1
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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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2
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Tingey M, Ruba A, Jiang Z, Yang W. Deciphering vesicle-assisted transport mechanisms in cytoplasm to cilium trafficking. Front Cell Neurosci 2024; 18:1379976. [PMID: 38860265 PMCID: PMC11163138 DOI: 10.3389/fncel.2024.1379976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/13/2024] [Indexed: 06/12/2024] Open
Abstract
The cilium, a pivotal organelle crucial for cell signaling and proper cell function, relies on meticulous macromolecular transport from the cytoplasm for its formation and maintenance. While the intraflagellar transport (IFT) pathway has traditionally been the focus of extensive study concerning ciliogenesis and ciliary maintenance, recent research highlights a complementary and alternative mechanism-vesicle-assisted transport (VAT) in cytoplasm to cilium trafficking. Despite its potential significance, the VAT pathway remains largely uncharacterized. This review explores recent studies providing evidence for the dynamics of vesicle-related diffusion and transport within the live primary cilium, employing high-speed super-resolution light microscopy. Additionally, we analyze the spatial distribution of vesicles in the cilium, mainly relying on electron microscopy data. By scrutinizing the VAT pathways that facilitate cargo transport into the cilium, with a specific emphasis on recent advancements and imaging data, our objective is to synthesize a comprehensive model of ciliary transport through the integration of IFT-VAT mechanisms.
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Affiliation(s)
| | | | | | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA, United States
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3
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Patel MB, Griffin PJ, Olson SF, Dai J, Hou Y, Malik T, Das P, Zhang G, Zhao W, Witman GB, Lechtreck KF. Distribution and bulk flow analyses of the intraflagellar transport (IFT) motor kinesin-2 support an "on-demand" model for Chlamydomonas ciliary length control. Cytoskeleton (Hoboken) 2024. [PMID: 38456596 DOI: 10.1002/cm.21851] [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: 10/30/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/09/2024]
Abstract
Most cells tightly control the length of their cilia. The regulation likely involves intraflagellar transport (IFT), a bidirectional motility of multi-subunit particles organized into trains that deliver building blocks into the organelle. In Chlamydomonas, the anterograde IFT motor kinesin-2 consists of the motor subunits FLA8 and FLA10 and the nonmotor subunit KAP. KAP dissociates from IFT at the ciliary tip and diffuses back to the cell body. This observation led to the diffusion-as-a-ruler model of ciliary length control, which postulates that KAP is progressively sequestered into elongating cilia because its return to the cell body will require increasingly more time, limiting motor availability at the ciliary base, train assembly, building block supply, and ciliary growth. Here, we show that Chlamydomonas FLA8 also returns to the cell body by diffusion. However, more than 95% of KAP and FLA8 are present in the cell body and, at a given time, just ~1% of the motor participates in IFT. After repeated photobleaching of both cilia, IFT of fluorescent kinesin subunits continued indicating that kinesin-2 cycles from the large cell-body pool through the cilia and back. Furthermore, growing and full-length cilia contained similar amounts of kinesin-2 subunits and the size of the motor pool at the base changed only slightly with ciliary length. These observations are incompatible with the diffusion-as-a-ruler model, but rather support an "on-demand model," in which the cargo load of the trains is regulated to assemble cilia of the desired length.
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Affiliation(s)
- Mansi B Patel
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Paul J Griffin
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Spencer F Olson
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Jin Dai
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Yuqing Hou
- Department of Radiology, UMass Chan Medical School, Worcester, Massachusetts, USA
| | - Tara Malik
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Poulomi Das
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Gui Zhang
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Winston Zhao
- Department of Radiology, UMass Chan Medical School, Worcester, Massachusetts, USA
| | - George B Witman
- Department of Radiology, UMass Chan Medical School, Worcester, Massachusetts, USA
| | - Karl F Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
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4
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Dougherty LL, Dutta S, Avasthi P. The ERK activator, BCI, inhibits ciliogenesis and causes defects in motor behavior, ciliary gating, and cytoskeletal rearrangement. Life Sci Alliance 2023; 6:e202301899. [PMID: 36914265 PMCID: PMC10011610 DOI: 10.26508/lsa.202301899] [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: 01/04/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/14/2023] Open
Abstract
MAPK pathways are well-known regulators of the cell cycle, but they have also been found to control ciliary length in a wide variety of organisms and cell types from Caenorhabditis elegans neurons to mammalian photoreceptors through unknown mechanisms. ERK1/2 is a MAP kinase in human cells that is predominantly phosphorylated by MEK1/2 and dephosphorylated by the phosphatase DUSP6. We have found that the ERK1/2 activator/DUSP6 inhibitor, (E)-2-benzylidene-3-(cyclohexylamino)-2,3-dihydro-1H-inden-1-one (BCI), inhibits ciliary maintenance in Chlamydomonas and hTERT-RPE1 cells and assembly in Chlamydomonas These effects involve inhibition of total protein synthesis, microtubule organization, membrane trafficking, and KAP-GFP motor dynamics. Our data provide evidence for various avenues for BCI-induced ciliary shortening and impaired ciliogenesis that gives mechanistic insight into how MAP kinases can regulate ciliary length.
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Affiliation(s)
- Larissa L Dougherty
- Biochemistry and Cell Biology Department, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
- Anatomy and Cell Biology Department, University of Kansas Medical Center, Kansas City, KS, USA
| | - Soumita Dutta
- Anatomy and Cell Biology Department, University of Kansas Medical Center, Kansas City, KS, USA
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Prachee Avasthi
- Biochemistry and Cell Biology Department, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
- Anatomy and Cell Biology Department, University of Kansas Medical Center, Kansas City, KS, USA
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5
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Chen H, Yang QL, Xu JX, Deng X, Zhang YJ, Liu T, Rots MG, Xu GL, Huang KY. Efficient methods for multiple types of precise gene-editing in Chlamydomonas. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 37310200 DOI: 10.1111/tpj.16265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 06/14/2023]
Abstract
Precise gene-editing using CRISPR/Cas9 technology remains a long-standing challenge, especially for genes with low expression and no selectable phenotypes in Chlamydomonas reinhardtii, a classic model for photosynthesis and cilia research. Here, we developed a multi-type and precise genetic manipulation method in which a DNA break was generated by Cas9 nuclease and the repair was mediated using a homologous DNA template. The efficacy of this method was demonstrated for several types of gene editing, including inactivation of two low-expression genes (CrTET1 and CrKU80), the introduction of a FLAG-HA epitope tag into VIPP1, IFT46, CrTET1 and CrKU80 genes, and placing a YFP tag into VIPP1 and IFT46 for live-cell imaging. We also successfully performed a single amino acid substitution for the FLA3, FLA10 and FTSY genes, and documented the attainment of the anticipated phenotypes. Lastly, we demonstrated that precise fragment deletion from the 3'-UTR of MAA7 and VIPP1 resulted in a stable knock-down effect. Overall, our study has established efficient methods for multiple types of precise gene editing in Chlamydomonas, enabling substitution, insertion and deletion at the base resolution, thus improving the potential of this alga in both basic research and industrial applications.
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Affiliation(s)
- Hui Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qing-Lin Yang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jia-Xi Xu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuan Deng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yun-Jie Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ting Liu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Marianne G Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, The Netherlands
| | - Guo-Liang Xu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Shanghai Key Laboratory of Medical Epigenetics, Laboratory of Cancer Epigenetics, Institutes of Biomedical Sciences, Medical College of Fudan University, Chinese Academy of Medical Sciences (RU069), Shanghai, China
| | - Kai-Yao Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
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6
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Arora S, Rana M, Sachdev A, D’Souza JS. Appearing and disappearing acts of cilia. J Biosci 2023. [DOI: 10.1007/s12038-023-00326-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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7
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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; 12:82901. [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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8
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Arora S, Rana M, Sachdev A, D'Souza JS. Appearing and disappearing acts of cilia. J Biosci 2023; 48:8. [PMID: 36924208 PMCID: PMC10005925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
The past few decades have seen a rise in research on vertebrate cilia and ciliopathy, with interesting collaborations between basic and clinical scientists. This work includes studies on ciliary architecture, composition, evolution, and organelle generation and its biological role. The human body has cells that harbour any of the following four types of cilia: 9+0 motile, 9+0 immotile, 9+2 motile, and 9+2 immotile. Depending on the type, cilia play an important role in cell/fluid movement, mating, sensory perception, and development. Defects in cilia are associated with a wide range of human diseases afflicting the brain, heart, kidneys, respiratory tract, and reproductive system. These are commonly known as ciliopathies and affect millions of people worldwide. Due to their complex genetic etiology, diagnosis and therapy have remained elusive. Although model organisms like Chlamydomonas reinhardtii have been a useful source for ciliary research, reports of a fascinating and rewarding translation of this research into mammalian systems, especially humans, are seen. The current review peeks into one of the complex features of this organelle, namely its birth, the common denominators across the formation of both 9+0 and 9+2 ciliary types, the molecules involved in ciliogenesis, and the steps that go towards regulating their assembly and disassembly.
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Affiliation(s)
- Shashank Arora
- School of Biological Sciences, UM-DAE Centre for Excellence in Basic Sciences, Kalina Campus, Santacruz (E), Mumbai 400098, India
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9
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Mechanisms of Regulation in Intraflagellar Transport. Cells 2022; 11:cells11172737. [PMID: 36078145 PMCID: PMC9454703 DOI: 10.3390/cells11172737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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10
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The physiological cargo adaptor of kinesin-2 functions as an evolutionary conserved lockpick. Proc Natl Acad Sci U S A 2022; 119:e2109378119. [PMID: 35947619 PMCID: PMC9388150 DOI: 10.1073/pnas.2109378119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Specific recognition of cellular cargo and efficient transport to its correct intracellular destination is an infrastructural challenge faced by most eukaryotic cells. This remarkable deed is accomplished by processive motor proteins that are subject to robust regulatory mechanisms. The first level of regulation entails the ability of the motor to suppress its own activity. This autoinhibition is eventually relieved by specific cargo binding. To better understand the role of the cargo during motor activation, we dissected the activation mechanism of the ciliary homodimeric kinesin-2 from Caenorhabditis elegans by its physiological cargo. In functional reconstitution assays, we identified two cargo adaptor proteins that together are necessary and sufficient to allosterically activate the autoinhibited motor. Surprisingly, the orthologous adaptor proteins from the unicellular green algae Chlamydomonas reinhardtii also fully activated the kinesin-2 from worm, even though C. reinhardtii itself lacks a homodimeric kinesin-2 motor. The latter suggested that a motor activation mechanism similar to the C. elegans model existed already well before metazoans evolved, and prompted us to scrutinize predicted homodimeric kinesin-2 orthologs in other evolutionarily distant eukaryotes. We show that the ciliate Tetrahymena thermophila not only possesses a homodimeric kinesin-2 but that it also shares the same allosteric activation mechanism that we delineated in the C. elegans model. Our results point to a much more fundamental role of homodimeric kinesin-2 in intraflagellar transport (IFT) than previously thought and warrant further scrutiny of distantly related organisms toward a comprehensive picture of the IFT process and its evolution.
