51
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Hibbard JVK, Vázquez N, Wallingford JB. Cilia proteins getting to work - how do they commute from the cytoplasm to the base of cilia? J Cell Sci 2022; 135:jcs259444. [PMID: 36073764 PMCID: PMC9482345 DOI: 10.1242/jcs.259444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cilia are multifunctional organelles that originated with the last eukaryotic common ancestor and play central roles in the life cycles of diverse organisms. The motile flagella that move single cells like sperm or unicellular organisms, the motile cilia on animal multiciliated cells that generate fluid flow in organs, and the immotile primary cilia that decorate nearly all cells in animals share many protein components in common, yet each also requires specialized proteins to perform their specialized functions. Despite a now-advanced understanding of how such proteins are transported within cilia, we still know very little about how they are transported from their sites of synthesis through the cytoplasm to the ciliary base. Here, we review the literature concerning this underappreciated topic in ciliary cell biology. We discuss both general mechanisms, as well as specific examples of motor-driven active transport and passive transport via diffusion-and-capture. We then provide deeper discussion of specific, illustrative examples, such as the diverse array of protein subunits that together comprise the intraflagellar transport (IFT) system and the multi-protein axonemal dynein motors that drive beating of motile cilia. We hope this Review will spur further work, shedding light not only on ciliogenesis and ciliary signaling, but also on intracellular transport in general.
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Affiliation(s)
| | | | - John B. Wallingford
- Department of Molecular Biosciences, University of Texas, Austin, TX 78751, USA
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52
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Dai J, Zhang G, Alkhofash RA, Mekonnen B, Saravanan S, Xue B, Fan ZC, Betleja E, Cole DG, Liu P, Lechtreck K. Loss of ARL13 impedes BBSome-dependent cargo export from Chlamydomonas cilia. J Cell Biol 2022; 221:213429. [PMID: 36040375 PMCID: PMC9436004 DOI: 10.1083/jcb.202201050] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/12/2022] [Accepted: 07/11/2022] [Indexed: 12/25/2022] Open
Abstract
The GTPase Arl13b participates in ciliary protein transport, but its contribution to intraflagellar transport (IFT), the main motor-based protein shuttle of cilia, remains largely unknown. Chlamydomonas arl13 mutant cilia were characterized by both abnormal reduction and accumulation of select membrane-associated proteins. With respect to the latter, a similar set of proteins including phospholipase D (PLD) also accumulated in BBSome-deficient cilia. IFT and BBSome traffic were apparently normal in arl13. However, transport of PLD, which in control cells moves by BBSome-dependent IFT, was impaired in arl13, causing PLD to accumulate in cilia. ARL13 only rarely and transiently traveled by IFT, indicating that it is not a co-migrating adapter securing PLD to IFT trains. In conclusion, the loss of Chlamydomonas ARL13 impedes BBSome-dependent protein transport, resulting in overlapping biochemical defects in arl13 and bbs mutant cilia.
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Affiliation(s)
- Jin Dai
- Cellular Biology, University of Georgia, Athens, GA
| | - Gui Zhang
- Cellular Biology, University of Georgia, Athens, GA
| | | | | | | | - Bin Xue
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Zhen-Chuan Fan
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | | | | | - Peiwei Liu
- College of Life Science, Shandong Normal University, Jinan, Shandong, China
| | - Karl Lechtreck
- Cellular Biology, University of Georgia, Athens, GA,Correspondence to Karl F. Lechtreck:
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53
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Jiang X, Shao W, Chai Y, Huang J, Mohamed MAA, Ökten Z, Li W, Zhu Z, Ou G. DYF-5/MAK-dependent phosphorylation promotes ciliary tubulin unloading. Proc Natl Acad Sci U S A 2022; 119:e2207134119. [PMID: 35969738 PMCID: PMC9407615 DOI: 10.1073/pnas.2207134119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/23/2022] [Indexed: 12/21/2022] Open
Abstract
Cilia are microtubule-based organelles that power cell motility and regulate sensation and signaling, and abnormal ciliary structure and function cause various ciliopathies. Cilium formation and maintenance requires intraflagellar transport (IFT), during which the kinesin-2 family motor proteins ferry IFT particles carrying axonemal precursors such as tubulins into cilia. Tubulin dimers are loaded to IFT machinery through an interaction between tubulin and the IFT-74/81 module; however, little is known of how tubulins are unloaded when arriving at the ciliary tip. Here, we show that the ciliary kinase DYF-5/MAK phosphorylates multiple sites within the tubulin-binding module of IFT-74, reducing the tubulin-binding affinity of IFT-74/81 approximately sixfold. Ablation or constitutive activation of IFT-74 phosphorylation abnormally elongates or shortens sensory cilia in Caenorhabditis elegans neurons. We propose that DYF-5/MAK-dependent phosphorylation plays a fundamental role in ciliogenesis by regulating tubulin unloading.
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Affiliation(s)
- Xuguang Jiang
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences and Ministry of Education Key Laboratory for Protein Science, Tsinghua University, Beijing 100084, China
| | - Wenxin Shao
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences and Ministry of Education Key Laboratory for Protein Science, Tsinghua University, Beijing 100084, China
| | - Yongping Chai
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences and Ministry of Education Key Laboratory for Protein Science, Tsinghua University, Beijing 100084, China
| | - Jingying Huang
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences and Ministry of Education Key Laboratory for Protein Science, Tsinghua University, Beijing 100084, China
| | - Mohamed A. A. Mohamed
- Center for Protein Assemblies, Physics Department, E22, Technical University of Munich, 85748 Garching, Germany
| | - Zeynep Ökten
- Center for Protein Assemblies, Physics Department, E22, Technical University of Munich, 85748 Garching, Germany
| | - Wei Li
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Zhiwen Zhu
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences and Ministry of Education Key Laboratory for Protein Science, Tsinghua University, Beijing 100084, China
| | - Guangshuo Ou
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences and Ministry of Education Key Laboratory for Protein Science, Tsinghua University, Beijing 100084, China
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54
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Abstract
Cilium formation and regeneration requires new protein synthesis, but the underlying cytosolic translational reprogramming remains largely unknown. Using ribosome footprinting, we performed global translatome profiling during cilia regeneration in Chlamydomonas and uncovered that flagellar genes undergo an early transcriptional activation but late translational repression. This pattern guided our identification of sphingolipid metabolism enzymes, including serine palmitoyltransferase (SPT), as essential regulators for ciliogenesis. Cryo-electron tomography showed that ceramide loss abnormally increased the membrane-axoneme distance and generated bulged cilia. We found that ceramides interact with intraflagellar transport (IFT) particle proteins that IFT motors transport along axoneme microtubules (MTs), suggesting that ceramide-IFT particle-IFT motor-MT interactions connect the ciliary membrane with the axoneme to form rod-shaped cilia. SPT-deficient vertebrate cells were defective in ciliogenesis, and SPT mutations from patients with hereditary sensory neuropathy disrupted cilia, which could be restored by sphingolipid supplementation. These results reveal a conserved role of sphingolipid in cilium formation and link compromised sphingolipid production with ciliopathies.
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55
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Guido I, Vilfan A, Ishibashi K, Sakakibara H, Shiraga M, Bodenschatz E, Golestanian R, Oiwa K. A Synthetic Minimal Beating Axoneme. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107854. [PMID: 35815940 DOI: 10.1002/smll.202107854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Cilia and flagella are beating rod-like organelles that enable the directional movement of microorganisms in fluids and fluid transport along the surface of biological organisms or inside organs. The molecular motor axonemal dynein drives their beating by interacting with microtubules. Constructing synthetic beating systems with axonemal dynein capable of mimicking ciliary beating still represents a major challenge. Here, the bottom-up engineering of a sustained beating synthoneme consisting of a pair of microtubules connected by a series of periodic arrays of approximately eight axonemal dyneins is reported. A model leads to the understanding of the motion through the cooperative, cyclic association-dissociation of the molecular motor from the microtubules. The synthoneme represents a bottom-up self-organized bio-molecular machine at the nanoscale with cilia-like properties.
