy chains that are modified by a cytosolic methyltransferase. Here, we have performed an extensive proteomic analysis of multiple independently derived cilia samples to assess the potential for SAM metabolism and the extent of methylation in these organelles. We find that cilia contain all the enzymes needed for generation of the SAM methyl donor and recycling of the S-adenosylhomocysteine and tetrahydrofolate byproducts. In addition, we find that at least 155 distinct ciliary proteins are methylated, in some cases at multiple sites. These data provide a comprehensive resource for studying the consequences of methyl marks on ciliary biology.
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Affiliation(s)
- Stephen M. King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 3305
| | - Miho Sakato-Antoku
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 3305
| | - Ramila S. Patel-King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 3305
| | - Jeremy L. Balsbaugh
- Proteomics and Metabolomics Facility, Center for Open Research Resources & Equipment, University of Connecticut, Storrs, CT 06269
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12
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Marshall WF. Chlamydomonas as a model system to study cilia and flagella using genetics, biochemistry, and microscopy. Front Cell Dev Biol 2024; 12:1412641. [PMID: 38872931 PMCID: PMC11169674 DOI: 10.3389/fcell.2024.1412641] [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: 04/05/2024] [Accepted: 05/13/2024] [Indexed: 06/15/2024] Open
Abstract
The unicellular green alga, Chlamydomonas reinhardtii, has played a central role in discovering much of what is currently known about the composition, assembly, and function of cilia and flagella. Chlamydomonas combines excellent genetics, such as the ability to grow cells as haploids or diploids and to perform tetrad analysis, with an unparalleled ability to detach and isolate flagella in a single step without cell lysis. The combination of genetics and biochemistry that is possible in Chlamydomonas has allowed many of the key components of the cilium to be identified by looking for proteins that are missing in a defined mutant. Few if any other model organisms allow such a seamless combination of genetic and biochemical approaches. Other major advantages of Chlamydomonas compared to other systems include the ability to induce flagella to regenerate in a highly synchronous manner, allowing the kinetics of flagellar growth to be measured, and the ability of Chlamydomonas flagella to adhere to glass coverslips allowing Intraflagellar Transport to be easily imaged inside the flagella of living cells, with quantitative precision and single-molecule resolution. These advantages continue to work in favor of Chlamydomonas as a model system going forward, and are now augmented by extensive genomic resources, a knockout strain collection, and efficient CRISPR gene editing. While Chlamydomonas has obvious limitations for studying ciliary functions related to animal development or organ physiology, when it comes to studying the fundamental biology of cilia and flagella, Chlamydomonas is simply unmatched in terms of speed, efficiency, cost, and the variety of approaches that can be brought to bear on a question.
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Affiliation(s)
- Wallace F. Marshall
- Department Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, United States
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13
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Wei D, Quaranta G, Aubin-Tam ME, Tam DSW. The younger flagellum sets the beat for Chlamydomonas reinhardtii. eLife 2024; 13:e86102. [PMID: 38752724 PMCID: PMC11098555 DOI: 10.7554/elife.86102] [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: 01/11/2023] [Accepted: 04/03/2024] [Indexed: 05/18/2024] Open
Abstract
Eukaryotes swim with coordinated flagellar (ciliary) beating and steer by fine-tuning the coordination. The model organism for studying flagellate motility, Chlamydomonas reinhardtii, employs synchronous, breaststroke-like flagellar beating to swim, and it modulates the beating amplitudes differentially to steer. This strategy hinges on both inherent flagellar asymmetries (e.g. different response to chemical messengers) and such asymmetries being effectively coordinated in the synchronous beating. In C. reinhardtii, the synchrony of beating is known to be supported by a mechanical connection between flagella; however, how flagellar asymmetries persist in the synchrony remains elusive. For example, it has been speculated for decades that one flagellum leads the beating, as its dynamic properties (i.e. frequency, waveform, etc.) appear to be copied by the other one. In this study, we combine experiments, computations, and modeling efforts to elucidate the roles played by each flagellum in synchronous beating. With a non-invasive technique to selectively load each flagellum, we show that the coordinated beating essentially only responds to load exerted on the cis flagellum; and that such asymmetry in response derives from a unilateral coupling between the two flagella. Our results highlight a distinct role for each flagellum in coordination and have implication for biflagellates' tactic behaviors.
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Affiliation(s)
- Da Wei
- Department of Bionanoscience, Delft University of TechnologyDelftNetherlands
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of SciencesBeijingChina
| | - Greta Quaranta
- Laboratory for Aero and Hydrodynamics, Delft University of TechnologyDelftNetherlands
| | - Marie-Eve Aubin-Tam
- Department of Bionanoscience, Delft University of TechnologyDelftNetherlands
| | - Daniel SW Tam
- Laboratory for Aero and Hydrodynamics, Delft University of TechnologyDelftNetherlands
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14
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Fu G, Augspurger K, Sakizadeh J, Reck J, Bower R, Tritschler D, Gui L, Nicastro D, Porter ME. The MBO2/FAP58 heterodimer stabilizes assembly of inner arm dynein b and reveals axoneme asymmetries involved in ciliary waveform. Mol Biol Cell 2024; 35:ar72. [PMID: 38568782 PMCID: PMC11151096 DOI: 10.1091/mbc.e23-11-0439] [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: 11/17/2023] [Revised: 03/05/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024] Open
Abstract
Cilia generate three-dimensional waveforms required for cell motility and transport of fluid, mucus, and particles over the cell surface. This movement is driven by multiple dynein motors attached to nine outer doublet microtubules that form the axoneme. The outer and inner arm dyneins are organized into 96-nm repeats tandemly arrayed along the length of the doublets. Motility is regulated in part by projections from the two central pair microtubules that contact radial spokes located near the base of the inner dynein arms in each repeat. Although much is known about the structures and protein complexes within the axoneme, many questions remain about the regulatory mechanisms that allow the cilia to modify their waveforms in response to internal or external stimuli. Here, we used Chlamydomonas mbo (move backwards only) mutants with altered waveforms to identify at least two conserved proteins, MBO2/CCDC146 and FAP58/CCDC147, that form part of a L-shaped structure that varies between doublet microtubules. Comparative proteomics identified additional missing proteins that are altered in other motility mutants, revealing overlapping protein defects. Cryo-electron tomography and epitope tagging revealed that the L-shaped, MBO2/FAP58 structure interconnects inner dynein arms with multiple regulatory complexes, consistent with its function in modifying the ciliary waveform.
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Affiliation(s)
- Gang Fu
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Katherine Augspurger
- Department of Genetics, Cell Biology, and Genetics, University of Minnesota, Minneapolis, MN 55455
| | - Jason Sakizadeh
- Department of Genetics, Cell Biology, and Genetics, University of Minnesota, Minneapolis, MN 55455
| | - Jaimee Reck
- Department of Genetics, Cell Biology, and Genetics, University of Minnesota, Minneapolis, MN 55455
| | - Raqual Bower
- Department of Genetics, Cell Biology, and Genetics, University of Minnesota, Minneapolis, MN 55455
| | - Douglas Tritschler
- Department of Genetics, Cell Biology, and Genetics, University of Minnesota, Minneapolis, MN 55455
| | - Long Gui
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Daniela Nicastro
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Mary E. Porter
- Department of Genetics, Cell Biology, and Genetics, University of Minnesota, Minneapolis, MN 55455
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15
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Vergou GA, Bajhaiya AK, Corredor L, Lema Asqui S, Timmerman E, Impens F, Funk C. In vivo proteolytic profiling of the type I and type II metacaspases in Chlamydomonas reinhardtii exposed to salt stress. PHYSIOLOGIA PLANTARUM 2024; 176:e14401. [PMID: 38899462 DOI: 10.1111/ppl.14401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 06/21/2024]
Abstract
Metacaspases are cysteine proteases present in plants, fungi and protists. While the association of metacaspases with cell death is studied in a range of organisms, their native substrates are largely unknown. Here, we explored the in vivo proteolytic landscape of the two metacaspases, CrMCA-I and CrMCA-II, present in the green freshwater alga Chlamydomonas reinhardtii, using mass spectrometry-based degradomics approach, during control conditions and salt stress. Comparison between the cleavage events of CrMCA-I and CrMCA-II in metacaspase mutants revealed unique cleavage preferences and substrate specificity. Degradome analysis demonstrated the relevance of the predicted metacaspase substrates to the physiology of C. reinhardtii cells and its adaptation during salt stress. Functional enrichment analysis indicated an involvement of CrMCA-I in the catabolism of carboxylic acids, while CrMCA-II plays an important role in photosynthesis and translation. Altogether, our findings suggest distinct cellular functions of the two metacaspases in C. reinhardtii during salt stress response.
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Affiliation(s)
| | | | | | | | - Evy Timmerman
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Francis Impens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
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16
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Pazour GJ. Cilia Structure and Function in Human Disease. CURRENT OPINION IN ENDOCRINE AND METABOLIC RESEARCH 2024; 34:100509. [PMID: 38836197 PMCID: PMC11147146 DOI: 10.1016/j.coemr.2024.100509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Ciliary dysfunction causes a large group of developmental and degenerative human diseases known as ciliopathies. These diseases reflect the critical roles that cilia play in sensing the environment and in force generation for motility. Sensory functions include our senses of vision and olfaction. In addition, primary and motile cilia throughout our body monitor the environment allowing cells to coordinate their biology with the cells around them. This coordination is critical to organ development and maintenance, and ciliary dysfunction causes diverse structural birth defects and degenerative diseases. Defects in motility cause lung disease due to the failure of mucociliary clearance, male infertility due to the failure of sperm motility and the ability of sperm to move through the efferent ducts, and disturbances of the left-right axis due to a failure of nodal cilia to establish proper left-right cues.