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11
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van den Hoek H, Klena N, Jordan MA, Alvarez Viar G, Righetto RD, Schaffer M, Erdmann PS, Wan W, Geimer S, Plitzko JM, Baumeister W, Pigino G, Hamel V, Guichard P, Engel BD. In situ architecture of the ciliary base reveals the stepwise assembly of intraflagellar transport trains. Science 2022; 377:543-548. [PMID: 35901159 DOI: 10.1126/science.abm6704] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The cilium is an antenna-like organelle that performs numerous cellular functions, including motility, sensing, and signaling. The base of the cilium contains a selective barrier that regulates the entry of large intraflagellar transport (IFT) trains, which carry cargo proteins required for ciliary assembly and maintenance. However, the native architecture of the ciliary base and the process of IFT train assembly remain unresolved. In this work, we used in situ cryo-electron tomography to reveal native structures of the transition zone region and assembling IFT trains at the ciliary base in Chlamydomonas. We combined this direct cellular visualization with ultrastructure expansion microscopy to describe the front-to-back stepwise assembly of IFT trains: IFT-B forms the backbone, onto which bind IFT-A, dynein-1b, and finally kinesin-2 before entry into the cilium.
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Affiliation(s)
- Hugo van den Hoek
- Biozentrum, University of Basel, 4056 Basel, Switzerland.,Helmholtz Pioneer Campus, Helmholtz Munich, 85764 Neuherberg, Germany.,Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Nikolai Klena
- Department of Molecular and Cellular Biology, Section of Biology, University of Geneva, 1211 Geneva, Switzerland.,Human Technopole, 20157 Milan, Italy
| | - Mareike A Jordan
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Gonzalo Alvarez Viar
- Human Technopole, 20157 Milan, Italy.,Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Ricardo D Righetto
- Biozentrum, University of Basel, 4056 Basel, Switzerland.,Helmholtz Pioneer Campus, Helmholtz Munich, 85764 Neuherberg, Germany
| | - Miroslava Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | | | - William Wan
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Stefan Geimer
- Cell Biology and Electron Microscopy, University of Bayreuth, 95447 Bayreuth, Germany
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Gaia Pigino
- Human Technopole, 20157 Milan, Italy.,Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Virginie Hamel
- Department of Molecular and Cellular Biology, Section of Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Paul Guichard
- Department of Molecular and Cellular Biology, Section of Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Benjamin D Engel
- Biozentrum, University of Basel, 4056 Basel, Switzerland.,Helmholtz Pioneer Campus, Helmholtz Munich, 85764 Neuherberg, Germany
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12
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Abstract
The intraflagellar transport (IFT) system is a remarkable molecular machine used by cells to assemble and maintain the cilium, a long organelle extending from eukaryotic cells that gives rise to motility, sensing and signaling. IFT plays a critical role in building the cilium by shuttling structural components and signaling receptors between the ciliary base and tip. To provide effective transport, IFT-A and IFT-B adaptor protein complexes assemble into highly repetitive polymers, called IFT trains, that are powered by the motors kinesin-2 and IFT-dynein to move bidirectionally along the microtubules. This dynamic system must be precisely regulated to shuttle different cargo proteins between the ciliary tip and base. In this Cell Science at a Glance article and the accompanying poster, we discuss the current structural and mechanistic understanding of IFT trains and how they function as macromolecular machines to assemble the structure of the cilium.
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Affiliation(s)
- Mareike A Jordan
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Gaia Pigino
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Pfotenhauerstraße 108, 01307 Dresden, Germany.,Human Technopole, Via Cristina Belgioioso 171, 20157 Milan, Italy
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13
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Fort C, Collingridge P, Brownlee C, Wheeler G. Ca 2+ elevations disrupt interactions between intraflagellar transport and the flagella membrane in Chlamydomonas. J Cell Sci 2021; 134:jcs.253492. [PMID: 33495279 DOI: 10.1242/jcs.253492] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/05/2021] [Indexed: 01/29/2023] Open
Abstract
The movement of ciliary membrane proteins is directed by transient interactions with intraflagellar transport (IFT) trains. The green alga Chlamydomonas has adapted this process for gliding motility, using retrograde IFT motors to move adhesive glycoproteins in the flagella membrane. Ca2+ signalling contributes directly to the gliding process, although uncertainty remains over the mechanism through which it acts. Here, we show that flagella Ca2+ elevations initiate the movement of paused retrograde IFT trains, which accumulate at the distal end of adherent flagella, but do not influence other IFT processes. On highly adherent surfaces, flagella exhibit high-frequency Ca2+ elevations that prevent the accumulation of paused retrograde IFT trains. Flagella Ca2+ elevations disrupt the IFT-dependent movement of microspheres along the flagella membrane, suggesting that Ca2+ acts by directly disrupting an interaction between retrograde IFT trains and flagella membrane glycoproteins. By regulating the extent to which glycoproteins on the flagella surface interact with IFT motor proteins on the axoneme, this signalling mechanism allows precise control of traction force and gliding motility in adherent flagella.
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Affiliation(s)
- Cecile Fort
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Peter Collingridge
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Colin Brownlee
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK.,School of Ocean and Earth Science, University of Southampton, Southampton SO14 3ZH, UK
| | - Glen Wheeler
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
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14
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Huang S, Dougherty LL, Avasthi P. Separable roles for RanGTP in nuclear and ciliary trafficking of a kinesin-2 subunit. J Biol Chem 2021; 296:100117. [PMID: 33234597 PMCID: PMC7948393 DOI: 10.1074/jbc.ra119.010936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 11/16/2020] [Accepted: 11/24/2020] [Indexed: 01/05/2023] Open
Abstract
Kinesin is part of the microtubule-binding motor protein superfamily, which serves important roles in cell division and intraorganellar transport. The heterotrimeric kinesin-2, consisting of the heterodimeric motor subunits, kinesin family member 3A/3B (KIF3A/3B), and kinesin-associated protein 3 (KAP3), is highly conserved across species from the unicellular eukaryote Chlamydomonas to humans. It plays diverse roles in cargo transport including anterograde (base to tip) trafficking in cilia. However, the molecular determinants mediating trafficking of heterotrimeric kinesin-2 itself are poorly understood. It has been previously suggested that ciliary transport is analogous to nuclear transport mechanisms. Using Chlamydomonas and human telomerase reverse transcriptase-retinal pigment epithelial cell line, we show that RanGTP, a small GTPase that dictates nuclear transport, regulates ciliary trafficking of KAP3, a key component for functional kinesin-2. We found that the armadillo-repeat region 6 to 9 (ARM6-9) of KAP3, required for its nuclear translocation, is also necessary and sufficient for its targeting to the ciliary base. Given that KAP3 is essential for cilium formation and there are the emerging roles for RanGTP/importin β in ciliary protein targeting, we further investigated the effect of RanGTP in cilium formation and maintenance. We found that precise control of RanGTP levels, revealed by different Ran mutants, is crucial for cilium formation and maintenance. Most importantly, we were able to provide orthogonal support in an algal model system that segregates RanGTP regulation of ciliary protein trafficking from its nuclear roles. Our work provides important support for the model that nuclear import mechanisms have been co-opted for independent roles in ciliary import.
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Affiliation(s)
- Shengping Huang
- Department of Ophthalmology, University of Kansas Medical Center, Kansas City, Kansas, USA.
| | - Larissa L Dougherty
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas, USA; Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, USA
| | - Prachee Avasthi
- Department of Ophthalmology, University of Kansas Medical Center, Kansas City, Kansas, USA; Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas, USA; Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, USA.
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15
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Webb S, Mukhopadhyay AG, Roberts AJ. Intraflagellar transport trains and motors: Insights from structure. Semin Cell Dev Biol 2020; 107:82-90. [PMID: 32684327 PMCID: PMC7561706 DOI: 10.1016/j.semcdb.2020.05.021] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/19/2020] [Accepted: 05/26/2020] [Indexed: 11/17/2022]
Abstract
Intraflagellar transport (IFT) sculpts the proteome of cilia and flagella; the antenna-like organelles found on the surface of virtually all human cell types. By delivering proteins to the growing ciliary tip, recycling turnover products, and selectively transporting signalling molecules, IFT has critical roles in cilia biogenesis, quality control, and signal transduction. IFT involves long polymeric arrays, termed IFT trains, which move to and from the ciliary tip under the power of the microtubule-based motor proteins kinesin-II and dynein-2. Recent top-down and bottom-up structural biology approaches are converging on the molecular architecture of the IFT train machinery. Here we review these studies, with a focus on how kinesin-II and dynein-2 assemble, attach to IFT trains, and undergo precise regulation to mediate bidirectional transport.
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Affiliation(s)
- Stephanie Webb
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London, United Kingdom
| | - Aakash G Mukhopadhyay
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London, United Kingdom
| | - Anthony J Roberts
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London, United Kingdom.