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Affiliation(s)
- Isabella Guido
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), 37077, Göttingen, Germany
| | - Andrej Vilfan
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), 37077, Göttingen, Germany
- Jožef Stefan Institute, Ljubljana, 1000, Slovenia
| | - Kenta Ishibashi
- Graduate School of Frontier Biosciences, Osaka University, Osaka, 5650871, Japan
- Center for Information and Neural Networks (CiNet), National Institute of Information and Communications Technology, Osaka, 565-0871, Japan
| | - Hitoshi Sakakibara
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, 651-2492, Japan
| | - Misaki Shiraga
- Graduate School of Life Science, University of Hyogo, Hyogo, 678-1297, Japan
| | - Eberhard Bodenschatz
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), 37077, Göttingen, Germany
- Institute for Dynamics of Complex Systems, Georg-August-University Göttingen, 37073, Göttingen, Germany
- Laboratory of Atomic and Solid-State Physics, Cornell University, Ithaca, NY, 14853, USA
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), 37077, Göttingen, Germany
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Kazuhiro Oiwa
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, 651-2492, Japan
- Graduate School of Life Science, University of Hyogo, Hyogo, 678-1297, Japan
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56
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Abstract
Flagellar-driven motility grants unicellular organisms the ability to gather more food and avoid predators, but the energetic costs of construction and operation of flagella are considerable. Paths of flagellar evolution depend on the deviations between fitness gains and energy costs. Using structural data available for all three major flagellar types (bacterial, archaeal, and eukaryotic), flagellar construction costs were determined for Escherichia coli, Pyrococcus furiosus, and Chlamydomonas reinhardtii. Estimates of cell volumes, flagella numbers, and flagellum lengths from the literature yield flagellar costs for another ~200 species. The benefits of flagellar investment were analysed in terms of swimming speed, nutrient collection, and growth rate; showing, among other things, that the cost-effectiveness of bacterial and eukaryotic flagella follows a common trend. However, a comparison of whole-cell costs and flagellum costs across the Tree of Life reveals that only cells with larger cell volumes than the typical bacterium could evolve the more expensive eukaryotic flagellum. These findings provide insight into the unsolved evolutionary question of why the three domains of life each carry their own type of flagellum.
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Affiliation(s)
- Paul E Schavemaker
- Biodesign Center for Mechanisms of Evolution, Arizona State UniversityTempeUnited States
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State UniversityTempeUnited States
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57
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Wang L, Wen X, Wang Z, Lin Z, Li C, Zhou H, Yu H, Li Y, Cheng Y, Chen Y, Lou G, Pan J, Cao M. Ciliary transition zone proteins coordinate ciliary protein composition and ectosome shedding. Nat Commun 2022; 13:3997. [PMID: 35810181 PMCID: PMC9271036 DOI: 10.1038/s41467-022-31751-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 06/30/2022] [Indexed: 11/09/2022] Open
Abstract
The transition zone (TZ) of the cilium/flagellum serves as a diffusion barrier that controls the entry/exit of ciliary proteins. Mutations of the TZ proteins disrupt barrier function and lead to multiple human diseases. However, the systematic regulation of ciliary composition and signaling-related processes by different TZ proteins is not completely understood. Here, we reveal that loss of TCTN1 in Chlamydomonas reinhardtii disrupts the assembly of wedge-shaped structures in the TZ. Proteomic analysis of cilia from WT and three TZ mutants, tctn1, cep290, and nphp4, shows a unique role of each TZ subunit in the regulation of ciliary composition, explaining the phenotypic diversity of different TZ mutants. Interestingly, we find that defects in the TZ impair the formation and biological activity of ciliary ectosomes. Collectively, our findings provide systematic insights into the regulation of ciliary composition by TZ proteins and reveal a link between the TZ and ciliary ectosomes. Cilia project from cells to serve sensory functions, and ciliary disruption can result in multiple disorders known as ciliopathies. Here the authors show that the ciliopathy gene TCTN1 functions to regulate the ciliary transition zone and ectosome formation.
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Affiliation(s)
- Liang Wang
- School of Life Sciences, Jiangsu Normal University, 221116, Xuzhou, China.
| | - Xin Wen
- School of Life Sciences, Jiangsu Normal University, 221116, Xuzhou, China
| | - Zhengmao Wang
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266071, Qingdao, China.,MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Zaisheng Lin
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Chunhong Li
- School of Life Sciences, Jiangsu Normal University, 221116, Xuzhou, China
| | - Huilin Zhou
- School of Life Sciences, Jiangsu Normal University, 221116, Xuzhou, China
| | - Huimin Yu
- School of Life Sciences, Jiangsu Normal University, 221116, Xuzhou, China
| | - Yuhan Li
- School of Life Sciences, Jiangsu Normal University, 221116, Xuzhou, China
| | - Yifei Cheng
- School of Life Sciences, Jiangsu Normal University, 221116, Xuzhou, China
| | - Yuling Chen
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Geer Lou
- Shanghai Biotree Biotech Co. Ltd, 201815, Shanghai, China
| | - Junmin Pan
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266071, Qingdao, China.,MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Muqing Cao
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
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58
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Martín-Salazar JE, Valverde D. CPLANE Complex and Ciliopathies. Biomolecules 2022; 12:biom12060847. [PMID: 35740972 PMCID: PMC9221175 DOI: 10.3390/biom12060847] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/10/2022] [Accepted: 06/16/2022] [Indexed: 02/04/2023] Open
Abstract
Primary cilia are non-motile organelles associated with the cell cycle, which can be found in most vertebrate cell types. Cilia formation occurs through a process called ciliogenesis, which involves several mechanisms including planar cell polarity (PCP) and the Hedgehog (Hh) signaling pathway. Some gene complexes, such as BBSome or CPLANE (ciliogenesis and planar polarity effector), have been linked to ciliogenesis. CPLANE complex is composed of INTU, FUZ and WDPCP, which bind to JBTS17 and RSG1 for cilia formation. Defects in these genes have been linked to a malfunction of intraflagellar transport and defects in the planar cell polarity, as well as defective activation of the Hedgehog signalling pathway. These faults lead to defective cilium formation, resulting in ciliopathies, including orofacial-digital syndrome (OFDS) and Bardet-Biedl syndrome (BBS). Considering the close relationship, between the CPLANE complex and cilium formation, it can be expected that defects in the genes that encode subunits of the CPLANE complex may be related to other ciliopathies.
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Affiliation(s)
| | - Diana Valverde
- CINBIO, Biomedical Research Centre, University of Vigo, 36310 Vigo, Spain;
- Galicia Sur Health Research Institute (IIS-GS), 36310 Vigo, Spain
- Correspondence:
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59
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Chen X, Shi Z, Yang F, Zhou T, Xie S. Deciphering cilia and ciliopathies using proteomic approaches. FEBS J 2022; 290:2590-2603. [PMID: 35633520 DOI: 10.1111/febs.16538] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/21/2022] [Accepted: 05/19/2022] [Indexed: 12/01/2022]
Abstract
Cilia are microtubule-based organelles that protrude from the cell surface and play crucial roles in cellular signaling pathways and extracellular fluid movement. Defects in the ciliary structures and functions are implicated in a set of hereditary disorders, including polycystic kidney disease, nephronophthisis, and Bardet-Biedl syndrome, which are collectively termed as ciliopathies. The application of mass spectrometry-based proteomic approaches to explore ciliary components provides important clues for understanding their physiological and pathological roles. In this review, we focus primarily on proteomic studies involving the identification of proteins in motile cilia and primary cilia, proteomes in ciliopathies, and interactomes of ciliopathy proteins. Collectively, the integration of these data sets will be beneficial for the comprehensive understanding of ciliary structures and exploring potential biomarkers and therapeutic targets for ciliopathies.
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Affiliation(s)
- Xiying Chen
- The Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China.,Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhouyuanjing Shi
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Feng Yang
- The Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China.,Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Tianhua Zhou
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Shanshan Xie
- The Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China.,Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, China
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60
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Cui G, Liew YJ, Konciute MK, Zhan Y, Hung SH, Thistle J, Gastoldi L, Schmidt-Roach S, Dekker J, Aranda M. Nutritional control regulates symbiont proliferation and life history in coral-dinoflagellate symbiosis. BMC Biol 2022; 20:103. [PMID: 35549698 PMCID: PMC9102920 DOI: 10.1186/s12915-022-01306-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 04/22/2022] [Indexed: 12/18/2022] Open
Abstract
Background The coral-Symbiodiniaceae symbiosis is fundamental for the coral reef ecosystem. Corals provide various inorganic nutrients to their algal symbionts in exchange for the photosynthates to meet their metabolic demands. When becoming symbionts, Symbiodiniaceae cells show a reduced proliferation rate and a different life history. While it is generally believed that the animal hosts play critical roles in regulating these processes, far less is known about the molecular underpinnings that allow the corals to induce the changes in their symbionts. Results We tested symbiont cell proliferation and life stage changes in vitro in response to different nutrient-limiting conditions to determine the key nutrients and to compare the respective symbiont transcriptomic profiles to cells in hospite. We then examined the effects of nutrient repletion on symbiont proliferation in coral hosts and quantified life stage transitions in vitro using time-lapse confocal imaging. Here, we show that symbionts in hospite share gene expression and pathway activation profiles with free-living cells under nitrogen-limited conditions, strongly suggesting that symbiont proliferation in symbiosis is limited by nitrogen availability. Conclusions We demonstrate that nitrogen limitation not only suppresses cell proliferation but also life stage transition to maintain symbionts in the immobile coccoid stage. Nutrient repletion experiments in corals further confirmed that nitrogen availability is the major factor limiting symbiont density in hospite. Our study emphasizes the importance of nitrogen in coral-algae interactions and, more importantly, sheds light on the crucial role of nitrogen in symbiont life history regulation. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01306-2.