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Affiliation(s)
- Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Biotech II, Worcester, Massachusetts, USA
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17
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Sakato-Antoku M, Patel-King RS, Balsbaugh JL, King SM. Methylation of ciliary dynein motors involves the essential cytosolic assembly factor DNAAF3/PF22. Proc Natl Acad Sci U S A 2024; 121:e2318522121. [PMID: 38261620 PMCID: PMC10835030 DOI: 10.1073/pnas.2318522121] [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: 10/23/2023] [Accepted: 12/15/2023] [Indexed: 01/25/2024] Open
Abstract
Axonemal dynein motors drive ciliary motility and can consist of up to twenty distinct components with a combined mass of ~2 MDa. In mammals, failure of dyneins to assemble within the axonemal superstructure leads to primary ciliary dyskinesia. Syndromic phenotypes include infertility, rhinitis, severe bronchial conditions, and situs inversus. Nineteen specific cytosolic factors (Dynein Axonemal Assembly Factors; DNAAFs) are necessary for axonemal dynein assembly, although the detailed mechanisms involved remain very unclear. Here, we identify the essential assembly factor DNAAF3 as a structural ortholog of S-adenosylmethionine-dependent methyltransferases. We demonstrate that dynein heavy chains, especially those forming the ciliary outer arms, are methylated on key residues within various nucleotide-binding sites and on microtubule-binding domain helices directly involved in the transition to low binding affinity. These variable modifications, which are generally missing in a Chlamydomonas null mutant for the DNAAF3 ortholog PF22 (DAB1), likely impact on motor mechanochemistry fine-tuning the activities of individual dynein complexes.
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Affiliation(s)
- Miho Sakato-Antoku
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT06030-3305
| | - Ramila S. Patel-King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT06030-3305
| | - Jeremy L. Balsbaugh
- Proteomics and Metabolomics Facility, Center for Open Research Resources & Equipment, University of Connecticut, Storrs, CT06269
| | - Stephen M. King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT06030-3305
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18
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Hwang J, Yanagisawa H, Davis KC, Hunter EL, Fox LA, Jimenez AR, Goodwin RE, Gordon SA, Stuart CDE, Bower R, Porter ME, Dutcher SK, Sale WS, Lechtreck KF, Alford LM. Assembly of FAP93 at the proximal axoneme in Chlamydomonas cilia. Cytoskeleton (Hoboken) 2024. [PMID: 38224153 DOI: 10.1002/cm.21818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 01/16/2024]
Abstract
To identify proteins specific to the proximal ciliary axoneme, we used iTRAQ to compare short (~2 μm) and full-length (~11 μm) axonemes of Chlamydomonas. Known compoents of the proximal axoneme such as minor dynein heavy chains and LF5 kinase as well as the ciliary tip proteins FAP256 (CEP104) and EB1 were enriched in short axonemes whereas proteins present along the length of the axoneme were of similar abundance in both samples. The iTRAQ analysis revealed that FAP93, a protein of unknown function, and protein phosphatase 2A (PP2A) are enriched in the short axonemes. Consistently, immunoblots show enrichment of FAP93 and PP2A in short axonemes and immunofluorescence confirms the localization of FAP93 and enrichment of PP2A at the proximal axoneme. Ciliary regeneration reveals that FAP93 assembles continuously but more slowly than other axonemal structures and terminates at 1.03 μm in steady-state axonemes. The length of FAP93 assembly correlates with ciliary length, demonstrating ciliary length-dependent assembly of FAP93. Dikaryon rescue experiments show that FAP93 can assemble independently of IFT transport. In addition, FRAP analysis of GFP-tagged FAP93 demonstrates that FAP93 is stably anchored in axoneme. FAP93 may function as a scaffold for assembly of other specific proteins at the proximal axoneme.
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Affiliation(s)
- Juyeon Hwang
- Department of Cell Biology, Emory University, Atlanta, Georgia, USA
| | | | - Keira C Davis
- Department of Cell Biology, Emory University, Atlanta, Georgia, USA
- College of Arts & Sciences, Clayton State University, Morrow, Georgia, USA
| | - Emily L Hunter
- Department of Cell Biology, Emory University, Atlanta, Georgia, USA
- Science Communication Group, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Laura A Fox
- Department of Cell Biology, Emory University, Atlanta, Georgia, USA
| | - Ariana R Jimenez
- Division of Natural Sciences, Oglethorpe University, Atlanta, Georgia, USA
| | - Reagan E Goodwin
- Division of Natural Sciences, Oglethorpe University, Atlanta, Georgia, USA
| | - Sarah A Gordon
- Division of Natural Sciences, Oglethorpe University, Atlanta, Georgia, USA
| | | | - Raqual Bower
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Mary E Porter
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Susan K Dutcher
- Department of Genetics, Washington University St. Louis, St. Louis, Missouri, USA
| | - Winfield S Sale
- Department of Cell Biology, Emory University, Atlanta, Georgia, USA
| | - Karl F Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Lea M Alford
- Division of Natural Sciences, Oglethorpe University, Atlanta, Georgia, USA
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19
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Das P, Mekonnen B, Alkhofash R, Ingle AV, Workman EB, Feather A, Zhang G, Chasen N, Liu P, Lechtreck KF. The Small Interactor of PKD2 protein promotes the assembly and ciliary entry of the Chlamydomonas PKD2-mastigoneme complexes. J Cell Sci 2024; 137:jcs261497. [PMID: 38063216 PMCID: PMC10846610 DOI: 10.1242/jcs.261497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 12/04/2023] [Indexed: 01/13/2024] Open
Abstract
In Chlamydomonas, the channel polycystin 2 (PKD2) is primarily present in the distal region of cilia, where it is attached to the axoneme and mastigonemes, extracellular polymers of MST1. In a smaller proximal ciliary region that lacks mastigonemes, PKD2 is more mobile. We show that the PKD2 regions are established early during ciliogenesis and increase proportionally in length as cilia elongate. In chimeric zygotes, tagged PKD2 rapidly entered the proximal region of PKD2-deficient cilia, whereas the assembly of the distal region was hindered, suggesting that axonemal binding of PKD2 requires de novo assembly of cilia. We identified the protein Small Interactor of PKD2 (SIP), a PKD2-related, single-pass transmembrane protein, as part of the PKD2-mastigoneme complex. In sip mutants, stability and proteolytic processing of PKD2 in the cell body were reduced and PKD2-mastigoneme complexes were absent from the cilia. Like the pkd2 and mst1 mutants, sip mutant cells swam with reduced velocity. Cilia of the pkd2 mutant beat with an increased frequency but were less efficient in moving the cells, suggesting a structural role for the PKD2-SIP-mastigoneme complex in increasing the effective surface of Chlamydomonas cilia.
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Affiliation(s)
- Poulomi Das
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Betlehem Mekonnen
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Rama Alkhofash
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Abha V. Ingle
- Department of Computer Science, University of Georgia, Athens, GA 30602, USA
| | - E. Blair Workman
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Alec Feather
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Gui Zhang
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Nathan Chasen
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Peiwei Liu
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Karl F. Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
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20
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Zhao X, Ge H, Xu W, Cheng C, Zhou W, Xu Y, Fan J, Liu Y, Tian X, Xu KF, Zhang X. Lack of CFAP54 causes primary ciliary dyskinesia in a mouse model and human patients. Front Med 2023; 17:1236-1249. [PMID: 37725231 DOI: 10.1007/s11684-023-0997-7] [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: 09/23/2022] [Accepted: 03/06/2023] [Indexed: 09/21/2023]
Abstract
Primary ciliary dyskinesia (PCD) is a highly heterogeneous recessive inherited disorder. FAP54, the homolog of CFAP54 in Chlamydomonas reinhardtii, was previously demonstrated as the C1d projection of the central microtubule apparatus of flagella. A Cfap54 knockout mouse model was then reported to have PCD-relevant phenotypes. Through whole-exome sequencing, compound heterozygous variants c.2649_2657delinC (p. E883Dfs*47) and c.7312_7313insCGCAGGCTGAATTCTTGG (p. T2438delinsTQAEFLA) in a new suspected PCD-relevant gene, CFAP54, were identified in an individual with PCD. Two missense variants, c.4112A>C (p. E1371A) and c.6559C>T (p. P2187S), in CFAP54 were detected in another unrelated patient. In this study, a minigene assay was conducted on the frameshift mutation showing a reduction in mRNA expression. In addition, a CFAP54 in-frame variant knock-in mouse model was established, which recapitulated the typical symptoms of PCD, including hydrocephalus, infertility, and mucus accumulation in nasal sinuses. Correspondingly, two missense variants were deleterious, with a dramatic reduction in mRNA abundance from bronchial tissue and sperm. The identification of PCD-causing variants of CFAP54 in two unrelated patients with PCD for the first time provides strong supportive evidence that CFAP54 is a new PCD-causing gene. This study further helps expand the disease-associated gene spectrum and improve genetic testing for PCD diagnosis in the future.
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Affiliation(s)
- Xinyue Zhao
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Haijun Ge
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Wenshuai Xu
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Chongsheng Cheng
- Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Wangji Zhou
- Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Yan Xu
- Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Junping Fan
- Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Yaping Liu
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
| | - Xinlun Tian
- Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.
| | - Kai-Feng Xu
- Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
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21
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Deretic J, Odabasi E, Firat-Karalar EN. The multifaceted roles of microtubule-associated proteins in the primary cilium and ciliopathies. J Cell Sci 2023; 136:jcs261148. [PMID: 38095645 DOI: 10.1242/jcs.261148] [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: 12/18/2023] Open
Abstract
The primary cilium is a conserved microtubule-based organelle that is critical for transducing developmental, sensory and homeostatic signaling pathways. It comprises an axoneme with nine parallel doublet microtubules extending from the basal body, surrounded by the ciliary membrane. The axoneme exhibits remarkable stability, serving as the skeleton of the cilium in order to maintain its shape and provide tracks to ciliary trafficking complexes. Although ciliary trafficking and signaling have been exhaustively characterized over the years, less is known about the unique structural and functional complexities of the axoneme. Recent work has yielded new insights into the mechanisms by which the axoneme is built with its proper length and architecture, particularly regarding the activity of microtubule-associated proteins (MAPs). In this Review, we first summarize current knowledge about the architecture, composition and specialized compartments of the primary cilium. Next, we discuss the mechanistic underpinnings of how a functional cilium is assembled, maintained and disassembled through the regulation of its axonemal microtubules. We conclude by examining the diverse localizations and functions of ciliary MAPs for the pathobiology of ciliary diseases.