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16
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Li S, Wan KY, Chen W, Tao H, Liang X, Pan J. Functional exploration of heterotrimeric kinesin-II in IFT and ciliary length control in Chlamydomonas. eLife 2020; 9:58868. [PMID: 33112235 PMCID: PMC7652414 DOI: 10.7554/elife.58868] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 10/28/2020] [Indexed: 12/27/2022] Open
Abstract
Heterodimeric motor organization of kinesin-II is essential for its function in anterograde IFT in ciliogenesis. However, the underlying mechanism is not well understood. In addition, the anterograde IFT velocity varies significantly in different organisms, but how this velocity affects ciliary length is not clear. We show that in Chlamydomonas motors are only stable as heterodimers in vivo, which is likely the key factor for the requirement of a heterodimer for IFT. Second, chimeric CrKinesin-II with human kinesin-II motor domains functioned in vitro and in vivo, leading to a ~ 2.8 fold reduced anterograde IFT velocity and a similar fold reduction in IFT injection rate that supposedly correlates with ciliary assembly activity. However, the ciliary length was only mildly reduced (~15%). Modeling analysis suggests a nonlinear scaling relationship between IFT velocity and ciliary length that can be accounted for by limitation of the motors and/or its ciliary cargoes, e.g. tubulin.
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Affiliation(s)
- Shufen Li
- MOE Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Kirsty Y Wan
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Wei Chen
- MOE Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Hui Tao
- MOE Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xin Liang
- MOE Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Junmin Pan
- MOE Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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17
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Douglas RL, Haltiwanger BM, Albisetti A, Wu H, Jeng RL, Mancuso J, Cande WZ, Welch MD. Trypanosomes have divergent kinesin-2 proteins that function differentially in flagellum biosynthesis and cell viability. J Cell Sci 2020; 133:jcs129213. [PMID: 32503938 DOI: 10.1242/jcs.129213] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 05/27/2020] [Indexed: 12/13/2022] Open
Abstract
Trypanosoma brucei, the causative agent of African sleeping sickness, has a flagellum that is crucial for motility, pathogenicity, and viability. In most eukaryotes, the intraflagellar transport (IFT) machinery drives flagellum biogenesis, and anterograde IFT requires kinesin-2 motor proteins. In this study, we investigated the function of the two T. brucei kinesin-2 proteins, TbKin2a and TbKin2b, in bloodstream form trypanosomes. We found that, compared to kinesin-2 proteins across other phyla, TbKin2a and TbKin2b show greater variation in neck, stalk and tail domain sequences. Both kinesins contributed additively to flagellar lengthening. Silencing TbKin2a inhibited cell proliferation, cytokinesis and motility, whereas silencing TbKin2b did not. TbKin2a was localized on the flagellum and colocalized with IFT components near the basal body, consistent with it performing a role in IFT. TbKin2a was also detected on the flagellar attachment zone, a specialized structure that connects the flagellum to the cell body. Our results indicate that kinesin-2 proteins in trypanosomes play conserved roles in flagellar biosynthesis and exhibit a specialized localization, emphasizing the evolutionary flexibility of motor protein function in an organism with a large complement of kinesins.
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Affiliation(s)
- Robert L Douglas
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Brett M Haltiwanger
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Anna Albisetti
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Haiming Wu
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Robert L Jeng
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Joel Mancuso
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
| | - W Zacheus Cande
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Matthew D Welch
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
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18
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Ma R, Hendel NL, Marshall WF, Qin H. Speed and Diffusion of Kinesin-2 Are Competing Limiting Factors in Flagellar Length-Control Model. Biophys J 2020; 118:2790-2800. [PMID: 32365327 DOI: 10.1016/j.bpj.2020.03.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 03/18/2020] [Accepted: 03/24/2020] [Indexed: 10/24/2022] Open
Abstract
Flagellar length control in Chlamydomonas is a tractable model system for studying the general question of organelle size regulation. We have previously proposed that the diffusive return of the kinesin motor that powers intraflagellar transport can play a key role in length regulation. Here, we explore how the motor speed and diffusion coefficient for the return of kinesin-2 affect flagellar growth kinetics. We find that the system can exist in two distinct regimes, one dominated by motor speed and one by diffusion coefficient. Depending on length, a flagellum can switch between these regimes. Our results indicate that mutations can affect the length in distinct ways. We discuss our theory's implication for flagellar growth influenced by beating and provide possible explanations for the experimental observation that a beating flagellum is usually longer than its immotile mutant. These results demonstrate how our simple model can suggest explanations for mutant phenotypes.
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Affiliation(s)
- Rui Ma
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Nathan L Hendel
- Department of Biochemistry and Biophysics, University of California, San Francisco, California; Bioinformatics Graduate Group, University of California, San Francisco, California
| | - Wallace F Marshall
- Department of Biochemistry and Biophysics, University of California, San Francisco, California
| | - Hongmin Qin
- Department of Biology, Texas A&M University, College Station, Texas.
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19
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Zhao Q, Li S, Shao S, Wang Z, Pan J. FLS2 is a CDK-like kinase that directly binds IFT70 and is required for proper ciliary disassembly in Chlamydomonas. PLoS Genet 2020; 16:e1008561. [PMID: 32134924 PMCID: PMC7077844 DOI: 10.1371/journal.pgen.1008561] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/17/2020] [Accepted: 02/01/2020] [Indexed: 02/06/2023] Open
Abstract
Intraflagellar transport (IFT) is required for ciliary assembly and maintenance. While disruption of IFT may trigger ciliary disassembly, we show here that IFT mediated transport of a CDK-like kinase ensures proper ciliary disassembly. Mutations in flagellar shortening 2 (FLS2), encoding a CDK-like kinase, lead to retardation of cilia resorption and delay of cell cycle progression. Stimulation for ciliary disassembly induces gradual dephosphorylation of FLS2 accompanied with gradual inactivation. Loss of FLS2 or its kinase activity induces early onset of kinesin13 phosphorylation in cilia. FLS2 is predominantly localized in the cell body, however, it is transported to cilia upon induction of ciliary disassembly. FLS2 directly interacts with IFT70 and loss of this interaction inhibits its ciliary transport, leading to dysregulation of kinesin13 phosphorylation and retardation of ciliary disassembly. Thus, this work demonstrates that IFT plays active roles in controlling proper ciliary disassembly by transporting a protein kinase to cilia to regulate a microtubule depolymerizer. Cilia or eukaryotic flagella are cellular surface protrusions that function in cell motility as well as sensing. They are dynamic structures that undergo assembly and disassembly. Cilia are resorbed during cell cycle progression. Dysregulation of cilia resorption may cause delay of cell cycle progression, which underlies aberrant cell differentiation and even cancer. Ciliary resorption requires depolmerization of axonemal microtubules that is mediated by kinesin13. Using the unicellular green alga, Chlamydomonas, we have identified a CDK-like kinase FLS2 that when mutated retards cilia resorption, leading to delay of cell cycle progression. FLS2, a cell body protein, is transported to cilia via intraflagellar transport upon induction of cilia resorption. FLS2 directly interacts with IFT70 and loss of this interaction inhibits transport of FLS2 to cilia and fails to regulate proper phosphorylation of kinesin13 in cilia.
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Affiliation(s)
- Qin Zhao
- MOE Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shufen Li
- MOE Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shangjin Shao
- MOE Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhengmao Wang
- MOE Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Junmin Pan
- MOE Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province, China
- * E-mail:
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20
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Sonar P, Youyen W, Cleetus A, Wisanpitayakorn P, Mousavi SI, Stepp WL, Hancock WO, Tüzel E, Ökten Z. Kinesin-2 from C. reinhardtii Is an Atypically Fast and Auto-inhibited Motor that Is Activated by Heterotrimerization for Intraflagellar Transport. Curr Biol 2020; 30:1160-1166.e5. [PMID: 32142698 DOI: 10.1016/j.cub.2020.01.046] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/04/2019] [Accepted: 01/14/2020] [Indexed: 11/17/2022]
Abstract
Construction and function of virtually all cilia require the universally conserved process of intraflagellar transport (IFT) [1, 2]. During the atypically fast IFT in the green alga C. reinhardtii, on average, 10 kinesin-2 motors "line up" in a tight assembly on the trains [3], provoking the question of how these motors coordinate their action to ensure smooth and fast transport along the flagellum without standing in each other's way. Here, we show that the heterodimeric FLA8/10 kinesin-2 alone is responsible for the atypically fast IFT in C. reinhardtii. Notably, in single-molecule studies, FLA8/10 moved at speeds matching those of in vivo IFT [4] but additionally displayed a slow velocity distribution, indicative of auto-inhibition. Addition of the KAP subunit to generate the heterotrimeric FLA8/10/KAP relieved this inhibition, thus providing a mechanistic rationale for heterotrimerization with the KAP subunit fully activating FLA8/10 for IFT in vivo. Finally, we linked fast FLA8/10 and slow KLP11/20 kinesin-2 from C. reinhardtii and C. elegans through a DNA tether to understand the molecular underpinnings of motor coordination during IFT in vivo. For motor pairs from both species, the co-transport velocities very nearly matched the single-molecule velocities, and both complexes spent roughly 80% of the time with only one of the two motors attached to the microtubule. Thus, irrespective of phylogeny and kinetic properties, kinesin-2 motors work mostly alone without sacrificing efficiency. Our findings thus offer a simple mechanism for how efficient IFT is achieved across diverse organisms despite being carried out by motors with different properties.
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Affiliation(s)
- Punam Sonar
- Physik Department E22, Technische Universität München, Garching 85748, Germany
| | - Wiphu Youyen
- Department of Physics, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
| | - Augustine Cleetus
- Physik Department E22, Technische Universität München, Garching 85748, Germany
| | | | - Sayed I Mousavi
- Department of Physics, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
| | - Willi L Stepp
- Physik Department E22, Technische Universität München, Garching 85748, Germany
| | - William O Hancock
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
| | - Erkan Tüzel
- Bioengineering Department, College of Engineering, Temple University, Philadelphia, PA 19122, USA
| | - Zeynep Ökten
- Physik Department E22, Technische Universität München, Garching 85748, Germany.