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Affiliation(s)
- Guoxin Cui
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Yi Jin Liew
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Migle K Konciute
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ye Zhan
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Shiou-Han Hung
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jana Thistle
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Lucia Gastoldi
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sebastian Schmidt-Roach
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Manuel Aranda
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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61
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Systematic characterization of gene function in the photosynthetic alga Chlamydomonas reinhardtii. Nat Genet 2022; 54:705-714. [PMID: 35513725 PMCID: PMC9110296 DOI: 10.1038/s41588-022-01052-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 03/15/2022] [Indexed: 12/12/2022]
Abstract
Most genes in photosynthetic organisms remain functionally uncharacterized. Here, using a barcoded mutant library of the model eukaryotic alga Chlamydomonas reinhardtii, we determined the phenotypes of more than 58,000 mutants under more than 121 different environmental growth conditions and chemical treatments. A total of 59% of genes are represented by at least one mutant that showed a phenotype, providing clues to the functions of thousands of genes. Mutant phenotypic profiles place uncharacterized genes into functional pathways such as DNA repair, photosynthesis, the CO2-concentrating mechanism and ciliogenesis. We illustrate the value of this resource by validating phenotypes and gene functions, including three new components of an actin cytoskeleton defense pathway. The data also inform phenotype discovery in land plants; mutants in Arabidopsis thaliana genes exhibit phenotypes similar to those we observed in their Chlamydomonas homologs. We anticipate that this resource will guide the functional characterization of genes across the tree of life. Systematic phenotyping of 58,101 mutants of the model eukaryotic alga Chlamydomonas reinhardtii under 121 environmental and chemical stress conditions provides a large resource for characterizing gene function.
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62
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Zehr EA, Roll-Mecak A. A look under the hood of the machine that makes cilia beat. Nat Struct Mol Biol 2022; 29:416-418. [PMID: 35578025 DOI: 10.1038/s41594-022-00778-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Elena A Zehr
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
| | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA. .,Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA.
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63
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Han L, Rao Q, Yang R, Wang Y, Chai P, Xiong Y, Zhang K. Cryo-EM structure of an active central apparatus. Nat Struct Mol Biol 2022; 29:472-482. [PMID: 35578022 PMCID: PMC9113940 DOI: 10.1038/s41594-022-00769-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 03/30/2022] [Indexed: 12/13/2022]
Abstract
Accurately regulated ciliary beating in time and space is critical for diverse cellular activities, which impact the survival and development of nearly all eukaryotic species. An essential beating regulator is the conserved central apparatus (CA) of motile cilia, composed of a pair of microtubules (C1 and C2) associated with hundreds of protein subunits per repeating unit. It is largely unclear how the CA plays its regulatory roles in ciliary motility. Here, we present high-resolution structures of Chlamydomonas reinhardtii CA by cryo-electron microscopy (cryo-EM) and its dynamic conformational behavior at multiple scales. The structures show how functionally related projection proteins of CA are clustered onto a spring-shaped scaffold of armadillo-repeat proteins, facilitated by elongated rachis-like proteins. The two halves of the CA are brought together by elastic chain-like bridge proteins to achieve coordinated activities. We captured an array of kinesin-like protein (KLP1) in two different stepping states, which are actively correlated with beating wave propagation of cilia. These findings establish a structural framework for understanding the role of the CA in cilia.
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Affiliation(s)
- Long Han
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Qinhui Rao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Renbin Yang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Center for Molecular Microscopy, Frederick National Laboratory for Cancer Research, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Yue Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Pengxin Chai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Kai Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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64
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Ishikawa H, Tian JL, Yu JE, Marshall WF, Qin H. Biosynthesis of Linear Protein Nanoarrays Using the Flagellar Axoneme. ACS Synth Biol 2022; 11:1454-1465. [PMID: 35271249 DOI: 10.1021/acssynbio.1c00439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Applications in biotechnology and synthetic biology often make use of soluble proteins, but there are many potential advantages of anchoring enzymes to a stable substrate, including stability and the possibility for substrate channeling. To avoid the necessity of protein purification and chemical immobilization, there has been growing interest in bio-assembly of protein-containing nanoparticles, exploiting the self-assembly of viral capsid proteins or other proteins that form polyhedral structures. However, these nanoparticles are limited in size, which constrains the packaging and the accessibility of the proteins. An axoneme, the insoluble protein core of the eukaryotic flagellum or cilium, is a highly ordered protein structure that can be several microns in length, orders of magnitude larger than other types of nanoparticles. We show that when proteins of interest are fused to specific axonemal proteins and expressed in living Chlamydomonas reinhardtii cells, they become incorporated into linear arrays, which have the advantages of high protein loading capacity and single-step purification with retention of biomass. The arrays can be isolated as membrane-enclosed vesicles or as exposed protein arrays. The approach is demonstrated for both a fluorescent protein and an enzyme (beta-lactamase), showing that incorporation into axonemes retains protein function in a stable, easily isolated array form.
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Affiliation(s)
- Hiroaki Ishikawa
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, California 94143, United States
- NSF Center for Cellular Construction, San Francisco, California 94143, United States
| | - Jie L. Tian
- Molecular & Environmental Plant Sciences, Texas A&M University, College Station, Texas 77845, United States
| | - Jefer E. Yu
- Department of Biology, Texas A&M University, College Station, Texas 77845, United States
| | - Wallace F. Marshall
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, California 94143, United States
- NSF Center for Cellular Construction, San Francisco, California 94143, United States
| | - Hongmin Qin
- Department of Biology, Texas A&M University, College Station, Texas 77845, United States
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Sakato-Antoku M, King SM. Developmental Changes in Ciliary Composition during Gametogenesis in Chlamydomonas. Mol Biol Cell 2022; 33:br10. [PMID: 35389765 PMCID: PMC9561859 DOI: 10.1091/mbc.e22-02-0033] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Chlamydomonas reinhardtii transitions from mitotically dividing vegetative cells to sexually competent gametes of two distinct mating types following nutrient deprivation. Gametes of opposite mating type interact via their cilia, initiating an intraciliary signaling cascade and ultimately fuse forming diploid zygotes. The process of gametogenesis is genetically encode, and a previous study revealed numerous significant changes in mRNA abundance during this life-cycle transition. Here we describe a proteomic analysis of cilia derived from vegetative and gametic cells of both mating types in an effort to assess the global changes that occur within the organelle during this process. We identify numerous membrane- and/or matrix-associated proteins in gametic cilia that were not detected in cilia from vegetative cells. This includes the pro-protein from which the GATI-amide gametic chemotactic modulator derives, as well as receptors, a dynamin-related protein, ammonium transporters, two proteins potentially involved in the intraciliary signaling cascade-driven increase in cAMP, and multiple proteins with a variety of interaction domains. These changes in ciliary composition likely directly affect the functional properties of this organelle as the cell transitions between life-cycle stages.
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Affiliation(s)
- Miho Sakato-Antoku
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030-3305, USA
| | - Stephen M King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030-3305, USA
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Zhang N, Pazouki L, Nguyen H, Jacobshagen S, Bigge BM, Xia M, Mattoon EM, Klebanovych A, Sorkin M, Nusinow DA, Avasthi P, Czymmek KJ, Zhang R. Comparative Phenotyping of Two Commonly Used Chlamydomonas reinhardtii Background Strains: CC-1690 (21gr) and CC-5325 (The CLiP Mutant Library Background). PLANTS (BASEL, SWITZERLAND) 2022; 11:585. [PMID: 35270055 PMCID: PMC8912731 DOI: 10.3390/plants11050585] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/07/2022] [Accepted: 02/14/2022] [Indexed: 05/02/2023]
Abstract
The unicellular green alga Chlamydomonas reinhardtii is an excellent model organism to investigate many essential cellular processes in photosynthetic eukaryotes. Two commonly used background strains of Chlamydomonas are CC-1690 and CC-5325. CC-1690, also called 21gr, has been used for the Chlamydomonas genome project and several transcriptome analyses. CC-5325 is the background strain for the Chlamydomonas Library Project (CLiP). Photosynthetic performance in CC-5325 has not been evaluated in comparison with CC-1690. Additionally, CC-5325 is often considered to be cell-wall deficient, although detailed analysis is missing. The circadian rhythms in CC-5325 are also unclear. To fill these knowledge gaps and facilitate the use of the CLiP mutant library for various screens, we performed phenotypic comparisons between CC-1690 and CC-5325. Our results showed that CC-5325 grew faster heterotrophically in dark and equally well in mixotrophic liquid medium as compared to CC-1690. CC-5325 had lower photosynthetic efficiency and was more heat-sensitive than CC-1690. Furthermore, CC-5325 had an intact cell wall which had comparable integrity to that in CC-1690 but appeared to have reduced thickness. Additionally, CC-5325 could perform phototaxis, but could not maintain a sustained circadian rhythm of phototaxis as CC1690 did. Finally, in comparison to CC-1690, CC-5325 had longer cilia in the medium with acetate but slower swimming speed in the medium without nitrogen and acetate. Our results will be useful for researchers in the Chlamydomonas community to choose suitable background strains for mutant analysis and employ the CLiP mutant library for genome-wide mutant screens under appropriate conditions, especially in the areas of photosynthesis, thermotolerance, cell wall, and circadian rhythms.