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Affiliation(s)
- Jovana Deretic
- Department of Molecular Biology and Genetics, Koç University, Istanbul 34450, Turkey
| | - Ezgi Odabasi
- Department of Molecular Biology and Genetics, Koç University, Istanbul 34450, Turkey
| | - Elif Nur Firat-Karalar
- Department of Molecular Biology and Genetics, Koç University, Istanbul 34450, Turkey
- School of Medicine, Koç University, Istanbul 34450, Turkey
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22
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Kruczek K, Swaroop A. Patient stem cell-derived in vitro disease models for developing novel therapies of retinal ciliopathies. Curr Top Dev Biol 2023; 155:127-163. [PMID: 38043950 DOI: 10.1016/bs.ctdb.2023.09.003] [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: 12/05/2023]
Abstract
Primary cilia are specialized organelles on the surface of almost all cells in vertebrate tissues and are primarily involved in the detection of extracellular stimuli. In retinal photoreceptors, cilia are uniquely modified to form outer segments containing components required for the detection of light in stacks of membrane discs. Not surprisingly, vision impairment is a frequent phenotype associated with ciliopathies, a heterogeneous class of conditions caused by mutations in proteins required for formation, maintenance and/or function of primary cilia. Traditionally, immortalized cell lines and model organisms have been used to provide insights into the biology of ciliopathies. The advent of methods for reprogramming human somatic cells into pluripotent stem cells has enabled the generation of in vitro disease models directly from patients suffering from ciliopathies. Such models help us in investigating pathological mechanisms specific to human physiology and in developing novel therapeutic approaches. In this article, we review current protocols to differentiate human pluripotent stem cells into retinal cell types, and discuss how these cellular and/or organoid models can be utilized to interrogate pathobiology of ciliopathies affecting the retina and for testing prospective treatments.
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Affiliation(s)
- Kamil Kruczek
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, United States.
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, United States.
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23
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Gopalakrishnan J, Feistel K, Friedrich BM, Grapin‐Botton A, Jurisch‐Yaksi N, Mass E, Mick DU, Müller R, May‐Simera H, Schermer B, Schmidts M, Walentek P, Wachten D. Emerging principles of primary cilia dynamics in controlling tissue organization and function. EMBO J 2023; 42:e113891. [PMID: 37743763 PMCID: PMC10620770 DOI: 10.15252/embj.2023113891] [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: 02/27/2023] [Revised: 08/07/2023] [Accepted: 09/08/2023] [Indexed: 09/26/2023] Open
Abstract
Primary cilia project from the surface of most vertebrate cells and are key in sensing extracellular signals and locally transducing this information into a cellular response. Recent findings show that primary cilia are not merely static organelles with a distinct lipid and protein composition. Instead, the function of primary cilia relies on the dynamic composition of molecules within the cilium, the context-dependent sensing and processing of extracellular stimuli, and cycles of assembly and disassembly in a cell- and tissue-specific manner. Thereby, primary cilia dynamically integrate different cellular inputs and control cell fate and function during tissue development. Here, we review the recently emerging concept of primary cilia dynamics in tissue development, organization, remodeling, and function.
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Affiliation(s)
- Jay Gopalakrishnan
- Institute for Human Genetics, Heinrich‐Heine‐UniversitätUniversitätsklinikum DüsseldorfDüsseldorfGermany
| | - Kerstin Feistel
- Department of Zoology, Institute of BiologyUniversity of HohenheimStuttgartGermany
| | | | - Anne Grapin‐Botton
- Cluster of Excellence Physics of Life, TU DresdenDresdenGermany
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Paul Langerhans Institute Dresden of the Helmholtz Center Munich at The University Hospital Carl Gustav Carus and Faculty of Medicine of the TU DresdenDresdenGermany
| | - Nathalie Jurisch‐Yaksi
- Department of Clinical and Molecular MedicineNorwegian University of Science and TechnologyTrondheimNorway
| | - Elvira Mass
- Life and Medical Sciences Institute, Developmental Biology of the Immune SystemUniversity of BonnBonnGermany
| | - David U Mick
- Center for Molecular Signaling (PZMS), Center of Human and Molecular Biology (ZHMB)Saarland School of MedicineHomburgGermany
| | - Roman‐Ulrich Müller
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Helen May‐Simera
- Institute of Molecular PhysiologyJohannes Gutenberg‐UniversityMainzGermany
| | - Bernhard Schermer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Miriam Schmidts
- Pediatric Genetics Division, Center for Pediatrics and Adolescent MedicineUniversity Hospital FreiburgFreiburgGermany
- CIBSS‐Centre for Integrative Biological Signalling StudiesUniversity of FreiburgFreiburgGermany
| | - Peter Walentek
- CIBSS‐Centre for Integrative Biological Signalling StudiesUniversity of FreiburgFreiburgGermany
- Renal Division, Internal Medicine IV, Medical CenterUniversity of FreiburgFreiburgGermany
| | - Dagmar Wachten
- Institute of Innate Immunity, Biophysical Imaging, Medical FacultyUniversity of BonnBonnGermany
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24
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Balasubramanian RN, Gao M, Umen J. Identification of cell-type specific alternative transcripts in the multicellular alga Volvox carteri. BMC Genomics 2023; 24:654. [PMID: 37904088 PMCID: PMC10617192 DOI: 10.1186/s12864-023-09558-0] [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: 03/09/2023] [Accepted: 08/06/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND Cell type specialization is a hallmark of complex multicellular organisms and is usually established through implementation of cell-type-specific gene expression programs. The multicellular green alga Volvox carteri has just two cell types, germ and soma, that have previously been shown to have very different transcriptome compositions which match their specialized roles. Here we interrogated another potential mechanism for differentiation in V. carteri, cell type specific alternative transcript isoforms (CTSAI). METHODS We used pre-existing predictions of alternative transcripts and de novo transcript assembly with HISAT2 and Ballgown software to compile a list of loci with two or more transcript isoforms, identified a small subset that were candidates for CTSAI, and manually curated this subset of genes to remove false positives. We experimentally verified three candidates using semi-quantitative RT-PCR to assess relative isoform abundance in each cell type. RESULTS Of the 1978 loci with two or more predicted transcript isoforms 67 of these also showed cell type isoform expression biases. After curation 15 strong candidates for CTSAI were identified, three of which were experimentally verified, and their predicted gene product functions were evaluated in light of potential cell type specific roles. A comparison of genes with predicted alternative splicing from Chlamydomonas reinhardtii, a unicellular relative of V. carteri, identified little overlap between ortholog pairs with alternative splicing in both species. Finally, we interrogated cell type expression patterns of 126 V. carteri predicted RNA binding protein (RBP) encoding genes and found 40 that showed either somatic or germ cell expression bias. These RBPs are potential mediators of CTSAI in V. carteri and suggest possible pre-adaptation for cell type specific RNA processing and a potential path for generating CTSAI in the early ancestors of metazoans and plants. CONCLUSIONS We predicted numerous instances of alternative transcript isoforms in Volvox, only a small subset of which showed cell type specific isoform expression bias. However, the validated examples of CTSAI supported existing hypotheses about cell type specialization in V. carteri, and also suggested new hypotheses about mechanisms of functional specialization for their gene products. Our data imply that CTSAI operates as a minor but important component of V. carteri cellular differentiation and could be used as a model for how alternative isoforms emerge and co-evolve with cell type specialization.
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Affiliation(s)
| | - Minglu Gao
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - James Umen
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
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25
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Kondo Y, Ogawa T, Kanno E, Hirono M, Kato-Minoura T, Kamiya R, Yagi T. IC2 participates in the cooperative activation of outer arm dynein densely attached to microtubules. Cell Struct Funct 2023; 48:175-185. [PMID: 37518064 DOI: 10.1247/csf.23044] [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: 08/01/2023] Open
Abstract
Ciliary outer-arm dynein (OAD) consists of heavy chains (HCs), intermediate chains (ICs), and light chains (LCs), of which HCs are the motor proteins that produce force. Studies using the green alga Chlamydomonas have revealed that ICs and LCs form a complex (IC/LC tower) at the base of the OAD tail and play a crucial role in anchoring OAD to specific sites on the microtubule. In this study, we isolated a novel slow-swimming Chlamydomonas mutant deficient in the IC2 protein. This mutation, E279K, is in the third of the seven WD repeat domains. No apparent abnormality was observed in electron microscope observations of axonemes or in SDS-PAGE analyses of dynein subunits. To explore the reason for the lowered motility in this mutant, in vitro microtubule sliding experiments were performed, which revealed that the motor activity of the mutant OAD was lowered. In particular, a large difference was observed between wild type (WT) and the mutant in the microtubule sliding velocity in microtubule bundles formed with the addition of OAD: ~35.3 μm/sec (WT) and ~4.3 μm/sec (mutant). From this and other results, we propose that IC2 in an OAD interacts with the β HC of the adjacent OAD, and that an OAD-OAD interaction is important for efficient beating of cilia and flagella.Key words: cilia, axoneme, dynein heavy chain, cooperativity.