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21
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Ahmed Z, Mazumdar S, Ray K. Kinesin associated protein, DmKAP, binding harnesses the C-terminal ends of the Drosophila kinesin-2 stalk heterodimer. Biochem Biophys Res Commun 2019; 522:506-511. [PMID: 31784087 DOI: 10.1016/j.bbrc.2019.11.111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 11/17/2019] [Indexed: 01/01/2023]
Abstract
The heterotrimeric kinesin-2 consists of two distinct motor subunits and an accessory protein, KAP, which binds to the coiled-coil stalk domains and one of the tail domains of the motor subunits. Genetic studies revealed that KAP is essential for the kinesin-2 functions in cilia, flagella, and axon. However, the structural significance of the KAP binding on kinesin-2 assembly and stability is not known. Here, using the Fluorescence Lifetime assay, we show that DmKAP binding selectively reduces the distance between the C-terminal ends of Drosophila kinesin-2 stalk heterodimer. Insertion of a missense mutation (E551K) in the Drosophila kinesin-2α stalk fragment, which was shown to reduce the structural dynamics of the stalk heterodimer earlier, also reduced the distances at both the N- and C-terminal ends of the stalk heterodimer independent of DmKAP. The zipping effect, particularly at the N-terminal end of the mutant stalk heterodimer, is further enhanced in the presence of DmKAP. Together, these results suggest that the KAP binding could alter the structural dynamics of kinesin-2 stalk heterodimer at the C-terminal end and stabilize the association between the stalk domains.
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Affiliation(s)
- Zoheb Ahmed
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India
| | - Shyamalava Mazumdar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India
| | - Krishanu Ray
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India.
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22
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Engelke MF, Waas B, Kearns SE, Suber A, Boss A, Allen BL, Verhey KJ. Acute Inhibition of Heterotrimeric Kinesin-2 Function Reveals Mechanisms of Intraflagellar Transport in Mammalian Cilia. Curr Biol 2019; 29:1137-1148.e4. [PMID: 30905605 PMCID: PMC6445692 DOI: 10.1016/j.cub.2019.02.043] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 01/02/2019] [Accepted: 02/18/2019] [Indexed: 10/27/2022]
Abstract
The trafficking of components within cilia, called intraflagellar transport (IFT), is powered by kinesin-2 and dynein-2 motors. Loss of function in any subunit of the heterotrimeric KIF3A/KIF3B/KAP kinesin-2 motor prevents ciliogenesis in mammalian cells and has hindered an understanding of how kinesin-2 motors function in cilium assembly and IFT. We used a chemical-genetic approach to generate an inhibitable KIF3A/KIF3B/KAP kinesin-2 motor (i3A/i3B) that is capable of rescuing wild-type (WT) motor function for cilium assembly and Hedgehog signaling in Kif3a/Kif3b double-knockout cells. We demonstrate that KIF3A/KIF3B function is required not just for cilium assembly but also for cilium maintenance, as inhibition of i3A/i3B blocks IFT within 2 min and leads to a complete loss of primary cilia within 8 h. In contrast, inhibition of dynein-2 has no effect on cilium maintenance within the same time frame. The kinetics of cilia loss indicate that two processes contribute to ciliary disassembly in response to cessation of anterograde IFT: a slow shortening that is steady over time and a rapid deciliation that occurs with stochastic onset. We also demonstrate that the kinesin-2 family members KIF3A/KIF3C and KIF17 cannot rescue ciliogenesis in Kif3a/Kif3b double-knockout cells or delay the loss of assembled cilia upon i3A/i3B inhibition. These results demonstrate that KIF3A/KIF3B/KAP is the sole and essential motor for cilium assembly and maintenance in mammalian cells. These findings highlight differences in how kinesin-2 motors were adapted for cilium assembly and IFT function across species.
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Affiliation(s)
- Martin F Engelke
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA.
| | - Bridget Waas
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Sarah E Kearns
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA; Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ayana Suber
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Allison Boss
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Benjamin L Allen
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Kristen J Verhey
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA.
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23
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Wang Q, Peng Z, Long H, Deng X, Huang K. Polyubiquitylation of α-tubulin at K304 is required for flagellar disassembly in Chlamydomonas. J Cell Sci 2019; 132:jcs.229047. [PMID: 30765466 DOI: 10.1242/jcs.229047] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 02/06/2019] [Indexed: 12/20/2022] Open
Abstract
Cilia/flagella are structurally conserved and dynamic organelles; their assembly and disassembly are coordinated with the cell cycle and cell differentiation. Several post-translational modifications, including acetylation, methylation, phosphorylation and ubiquitylation, participate in ciliary disassembly. However, the detailed mechanism and the role of ubiquitylation in ciliary disassembly are unclear. This study identified 20 proteins that were ubiquitylated in shortening flagella of Chlamydomonas α-Tubulin was the most abundant ubiquitylated protein and it was labeled with K63 polyubiquitin chains primarily at K304. Expression of an α-tubulin mutant (K304R), which could not be ubiquitylated, decreased the rate of flagellar disassembly and resulted in an enrichment of the mutant form in the axoneme, suggesting that ubiquitylation of α-tubulin is required for the normal kinetics of axonemal disassembly. Immunoprecipitation and glutathione-S-transferase pulldown assays demonstrated that the retrograde intraflagellar transport (IFT) protein, IFT139, interacted with a variety of ubiquitylated proteins, including α-tubulin, suggesting that IFT-A was responsible for transporting ubiquitylated proteins out of the flagella. Our data suggest an important role for ubiquitylation and retrograde IFT in ciliary disassembly.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Qiyu Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China.,University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhao Peng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China.,University of Chinese Academy of Sciences, Beijing 100039, China
| | - Huan Long
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Xuan Deng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Kaiyao Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
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24
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Hendel NL, Thomson M, Marshall WF. Diffusion as a Ruler: Modeling Kinesin Diffusion as a Length Sensor for Intraflagellar Transport. Biophys J 2019; 114:663-674. [PMID: 29414712 PMCID: PMC5985012 DOI: 10.1016/j.bpj.2017.11.3784] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/30/2017] [Accepted: 11/29/2017] [Indexed: 02/01/2023] Open
Abstract
An important question in cell biology is whether cells are able to measure size, either whole cell size or organelle size. Perhaps cells have an internal chemical representation of size that can be used to precisely regulate growth, or perhaps size is just an accident that emerges due to constraint of nutrients. The eukaryotic flagellum is an ideal model for studying size sensing and control because its linear geometry makes it essentially one-dimensional, greatly simplifying mathematical modeling. The assembly of flagella is regulated by intraflagellar transport (IFT), in which kinesin motors carry cargo adaptors for flagellar proteins along the flagellum and then deposit them at the tip, lengthening the flagellum. The rate at which IFT motors are recruited to begin transport into the flagellum is anticorrelated with the flagellar length, implying some kind of communication between the base and the tip and possibly indicating that cells contain some mechanism for measuring flagellar length. Although it is possible to imagine many complex scenarios in which additional signaling molecules sense length and carry feedback signals to the cell body to control IFT, might the already-known components of the IFT system be sufficient to allow length dependence of IFT? Here we investigate a model in which the anterograde kinesin motors unbind after cargo delivery, diffuse back to the base, and are subsequently reused to power entry of new IFT trains into the flagellum. By mathematically modeling and simulating such a system, we are able to show that the diffusion time of the motors can in principle be sufficient to serve as a proxy for length measurement. We found that the diffusion model can not only achieve a stable steady-state length without the addition of any other signaling molecules or pathways, but also is able to produce the anticorrelation between length and IFT recruitment rate that has been observed in quantitative imaging studies.
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Affiliation(s)
- Nathan L Hendel
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California; Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, California
| | - Matthew Thomson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | - Wallace F Marshall
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California.
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25
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Cilium structure, assembly, and disassembly regulated by the cytoskeleton. Biochem J 2018; 475:2329-2353. [PMID: 30064990 PMCID: PMC6068341 DOI: 10.1042/bcj20170453] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/02/2018] [Accepted: 07/04/2018] [Indexed: 12/17/2022]
Abstract
The cilium, once considered a vestigial structure, is a conserved, microtubule-based organelle critical for transducing extracellular chemical and mechanical signals that control cell polarity, differentiation, and proliferation. The cilium undergoes cycles of assembly and disassembly that are controlled by complex inter-relationships with the cytoskeleton. Microtubules form the core of the cilium, the axoneme, and are regulated by post-translational modifications, associated proteins, and microtubule dynamics. Although actin and septin cytoskeletons are not major components of the axoneme, they also regulate cilium organization and assembly state. Here, we discuss recent advances on how these different cytoskeletal systems affect cilium function, structure, and organization.
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26
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Bower R, Tritschler D, Mills KV, Heuser T, Nicastro D, Porter ME. DRC2/CCDC65 is a central hub for assembly of the nexin-dynein regulatory complex and other regulators of ciliary and flagellar motility. Mol Biol Cell 2017; 29:137-153. [PMID: 29167384 PMCID: PMC5909927 DOI: 10.1091/mbc.e17-08-0510] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 11/13/2017] [Accepted: 11/15/2017] [Indexed: 02/01/2023] Open
Abstract
DRC2 is a subunit of the nexin–dynein regulatory complex linked to primary ciliary dyskinesia. Little is known about the impact of drc2 mutations on axoneme composition and structure. We used proteomic and structural approaches to reveal that DRC2 coassembles with DRC1 to attach the N-DRC to the A-tubule and mediate interactions with other regulatory structures. The nexin–dynein regulatory complex (N-DRC) plays a central role in the regulation of ciliary and flagellar motility. In most species, the N-DRC contains at least 11 subunits, but the specific function of each subunit is unknown. Mutations in three subunits (DRC1, DRC2/CCDC65, DRC4/GAS8) have been linked to defects in ciliary motility in humans and lead to a ciliopathy known as primary ciliary dyskinesia (PCD). Here we characterize the biochemical, structural, and motility phenotypes of two mutations in the DRC2 gene of Chlamydomonas. Using high-resolution proteomic and structural approaches, we find that the C-terminal region of DRC2 is critical for the coassembly of DRC2 and DRC1 to form the base plate of N-DRC and its attachment to the outer doublet microtubule. Loss of DRC2 in drc2 mutants disrupts the assembly of several other N-DRC subunits and also destabilizes the assembly of several closely associated structures such as the inner dynein arms, the radial spokes, and the calmodulin- and spoke-associated complex. Our study provides new insights into the range of ciliary defects that can lead to PCD.