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Affiliation(s)
- Ningning Zhang
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Leila Pazouki
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Huong Nguyen
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Sigrid Jacobshagen
- Department of Biology, Western Kentucky University, Bowling Green, KY 42101, USA;
| | - Brae M. Bigge
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA; (B.M.B.); (P.A.)
| | - Ming Xia
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Erin M. Mattoon
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
- Plant and Microbial Biosciences Program, Division of Biology and Biomedical Sciences, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Anastasiya Klebanovych
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Maria Sorkin
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
- Plant and Microbial Biosciences Program, Division of Biology and Biomedical Sciences, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Dmitri A. Nusinow
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Prachee Avasthi
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA; (B.M.B.); (P.A.)
| | - Kirk J. Czymmek
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Ru Zhang
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
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Omolaoye TS, Hachim MY, du Plessis SS. Using publicly available transcriptomic data to identify mechanistic and diagnostic biomarkers in azoospermia and overall male infertility. Sci Rep 2022; 12:2584. [PMID: 35173218 PMCID: PMC8850557 DOI: 10.1038/s41598-022-06476-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 01/28/2022] [Indexed: 12/23/2022] Open
Abstract
Azoospermia, which is the absence of spermatozoa in an ejaculate occurring due to defects in sperm production, or the obstruction of the reproductive tract, affects about 1% of all men and is prevalent in up to 10–15% of infertile males. Conventional semen analysis remains the gold standard for diagnosing and treating male infertility; however, advances in molecular biology and bioinformatics now highlight the insufficiency thereof. Hence, the need to widen the scope of investigating the aetiology of male infertility stands pertinent. The current study aimed to identify common differentially expressed genes (DEGs) that might serve as potential biomarkers for non-obstructive azoospermia (NOA) and overall male infertility. DEGs across different datasets of transcriptomic profiling of testis from human patients with different causes of infertility/ impaired spermatogenesis and/or azoospermia were explored using the gene expression omnibus (GEO) database. Following the search using the GEOquery, 30 datasets were available, with 5 meeting the inclusion criteria. The DEGs for datasets were identified using limma R packages through the GEO2R tool. The annotated genes of the probes in each dataset were intersected with DEGs from all other datasets. Enriched Ontology Clustering for the identified genes was performed using Metascape to explore the possible connection or interaction between the genes. Twenty-five DEGs were shared between most of the datasets, which might indicate their role in the pathogenesis of male infertility. Of the 25 DEGs, eight genes (THEG, SPATA20, ROPN1L, GSTF1, TSSK1B, CABS1, ADAD1, RIMBP3) are either involved in the overall spermatogenic processes or at specific phases of spermatogenesis. We hypothesize that alteration in the expression of these genes leads to impaired spermatogenesis and, ultimately, male infertility. Thus, these genes can be used as potential biomarkers for the early detection of NOA.
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Affiliation(s)
- Temidayo S Omolaoye
- Department of Basic Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Mahmood Yaseen Hachim
- Department of Basic Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE.
| | - Stefan S du Plessis
- Department of Basic Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE.,Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
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Weiner E, Pinskey JM, Nicastro D, Otegui MS. Electron microscopy for imaging organelles in plants and algae. PLANT PHYSIOLOGY 2022; 188:713-725. [PMID: 35235662 PMCID: PMC8825266 DOI: 10.1093/plphys/kiab449] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/23/2021] [Indexed: 05/31/2023]
Abstract
Recent developments in both instrumentation and image analysis algorithms have allowed three-dimensional electron microscopy (3D-EM) to increase automated image collections through large tissue volumes using serial block-face scanning EM (SEM) and to achieve near-atomic resolution of macromolecular complexes using cryo-electron tomography (cryo-ET) and sub-tomogram averaging. In this review, we discuss applications of cryo-ET to cell biology research on plant and algal systems and the special opportunities they offer for understanding the organization of eukaryotic organelles with unprecedently resolution. However, one of the most challenging aspects for cryo-ET is sample preparation, especially for multicellular organisms. We also discuss correlative light and electron microscopy (CLEM) approaches that have been developed for ET at both room and cryogenic temperatures.
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Affiliation(s)
- Ethan Weiner
- Department of Botany, University of Wisconsin, Madison 53706, Wisconsin
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison 53706, Wisconsin
| | - Justine M Pinskey
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas 75390, Texas
| | - Daniela Nicastro
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas 75390, Texas
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin, Madison 53706, Wisconsin
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison 53706, Wisconsin
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Niziolek M, Bicka M, Osinka A, Samsel Z, Sekretarska J, Poprzeczko M, Bazan R, Fabczak H, Joachimiak E, Wloga D. PCD Genes-From Patients to Model Organisms and Back to Humans. Int J Mol Sci 2022; 23:ijms23031749. [PMID: 35163666 PMCID: PMC8836003 DOI: 10.3390/ijms23031749] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/25/2022] [Accepted: 01/31/2022] [Indexed: 01/27/2023] Open
Abstract
Primary ciliary dyskinesia (PCD) is a hereditary genetic disorder caused by the lack of motile cilia or the assembxly of dysfunctional ones. This rare human disease affects 1 out of 10,000-20,000 individuals and is caused by mutations in at least 50 genes. The past twenty years brought significant progress in the identification of PCD-causative genes and in our understanding of the connections between causative mutations and ciliary defects observed in affected individuals. These scientific advances have been achieved, among others, due to the extensive motile cilia-related research conducted using several model organisms, ranging from protists to mammals. These are unicellular organisms such as the green alga Chlamydomonas, the parasitic protist Trypanosoma, and free-living ciliates, Tetrahymena and Paramecium, the invertebrate Schmidtea, and vertebrates such as zebrafish, Xenopus, and mouse. Establishing such evolutionarily distant experimental models with different levels of cell or body complexity was possible because both basic motile cilia ultrastructure and protein composition are highly conserved throughout evolution. Here, we characterize model organisms commonly used to study PCD-related genes, highlight their pros and cons, and summarize experimental data collected using these models.
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Affiliation(s)
- Michal Niziolek
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
| | - Marta Bicka
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
- Faculty of Chemistry, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
| | - Anna Osinka
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
| | - Zuzanna Samsel
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
| | - Justyna Sekretarska
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
| | - Martyna Poprzeczko
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
- Laboratory of Immunology, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawinskiego Street, 02-106 Warsaw, Poland
| | - Rafal Bazan
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
| | - Hanna Fabczak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
- Correspondence: (E.J.); (D.W.); Tel.: +48-22-58-92-338 (E.J. & D.W.)
| | - Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
- Correspondence: (E.J.); (D.W.); Tel.: +48-22-58-92-338 (E.J. & D.W.)
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Lechtreck KF, Liu Y, Dai J, Alkhofash RA, Butler J, Alford L, Yang P. Chlamydomonas ARMC2/PF27 is an obligate cargo adapter for intraflagellar transport of radial spokes. eLife 2022; 11:74993. [PMID: 34982025 PMCID: PMC8789290 DOI: 10.7554/elife.74993] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/03/2022] [Indexed: 12/19/2022] Open
Abstract
Intraflagellar transport (IFT) carries proteins into flagella but how IFT trains interact with the large number of diverse proteins required to assemble flagella remains largely unknown. Here, we show that IFT of radial spokes in Chlamydomonas requires ARMC2/PF27, a conserved armadillo repeat protein associated with male infertility and reduced lung function. Chlamydomonas ARMC2 was highly enriched in growing flagella and tagged ARMC2 and the spoke protein RSP3 co-migrated on anterograde trains. In contrast, a cargo and an adapter of inner and outer dynein arms moved independently of ARMC2, indicating that unrelated cargoes distribute stochastically onto the IFT trains. After concomitant unloading at the flagellar tip, RSP3 attached to the axoneme whereas ARMC2 diffused back to the cell body. In armc2/pf27 mutants, IFT of radial spokes was abolished and the presence of radial spokes was limited to the proximal region of flagella. We conclude that ARMC2 is a cargo adapter required for IFT of radial spokes to ensure their assembly along flagella. ARMC2 belongs to a growing class of cargo-specific adapters that enable flagellar transport of preassembled axonemal substructures by IFT.