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Affiliation(s)
- Yusuke Kondo
- Department of Life and Environmental Sciences, Faculty of Bioresource Sciences, Prefectural University of Hiroshima
| | - Tomoka Ogawa
- Department of Life and Environmental Sciences, Faculty of Bioresource Sciences, Prefectural University of Hiroshima
| | - Emiri Kanno
- Department of Biological Sciences, Chuo University
| | | | | | - Ritsu Kamiya
- Department of Biological Sciences, Chuo University
| | - Toshiki Yagi
- Department of Life and Environmental Sciences, Faculty of Bioresource Sciences, Prefectural University of Hiroshima
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26
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Chinipardaz Z, Yuan G, Liu M, Graves DT, Yang S. Diabetes impairs fracture healing through Foxo1 mediated disruption of ciliogenesis. Cell Death Discov 2023; 9:299. [PMID: 37591875 PMCID: PMC10435563 DOI: 10.1038/s41420-023-01562-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/12/2023] [Accepted: 07/17/2023] [Indexed: 08/19/2023] Open
Abstract
Foxo1 upregulation is linked to defective fracture healing under diabetic conditions. Previous studies demonstrated that diabetes upregulates Foxo1 expression and activation and diabetes impairs ciliogenesis resulting in defective fracture repair. However, the mechanism by which diabetes causes cilia loss during fracture healing remains elusive. We report here that streptozotocin (STZ)-induced type 1 diabetes mellitus (T1DM) dramatically increased Foxo1 expression in femoral fracture calluses, which thereby caused a significant decrease in the expression of IFT80 and primary cilia number. Ablation of Foxo1 in osteoblasts in OSXcretTAFoxo1f/f mice rescued IFT80 expression and ciliogenesis and restored bone formation and mechanical strength in diabetic fracture calluses. In vitro, advanced glycation end products (AGEs) impaired cilia formation in osteoblasts and reduced the production of a mineralizing matrix, which were rescued by Foxo1 deletion. Mechanistically, AGEs increased Foxo1 expression and transcriptional activity to inhibit IFT80 expression causing impaired cilia formation. Thus, our findings demonstrate that diabetes impairs fracture healing through Foxo1 mediated inhibition of ciliary IFT80 expression and primary cilia formation, resulting in impaired osteogenesis. Inhibition of Foxo1 and/or restoration of cilia formation has the potential to promote diabetes-impaired fracture healing.
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Affiliation(s)
- Zahra Chinipardaz
- Department of Basic and Translation Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Periodontology, Tufts University School of Dental Medicine, Boston, MA, 02111, USA
| | - Gongsheng Yuan
- Department of Basic and Translation Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Min Liu
- Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Dana T Graves
- Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Shuying Yang
- Department of Basic and Translation Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Center for Innovation & Precision Dentistry, School of Dental Medicine, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- The Penn Center for Musculoskeletal Disorders, School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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27
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Dobbelaere J, Su TY, Erdi B, Schleiffer A, Dammermann A. A phylogenetic profiling approach identifies novel ciliogenesis genes in Drosophila and C. elegans. EMBO J 2023; 42:e113616. [PMID: 37317646 PMCID: PMC10425847 DOI: 10.15252/embj.2023113616] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 05/22/2023] [Accepted: 06/01/2023] [Indexed: 06/16/2023] Open
Abstract
Cilia are cellular projections that perform sensory and motile functions in eukaryotic cells. A defining feature of cilia is that they are evolutionarily ancient, yet not universally conserved. In this study, we have used the resulting presence and absence pattern in the genomes of diverse eukaryotes to identify a set of 386 human genes associated with cilium assembly or motility. Comprehensive tissue-specific RNAi in Drosophila and mutant analysis in C. elegans revealed signature ciliary defects for 70-80% of novel genes, a percentage similar to that for known genes within the cluster. Further characterization identified different phenotypic classes, including a set of genes related to the cartwheel component Bld10/CEP135 and two highly conserved regulators of cilium biogenesis. We propose this dataset defines the core set of genes required for cilium assembly and motility across eukaryotes and presents a valuable resource for future studies of cilium biology and associated disorders.
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Affiliation(s)
- Jeroen Dobbelaere
- Max Perutz LabsUniversity of Vienna, Vienna Biocenter (VBC)ViennaAustria
| | - Tiffany Y Su
- Max Perutz LabsUniversity of Vienna, Vienna Biocenter (VBC)ViennaAustria
- Vienna BioCenter PhD ProgramDoctoral School of the University of Vienna and Medical University of ViennaViennaAustria
| | - Balazs Erdi
- Max Perutz LabsUniversity of Vienna, Vienna Biocenter (VBC)ViennaAustria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology, Vienna Biocenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC)ViennaAustria
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28
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Wang L, Patena W, Van Baalen KA, Xie Y, Singer ER, Gavrilenko S, Warren-Williams M, Han L, Harrigan HR, Hartz LD, Chen V, Ton VTNP, Kyin S, Shwe HH, Cahn MH, Wilson AT, Onishi M, Hu J, Schnell DJ, McWhite CD, Jonikas MC. A chloroplast protein atlas reveals punctate structures and spatial organization of biosynthetic pathways. Cell 2023; 186:3499-3518.e14. [PMID: 37437571 DOI: 10.1016/j.cell.2023.06.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 05/06/2023] [Accepted: 06/11/2023] [Indexed: 07/14/2023]
Abstract
Chloroplasts are eukaryotic photosynthetic organelles that drive the global carbon cycle. Despite their importance, our understanding of their protein composition, function, and spatial organization remains limited. Here, we determined the localizations of 1,034 candidate chloroplast proteins using fluorescent protein tagging in the model alga Chlamydomonas reinhardtii. The localizations provide insights into the functions of poorly characterized proteins; identify novel components of nucleoids, plastoglobules, and the pyrenoid; and reveal widespread protein targeting to multiple compartments. We discovered and further characterized cellular organizational features, including eleven chloroplast punctate structures, cytosolic crescent structures, and unexpected spatial distributions of enzymes within the chloroplast. We also used machine learning to predict the localizations of other nuclear-encoded Chlamydomonas proteins. The strains and localization atlas developed here will serve as a resource to accelerate studies of chloroplast architecture and functions.
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Affiliation(s)
- Lianyong Wang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Weronika Patena
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Kelly A Van Baalen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Yihua Xie
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Emily R Singer
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sophia Gavrilenko
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | | | - Linqu Han
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI 48824, USA
| | - Henry R Harrigan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Linnea D Hartz
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Vivian Chen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Vinh T N P Ton
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Saw Kyin
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Henry H Shwe
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Matthew H Cahn
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Alexandra T Wilson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Masayuki Onishi
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Jianping Hu
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI 48824, USA
| | - Danny J Schnell
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Claire D McWhite
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA.
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29
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Kreutzberger MAB, Cvirkaite-Krupovic V, Liu Y, Baquero DP, Liu J, Sonani RR, Calladine CR, Wang F, Krupovic M, Egelman EH. The evolution of archaeal flagellar filaments. Proc Natl Acad Sci U S A 2023; 120:e2304256120. [PMID: 37399404 PMCID: PMC10334743 DOI: 10.1073/pnas.2304256120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/08/2023] [Indexed: 07/05/2023] Open
Abstract
Flagellar motility has independently arisen three times during evolution: in bacteria, archaea, and eukaryotes. In prokaryotes, the supercoiled flagellar filaments are composed largely of a single protein, bacterial or archaeal flagellin, although these two proteins are not homologous, while in eukaryotes, the flagellum contains hundreds of proteins. Archaeal flagellin and archaeal type IV pilin are homologous, but how archaeal flagellar filaments (AFFs) and archaeal type IV pili (AT4Ps) diverged is not understood, in part, due to the paucity of structures for AFFs and AT4Ps. Despite having similar structures, AFFs supercoil, while AT4Ps do not, and supercoiling is essential for the function of AFFs. We used cryo-electron microscopy to determine the atomic structure of two additional AT4Ps and reanalyzed previous structures. We find that all AFFs have a prominent 10-strand packing, while AT4Ps show a striking structural diversity in their subunit packing. A clear distinction between all AFF and all AT4P structures involves the extension of the N-terminal α-helix with polar residues in the AFFs. Additionally, we characterize a flagellar-like AT4P from Pyrobaculum calidifontis with filament and subunit structure similar to that of AFFs which can be viewed as an evolutionary link, showing how the structural diversity of AT4Ps likely allowed for an AT4P to evolve into a supercoiling AFF.
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Affiliation(s)
- Mark A. B. Kreutzberger
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA22903
| | | | - Ying Liu
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris75015, France
| | - Diana P. Baquero
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris75015, France
| | - Junfeng Liu
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris75015, France
| | - Ravi R. Sonani
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA22903
| | - Chris R. Calladine
- Department of Engineering, University of Cambridge, CambridgeCB2 1PZ, United Kingdom
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA22903
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris75015, France
| | - Edward H. Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA22903
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30
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Das P, Mekonnen B, Alkhofash R, Ingle A, Workman EB, Feather A, Liu P, Lechtreck KF. Small Interactor of PKD2 (SIP), a novel PKD2-related single-pass transmembrane protein, is required for proteolytic processing and ciliary import of Chlamydomonas PKD2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544839. [PMID: 37398320 PMCID: PMC10312728 DOI: 10.1101/2023.06.13.544839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
In Chlamydomonas cilia, the ciliopathy-relevant TRP channel PKD2 is spatially compartmentalized into a distal region, in which PKD2 binds the axoneme and extracellular mastigonemes, and a smaller proximal region, in which PKD2 is more mobile and lacks mastigonemes. Here, we show that the two PKD2 regions are established early during cilia regeneration and increase in length as cilia elongate. In abnormally long cilia, only the distal region elongated whereas both regions adjusted in length during cilia shortening. In dikaryon rescue experiments, tagged PKD2 rapidly entered the proximal region of PKD2-deficient cilia whereas assembly of the distal region was hindered, suggesting that axonemal docking of PKD2 requires de novo ciliary assembly. We identified Small Interactor of PKD2 (SIP), a small PKD2-related protein, as a novel component of the PKD2-mastigoneme complex. In sip mutants, stability and proteolytic processing of PKD2 in the cell body were reduced and PKD2-mastigoneme complexes were absent from mutant cilia. Like the pkd2 and mst1 mutants, sip swims with reduced velocity. Cilia of the pkd2 mutant beat with normal frequency and bending pattern but were less efficient in moving cells supporting a passive role of the PKD2-SIP-mastigoneme complexes in increasing the effective surface of Chlamydomonas cilia.