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Affiliation(s)
- Raqual Bower
- Department of Genetics, Cell Biology, and Development, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Douglas Tritschler
- Department of Genetics, Cell Biology, and Development, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Kristyn VanderWaal Mills
- Department of Genetics, Cell Biology, and Development, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Thomas Heuser
- Biology Department and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454.,Vienna Biocenter Core Facilities, 1030 Vienna, Austria
| | - Daniela Nicastro
- Biology Department and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454.,Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Mary E Porter
- Department of Genetics, Cell Biology, and Development, University of Minnesota Medical School, Minneapolis, MN 55455
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27
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Dong B, Wu S, Wang J, Liu YX, Peng Z, Meng DM, Huang K, Wu M, Fan ZC. Chlamydomonas IFT25 is dispensable for flagellar assembly but required to export the BBSome from flagella. Biol Open 2017; 6:1680-1691. [PMID: 28838966 PMCID: PMC5703605 DOI: 10.1242/bio.026278] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Intraflagellar transport (IFT) particles are composed of polyprotein complexes IFT-A and IFT-B as well as cargo adaptors such as the BBSome. Two IFT-B subunits, IFT25 and IFT27 were found to form a heterodimer, which is essential in exporting the BBSome out of the cilium but not involved in flagellar assembly and cytokinesis in vertebrates. Controversial results were, however, recorded to show that defects in IFT, flagellar assembly and even cytokinesis were caused by IFT27 knockdown in Chlamydomonas reinhardtii. Using C. reinhardtii as a model organism, we report that depletion of IFT25 has no effect on flagellar assembly and does not affect the entry of the BBSome into the flagellum, but IFT25 depletion did impair BBSome movement out of the flagellum, clarifying the evolutionally conserved role of IFT25 in regulating the exit of the BBSome from the flagellum cross species. Interestingly, depletion of IFT25 causes dramatic reduction of IFT27 as expected, which does not cause defects in flagellar assembly and cytokinesis in C. reinhardtii. Our data thus support that Chlamydomonas IFT27, like its vertebrate homologues, is not involved in flagellar assembly and cytokinesis. Summary: Chlamydomonas IFT25 is not involved in flagellar assembly, but is required for export of the BBSome from the flagellum.
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Affiliation(s)
- Bin Dong
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Institute of Health Biotechnology, International Collaborative Research Center for Health Biotechnology, College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Song Wu
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Institute of Health Biotechnology, International Collaborative Research Center for Health Biotechnology, College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Jing Wang
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Institute of Health Biotechnology, International Collaborative Research Center for Health Biotechnology, College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Yan-Xia Liu
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Institute of Health Biotechnology, International Collaborative Research Center for Health Biotechnology, College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Zhao Peng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
| | - De-Mei Meng
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Institute of Health Biotechnology, International Collaborative Research Center for Health Biotechnology, College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Kaiyao Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
| | - Mingfu Wu
- Cardiovascular Science Center, Albany Medical College, Albany, New York 12208, USA
| | - Zhen-Chuan Fan
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Institute of Health Biotechnology, International Collaborative Research Center for Health Biotechnology, College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China .,Obesita & Algaegen LLC, College Station, Texas 77845, USA
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28
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Chien A, Shih SM, Bower R, Tritschler D, Porter ME, Yildiz A. Dynamics of the IFT machinery at the ciliary tip. eLife 2017; 6:28606. [PMID: 28930071 PMCID: PMC5662288 DOI: 10.7554/elife.28606] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 09/12/2017] [Indexed: 12/15/2022] Open
Abstract
Intraflagellar transport (IFT) is essential for the elongation and maintenance of eukaryotic cilia and flagella. Due to the traffic jam of multiple trains at the ciliary tip, how IFT trains are remodeled in these turnaround zones cannot be determined by conventional imaging. Using PhotoGate, we visualized the full range of movement of single IFT trains and motors in Chlamydomonas flagella. Anterograde trains split apart and IFT complexes mix with each other at the tip to assemble retrograde trains. Dynein-1b is carried to the tip by kinesin-II as inactive cargo on anterograde trains. Unlike dynein-1b, kinesin-II detaches from IFT trains at the tip and diffuses in flagella. As the flagellum grows longer, diffusion delays return of kinesin-II to the basal body, depleting kinesin-II available for anterograde transport. Our results suggest that dissociation of kinesin-II from IFT trains serves as a negative feedback mechanism that facilitates flagellar length control in Chlamydomonas.
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Affiliation(s)
- Alexander Chien
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States
| | - Sheng Min Shih
- Physics Department, University of California, Berkeley, Berkeley, United States
| | - Raqual Bower
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, United States
| | - Douglas Tritschler
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, United States
| | - Mary E Porter
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, United States
| | - Ahmet Yildiz
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States.,Physics Department, University of California, Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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29
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Ishikawa H, Marshall WF. Testing the time-of-flight model for flagellar length sensing. Mol Biol Cell 2017; 28:3447-3456. [PMID: 28931591 PMCID: PMC5687043 DOI: 10.1091/mbc.e17-06-0384] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 11/23/2022] Open
Abstract
A combination of quantitative imaging, modeling, and genetics has been used to test a proposed mechanism for measuring the size of an organelle. One way to measure distance is to send a clock out on a train and measure the elapsed time when the train returns. We tested a molecular version of this model as a possible regulator of intraflagellar transport by altering the return speed of the transport machinery and probing the effect on a known length-dependent process. Cilia and flagella are microtubule-based organelles that protrude from the surface of most cells, are important to the sensing of extracellular signals, and make a driving force for fluid flow. Maintenance of flagellar length requires an active transport process known as intraflagellar transport (IFT). Recent studies reveal that the amount of IFT injection negatively correlates with the length of flagella. These observations suggest that a length-dependent feedback regulates IFT. However, it is unknown how cells recognize the length of flagella and control IFT. Several theoretical models try to explain this feedback system. We focused on one of the models, the “time-of-flight” model, which measures the length of flagella on the basis of the travel time of IFT protein in the flagellar compartment. We tested the time-of-flight model using Chlamydomonas dynein mutant cells, which show slower retrograde transport speed. The amount of IFT injection in dynein mutant cells was higher than that in control cells. This observation does not support the prediction of the time-of-flight model and suggests that Chlamydomonas uses another length-control feedback system rather than that described by the time-of-flight model.
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Affiliation(s)
- Hiroaki Ishikawa
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143
| | - Wallace F Marshall
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143
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30
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Prevo B, Scholey JM, Peterman EJG. Intraflagellar transport: mechanisms of motor action, cooperation, and cargo delivery. FEBS J 2017; 284:2905-2931. [PMID: 28342295 PMCID: PMC5603355 DOI: 10.1111/febs.14068] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 02/20/2017] [Accepted: 03/23/2017] [Indexed: 02/06/2023]
Abstract
Intraflagellar transport (IFT) is a form of motor-dependent cargo transport that is essential for the assembly, maintenance, and length control of cilia, which play critical roles in motility, sensory reception, and signal transduction in virtually all eukaryotic cells. During IFT, anterograde kinesin-2 and retrograde IFT dynein motors drive the bidirectional transport of IFT trains that deliver cargo, for example, axoneme precursors such as tubulins as well as molecules of the signal transduction machinery, to their site of assembly within the cilium. Following its discovery in Chlamydomonas, IFT has emerged as a powerful model system for studying general principles of motor-dependent cargo transport and we now appreciate the diversity that exists in the mechanism of IFT within cilia of different cell types. The absence of heterotrimeric kinesin-2 function, for example, causes a complete loss of both IFT and cilia in Chlamydomonas, but following its loss in Caenorhabditis elegans, where its primary function is loading the IFT machinery into cilia, homodimeric kinesin-2-driven IFT persists and assembles a full-length cilium. Generally, heterotrimeric kinesin-2 and IFT dynein motors are thought to play widespread roles as core IFT motors, whereas homodimeric kinesin-2 motors are accessory motors that mediate different functions in a broad range of cilia, in some cases contributing to axoneme assembly or the delivery of signaling molecules but in many other cases their ciliary functions, if any, remain unknown. In this review, we focus on mechanisms of motor action, motor cooperation, and motor-dependent cargo delivery during IFT.