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Affiliation(s)
- Karl F Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, United States
| | - Yi Liu
- Department of Biological Sciences, Marquette University, Milwaukee, United States
| | - Jin Dai
- Department of Cellular Biology, University of Georgia, Athens, United States
| | - Rama A Alkhofash
- Department of Cellular Biology, University of Georgia, Athens, United States
| | - Jack Butler
- Department of Cellular Biology, University of Georgia, Athens, United States
| | - Lea Alford
- Division of Natural Sciences,, Oglethorpe University, Atlanta, United States
| | - Pinfen Yang
- Department of Biological Sciences, Marquette University, Milwaukee, United States
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71
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Pablos M, Casanueva-Álvarez E, González-Casimiro CM, Merino B, Perdomo G, Cózar-Castellano I. Primary Cilia in Pancreatic β- and α-Cells: Time to Revisit the Role of Insulin-Degrading Enzyme. Front Endocrinol (Lausanne) 2022; 13:922825. [PMID: 35832432 PMCID: PMC9271624 DOI: 10.3389/fendo.2022.922825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/24/2022] [Indexed: 12/25/2022] Open
Abstract
The primary cilium is a narrow organelle located at the surface of the cell in contact with the extracellular environment. Once underappreciated, now is thought to efficiently sense external environmental cues and mediate cell-to-cell communication, because many receptors, ion channels, and signaling molecules are highly or differentially expressed in primary cilium. Rare genetic disorders that affect cilia integrity and function, such as Bardet-Biedl syndrome and Alström syndrome, have awoken interest in studying the biology of cilium. In this review, we discuss recent evidence suggesting emerging roles of primary cilium and cilia-mediated signaling pathways in the regulation of pancreatic β- and α-cell functions, and its implications in regulating glucose homeostasis.
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Affiliation(s)
- Marta Pablos
- Department of Biochemistry, Molecular Biology and Physiology, School of Medicine, University of Valladolid, Valladolid, Spain
- *Correspondence: Marta Pablos,
| | - Elena Casanueva-Álvarez
- Unidad de Excelencia Instituto de Biología y Genética Molecular, University of Valladolid Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
| | - Carlos M. González-Casimiro
- Unidad de Excelencia Instituto de Biología y Genética Molecular, University of Valladolid Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
| | - Beatriz Merino
- Unidad de Excelencia Instituto de Biología y Genética Molecular, University of Valladolid Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
| | - Germán Perdomo
- Unidad de Excelencia Instituto de Biología y Genética Molecular, University of Valladolid Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
| | - Irene Cózar-Castellano
- Department of Biochemistry, Molecular Biology and Physiology, School of Medicine, University of Valladolid, Valladolid, Spain
- Unidad de Excelencia Instituto de Biología y Genética Molecular, University of Valladolid Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
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Collesano L, Guido I, Golestanian R, Vilfan A. Active beating modes of two clamped filaments driven by molecular motors. J R Soc Interface 2022; 19:20210693. [PMID: 34983201 PMCID: PMC8728166 DOI: 10.1098/rsif.2021.0693] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/02/2021] [Indexed: 12/11/2022] Open
Abstract
Biological cilia pump the surrounding fluid by asymmetric beating that is driven by dynein motors between sliding microtubule doublets. The complexity of biological cilia raises the question about minimal systems that can re-create similar patterns of motion. One such system consists of a pair of microtubules that are clamped at the proximal end. They interact through dynein motors that cover one of the filaments and pull against the other one. Here, we study theoretically the static shapes and the active dynamics of such a system. Using the theory of elastica, we analyse the shapes of two filaments of different lengths with clamped ends. Starting from equal lengths, we observe a transition similar to Euler buckling leading to a planar shape. When further increasing the length ratio, the system assumes a non-planar shape with spontaneously broken chiral symmetry after a secondary bifurcation and then transitions to planar again. The predicted curves agree with experimentally observed shapes of microtubule pairs. The dynamical system can have a stable fixed point, with either bent or straight filaments, or limit cycle oscillations. The latter match many properties of ciliary motility, demonstrating that a two-filament system can serve as a minimal actively beating model.
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Affiliation(s)
- Laura Collesano
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), Göttingen 37077, Germany
| | - Isabella Guido
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), Göttingen 37077, Germany
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), Göttingen 37077, Germany
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Andrej Vilfan
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), Göttingen 37077, Germany
- Jožef Stefan Institute, Ljubljana 1000, Slovenia
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73
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Li S, Fernandez JJ, Fabritius AS, Agard DA, Winey M. Electron cryo-tomography structure of axonemal doublet microtubule from Tetrahymena thermophila. Life Sci Alliance 2022; 5:5/3/e202101225. [PMID: 34969817 PMCID: PMC8742875 DOI: 10.26508/lsa.202101225] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 11/24/2022] Open
Abstract
Doublet microtubules (DMTs) provide a scaffold for axoneme assembly in motile cilia. Aside from α/β tubulins, the DMT comprises a large number of non-tubulin proteins in the luminal wall of DMTs, collectively named the microtubule inner proteins (MIPs). We used cryoET to study axoneme DMT isolated from Tetrahymena We present the structures of DMT at nanometer and sub-nanometer resolution. The structures confirm that MIP RIB72A/B binds to the luminal wall of DMT by multiple DM10 domains. We found FAP115, an MIP-containing multiple EF-hand domains, located at the interface of four-tubulin dimers in the lumen of A-tubule. It contacts both lateral and longitudinal tubulin interfaces and playing a critical role in DMT stability. We observed substantial structure heterogeneity in DMT in an FAP115 knockout strain, showing extensive structural defects beyond the FAP115-binding site. The defects propagate along the axoneme. Finally, by comparing DMT structures from Tetrahymena and Chlamydomonas, we have identified a number of conserved MIPs as well as MIPs that are unique to each organism. This conservation and diversity of the DMT structures might be linked to their specific functions. Our work provides structural insights essential for understanding the roles of MIPs during motile cilium assembly and function, as well as their relationships to human ciliopathies.
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Affiliation(s)
- Sam Li
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Jose-Jesus Fernandez
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Health Research Institute of Asturias (ISPA), Oviedo, Spain
| | - Amy S Fabritius
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA, USA
| | - David A Agard
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Mark Winey
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA, USA
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74
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Abstract
Cilia are tail-like organelles responsible for motility, transportation, and sensory functions in eukaryotic cells. Cilia research has been providing multifaceted questions, attracting biologists of various areas and inducing interdisciplinary studies. In this chapter, we mainly focus on efforts to elucidate the molecular mechanism of ciliary beating motion, a field of research that has a long history and is still ongoing. We also overview topics closely related to the motility mechanism, such as ciliogenesis, cilia-related diseases, and sensory cilia. Subnanometer-scale to submillimeter-scale 3D imaging of the axoneme and the basal body resulted in a wide variety of insights into these questions.
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Affiliation(s)
- Takashi Ishikawa
- Department of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland.
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75
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Lindemann CB. The flagellar germ-line hypothesis: How flagellate and ciliate gametes significantly shaped the evolution of organismal complexity. Bioessays 2021; 44:e2100143. [PMID: 34967029 DOI: 10.1002/bies.202100143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 12/10/2021] [Accepted: 12/15/2021] [Indexed: 11/10/2022]
Abstract
This essay presents a hypothesis which contends that the development of organismic complexity in the eukaryotes depended extensively on propagation via flagellated and ciliated gametes. Organisms utilizing flagellate and ciliate gametes to propagate their germ line have contributed most of the organismic complexity found in the higher animals. The genes of the flagellum and the flagellar assembly system (intraflagellar transport) have played a disproportionately important role in the construction of complex tissues and organs. The hypothesis also proposes that competition between large numbers of haploid flagellated male gametes rigorously conserved the functionality of a key set of flagellar genes for more than 700 million years. This in turn has insured that a large set (>600) of highly functional cytoskeletal and signal pathway genes is always present in the lineage of organisms with flagellated or ciliated gametes to act as a dependable resource, or "toolkit," for organ elaboration.
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76
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Vasquez SSV, van Dam J, Wheway G. An updated SYSCILIA gold standard (SCGSv2) of known ciliary genes, revealing the vast progress that has been made in the cilia research field. Mol Biol Cell 2021; 32:br13. [PMID: 34613793 PMCID: PMC8694072 DOI: 10.1091/mbc.e21-05-0226] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Cilia are microtubule-based organelles with important functions in motility and sensation. They contribute to a broad spectrum of developmental disorders called ciliopathies and have recently been linked to common conditions such as cancers and congenital heart disease. There has been increasing interest in the biology of cilia and their contribution to disease over the past two decades. In 2013 we published a "Gold Standard" list of genes confirmed to be associated with cilia. This was published as part of the SYSCILIA consortium for systems biology study dissecting the contribution of cilia to human health and disease, and was named the Syscilia Gold Standard (SCGS). Since this publication, interest in cilia and understanding of their functions have continued to grow, and we now present an updated SCGS version 2. This includes an additional 383 genes, more than doubling the size of SCGSv1. We use this dataset to conduct a review of advances in understanding of cilia biology 2013- 2021 and offer perspectives on the future of cilia research. We hope that this continues to be a useful resource for the cilia community.