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Affiliation(s)
- Poulomi Das
- Department of Cellular Biology, University of Georgia, Athens, GA 30602
| | - Betlehem Mekonnen
- Department of Cellular Biology, University of Georgia, Athens, GA 30602
| | - Rama Alkhofash
- Department of Cellular Biology, University of Georgia, Athens, GA 30602
| | - Abha Ingle
- Department of Computer Science, University of Georgia, Athens, GA 30602
| | - E. Blair Workman
- Department of Cellular Biology, University of Georgia, Athens, GA 30602
| | - Alec Feather
- Department of Cellular Biology, University of Georgia, Athens, GA 30602
| | | | - Karl F. Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, GA 30602
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31
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Walton T, Gui M, Velkova S, Fassad MR, Hirst RA, Haarman E, O'Callaghan C, Bottier M, Burgoyne T, Mitchison HM, Brown A. Axonemal structures reveal mechanoregulatory and disease mechanisms. Nature 2023; 618:625-633. [PMID: 37258679 PMCID: PMC10266980 DOI: 10.1038/s41586-023-06140-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 04/27/2023] [Indexed: 06/02/2023]
Abstract
Motile cilia and flagella beat rhythmically on the surface of cells to power the flow of fluid and to enable spermatozoa and unicellular eukaryotes to swim. In humans, defective ciliary motility can lead to male infertility and a congenital disorder called primary ciliary dyskinesia (PCD), in which impaired clearance of mucus by the cilia causes chronic respiratory infections1. Ciliary movement is generated by the axoneme, a molecular machine consisting of microtubules, ATP-powered dynein motors and regulatory complexes2. The size and complexity of the axoneme has so far prevented the development of an atomic model, hindering efforts to understand how it functions. Here we capitalize on recent developments in artificial intelligence-enabled structure prediction and cryo-electron microscopy (cryo-EM) to determine the structure of the 96-nm modular repeats of axonemes from the flagella of the alga Chlamydomonas reinhardtii and human respiratory cilia. Our atomic models provide insights into the conservation and specialization of axonemes, the interconnectivity between dyneins and their regulators, and the mechanisms that maintain axonemal periodicity. Correlated conformational changes in mechanoregulatory complexes with their associated axonemal dynein motors provide a mechanism for the long-hypothesized mechanotransduction pathway to regulate ciliary motility. Structures of respiratory-cilia doublet microtubules from four individuals with PCD reveal how the loss of individual docking factors can selectively eradicate periodically repeating structures.
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Affiliation(s)
- Travis Walton
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Miao Gui
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Simona Velkova
- Genetics and Genomic Medicine Department, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Mahmoud R Fassad
- Genetics and Genomic Medicine Department, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Robert A Hirst
- Centre for PCD Diagnosis and Research, Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Eric Haarman
- Department of Pediatric Respiratory Medicine and Allergy, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Christopher O'Callaghan
- Infection, Immunity & Inflammation Department, NIHR GOSH BRC, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Mathieu Bottier
- Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Thomas Burgoyne
- Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
- Institute of Ophthalmology, University College London, London, UK
| | - Hannah M Mitchison
- Genetics and Genomic Medicine Department, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Alan Brown
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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32
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Wu B, Li R, Ma S, Ma Y, Fan L, Gong C, Liu C, Sun L, Yuan L. The cilia and flagella associated protein CFAP52 orchestrated with CFAP45 is required for sperm motility in mice. J Biol Chem 2023:104858. [PMID: 37236356 PMCID: PMC10319328 DOI: 10.1016/j.jbc.2023.104858] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Asthenozoospermia characterized by decreased sperm motility is a major cause of male infertility, but the majority of their etiology remains unknown. Here, we showed that the cilia and flagella associated protein 52 (Cfap52) gene was predominantly expressed in testis and its deletion in a Cfap52 knockout mouse model resulted in decreased sperm motility and male infertility. Cfap52 knockout also led to the disorganization of midpiece-principal piece junction of the sperm tail, but had no effect on the axoneme ultrastructure in spermatozoa. Furthermore, we found that CFAP52 interacted with the cilia and flagella associated protein 45 (CFAP45), and knockout of Cfap52 decreased the expression level of CFAP45 in sperm flagellum, which further disrupted the microtubule sliding produced by dynein ATPase. Together, our studies demonstrate that CFAP52 plays an essential role in sperm motility by interacting with CFAP45 in sperm flagellum, providing insights into the potential pathogenesis of the infertility of the human CFAP52 mutations.
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Affiliation(s)
- Bingbing Wu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623 Guangzhou, China; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Rachel Li
- Beijing Academy International Division, Beijing, 100018, China
| | - Shuang Ma
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623 Guangzhou, China; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yanjie Ma
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623 Guangzhou, China; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Lijun Fan
- Department of Endocrinology, Genetics, Metabolism, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Chunxiu Gong
- Department of Endocrinology, Genetics, Metabolism, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Chao Liu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623 Guangzhou, China
| | - Ling Sun
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623 Guangzhou, China.
| | - Li Yuan
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China.
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33
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Ewerling A, Maissl V, Wickstead B, May-Simera HL. Neofunctionalization of ciliary BBS proteins to nuclear roles is likely a frequent innovation across eukaryotes. iScience 2023; 26:106410. [PMID: 37034981 PMCID: PMC10074162 DOI: 10.1016/j.isci.2023.106410] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/20/2022] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
The eukaryotic BBSome is a transport complex within cilia and assembled by chaperonin-like BBS proteins. Recent work indicates nuclear functions for BBS proteins in mammals, but it is unclear how common these are in extant proteins or when they evolved. We screened for BBS orthologues across a diverse set of eukaryotes, consolidated nuclear association via signal sequence predictions and permutation analysis, and validated nuclear localization in mammalian cells via fractionation and immunocytochemistry. BBS proteins are-with exceptions-conserved as a set in ciliated species. Predictions highlight five most likely nuclear proteins and suggest that nuclear roles evolved independently of nuclear access during mitosis. Nuclear localization was confirmed in human cells. These findings suggest that nuclear BBS functions are potentially not restricted to mammals, but may be a common frequently co-opted eukaryotic feature. Understanding the functional spectrum of BBS proteins will help elucidating their role in gene regulation, development, and disease.
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Affiliation(s)
- Alexander Ewerling
- Institute of Molecular Physiology, Faculty of Biology, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Vanessa Maissl
- Institute of Molecular Physiology, Faculty of Biology, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Bill Wickstead
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Helen Louise May-Simera
- Institute of Molecular Physiology, Faculty of Biology, Johannes Gutenberg-University Mainz, Mainz, Germany
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34
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Zimmermann N, Noga A, Obbineni JM, Ishikawa T. ATP-induced conformational change of axonemal outer dynein arms revealed by cryo-electron tomography. EMBO J 2023:e112466. [PMID: 37051721 DOI: 10.15252/embj.2022112466] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 03/08/2023] [Accepted: 03/16/2023] [Indexed: 04/14/2023] Open
Abstract
Axonemal outer dynein arm (ODA) motors generate force for ciliary beating. We analyzed three states of the ODA during the power stroke cycle using in situ cryo-electron tomography, subtomogram averaging, and classification. These states of force generation depict the prepower stroke, postpower stroke, and intermediate state conformations. Comparison of these conformations to published in vitro atomic structures of cytoplasmic dynein, ODA, and the Shulin-ODA complex revealed differences in the orientation and position of the dynein head. Our analysis shows that in the absence of ATP, all dynein linkers interact with the AAA3/AAA4 domains, indicating that interactions with the adjacent microtubule doublet B-tubule direct dynein orientation. For the prepower stroke conformation, there were changes in the tail that is anchored on the A-tubule. We built models starting with available high-resolution structures to generate a best-fitting model structure for the in situ pre- and postpower stroke ODA conformations, thereby showing that ODA in a complex with Shulin adopts a similar conformation as the active prepower stroke ODA in the axoneme.