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Affiliation(s)
- Bram Prevo
- Department of Cellular & Molecular Medicine, University of California San Diego, CA, USA
- Ludwig Institute for Cancer Research, San Diego, CA, USA
| | - Jonathan M Scholey
- Department of Molecular & Cell Biology, University of California Davis, CA, USA
| | - Erwin J G Peterman
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit, Amsterdam, The Netherlands
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31
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Wingfield JL, Mengoni I, Bomberger H, Jiang YY, Walsh JD, Brown JM, Picariello T, Cochran DA, Zhu B, Pan J, Eggenschwiler J, Gaertig J, Witman GB, Kner P, Lechtreck K. IFT trains in different stages of assembly queue at the ciliary base for consecutive release into the cilium. eLife 2017; 6. [PMID: 28562242 PMCID: PMC5451262 DOI: 10.7554/elife.26609] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/16/2017] [Indexed: 12/13/2022] Open
Abstract
Intraflagellar transport (IFT) trains, multimegadalton assemblies of IFT proteins and motors, traffic proteins in cilia. To study how trains assemble, we employed fluorescence protein-tagged IFT proteins in Chlamydomonas reinhardtii. IFT-A and motor proteins are recruited from the cell body to the basal body pool, assembled into trains, move through the cilium, and disperse back into the cell body. In contrast to this ‘open’ system, IFT-B proteins from retrograde trains reenter the pool and a portion is reused directly in anterograde trains indicating a ‘semi-open’ system. Similar IFT systems were also observed in Tetrahymena thermophila and IMCD3 cells. FRAP analysis indicated that IFT proteins and motors of a given train are sequentially recruited to the basal bodies. IFT dynein and tubulin cargoes are loaded briefly before the trains depart. We conclude that the pool contains IFT trains in multiple stages of assembly queuing for successive release into the cilium upon completion. DOI:http://dx.doi.org/10.7554/eLife.26609.001
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Affiliation(s)
- Jenna L Wingfield
- Department of Cellular Biology, University of Georgia, Athens, United States
| | - Ilaria Mengoni
- Department of Cellular Biology, University of Georgia, Athens, United States
| | - Heather Bomberger
- Department of Cellular Biology, University of Georgia, Athens, United States.,College of Engineering, University of Georgia, Athens, United States
| | - Yu-Yang Jiang
- Department of Cellular Biology, University of Georgia, Athens, United States
| | - Jonathon D Walsh
- Department of Genetics, University of Georgia, Athens, United States
| | - Jason M Brown
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, United States.,Department of Biology, Salem State University, Salem, United States
| | - Tyler Picariello
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, United States
| | - Deborah A Cochran
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, United States
| | - Bing Zhu
- MOE Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Junmin Pan
- MOE Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | | | - Jacek Gaertig
- Department of Cellular Biology, University of Georgia, Athens, United States
| | - George B Witman
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, United States
| | - Peter Kner
- College of Engineering, University of Georgia, Athens, United States
| | - Karl Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, United States
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32
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Mizuno K, Sloboda RD. Protein arginine methyltransferases interact with intraflagellar transport particles and change location during flagellar growth and resorption. Mol Biol Cell 2017; 28:1208-1222. [PMID: 28298486 PMCID: PMC5415017 DOI: 10.1091/mbc.e16-11-0774] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/03/2017] [Accepted: 03/08/2017] [Indexed: 01/09/2023] Open
Abstract
Protein arginine methyl transferases are located at specific sites in the flagellum. They change location during changes in flagellar dynamics (i.e., resorption and regeneration) via interaction with intraflagellar transport trains. Changes in protein by posttranslational modifications comprise an important mechanism for the control of many cellular processes. Several flagellar proteins are methylated on arginine residues during flagellar resorption; however, the function is not understood. To learn more about the role of protein methylation during flagellar dynamics, we focused on protein arginine methyltransferases (PRMTs) 1, 3, 5, and 10. These PRMTs localize to the tip of flagella and in a punctate pattern along the length, very similar, but not identical, to that of intraflagellar transport (IFT) components. In addition, we found that PRMT 1 and 3 are also highly enriched at the base of the flagella, and the basal localization of these PRMTs changes during flagellar regeneration and resorption. Proteins with methyl arginine residues are also enriched at the tip and base of flagella, and their localization also changes during flagellar assembly and disassembly. PRMTs are lost from the flagella of fla10-1 cells, which carry a temperature-sensitive mutation in the anterograde motor for IFT. The data define the distribution of specific PRMTs and their target proteins in flagella and demonstrate that PRMTs are cargo for translocation within flagella by the process of IFT.
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Affiliation(s)
- Katsutoshi Mizuno
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755
| | - Roger D Sloboda
- Marine Biological Laboratory, Woods Hole, MA 02543 .,Marine Biological Laboratory, Woods Hole, MA 02543
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33
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Jiang X, Hernandez D, Hernandez C, Ding Z, Nan B, Aufderheide K, Qin H. IFT57 stabilizes assembled intraflagellar transport complex and mediates transport of motility-related flagellar cargo. J Cell Sci 2017; 130:879-891. [DOI: 10.1242/jcs.199117] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 01/11/2017] [Indexed: 11/20/2022] Open
Abstract
Intraflagellar Transport (IFT) is essential for flagella/cilia assembly and maintenance. Recent biochemical studies have shown that IFT-B is comprised of two subcomplexes, IFT-B1 and IFT-B2. The IFT-B2 subunit IFT57 lies at the interface between IFT-B1 and IFT-B2. Here, using a Chlamydomonas mutant for IFT57, we tested whether IFT57 is critical for IFT-B complex assembly by bridging IFT-B1 and IFT-B2 together. In the ift57-1 mutant, IFT57 and other IFT-B proteins were greatly reduced at the whole-cell level. Strikingly, in the protease free flagellar compartment, while the level of IFT57 was reduced, other IFT particle proteins were not concomitantly reduced but present at the wild-type level. The IFT movement of the IFT57-deficient-IFT particles was also unchanged. Moreover, IFT57 depletion disrupted the flagellar waveform, leading to cell swimming defects. Analysis of the mutant flagellar protein composition showed that certain axonemal proteins were altered. Taken together, these findings suggest that IFT57 does not play an essential structural role in the IFT particle complex but rather functions to prevent it from degradation. Additionally, IFT57 is involved in transporting specific motility-related proteins.
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Affiliation(s)
- Xue Jiang
- Department of Biology, Texas A&M University, College Station, Texas 77843-3258, USA
| | - Daniel Hernandez
- Department of Biology, Texas A&M University, College Station, Texas 77843-3258, USA
| | - Catherine Hernandez
- Department of Biology, Texas A&M University, College Station, Texas 77843-3258, USA
| | - Zhaolan Ding
- Department of Biology, Texas A&M University, College Station, Texas 77843-3258, USA
| | - Beiyan Nan
- Department of Biology, Texas A&M University, College Station, Texas 77843-3258, USA
| | - Karl Aufderheide
- Department of Biology, Texas A&M University, College Station, Texas 77843-3258, USA
| | - Hongmin Qin
- Department of Biology, Texas A&M University, College Station, Texas 77843-3258, USA
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34
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Stepanek L, Pigino G. Millisecond time resolution correlative light and electron microscopy for dynamic cellular processes. Methods Cell Biol 2017; 140:1-20. [DOI: 10.1016/bs.mcb.2017.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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35
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Albracht CD, Guzik-Lendrum S, Rayment I, Gilbert SP. Heterodimerization of Kinesin-2 KIF3AB Modulates Entry into the Processive Run. J Biol Chem 2016; 291:23248-23256. [PMID: 27637334 DOI: 10.1074/jbc.m116.752196] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Indexed: 11/06/2022] Open
Abstract
Mammalian KIF3AB is an N-terminal processive kinesin-2 that is best known for its roles in intracellular transport. There has been significant interest in KIF3AB to define the key principles that underlie its processivity but also to define the mechanistic basis of its sensitivity to force. In this study, the kinetics for entry into the processive run were quantified. The results show for KIF3AB that the kinetics of microtubule association at 7 μm-1 s-1 is less than the rates observed for KIF3AA at 13 μm-1 s-1 or KIF3BB at 11.9 μm-1 s-1 ADP release after microtubule association for KIF3AB is 33 s-1 and is significantly slower than ADP release from homodimeric KIF3AA and KIF3BB, which reach 80-90 s-1 To explore the interhead communication implied by the rate differences at these first steps, we compared the kinetics of KIF3AB microtubule association followed by ADP release with the kinetics for mixtures of KIF3AA plus KIF3BB. Surprisingly, the kinetics of KIF3AB are not equivalent to any of the mixtures of KIF3AA + KIF3BB. In fact, the transients for each of the mixtures overlay the transients for KIF3AA and KIF3BB. These results reveal that intermolecular communication within the KIF3AB heterodimer modulates entry into the processive run, and the results suggest that it is the high rate of microtubule association that drives rebinding to the microtubule after force-dependent motor detachment.
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Affiliation(s)
- Clayton D Albracht
- From the Department of Biological Sciences and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180 and
| | - Stephanie Guzik-Lendrum
- From the Department of Biological Sciences and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180 and
| | - Ivan Rayment
- the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Susan P Gilbert
- From the Department of Biological Sciences and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180 and
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36
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Reck J, Schauer AM, VanderWaal Mills K, Bower R, Tritschler D, Perrone CA, Porter ME. The role of the dynein light intermediate chain in retrograde IFT and flagellar function in Chlamydomonas. Mol Biol Cell 2016; 27:2404-22. [PMID: 27251063 PMCID: PMC4966982 DOI: 10.1091/mbc.e16-03-0191] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/26/2016] [Indexed: 12/28/2022] Open
Abstract
The assembly of cilia and flagella depends on the activity of two microtubule motor complexes, kinesin-2 and dynein-2/1b, but the specific functions of the different subunits are poorly defined. Here we analyze Chlamydomonas strains expressing different amounts of the dynein 1b light intermediate chain (D1bLIC). Disruption of D1bLIC alters the stability of the dynein 1b complex and reduces both the frequency and velocity of retrograde intraflagellar transport (IFT), but it does not eliminate retrograde IFT. Flagellar assembly, motility, gliding, and mating are altered in a dose-dependent manner. iTRAQ-based proteomics identifies a small subset of proteins that are significantly reduced or elevated in d1blic flagella. Transformation with D1bLIC-GFP rescues the mutant phenotypes, and D1bLIC-GFP assembles into the dynein 1b complex at wild-type levels. D1bLIC-GFP is transported with anterograde IFT particles to the flagellar tip, dissociates into smaller particles, and begins processive retrograde IFT in <2 s. These studies demonstrate the role of D1bLIC in facilitating the recycling of IFT subunits and other proteins, identify new components potentially involved in the regulation of IFT, flagellar assembly, and flagellar signaling, and provide insight into the role of D1bLIC and retrograde IFT in other organisms.
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Affiliation(s)
- Jaimee Reck
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455 R&D Systems, Minneapolis, MN 55413
| | - Alexandria M Schauer
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455 College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108
| | - Kristyn VanderWaal Mills
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455 Anoka Technical College, Anoka, MN 55303
| | - Raqual Bower
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455
| | - Douglas Tritschler
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455
| | - Catherine A Perrone
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455 Medtronic, Minneapolis, MN 55432
| | - Mary E Porter
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455
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37
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Ludington WB, Ishikawa H, Serebrenik YV, Ritter A, Hernandez-Lopez RA, Gunzenhauser J, Kannegaard E, Marshall WF. A systematic comparison of mathematical models for inherent measurement of ciliary length: how a cell can measure length and volume. Biophys J 2016; 108:1361-1379. [PMID: 25809250 DOI: 10.1016/j.bpj.2014.12.051] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 12/15/2014] [Accepted: 12/19/2014] [Indexed: 10/23/2022] Open
Abstract
Cells control organelle size with great precision and accuracy to maintain optimal physiology, but the mechanisms by which they do so are largely unknown. Cilia and flagella are simple organelles in which a single measurement, length, can represent size. Maintenance of flagellar length requires an active transport process known as intraflagellar transport, and previous measurements suggest that a length-dependent feedback regulates intraflagellar transport. But the question remains: how is a length-dependent signal produced to regulate intraflagellar transport appropriately? Several conceptual models have been suggested, but testing these models quantitatively requires that they be cast in mathematical form. Here, we derive a set of mathematical models that represent the main broad classes of hypothetical size-control mechanisms currently under consideration. We use these models to predict the relation between length and intraflagellar transport, and then compare the predicted relations for each model with experimental data. We find that three models-an initial bolus formation model, an ion current model, and a diffusion-based model-show particularly good agreement with available experimental data. The initial bolus and ion current models give mathematically equivalent predictions for length control, but fluorescence recovery after photobleaching experiments rule out the initial bolus model, suggesting that either the ion current model or a diffusion-based model is more likely correct. The general biophysical principles of the ion current and diffusion-based models presented here to measure cilia and flagellar length can be generalized to measure any membrane-bound organelle volume, such as the nucleus and endoplasmic reticulum.