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Affiliation(s)
| | - John van Dam
- Theoretical Biology and Bioinformatics, Department of Biology, Science Faculty, Utrecht University, 3584 CH Utrecht, Netherlands
| | - Gabrielle Wheway
- Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, United Kingdom
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77
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Hao K, Chen Y, Yan X, Zhu X. Cilia locally synthesize proteins to sustain their ultrastructure and functions. Nat Commun 2021; 12:6971. [PMID: 34848703 PMCID: PMC8632896 DOI: 10.1038/s41467-021-27298-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 11/09/2021] [Indexed: 12/26/2022] Open
Abstract
Cilia are microtubule-based hair-like organelles propelling locomotion and extracellular liquid flow or sensing environmental stimuli. As cilia are diffusion barrier-gated subcellular compartments, their protein components are thought to come from the cell body through intraflagellar transport or diffusion. Here we show that cilia locally synthesize proteins to maintain their structure and functions. Multicilia of mouse ependymal cells are abundant in ribosomal proteins, translation initiation factors, and RNA, including 18 S rRNA and tubulin mRNA. The cilia actively generate nascent peptides, including those of tubulin. mRNA-binding protein Fmrp localizes in ciliary central lumen and appears to function in mRNA delivery into the cilia. Its depletion by RNAi impairs ciliary local translation and induces multicilia degeneration. Expression of exogenous Fmrp, but not an isoform tethered to mitochondria, rescues the degeneration defects. Therefore, local translation defects in cilia might contribute to the pathology of ciliopathies and other diseases such as Fragile X syndrome.
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Affiliation(s)
- Kai Hao
- grid.507739.f0000 0001 0061 254XState Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 320 Yueyang Road, 200031 Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Yawen Chen
- grid.507739.f0000 0001 0061 254XState Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 320 Yueyang Road, 200031 Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Xiumin Yan
- Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Institute of Early Life Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, 200092, Shanghai, China.
| | - Xueliang Zhu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China. .,University of Chinese Academy of Sciences, 100049, Beijing, China. .,School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 310024, Hangzhou, China.
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78
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Perlaza K, Mirvis M, Ishikawa H, Marshall W. The short flagella 1 (SHF1) gene in Chlamydomonas encodes a Crescerin TOG-domain protein required for late stages of flagellar growth. Mol Biol Cell 2021; 33:ar12. [PMID: 34818077 PMCID: PMC9236146 DOI: 10.1091/mbc.e21-09-0472] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Length control of flagella represents a simple and tractable system to investigate the dynamics of organelle size. Models for flagellar length control in the model organism, Chlamydomonas reinhardtii have focused on the length-dependence of the intraflagellar transport (IFT) system which manages the delivery and removal of axonemal subunits at the tip of the flagella. One of these cargoes, tubulin, is the major axonemal subunit, and its frequency of arrival at the tip plays a central role in size control models. However, the mechanisms determining tubulin dynamics at the tip are still poorly understood. We discovered a loss-of-function mutation that leads to shortened flagella, and found that this was an allele of a previously described gene, SHF1, whose molecular identity had not previously been determined. We found that SHF1 encodes a Chlamydomonas ortholog of Crescerin, previously identified as a cilia-specific TOG-domain array protein that can bind tubulin via its TOG domains and increase tubulin polymerization rates. In this mutant, flagellar regeneration occurs with the same initial kinetics as wild-type cells, but plateaus at a shorter length. Using a computational model in which the flagellar microtubules are represented by a differential equation for flagellar length combined with a stochastic model for cytoplasmic microtubule dynamics, we found that our experimental results are best described by a model in which Crescerin/SHF1 binds tubulin dimers in the cytoplasm and transports them into the flagellum. We suggest that this TOG-domain protein is necessary to efficiently and preemptively increase intra-flagella tubulin levels to offset decreasing IFT cargo at the tip as flagellar assembly progresses.
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Affiliation(s)
- Karina Perlaza
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143
| | - Mary Mirvis
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143
| | - Hiroaki Ishikawa
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143
| | - Wallace Marshall
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143
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79
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Boselli F, Jullien J, Lauga E, Goldstein RE. Fluid Mechanics of Mosaic Ciliated Tissues. PHYSICAL REVIEW LETTERS 2021; 127:198102. [PMID: 34797132 PMCID: PMC7616087 DOI: 10.1103/physrevlett.127.198102] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 10/07/2021] [Indexed: 06/13/2023]
Abstract
In tissues as diverse as amphibian skin and the human airway, the cilia that propel fluid are grouped in sparsely distributed multiciliated cells (MCCs). We investigate fluid transport in this "mosaic" architecture, with emphasis on the trade-offs that may have been responsible for its evolutionary selection. Live imaging of MCCs in embryos of the frog Xenopus laevis shows that cilia bundles behave as active vortices that produce a flow field accurately represented by a local force applied to the fluid. A coarse-grained model that self-consistently couples bundles to the ambient flow reveals that hydrodynamic interactions between MCCs limit their rate of work so that they best shear the tissue at a finite but low area coverage, a result that mirrors findings for other sparse distributions such as cell receptors and leaf stomata.
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Affiliation(s)
- Francesco Boselli
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge CB3 0WA, United Kingdom
| | - Jerome Jullien
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge CB2 1QN, United Kingdom
- Inserm, Nantes Université, CHU Nantes, CRTI-UMR 1064, F-44000 Nantes, France
| | - Eric Lauga
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge CB3 0WA, United Kingdom
| | - Raymond E. Goldstein
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge CB3 0WA, United Kingdom
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80
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Hammond M, Zoltner M, Garrigan J, Butterfield E, Varga V, Lukeš J, Field MC. The distinctive flagellar proteome of Euglena gracilis illuminates the complexities of protistan flagella adaptation. THE NEW PHYTOLOGIST 2021; 232:1323-1336. [PMID: 34292600 DOI: 10.1111/nph.17638] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
The eukaryotic flagellum/cilium is a prominent organelle with conserved structure and diverse functions. Euglena gracilis, a photosynthetic and highly adaptable protist, employs its flagella for both locomotion and environmental sensing. Using proteomics of isolated E. gracilis flagella we identify nearly 1700 protein groups, which challenges previous estimates of the protein complexity of motile eukaryotic flagella. We not only identified several unexpected similarities shared with mammalian flagella, including an entire glycolytic pathway and proteasome, but also document a vast array of flagella-based signal transduction components that coordinate gravitaxis and phototactic motility. By contrast, the pellicle was found to consist of > 900 protein groups, containing additional structural and signalling components. Our data identify significant adaptations within the E. gracilis flagellum, many of which are clearly linked to the highly flexible lifestyle.
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Affiliation(s)
- Michael Hammond
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), 370 05, Czech Republic
| | - Martin Zoltner
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Department of Parasitology, Faculty of Science, BIOCEV, Charles University, Vestec, 252 50, Czech Republic
| | - Jack Garrigan
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Erin Butterfield
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Vladimir Varga
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, 142 20, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), 370 05, Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), 370 05, Czech Republic
| | - Mark C Field
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), 370 05, Czech Republic
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
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81
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Noguchi T, Nakamura K, Satoda Y, Katoh Y, Nakayama K. CCRK/CDK20 regulates ciliary retrograde protein trafficking via interacting with BROMI/TBC1D32. PLoS One 2021; 16:e0258497. [PMID: 34624068 PMCID: PMC8500422 DOI: 10.1371/journal.pone.0258497] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/28/2021] [Indexed: 01/02/2023] Open
Abstract
CCRK/CDK20 was reported to interact with BROMI/TBC1D32 and regulate ciliary Hedgehog signaling. In various organisms, mutations in the orthologs of CCRK and those of the kinase ICK/CILK1, which is phosphorylated by CCRK, are known to result in cilia elongation. Furthermore, we recently showed that ICK regulates retrograde ciliary protein trafficking and/or the turnaround event at the ciliary tips, and that its mutations result in the elimination of intraflagellar transport (IFT) proteins that have overaccumulated at the bulged ciliary tips as extracellular vesicles, in addition to cilia elongation. However, how these proteins cooperate to regulate ciliary protein trafficking has remained unclear. We here show that the phenotypes of CCRK-knockout (KO) cells closely resemble those of ICK-KO cells; namely, the overaccumulation of IFT proteins at the bulged ciliary tips, which appear to be eliminated as extracellular vesicles, and the enrichment of GPR161 and Smoothened on the ciliary membrane. The abnormal phenotypes of CCRK-KO cells were rescued by the exogenous expression of wild-type CCRK but not its kinase-dead mutant or a mutant defective in BROMI binding. These results together indicate that CCRK regulates the turnaround process at the ciliary tips in concert with BROMI and probably via activating ICK.