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Affiliation(s)
- Noemi Zimmermann
- Paul Scherrer Institut (PSI), Laboratory of Nanoscale Biology, Villigen PSI, Switzerland
| | - Akira Noga
- Paul Scherrer Institut (PSI), Laboratory of Nanoscale Biology, Villigen PSI, Switzerland
| | - Jagan Mohan Obbineni
- Paul Scherrer Institut (PSI), Laboratory of Nanoscale Biology, Villigen PSI, Switzerland
- VIT School for Agricultural Innovations and Advanced, Learning (VAIAL), VIT, Vellore, India
| | - Takashi Ishikawa
- Paul Scherrer Institut (PSI), Laboratory of Nanoscale Biology, Villigen PSI, Switzerland
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35
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Kupriyanova EV, Pronina NA, Los DA. Adapting from Low to High: An Update to CO 2-Concentrating Mechanisms of Cyanobacteria and Microalgae. PLANTS (BASEL, SWITZERLAND) 2023; 12:1569. [PMID: 37050194 PMCID: PMC10096703 DOI: 10.3390/plants12071569] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
The intracellular accumulation of inorganic carbon (Ci) by microalgae and cyanobacteria under ambient atmospheric CO2 levels was first documented in the 80s of the 20th Century. Hence, a third variety of the CO2-concentrating mechanism (CCM), acting in aquatic photoautotrophs with the C3 photosynthetic pathway, was revealed in addition to the then-known schemes of CCM, functioning in CAM and C4 higher plants. Despite the low affinity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) of microalgae and cyanobacteria for the CO2 substrate and low CO2/O2 specificity, CCM allows them to perform efficient CO2 fixation in the reductive pentose phosphate (RPP) cycle. CCM is based on the coordinated operation of strategically located carbonic anhydrases and CO2/HCO3- uptake systems. This cooperation enables the intracellular accumulation of HCO3-, which is then employed to generate a high concentration of CO2 molecules in the vicinity of Rubisco's active centers compensating up for the shortcomings of enzyme features. CCM functions as an add-on to the RPP cycle while also acting as an important regulatory link in the interaction of dark and light reactions of photosynthesis. This review summarizes recent advances in the study of CCM molecular and cellular organization in microalgae and cyanobacteria, as well as the fundamental principles of its functioning and regulation.
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36
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Liu YX, Li WJ, Zhang RK, Sun SN, Fan ZC. Unraveling the intricate cargo-BBSome coupling mechanism at the ciliary tip. Proc Natl Acad Sci U S A 2023; 120:e2218819120. [PMID: 36943875 PMCID: PMC10068815 DOI: 10.1073/pnas.2218819120] [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: 11/03/2022] [Accepted: 02/13/2023] [Indexed: 03/23/2023] Open
Abstract
Certain ciliary transmembrane and membrane-tethered signaling proteins migrate from the ciliary tip to base via retrograde intraflagellar transport (IFT), essential for maintaining their ciliary dynamics to enable cells to sense and transduce extracellular stimuli inside the cell. During this process, the BBSome functions as an adaptor between retrograde IFT trains and these signaling protein cargoes. The Arf-like 13 (ARL13) small GTPase resembles ARL6/BBS3 in facilitating these signaling cargoes to couple with the BBSome at the ciliary tip prior to loading onto retrograde IFT trains for transporting towards the ciliary base, while the molecular basis for how this intricate coupling event happens remains elusive. Here, we report that Chlamydomonas ARL13 only in a GTP-bound form (ARL13GTP) anchors to the membrane for diffusing into cilia. Upon entering cilia, ARL13 undergoes GTPase cycle for shuttling between the ciliary membrane (ARL13GTP) and matrix (ARL13GDP). To achieve this goal, the ciliary membrane-anchored BBS3GTP binds the ciliary matrix-residing ARL13GDP to activate the latter as an ARL13 guanine nucleotide exchange factor. At the ciliary tip, ARL13GTP recruits the ciliary matrix-residing and post-remodeled BBSome as an ARL13 effector to anchor to the ciliary membrane. This makes the BBSome spatiotemporally become available for the ciliary membrane-tethered phospholipase D (PLD) to couple with. Afterward, ARL13GTP hydrolyzes GTP for releasing the PLD-laden BBSome to load onto retrograde IFT trains. According to this model, hedgehog signaling defects associated with ARL13b and BBS3 mutations in humans could be satisfactorily explained, providing us a mechanistic understanding behind BBSome-cargo coupling required for proper ciliary signaling.
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Affiliation(s)
- Yan-Xia Liu
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin300457, China
| | - Wen-Juan Li
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin300457, China
| | - Rui-Kai Zhang
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin300457, China
| | - Sheng-Nan Sun
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin300457, China
| | - Zhen-Chuan Fan
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin300457, China
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37
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Hou Y, Bando Y, Carrasco Flores D, Hotter V, Das R, Schiweck B, Melzer T, Arndt HD, Mittag M. A cyclic lipopeptide produced by an antagonistic bacterium relies on its tail and transient receptor potential-type Ca 2+ channels to immobilize a green alga. THE NEW PHYTOLOGIST 2023; 237:1620-1635. [PMID: 36464797 DOI: 10.1111/nph.18658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
The antagonistic bacterium Pseudomonas protegens secretes the cyclic lipopeptide (CLiP) orfamide A, which triggers a Ca2+ signal causing rapid deflagellation of the microalga Chlamydomonas reinhardtii. We performed chemical synthesis of orfamide A derivatives and used an aequorin reporter line to measure their Ca2+ responses. Immobilization of algae was studied using a modulator and mutants of transient receptor potential (TRP)-type channels. By investigating targeted synthetic orfamide A derivatives, we found that N-terminal amino acids of the linear part and the terminal fatty acid region are important for the specificity of the Ca2+ -signal causing deflagellation. Molecular editing indicates that at least two distinct Ca2+ -signaling pathways are triggered. One is involved in deflagellation (Thr3 change, fatty acid tail shortened by 4C), whereas the other still causes an increase in cytosolic Ca2+ in the algal cells, but does not cause substantial deflagellation (Leu1 change, fatty acid hydroxylation, fatty acid changes by 2C). Using mutants, we define four TRP-type channels that are involved in orfamide A signaling; only one (ADF1) responds additionally to low pH. These results suggest that the linear part of the CLiP plays one major role in Ca2+ signaling, and that orfamide A uses a network of algal TRP-type channels for deflagellation.
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Affiliation(s)
- Yu Hou
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Yuko Bando
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - David Carrasco Flores
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Vivien Hotter
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Ritam Das
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Bastian Schiweck
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Tommy Melzer
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Hans-Dieter Arndt
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743, Jena, Germany
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38
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Using the Culex pipiens sperm proteome to identify elements essential for mosquito reproduction. PLoS One 2023; 18:e0280013. [PMID: 36795667 PMCID: PMC9934393 DOI: 10.1371/journal.pone.0280013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 12/19/2022] [Indexed: 02/17/2023] Open
Abstract
Mature sperm from Culex pipiens were isolated and analyzed by mass spectrometry to generate a mature sperm proteome dataset. In this study, we highlight subsets of proteins related to flagellar structure and sperm motility and compare the identified protein components to previous studies examining essential functions of sperm. The proteome includes 1700 unique protein IDs, including a number of uncharacterized proteins. Here we discuss those proteins that may contribute to the unusual structure of the Culex sperm flagellum, as well as potential regulators of calcium mobilization and phosphorylation pathways that regulate motility. This database will prove useful for understanding the mechanisms that activate and maintain sperm motility as well as identify potential molecular targets for mosquito population control.
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39
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Ishikawa H, Moore J, Diener DR, Delling M, Marshall WF. Testing the ion-current model for flagellar length sensing and IFT regulation. eLife 2023; 12:e82901. [PMID: 36637158 PMCID: PMC9891718 DOI: 10.7554/elife.82901] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 01/12/2023] [Indexed: 01/14/2023] Open
Abstract
Eukaryotic cilia and flagella are microtubule-based organelles whose relatively simple shape makes them ideal for investigating the fundamental question of organelle size regulation. Most of the flagellar materials are transported from the cell body via an active transport process called intraflagellar transport (IFT). The rate of IFT entry into flagella, known as IFT injection, has been shown to negatively correlate with flagellar length. However, it remains unknown how the cell measures the length of its flagella and controls IFT injection. One of the most-discussed theoretical models for length sensing to control IFT is the ion-current model, which posits that there is a uniform distribution of Ca2+ channels along the flagellum and that the Ca2+ current from the flagellum into the cell body increases linearly with flagellar length. In this model, the cell uses the Ca2+ current to negatively regulate IFT injection. The recent discovery that IFT entry into flagella is regulated by the phosphorylation of kinesin through a calcium-dependent protein kinase has provided further impetus for the ion-current model. To test this model, we measured and manipulated the levels of Ca2+ inside of Chlamydomonas flagella and quantified IFT injection. Although the concentration of Ca2+ inside of flagella was weakly correlated with the length of flagella, we found that IFT injection was reduced in calcium-deficient flagella, rather than increased as the model predicted, and that variation in IFT injection was uncorrelated with the occurrence of flagellar Ca2+ spikes. Thus, Ca2+ does not appear to function as a negative regulator of IFT injection, hence it cannot form the basis of a stable length control system.
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Affiliation(s)
- Hiroaki Ishikawa
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Jeremy Moore
- Kenyon College, Gambier, and Summer Research Training Program at University of California San FranciscoSan FranciscoUnited States
| | - Dennis R Diener
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Markus Delling
- Department of Physiology, University of California, San FranciscoSan FranciscoUnited States
| | - Wallace F Marshall
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
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40
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Brunet T, Booth DS. Cell polarity in the protist-to-animal transition. Curr Top Dev Biol 2023; 154:1-36. [PMID: 37100515 DOI: 10.1016/bs.ctdb.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
A signature feature of the animal kingdom is the presence of epithelia: sheets of polarized cells that both insulate the organism from its environment and mediate interactions with it. Epithelial cells display a marked apico-basal polarity, which is highly conserved across the animal kingdom, both in terms of morphology and of molecular regulators. How did this architecture first evolve? Although the last eukaryotic common ancestor almost certainly possessed a simple form of apico-basal polarity (marked by the presence of one or several flagella at a single cellular pole), comparative genomics and evolutionary cell biology reveal that the polarity regulators of animal epithelial cells have a surprisingly complex and stepwise evolutionary history. Here, we retrace their evolutionary assembly. We suggest that the "polarity network" that polarized animal epithelial cells evolved by integration of initially independent cellular modules that evolved at distinct steps of our evolutionary ancestry. The first module dates back to the last common ancestor of animals and amoebozoans and involved Par1, extracellular matrix proteins, and the integrin-mediated adhesion complex. Other regulators, such as Cdc42, Dlg, Par6 and cadherins evolved in ancient unicellular opisthokonts, and might have first been involved in F-actin remodeling and filopodial dynamics. Finally, the bulk of "polarity proteins" as well as specialized adhesion complexes evolved in the metazoan stem-line, in concert with the newly evolved intercellular junctional belts. Thus, the polarized architecture of epithelia can be understood as a palimpsest of components of distinct histories and ancestral functions, which have become tightly integrated in animal tissues.