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Affiliation(s)
- William B Ludington
- Department of Biophysics and Biochemistry, University of California, San Francisco, San Francisco, California
| | - Hiroaki Ishikawa
- Department of Biophysics and Biochemistry, University of California, San Francisco, San Francisco, California
| | - Yevgeniy V Serebrenik
- Department of Biophysics and Biochemistry, University of California, San Francisco, San Francisco, California
| | - Alex Ritter
- Physiology Course, Marine Biological Laboratory, Woods Hole, Massachusetts
| | | | - Julia Gunzenhauser
- Physiology Course, Marine Biological Laboratory, Woods Hole, Massachusetts
| | - Elisa Kannegaard
- Department of Biophysics and Biochemistry, University of California, San Francisco, San Francisco, California
| | - Wallace F Marshall
- Department of Biophysics and Biochemistry, University of California, San Francisco, San Francisco, California.
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Sloboda RD. Purification and Localization of Intraflagellar Transport Particles and Polypeptides. Methods Mol Biol 2016; 1365:119-37. [PMID: 26498782 DOI: 10.1007/978-1-4939-3124-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The growth and maintenance of almost all cilia and flagella are dependent on the proper functioning of the process of intraflagellar transport (IFT). This includes the primary cilia of most human cells that are in the Go phase of the cell cycle. The model system for the study of IFT is the flagella of the biflagellate green alga Chlamydomonas. It is in this organism that IFT was first discovered, and genetic data from a Chlamydomonas mutant first linked the process of IFT to polycystic kidney disease in humans. The information provided in this chapter addresses procedures to purify IFT particles from flagella and localize these particles, and their associated motor proteins, in flagella using light and electron microscopic approaches.
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Affiliation(s)
- Roger D Sloboda
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA.
- The Marine Biological Laboratory, Woods Hole, MA, 02543, USA.
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Abstract
The assembly of cilia and eukaryotic flagella (interchangeable terms) requires the import of numerous proteins from the cell body into the growing organelle. Proteins move into and inside cilia by diffusion and by motor-based intraflagellar transport (IFT). Many aspects of ciliary protein transport such as the distribution of unloading sites and the frequency of transport can be analyzed using direct in vivo imaging of fluorescently tagged proteins. Here, we will describe how to use total internal reflection fluorescence microcopy (TIRFM) to analyze protein transport in the flagella of the unicellular alga Chlamydomonas reinhardtii, a widely used model for cilia and cilia-related disease.
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40
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Lechtreck KF. IFT-Cargo Interactions and Protein Transport in Cilia. Trends Biochem Sci 2015; 40:765-778. [PMID: 26498262 PMCID: PMC4661101 DOI: 10.1016/j.tibs.2015.09.003] [Citation(s) in RCA: 226] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/07/2015] [Accepted: 09/11/2015] [Indexed: 12/30/2022]
Abstract
The motile and sensory functions of cilia and flagella are indispensable for human health. Cilia assembly requires a dedicated protein shuttle, intraflagellar transport (IFT), a bidirectional motility of multi-megadalton protein arrays along ciliary microtubules. IFT functions as a protein carrier delivering hundreds of distinct proteins into growing cilia. IFT-based protein import and export continue in fully grown cilia and are required for ciliary maintenance and sensing. Large ciliary building blocks might depend on IFT to move through the transition zone, which functions as a ciliary gate. Smaller, freely diffusing proteins, such as tubulin, depend on IFT to be concentrated or removed from cilia. As I discuss here, recent work provides insights into how IFT interacts with its cargoes and how the transport is regulated.
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Affiliation(s)
- Karl F Lechtreck
- Department of Cellular Biology, University of Georgia, 635C Biological Science Building, 1000 Cedar Street, Athens, GA 30602, USA.
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41
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Prevo B, Mangeol P, Oswald F, Scholey JM, Peterman EJG. Functional differentiation of cooperating kinesin-2 motors orchestrates cargo import and transport in C. elegans cilia. Nat Cell Biol 2015; 17:1536-45. [PMID: 26523365 DOI: 10.1038/ncb3263] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 09/30/2015] [Indexed: 12/19/2022]
Abstract
Intracellular transport depends on cooperation between distinct motor proteins. Two anterograde intraflagellar transport (IFT) motors, heterotrimeric kinesin-II and homodimeric OSM-3, cooperate to move cargo along Caenorhabditis elegans cilia. Here, using quantitative fluorescence microscopy, with single-molecule sensitivity, of IFT in living strains containing single-copy transgenes encoding fluorescent IFT proteins, we show that kinesin-II transports IFT trains through the ciliary base and transition zone to a 'handover zone' on the proximal axoneme. There, OSM-3 gradually replaces kinesin-II, yielding velocity profiles inconsistent with in vitro motility assays, and then drives transport to the ciliary tip. Dissociated kinesin-II motors undergo rapid turnaround and recycling to the ciliary base, whereas OSM-3 is recycled mainly to the handover zone. This reveals a functional differentiation in which the slower, less processive kinesin-II imports IFT trains into the cilium and OSM-3 drives their long-range transport, thereby optimizing cargo delivery.
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Affiliation(s)
- Bram Prevo
- Department of Physics and Astronomy and LaserLaB Amsterdam, VU University Amsterdam, De Boelelaan 1081 1081 HV Amsterdam, The Netherlands
| | - Pierre Mangeol
- Department of Physics and Astronomy and LaserLaB Amsterdam, VU University Amsterdam, De Boelelaan 1081 1081 HV Amsterdam, The Netherlands
| | - Felix Oswald
- Department of Physics and Astronomy and LaserLaB Amsterdam, VU University Amsterdam, De Boelelaan 1081 1081 HV Amsterdam, The Netherlands
| | - Jonathan M Scholey
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, California 95616, USA
| | - Erwin J G Peterman
- Department of Physics and Astronomy and LaserLaB Amsterdam, VU University Amsterdam, De Boelelaan 1081 1081 HV Amsterdam, The Netherlands
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Abstract
All of the same conceptual questions about size in organisms apply equally at the level of single cells. What determines the size, not only of the whole cell, but of all of its parts? What ensures that subcellular components are properly proportioned relative to the whole cell? How does alteration in organelle size affect biochemical function? Answering such fundamental questions requires us to understand how the size of individual organelles and other cellular structures is determined. Knowledge of organelle biogenesis and dynamics has advanced rapidly in recent years. Does this knowledge give us enough information to formulate reasonable models for organelle size control, or are we still missing something?
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Affiliation(s)
- Wallace F Marshall
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, California 94158
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Lin H, Dutcher SK. Genetic and genomic approaches to identify genes involved in flagellar assembly in Chlamydomonas reinhardtii. Methods Cell Biol 2015; 127:349-86. [PMID: 25837400 DOI: 10.1016/bs.mcb.2014.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Flagellar assembly requires intraflagellar transport of components from the cell body to the flagellar tip for assembly. The understanding of flagellar assembly has been aided by the ease of biochemistry and the availability of mutants in the unicellular green alga, Chlamydomonas reinhardtii. In this chapter, we discuss means to identify genes involved in these processes using forward and reverse genetics. In particular, the ease and low cost of whole genome sequencing (WGS) will help to make gene identification easier and promote the understanding of this important process.
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Affiliation(s)
- Huawen Lin
- Department of Genetics, Washington University, St. Louis, MO, USA
| | - Susan K Dutcher
- Department of Genetics, Washington University, St. Louis, MO, USA.
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Craft JM, Harris JA, Hyman S, Kner P, Lechtreck KF. Tubulin transport by IFT is upregulated during ciliary growth by a cilium-autonomous mechanism. ACTA ACUST UNITED AC 2015; 208:223-37. [PMID: 25583998 PMCID: PMC4298693 DOI: 10.1083/jcb.201409036] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In Chlamydomonas cilia, IFT concentrates soluble tubulin by regulating IFT train occupancy and thereby promotes elongation of axonemal microtubules. The assembly of the axoneme, the structural scaffold of cilia and flagella, requires translocation of a vast quantity of tubulin into the growing cilium, but the mechanisms that regulate the targeting, quantity, and timing of tubulin transport are largely unknown. In Chlamydomonas, GFP-tagged α-tubulin enters cilia as an intraflagellar transport (IFT) cargo and by diffusion. IFT-based transport of GFP-tubulin is elevated in growing cilia and IFT trains carry more tubulin. Cells possessing both nongrowing and growing cilia selectively target GFP-tubulin into the latter. The preferential delivery of tubulin boosts the concentration of soluble tubulin in the matrix of growing versus steady-state cilia. Cilia length mutants show abnormal kinetics of tubulin transport. We propose that cells regulate the extent of occupancy of IFT trains by tubulin cargoes. During ciliary growth, IFT concentrates soluble tubulin in cilia and thereby promotes elongation of the axonemal microtubules.