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Affiliation(s)
- Tatsuro Noguchi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Kentaro Nakamura
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yuuki Satoda
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
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82
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Sudhakar A, Kamanna S, Bojja M, Tatu U. Proteomic analysis of Giardia lamblia and Trichomonas vaginalis flagella reveal unique post-translational modifications in tubulin that provide clues to regulation of their motilities. Proteomics 2021; 21:e2100004. [PMID: 34558204 DOI: 10.1002/pmic.202100004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 08/17/2021] [Indexed: 11/07/2022]
Abstract
All eukaryotic flagella are made of microtubules and driven by dynein motor proteins. However, every organism is unique in terms of its flagellar waveform, beat frequency, and its general motility pattern. With recent research, it is becoming clear that despite overall conservation in flagellar structure, the pattern of tubulin post-translational modifications within the flagella are diverse and may contribute to variations in their patterns of motility. In this study, we have analyzed the tubulin post-translational modification in the protozoan parasites Giardia lamblia and Trichomonas vaginalis using global, untargeted mass spectrometry. We show that tubulin monoglycylation is a modification localized to the flagella present in G. lamblia but absent in T. vaginalis. We also show the presence of glutamylated tubulin in both G. lamblia and T. vaginalis. Using MS/MS, we were also able to identify the previously unknown sites of monoglycylation in β-tubulin at E438 and E439 in G. lamblia. Using isolated flagella, we also characterized the flagellar proteome in G. lamblia and T. vaginalis and identified 475 proteins in G. lamblia and 386 proteins in T. vaginalis flagella. Altogether, the flagellar proteomes as well as the sites of tubulin PTMs in these organisms, reveal potential mechanisms in regulating flagellar motilities in these neglected protozoan parasites.
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Affiliation(s)
- Aparna Sudhakar
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Sathisha Kamanna
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Mallikarjun Bojja
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Utpal Tatu
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
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83
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Kubo S, Yang SK, Black CS, Dai D, Valente-Paterno M, Gaertig J, Ichikawa M, Bui KH. Remodeling and activation mechanisms of outer arm dyneins revealed by cryo-EM. EMBO Rep 2021; 22:e52911. [PMID: 34338432 PMCID: PMC8419702 DOI: 10.15252/embr.202152911] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/15/2021] [Accepted: 06/30/2021] [Indexed: 12/11/2022] Open
Abstract
Cilia are thin microtubule-based protrusions of eukaryotic cells. The swimming of ciliated protists and sperm cells is propelled by the beating of cilia. Cilia propagate the flow of mucus in the trachea and protect the human body from viral infections. The main force generators of ciliary beating are the outer dynein arms (ODAs) which attach to the doublet microtubules. The bending of cilia is driven by the ODAs' conformational changes caused by ATP hydrolysis. Here, we report the native ODA complex structure attaching to the doublet microtubule by cryo-electron microscopy. The structure reveals how the ODA complex is attached to the doublet microtubule via the docking complex in its native state. Combined with coarse-grained molecular dynamic simulations, we present a model of how the attachment of the ODA to the doublet microtubule induces remodeling and activation of the ODA complex.
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Affiliation(s)
- Shintaroh Kubo
- Department of Anatomy and Cell BiologyMcGill UniversityMontréalQCCanada
| | - Shun Kai Yang
- Department of Anatomy and Cell BiologyMcGill UniversityMontréalQCCanada
| | - Corbin S Black
- Department of Anatomy and Cell BiologyMcGill UniversityMontréalQCCanada
| | - Daniel Dai
- Department of Anatomy and Cell BiologyMcGill UniversityMontréalQCCanada
| | | | - Jacek Gaertig
- Department of Cellular BiologyUniversity of GeorgiaAthensGAUSA
| | - Muneyoshi Ichikawa
- Division of Biological ScienceGraduate School of Science and TechnologyNara Institute of Science and TechnologyIkomaJapan
- PRESTOJapan Science and Technology AgencyKawaguchiJapan
| | - Khanh Huy Bui
- Department of Anatomy and Cell BiologyMcGill UniversityMontréalQCCanada
- Centre de Recherche en Biologie StructuraleMcGill UniversityMontréalQCCanada
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84
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Chlamydomonas LZTFL1 mediates phototaxis via controlling BBSome recruitment to the basal body and its reassembly at the ciliary tip. Proc Natl Acad Sci U S A 2021; 118:2101590118. [PMID: 34446551 DOI: 10.1073/pnas.2101590118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Many G protein-coupled receptors and other signaling proteins localize to the ciliary membrane for regulating diverse cellular processes. The BBSome composed of multiple Bardet-Biedl syndrome (BBS) proteins is an intraflagellar transport (IFT) cargo adaptor essential for sorting signaling proteins in and/or out of cilia via IFT. Leucine zipper transcription factor-like 1 (LZTFL1) protein mediates ciliary signaling by controlling BBSome ciliary content, reflecting how LZTFL1 mutations could cause BBS. However, the mechanistic mechanism underlying this process remains elusive thus far. Here, we show that LZTFL1 maintains BBSome ciliary dynamics by finely controlling BBSome recruitment to the basal body and its reassembly at the ciliary tip simultaneously in Chlamydomonas reinhardtii LZTFL1 directs BBSome recruitment to the basal body via promoting basal body targeting of Arf-like 6 GTPase BBS3, thus deciding the BBSome amount available for loading onto anterograde IFT trains for entering cilia. Meanwhile, LZTFL1 stabilizes the IFT25/27 component of the IFT-B1 subcomplex in the cell body so as to control its presence and amount at the basal body for entering cilia. Since IFT25/27 promotes BBSome reassembly at the ciliary tip for loading onto retrograde IFT trains, LZTFL1 thus also directs BBSome removal out of cilia. Therefore, LZTFL1 dysfunction deprives the BBSome of ciliary presence and generates Chlamydomonas cells defective in phototaxis. In summary, our data propose that LZTFL1 maintains BBSome dynamics in cilia by such a dual-mode system, providing insights into how LZTFL1 mediates ciliary signaling through maintaining BBSome ciliary dynamics and the pathogenetic mechanism of the BBS disorder as well.
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85
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Pivato M, Ballottari M. Chlamydomonas reinhardtii cellular compartments and their contribution to intracellular calcium signalling. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5312-5335. [PMID: 34077536 PMCID: PMC8318260 DOI: 10.1093/jxb/erab212] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/11/2021] [Indexed: 05/12/2023]
Abstract
Calcium (Ca2+)-dependent signalling plays a well-characterized role in the response to different environmental stimuli, in both plant and animal cells. In the model organism for green algae, Chlamydomonas reinhardtii, Ca2+ signals were reported to have a crucial role in different physiological processes, such as stress responses, photosynthesis, and flagella functions. Recent reports identified the underlying components of the Ca2+ signalling machinery at the level of specific subcellular compartments and reported in vivo imaging of cytosolic Ca2+ concentration in response to environmental stimuli. The characterization of these Ca2+-related mechanisms and proteins in C. reinhardtii is providing knowledge on how microalgae can perceive and respond to environmental stimuli, but also on how this Ca2+ signalling machinery has evolved. Here, we review current knowledge on the cellular mechanisms underlying the generation, shaping, and decoding of Ca2+ signals in C. reinhardtii, providing an overview of the known and possible molecular players involved in the Ca2+ signalling of its different subcellular compartments. The advanced toolkits recently developed to measure time-resolved Ca2+ signalling in living C. reinhardtii cells are also discussed, suggesting how they can improve the study of the role of Ca2+ signals in the cellular response of microalgae to environmental stimuli.
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Affiliation(s)
- Matteo Pivato
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Matteo Ballottari
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
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86
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Fu G, Scarbrough C, Song K, Phan N, Wirschell M, Nicastro D. Structural organization of the intermediate and light chain complex of Chlamydomonas ciliary I1 dynein. FASEB J 2021; 35:e21646. [PMID: 33993568 DOI: 10.1096/fj.202001857r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 04/01/2021] [Accepted: 04/21/2021] [Indexed: 12/18/2022]
Abstract
Axonemal I1 dynein (dynein f) is the largest inner dynein arm in cilia and a key regulator of ciliary beating. It consists of two dynein heavy chains, and an intermediate chain/light chain (ICLC) complex. However, the structural organization of the nine ICLC subunits remains largely unknown. Here, we used biochemical and genetic approaches, and cryo-electron tomography imaging in Chlamydomonas to dissect the molecular architecture of the I1 dynein ICLC complex. Using a strain expressing SNAP-tagged IC140, tomography revealed the location of the IC140 N-terminus at the proximal apex of the ICLC structure. Mass spectrometry of a tctex2b mutant showed that TCTEX2B dynein light chain is required for the stable assembly of TCTEX1 and inner dynein arm interacting proteins IC97 and FAP120. The structural defects observed in tctex2b located these 4 subunits in the center and bottom regions of the ICLC structure, which overlaps with the location of the IC138 regulatory subcomplex, which contains IC138, IC97, FAP120, and LC7b. These results reveal the three-dimensional organization of the native ICLC complex and indicate potential protein-protein interactions that are involved in the pathway by which I1 regulates ciliary motility.