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Abstract
The assembly and maintenance of most cilia and eukaryotic flagella depends on intraflagellar transport (IFT), the bidirectional movement of multi-megadalton IFT trains along the axonemal microtubules. These IFT trains function as carriers, moving ciliary proteins between the cell body and the organelle. Whereas tubulin, the principal protein of cilia, binds directly to IFT particle proteins, the transport of other ciliary proteins and complexes requires adapters that link them to the trains. Large axonemal substructures, such as radial spokes, outer dynein arms and inner dynein arms, assemble in the cell body before attaching to IFT trains, using the adapters ARMC2, ODA16 and IDA3, respectively. Ciliary import of several membrane proteins involves the putative adapter tubby-like protein 3 (TULP3), whereas membrane protein export involves the BBSome, an octameric complex that co-migrates with IFT particles. Thus, cells employ a variety of adapters, each of which is substoichiometric to the core IFT machinery, to expand the cargo range of the IFT trains. This Review summarizes the individual and shared features of the known cargo adapters and discusses their possible role in regulating the transport capacity of the IFT pathway.
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Affiliation(s)
- Karl Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
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42
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Park K, Leroux MR. Composition, organization and mechanisms of the transition zone, a gate for the cilium. EMBO Rep 2022; 23:e55420. [PMID: 36408840 PMCID: PMC9724682 DOI: 10.15252/embr.202255420] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/08/2022] [Accepted: 10/31/2022] [Indexed: 11/22/2022] Open
Abstract
The cilium evolved to provide the ancestral eukaryote with the ability to move and sense its environment. Acquiring these functions required the compartmentalization of a dynein-based motility apparatus and signaling proteins within a discrete subcellular organelle contiguous with the cytosol. Here, we explore the potential molecular mechanisms for how the proximal-most region of the cilium, termed transition zone (TZ), acts as a diffusion barrier for both membrane and soluble proteins and helps to ensure ciliary autonomy and homeostasis. These include a unique complement and spatial organization of proteins that span from the microtubule-based axoneme to the ciliary membrane; a protein picket fence; a specialized lipid microdomain; differential membrane curvature and thickness; and lastly, a size-selective molecular sieve. In addition, the TZ must be permissive for, and functionally integrates with, ciliary trafficking systems (including intraflagellar transport) that cross the barrier and make the ciliary compartment dynamic. The quest to understand the TZ continues and promises to not only illuminate essential aspects of human cell signaling, physiology, and development, but also to unravel how TZ dysfunction contributes to ciliopathies that affect multiple organ systems, including eyes, kidney, and brain.
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Affiliation(s)
- Kwangjin Park
- Department of Molecular Biology and BiochemistrySimon Fraser UniversityBurnabyBCCanada
- Centre for Cell Biology, Development, and DiseaseSimon Fraser UniversityBurnabyBCCanada
- Present address:
Terry Fox LaboratoryBC CancerVancouverBCCanada
- Present address:
Department of Medical GeneticsUniversity of British ColumbiaVancouverBCCanada
| | - Michel R Leroux
- Department of Molecular Biology and BiochemistrySimon Fraser UniversityBurnabyBCCanada
- Centre for Cell Biology, Development, and DiseaseSimon Fraser UniversityBurnabyBCCanada
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43
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Pinskey JM, Lagisetty A, Gui L, Phan N, Reetz E, Tavakoli A, Fu G, Nicastro D. Three-dimensional flagella structures from animals' closest unicellular relatives, the Choanoflagellates. eLife 2022; 11:e78133. [PMID: 36384644 PMCID: PMC9671500 DOI: 10.7554/elife.78133] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 11/01/2022] [Indexed: 11/18/2022] Open
Abstract
In most eukaryotic organisms, cilia and flagella perform a variety of life-sustaining roles related to environmental sensing and motility. Cryo-electron microscopy has provided considerable insight into the morphology and function of flagellar structures, but studies have been limited to less than a dozen of the millions of known eukaryotic species. Ultrastructural information is particularly lacking for unicellular organisms in the Opisthokonta clade, leaving a sizeable gap in our understanding of flagella evolution between unicellular species and multicellular metazoans (animals). Choanoflagellates are important aquatic heterotrophs, uniquely positioned within the opisthokonts as the metazoans' closest living unicellular relatives. We performed cryo-focused ion beam milling and cryo-electron tomography on flagella from the choanoflagellate species Salpingoeca rosetta. We show that the axonemal dyneins, radial spokes, and central pair complex in S. rosetta more closely resemble metazoan structures than those of unicellular organisms from other suprakingdoms. In addition, we describe unique features of S. rosetta flagella, including microtubule holes, microtubule inner proteins, and the flagellar vane: a fine, net-like extension that has been notoriously difficult to visualize using other methods. Furthermore, we report barb-like structures of unknown function on the extracellular surface of the flagellar membrane. Together, our findings provide new insights into choanoflagellate biology and flagella evolution between unicellular and multicellular opisthokonts.
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Affiliation(s)
- Justine M Pinskey
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Adhya Lagisetty
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Long Gui
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Nhan Phan
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Evan Reetz
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Amirrasoul Tavakoli
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Gang Fu
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Daniela Nicastro
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
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44
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Finetti F, Onnis A, Baldari CT. IFT20: An Eclectic Regulator of Cellular Processes beyond Intraflagellar Transport. Int J Mol Sci 2022; 23:ijms232012147. [PMID: 36292997 PMCID: PMC9603483 DOI: 10.3390/ijms232012147] [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: 08/12/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022] Open
Abstract
Initially discovered as the smallest component of the intraflagellar transport (IFT) system, the IFT20 protein has been found to be implicated in several unconventional mechanisms beyond its essential role in the assembly and maintenance of the primary cilium. IFT20 is now considered a key player not only in ciliogenesis but also in vesicular trafficking of membrane receptors and signaling proteins. Moreover, its ability to associate with a wide array of interacting partners in a cell-type specific manner has expanded the function of IFT20 to the regulation of intracellular degradative and secretory pathways. In this review, we will present an overview of the multifaceted role of IFT20 in both ciliated and non-ciliated cells.
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Howard J, Chasteen A, Ouyang X, Geyer VF, Sartori P. Predicting the locations of force-generating dyneins in beating cilia and flagella. Front Cell Dev Biol 2022; 10:995847. [PMID: 36303602 PMCID: PMC9592896 DOI: 10.3389/fcell.2022.995847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 09/13/2022] [Indexed: 11/18/2022] Open
Abstract
Cilia and flagella are slender cylindrical organelles whose bending waves propel cells through fluids and drive fluids across epithelia. The bending waves are generated by dynein motor proteins, ATPases whose force-generating activity changes over time and with position along the axoneme, the motile structure within the cilium. A key question is: where, in an actively beating axoneme, are the force-generating dyneins located? Answering this question is crucial for determining which of the conformational states adopted by the dynein motors generate the forces that bend the axoneme. The question is difficult to answer because the flagellum contains a large number of dyneins in a complex three-dimensional architecture. To circumvent this complexity, we used a molecular-mechanics approach to show how the bending moments produced by single pairs of dynein motors work against elastic and hydrodynamic forces. By integrating the individual motor activities over the length of the axoneme, we predict the locations of the force-generating dyneins in a beating axoneme. The predicted location depends on the beat frequency, the wavelength, and the elastic and hydrodynamic properties of the axoneme. To test these predictions using cryogenic electron microscopy, cilia with shorter wavelengths, such as found in Chlamydomonas, are more suitable than sperm flagella with longer wavelengths because, in the former, the lag between force and curvature is less dependent on the specific mechanical properties and experimental preparation.
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Affiliation(s)
- Jonathon Howard
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, United States
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Department of Physics, Yale University, New Haven, United States
- Yale Quantitative Biology Institute, New Haven, United States
- *Correspondence: Jonathon Howard,
| | - Alexander Chasteen
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, United States
| | - Xiaoyi Ouyang
- Department of Physics, Yale University, New Haven, United States
| | - Veikko F. Geyer
- Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
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Liu YX, Sun WY, Xue B, Zhang RK, Li WJ, Xie X, Fan ZC. ARL3 mediates BBSome ciliary turnover by promoting its outward movement across the transition zone. J Cell Biol 2022; 221:213491. [PMID: 36129685 PMCID: PMC9499826 DOI: 10.1083/jcb.202111076] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/13/2022] [Accepted: 07/11/2022] [Indexed: 01/16/2023] Open
Abstract
Ciliary receptors and their certain downstream signaling components undergo intraflagellar transport (IFT) as BBSome cargoes to maintain their ciliary dynamics for sensing and transducing extracellular stimuli inside the cell. Cargo-laden BBSomes pass the transition zone (TZ) for ciliary retrieval, but how this passage is controlled remains elusive. Here, we show that phospholipase D (PLD)-laden BBSomes shed from retrograde IFT trains at the proximal ciliary region right above the TZ to act as Arf-like 3 (ARL3) GTPase-specific effectors in Chlamydomonas cilia. Under physiological condition, ARL3GDP binds to the membrane for diffusing into cilia. Following nucleotide exchange, ARL3GTP detaches from the ciliary membrane, binds to retrograde IFT train-shed and PLD-laden BBSomes at the proximal ciliary region right above the TZ, and recruits them to pass the TZ for ciliary retrieval likely via diffusion. ARL3 mediates the ciliary dynamics of certain signaling molecules through facilitating BBSome ciliary retrieval, providing a mechanistic understanding behind why ARL3-related Joubert syndrome shares overlapping phenotypes with Bardet-Biedl syndrome.