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Affiliation(s)
- Julie M Craft
- Department of Cellular Biology and College of Engineering, University of Georgia, Athens, GA 30602
| | - J Aaron Harris
- Department of Cellular Biology and College of Engineering, University of Georgia, Athens, GA 30602
| | - Sebastian Hyman
- Department of Cellular Biology and College of Engineering, University of Georgia, Athens, GA 30602
| | - Peter Kner
- Department of Cellular Biology and College of Engineering, University of Georgia, Athens, GA 30602
| | - Karl F Lechtreck
- Department of Cellular Biology and College of Engineering, University of Georgia, Athens, GA 30602
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Awata J, Takada S, Standley C, Lechtreck KF, Bellvé KD, Pazour GJ, Fogarty KE, Witman GB. NPHP4 controls ciliary trafficking of membrane proteins and large soluble proteins at the transition zone. J Cell Sci 2014; 127:4714-27. [PMID: 25150219 DOI: 10.1242/jcs.155275] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The protein nephrocystin-4 (NPHP4) is widespread in ciliated organisms, and defects in NPHP4 cause nephronophthisis and blindness in humans. To learn more about the function of NPHP4, we have studied it in Chlamydomonas reinhardtii. NPHP4 is stably incorporated into the distal part of the flagellar transition zone, close to the membrane and distal to CEP290, another transition zone protein. Therefore, these two proteins, which are incorporated into the transition zone independently of each other, define different domains of the transition zone. An nphp4-null mutant forms flagella with nearly normal length, ultrastructure and intraflagellar transport. When fractions from isolated wild-type and nphp4 flagella were compared, few differences were observed between the axonemes, but the amounts of certain membrane proteins were greatly reduced in the mutant flagella, and cellular housekeeping proteins >50 kDa were no longer excluded from mutant flagella. Therefore, NPHP4 functions at the transition zone as an essential part of a barrier that regulates both membrane and soluble protein composition of flagella. The phenotypic consequences of NPHP4 mutations in humans likely follow from protein mislocalization due to defects in the transition zone barrier.
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Affiliation(s)
- Junya Awata
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Saeko Takada
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Clive Standley
- Biomedical Imaging Group, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Karl F Lechtreck
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Karl D Bellvé
- Biomedical Imaging Group, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Kevin E Fogarty
- Biomedical Imaging Group, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - George B Witman
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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Bhogaraju S, Weber K, Engel BD, Lechtreck KF, Lorentzen E. Getting tubulin to the tip of the cilium: One IFT train, many different tubulin cargo-binding sites? Bioessays 2014; 36:463-7. [DOI: 10.1002/bies.201400007] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Sagar Bhogaraju
- Department of Structural Cell Biology; Max-Planck-Institute of Biochemistry; Martinsried Germany
| | - Kristina Weber
- Department of Structural Cell Biology; Max-Planck-Institute of Biochemistry; Martinsried Germany
| | - Benjamin D. Engel
- Department of Molecular Structural Biology; Max-Planck-Institute of Biochemistry; Martinsried Germany
| | | | - Esben Lorentzen
- Department of Structural Cell Biology; Max-Planck-Institute of Biochemistry; Martinsried Germany
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47
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Ishikawa H, Ide T, Yagi T, Jiang X, Hirono M, Sasaki H, Yanagisawa H, Wemmer KA, Stainier DY, Qin H, Kamiya R, Marshall WF. TTC26/DYF13 is an intraflagellar transport protein required for transport of motility-related proteins into flagella. eLife 2014; 3:e01566. [PMID: 24596149 PMCID: PMC3936282 DOI: 10.7554/elife.01566] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Cilia/flagella are assembled and maintained by the process of intraflagellar transport (IFT), a highly conserved mechanism involving more than 20 IFT proteins. However, the functions of individual IFT proteins are mostly unclear. To help address this issue, we focused on a putative IFT protein TTC26/DYF13. Using live imaging and biochemical approaches we show that TTC26/DYF13 is an IFT complex B protein in mammalian cells and Chlamydomonas reinhardtii. Knockdown of TTC26/DYF13 in zebrafish embryos or mutation of TTC26/DYF13 in C. reinhardtii, produced short cilia with abnormal motility. Surprisingly, IFT particle assembly and speed were normal in dyf13 mutant flagella, unlike in other IFT complex B mutants. Proteomic and biochemical analyses indicated a particular set of proteins involved in motility was specifically depleted in the dyf13 mutant. These results support the concept that different IFT proteins are responsible for different cargo subsets, providing a possible explanation for the complexity of the IFT machinery. DOI: http://dx.doi.org/10.7554/eLife.01566.001.
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Affiliation(s)
- Hiroaki Ishikawa
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
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Wren KN, Craft JM, Tritschler D, Schauer A, Patel DK, Smith EF, Porter ME, Kner P, Lechtreck KF. A differential cargo-loading model of ciliary length regulation by IFT. Curr Biol 2013; 23:2463-71. [PMID: 24316207 DOI: 10.1016/j.cub.2013.10.044] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 09/23/2013] [Accepted: 10/14/2013] [Indexed: 01/07/2023]
Abstract
BACKGROUND During the assembly and maintenance of cilia, precursor proteins need to be transported from the cell body into the organelle. Intraflagellar transport (IFT) is assumed to be the predominant protein transport pathway in cilia, but it remains largely unknown how ciliary proteins use IFT to reach their destination sites in the cilium and whether the amount of cargo transported by IFT is regulated. RESULTS Single-particle imaging showed that DRC4, a structural protein of the axoneme, moves in association with IFT particles inside Chlamydomonas reinhardtii cilia. IFT is required for DRC4 transport both into and within the cilium. DRC4 cargoes dissociate from IFT trains at the tip as well as at various sites along the length of the cilium. Unloaded DRC4 diffuses before docking at its axonemal assembly site. In growing cilia, DRC4 transport by IFT was strongly increased over the steady-state level, and the frequency decreased linearly with the increasing ciliary length. The frequency of DRC4 transport was similarly elevated in short growth-arrested cilia and remained high even when the amount of DRC4 available in the cell body was reduced. CONCLUSIONS DRC4 is a bona fide cargo of IFT. Incompletely assembled cilia trigger an increase in the amount of DRC4 cargo transported by IFT particles, and DRC4 transport is downregulated as cilia approach their steady-state length. We propose a model in which ciliary length is controlled by regulating the amount of cargo transported by IFT particles.
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Affiliation(s)
- Kathryne N Wren
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Julie M Craft
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Douglas Tritschler
- Department of Genetics, Cell Biology and Development, University of Minnesota, MN 55455, USA
| | - Alexandria Schauer
- Department of Genetics, Cell Biology and Development, University of Minnesota, MN 55455, USA
| | - Deep K Patel
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Elizabeth F Smith
- Department of Biological Science, Dartmouth College, Hanover, NH 03755, USA
| | - Mary E Porter
- Department of Genetics, Cell Biology and Development, University of Minnesota, MN 55455, USA
| | - Peter Kner
- College of Engineering, 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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Morga B, Bastin P. Getting to the heart of intraflagellar transport using Trypanosoma and Chlamydomonas models: the strength is in their differences. Cilia 2013; 2:16. [PMID: 24289478 PMCID: PMC4015504 DOI: 10.1186/2046-2530-2-16] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 11/11/2013] [Indexed: 11/22/2022] Open
Abstract
Cilia and flagella perform diverse roles in motility and sensory perception, and defects in their construction or their function are responsible for human genetic diseases termed ciliopathies. Cilia and flagella construction relies on intraflagellar transport (IFT), the bi-directional movement of ‘trains’ composed of protein complexes found between axoneme microtubules and the flagellum membrane. Although extensive information about IFT components and their mode of action were discovered in the green algae Chlamydomonas reinhardtii, other model organisms have revealed further insights about IFT. This is the case of Trypanosoma brucei, a flagellated protist responsible for sleeping sickness that is turning out to be an emerging model for studying IFT. In this article, we review different aspects of IFT, based on studies of Chlamydomonas and Trypanosoma. Data available from both models are examined to ask challenging questions about IFT such as the initiation of flagellum construction, the setting-up of IFT and the mode of formation of IFT trains, and their remodeling at the tip as well as their recycling at the base. Another outstanding question is the individual role played by the multiple IFT proteins. The use of different models, bringing their specific biological and experimental advantages, will be invaluable in order to obtain a global understanding of IFT.
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Affiliation(s)
- Benjamin Morga
- Trypanosome Cell Biology Unit, Institut Pasteur and CNRS, URA 2581, 25 rue du Docteur Roux, 75015, Paris, France.
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50
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Flagellar central pair assembly in Chlamydomonas reinhardtii. Cilia 2013; 2:15. [PMID: 24283352 PMCID: PMC3895805 DOI: 10.1186/2046-2530-2-15] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 11/13/2013] [Indexed: 11/21/2022] Open
Abstract
Background Most motile cilia and flagella have nine outer doublet and two central pair (CP) microtubules. Outer doublet microtubules are continuous with the triplet microtubules of the basal body, are templated by the basal body microtubules, and grow by addition of new subunits to their distal (“plus”) ends. In contrast, CP microtubules are not continuous with basal body microtubules, raising the question of how these microtubules are assembled and how their polarity is established. Methods CP assembly in Chlamydomonas reinhardtii was analyzed by electron microscopy and wide-field and super-resolution immunofluorescence microscopy. To analyze CP assembly independently from flagellar assembly, the CP-deficient katanin mutants pf15 or pf19 were mated to wild-type cells. HA-tagged tubulin and the CP-specific protein hydin were used as markers to analyze de novo CP assembly inside the formerly mutant flagella. Results In regenerating flagella, the CP and its projections assemble near the transition zone soon after the onset of outer doublet elongation. During de novo CP assembly in full-length flagella, the nascent CP was first apparent in a subdistal region of the flagellum. The developing CP replaces a fibrous core that fills the axonemal lumen of CP-deficient flagella. The fibrous core contains proteins normally associated with the C1 CP microtubule and proteins involved in intraflagellar transport (IFT). In flagella of the radial spoke-deficient mutant pf14, two pairs of CPs are frequently present with identical correct polarities. Conclusions The temporal separation of flagellar and CP assembly in dikaryons formed by mating CP-deficient gametes to wild-type gametes revealed that the formation of the CP does not require proximity to the basal body or transition zone, or to the flagellar tip. The observations on pf14 provide further support that the CP self-assembles without a template and eliminate the possibility that CP polarity is established by interaction with axonemal radial spokes. Polarity of the developing CP may be determined by the proximal-to-distal gradient of precursor molecules. IFT proteins accumulate in flagella of CP mutants; the abnormal distribution of IFT proteins may explain why these flagella are often shorter than normal.
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