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Affiliation(s)
- Yan-Xia Liu
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Wei-Yue Sun
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Bin Xue
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Rui-Kai Zhang
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Wen-Juan Li
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Xixian Xie
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Zhen-Chuan Fan
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Correspondence to Zhen-Chuan Fan:
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Pochitaloff M, Miranda M, Richard M, Chaiyasitdhi A, Takagi Y, Cao W, De La Cruz EM, Sellers JR, Joanny JF, Jülicher F, Blanchoin L, Martin P. Flagella-like beating of actin bundles driven by self-organized myosin waves. NATURE PHYSICS 2022; 18:1240-1247. [PMID: 37396880 PMCID: PMC10312380 DOI: 10.1038/s41567-022-01688-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 06/23/2022] [Indexed: 07/04/2023]
Abstract
Wave-like beating of eukaryotic cilia and flagella-threadlike protrusions found in many cells and microorganisms-is a classic example of spontaneous mechanical oscillations in biology. This type of self-organized active matter raises the question of the coordination mechanism between molecular motor activity and cytoskeletal filament bending. Here we show that in the presence of myosin motors, polymerizing actin filaments self-assemble into polar bundles that exhibit wave-like beating. Importantly, filament beating is associated with myosin density waves initiated at twice the frequency of the actin-bending waves. A theoretical description based on curvature control of motor binding to the filaments and of motor activity explains our observations in a regime of high internal friction. Overall, our results indicate that the binding of myosin to actin depends on the actin bundle shape, providing a feedback mechanism between the myosin activity and filament deformations for the self-organization of large motor filament assemblies.
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Affiliation(s)
- Marie Pochitaloff
- Laboratoire Physico-Chimie Curie, Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Paris, France
- Present address: Department of Mechanical Engineering, UC Santa Barbara, Santa Barbara, CA, USA
| | - Martin Miranda
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Mathieu Richard
- Laboratoire Physico-Chimie Curie, Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Paris, France
| | - Atitheb Chaiyasitdhi
- Laboratoire Physico-Chimie Curie, Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Paris, France
| | - Yasuharu Takagi
- Laboratory of Molecular Physiology, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
| | - Wenxiang Cao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Enrique M. De La Cruz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - James R. Sellers
- Laboratory of Molecular Physiology, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
| | - Jean-François Joanny
- Laboratoire Physico-Chimie Curie, Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Paris, France
- Collège de France, Paris, France
| | - Frank Jülicher
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden, Germany
| | - Laurent Blanchoin
- CytomorphoLab, Biosciences and Biotechnology Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, Université Grenoble-Alpes/CEA/CNRS/INRA, Grenoble, France
- CytomorphoLab, Hôpital Saint Louis, Institut Universitaire d’Hématologie, UMRS1160, INSERM/AP-HP/Université Paris Diderot, Paris, France
| | - Pascal Martin
- Laboratoire Physico-Chimie Curie, Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Paris, France
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Faubel RJ, Santos Canellas VS, Gaesser J, Beluk NH, Feinstein TN, Wang Y, Yankova M, Karunakaran KB, King SM, Ganapathiraju MK, Lo CW. Flow blockage disrupts cilia-driven fluid transport in the epileptic brain. Acta Neuropathol 2022; 144:691-706. [PMID: 35980457 DOI: 10.1007/s00401-022-02463-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 01/28/2023]
Abstract
A carpet of ependymal motile cilia lines the brain ventricular system, forming a network of flow channels and barriers that pattern cerebrospinal fluid (CSF) flow at the surface. This CSF transport system is evolutionary conserved, but its physiological function remains unknown. Here we investigated its potential role in epilepsy with studies focused on CDKL5 deficiency disorder (CDD), a neurodevelopmental disorder with early-onset epilepsy refractory to seizure medications and the most common cause of infant epilepsy. CDKL5 is a highly conserved X-linked gene suggesting its function in regulating cilia length and motion in the green alga Chlamydomonas might have implication in the etiology of CDD. Examination of the structure and function of airway motile cilia revealed both the CDD patients and the Cdkl5 knockout mice exhibit cilia lengthening and abnormal cilia motion. Similar defects were observed for brain ventricular cilia in the Cdkl5 knockout mice. Mapping ependymal cilia generated flow in the ventral third ventricle (v3V), a brain region with important physiological functions showed altered patterning of flow. Tracing of cilia-mediated inflow into v3V with fluorescent dye revealed the appearance of a flow barrier at the inlet of v3V in Cdkl5 knockout mice. Analysis of mice with a mutation in another epilepsy-associated kinase, Yes1, showed the same disturbance of cilia motion and flow patterning. The flow barrier was also observed in the Foxj1± and FOXJ1CreERT:Cdkl5y/fl mice, confirming the contribution of ventricular cilia to the flow disturbances. Importantly, mice exhibiting altered cilia-driven flow also showed increased susceptibility to anesthesia-induced seizure-like activity. The cilia-driven flow disturbance arises from altered cilia beating orientation with the disrupted polarity of the cilia anchoring rootlet meshwork. Together these findings indicate motile cilia disturbances have an essential role in CDD-associated seizures and beyond, suggesting cilia regulating kinases may be a therapeutic target for medication-resistant epilepsy.
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Affiliation(s)
- Regina J Faubel
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15201, USA
| | - Veronica S Santos Canellas
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15201, USA
| | - Jenna Gaesser
- Division of Child Neurology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15201, USA
| | - Nancy H Beluk
- Division of Radiology, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Tim N Feinstein
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15201, USA
| | - Yong Wang
- Laboratory for Fluid Physics, Pattern Formation and Biocomplexity, Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077, Göttingen, Germany
| | - Maya Yankova
- Department of Molecular Biology and Biophysics, And Electron Microscopy Facility, University of Connecticut Health Center, Farmington, CT, 06030-3305, USA
| | - Kalyani B Karunakaran
- Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, 560012, India
| | - Stephen M King
- Department of Molecular Biology and Biophysics, And Electron Microscopy Facility, University of Connecticut Health Center, Farmington, CT, 06030-3305, USA
| | - Madhavi K Ganapathiraju
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15201, USA
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15201, USA.
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Kreutzberger MAB, Sonani RR, Liu J, Chatterjee S, Wang F, Sebastian AL, Biswas P, Ewing C, Zheng W, Poly F, Frankel G, Luisi BF, Calladine CR, Krupovic M, Scharf BE, Egelman EH. Convergent evolution in the supercoiling of prokaryotic flagellar filaments. Cell 2022; 185:3487-3500.e14. [PMID: 36057255 PMCID: PMC9500442 DOI: 10.1016/j.cell.2022.08.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/04/2022] [Accepted: 08/04/2022] [Indexed: 02/02/2023]
Abstract
The supercoiling of bacterial and archaeal flagellar filaments is required for motility. Archaeal flagellar filaments have no homology to their bacterial counterparts and are instead homologs of bacterial type IV pili. How these prokaryotic flagellar filaments, each composed of thousands of copies of identical subunits, can form stable supercoils under torsional stress is a fascinating puzzle for which structural insights have been elusive. Advances in cryoelectron microscopy (cryo-EM) make it now possible to directly visualize the basis for supercoiling, and here, we show the atomic structures of supercoiled bacterial and archaeal flagellar filaments. For the bacterial flagellar filament, we identify 11 distinct protofilament conformations with three broad classes of inter-protomer interface. For the archaeal flagellar filament, 10 protofilaments form a supercoil geometry supported by 10 distinct conformations, with one inter-protomer discontinuity creating a seam inside of the curve. Our results suggest that convergent evolution has yielded stable superhelical geometries that enable microbial locomotion.
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Affiliation(s)
- Mark A B Kreutzberger
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Ravi R Sonani
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Junfeng Liu
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Archaeal Virology Unit, 75015 Paris, France
| | - Sharanya Chatterjee
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Amanda L Sebastian
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Priyanka Biswas
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - Cheryl Ewing
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, MD 20910, USA
| | - Weili Zheng
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Frédéric Poly
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, MD 20910, USA
| | - Gad Frankel
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - B F Luisi
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Chris R Calladine
- Department of Engineering, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ, UK
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Archaeal Virology Unit, 75015 Paris, France
| | - Birgit E Scharf
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA.
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50
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Mul W, Mitra A, Peterman EJG. Mechanisms of Regulation in Intraflagellar Transport. Cells 2022; 11:2737. [PMID: 36078145 PMCID: PMC9454703 DOI: 10.3390/cells11172737] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/30/2022] Open
Abstract
Cilia are eukaryotic organelles essential for movement, signaling or sensing. Primary cilia act as antennae to sense a cell's environment and are involved in a wide range of signaling pathways essential for development. Motile cilia drive cell locomotion or liquid flow around the cell. Proper functioning of both types of cilia requires a highly orchestrated bi-directional transport system, intraflagellar transport (IFT), which is driven by motor proteins, kinesin-2 and IFT dynein. In this review, we explore how IFT is regulated in cilia, focusing from three different perspectives on the issue. First, we reflect on how the motor track, the microtubule-based axoneme, affects IFT. Second, we focus on the motor proteins, considering the role motor action, cooperation and motor-train interaction plays in the regulation of IFT. Third, we discuss the role of kinases in the regulation of the motor proteins. Our goal is to provide mechanistic insights in IFT regulation in cilia and to suggest directions of future research.
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Affiliation(s)
| | | | - Erwin J. G. Peterman
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
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