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Affiliation(s)
- Gang Fu
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, China
| | - Chasity Scarbrough
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Kangkang Song
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nhan Phan
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Maureen Wirschell
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Daniela Nicastro
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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87
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Cardenas-Rodriguez M, Austin-Tse C, Bergboer JGM, Molinari E, Sugano Y, Bachmann-Gagescu R, Sayer JA, Drummond IA. Genetic compensation for cilia defects in cep290 mutants by upregulation of cilia-associated small GTPases. J Cell Sci 2021; 134:jcs258568. [PMID: 34155518 PMCID: PMC8325957 DOI: 10.1242/jcs.258568] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/02/2021] [Indexed: 12/13/2022] Open
Abstract
Mutations in CEP290 (also known as NPHP6), a large multidomain coiled coil protein, are associated with multiple cilia-associated syndromes. Over 130 CEP290 mutations have been linked to a wide spectrum of human ciliopathies, raising the question of how mutations in a single gene cause different disease syndromes. In zebrafish, the expressivity of cep290 deficiencies were linked to the type of genetic ablation: acute cep290 morpholino knockdown caused severe cilia-related phenotypes, whereas deficiencies in a CRISPR/Cas9 genetic mutant were restricted to photoreceptor defects. Here, we show that milder phenotypes in genetic mutants were associated with the upregulation of genes encoding the cilia-associated small GTPases arl3, arl13b and unc119b. Upregulation of UNC119b was also observed in urine-derived renal epithelial cells from human Joubert syndrome CEP290 patients. Ectopic expression of arl3, arl13b and unc119b in cep290 morphant zebrafish embryos rescued Kupffer's vesicle cilia and partially rescued photoreceptor outer segment defects. The results suggest that genetic compensation by upregulation of genes involved in a common subcellular process, lipidated protein trafficking to cilia, may be a conserved mechanism contributing to genotype-phenotype variations observed in CEP290 deficiencies. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Magdalena Cardenas-Rodriguez
- Department of Medicine, Nephrology Division, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129, USA
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
| | - Christina Austin-Tse
- Department of Pathology, Massachusetts General Hospital, 185 Cambridge St, Boston, MA 02114, USA
| | | | - Elisa Molinari
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle NE1 3BZ, UK
| | - Yuya Sugano
- Institute of Anatomy, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | | | - John A. Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle NE1 3BZ, UK
- Renal Services, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Freeman Road, Newcastle NE7 7DN, UK
| | - Iain A. Drummond
- Department of Medicine, Nephrology Division, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129, USA
- Davis Center for Regenerative Biology and Aging, Mount Desert Island Biological Laboratory, Salisbury Cove, Bar Harbor, ME 04609, USA
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88
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Beckers A, Fuhl F, Ott T, Boldt K, Brislinger MM, Walentek P, Schuster-Gossler K, Hegermann J, Alten L, Kremmer E, Przykopanski A, Serth K, Ueffing M, Blum M, Gossler A. The highly conserved FOXJ1 target CFAP161 is dispensable for motile ciliary function in mouse and Xenopus. Sci Rep 2021; 11:13333. [PMID: 34172766 PMCID: PMC8233316 DOI: 10.1038/s41598-021-92495-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 06/08/2021] [Indexed: 12/14/2022] Open
Abstract
Cilia are protrusions of the cell surface and composed of hundreds of proteins many of which are evolutionary and functionally well conserved. In cells assembling motile cilia the expression of numerous ciliary components is under the control of the transcription factor FOXJ1. Here, we analyse the evolutionary conserved FOXJ1 target CFAP161 in Xenopus and mouse. In both species Cfap161 expression correlates with the presence of motile cilia and depends on FOXJ1. Tagged CFAP161 localises to the basal bodies of multiciliated cells of the Xenopus larval epidermis, and in mice CFAP161 protein localises to the axoneme. Surprisingly, disruption of the Cfap161 gene in both species did not lead to motile cilia-related phenotypes, which contrasts with the conserved expression in cells carrying motile cilia and high sequence conservation. In mice mutation of Cfap161 stabilised the mutant mRNA making genetic compensation triggered by mRNA decay unlikely. However, genes related to microtubules and cilia, microtubule motor activity and inner dyneins were dysregulated, which might buffer the Cfap161 mutation.
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Affiliation(s)
- Anja Beckers
- Institute for Molecular Biology, OE5250, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Franziska Fuhl
- Institute of Biology, University of Hohenheim, Garbenstraße 30, 70593, Stuttgart, Germany
| | - Tim Ott
- Institute of Biology, University of Hohenheim, Garbenstraße 30, 70593, Stuttgart, Germany
| | - Karsten Boldt
- Institute of Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, 72076, Tübingen, Germany
| | - Magdalena Maria Brislinger
- Institute of Biology, University of Hohenheim, Garbenstraße 30, 70593, Stuttgart, Germany.,Renal Division, Department of Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine & CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Habsburger Str. 49, 79104, Freiburg, Germany
| | - Peter Walentek
- Renal Division, Department of Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine & CIBSS-Centre for Integrative Biological Signaling Studies, University of Freiburg, Habsburger Str. 49, 79104, Freiburg, Germany
| | - Karin Schuster-Gossler
- Institute for Molecular Biology, OE5250, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Jan Hegermann
- Institute of Functional and Applied Anatomy, Research Core Unit Electron Microscopy, OE8840, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Leonie Alten
- Institute for Molecular Biology, OE5250, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.,Twist Bioscience, 681 Gateway Blvd South, South San Francisco, CA, 94080, USA
| | - Elisabeth Kremmer
- Institute of Molecular Immunology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Core Facility Monoclonal Antibodies, Marchioninistr. 25, 81377, München, Germany.,Department of Biology II, Ludwig-Maximilians University, Großhaderner Straße 2, 82152, Martinsried, Germany
| | - Adina Przykopanski
- Institute for Molecular Biology, OE5250, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.,Institute for Toxicology, OE 5340, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Katrin Serth
- Institute for Molecular Biology, OE5250, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Marius Ueffing
- Institute of Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, 72076, Tübingen, Germany
| | - Martin Blum
- Institute of Biology, University of Hohenheim, Garbenstraße 30, 70593, Stuttgart, Germany.
| | - Achim Gossler
- Institute for Molecular Biology, OE5250, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
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89
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Lv B, Stuck MW, Desai PB, Cabrera OA, Pazour GJ. E3 ubiquitin ligase Wwp1 regulates ciliary dynamics of the Hedgehog receptor Smoothened. J Cell Biol 2021; 220:212435. [PMID: 34161574 PMCID: PMC8236919 DOI: 10.1083/jcb.202010177] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 05/01/2021] [Accepted: 06/01/2021] [Indexed: 12/26/2022] Open
Abstract
The Hedgehog pathway, critical to vertebrate development, is organized in primary cilia. Activation of signaling causes the Hedgehog receptor Ptch1 to exit cilia, allowing a second receptor, Smo, to accumulate in cilia and activate the downstream steps of the pathway. Mechanisms regulating the dynamics of these receptors are unknown, but the ubiquitination of Smo regulates its interaction with the intraflagellar transport system to control ciliary levels. A focused screen of ubiquitin-related genes identified nine required for maintaining low ciliary Smo at the basal state. These included cytoplasmic E3s (Arih2, Mgrn1, and Maea), a ciliary localized E3 (Wwp1), a ciliary localized E2 (Ube2l3), a deubiquitinase (Bap1), and three adaptors (Kctd5, Skp1a, and Skp2). The ciliary E3, Wwp1, binds Ptch1 and localizes to cilia at the basal state. Activation of signaling removes both Ptch1 and Wwp1 from cilia, thus providing an elegant mechanism for Ptch1 to regulate ciliary Smo levels.
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Affiliation(s)
- Bo Lv
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Michael W Stuck
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Paurav B Desai
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Oscar A Cabrera
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA
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90
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Ahmad R, Kleineberg C, Nasirimarekani V, Su YJ, Goli Pozveh S, Bae A, Sundmacher K, Bodenschatz E, Guido I, Vidaković-koch T, Gholami A. Light-Powered Reactivation of Flagella and Contraction of Microtubule Networks: Toward Building an Artificial Cell. ACS Synth Biol 2021; 10:1490-1504. [PMID: 33761235 PMCID: PMC8218302 DOI: 10.1021/acssynbio.1c00071] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Artificial systems
capable of self-sustained movement with self-sufficient
energy are of high interest with respect to the development of many
challenging applications, including medical treatments, but also technical
applications. The bottom-up assembly of such systems in the context
of synthetic biology is still a challenging task. In this work, we
demonstrate the biocompatibility and efficiency of an artificial light-driven
energy module and a motility functional unit by integrating light-switchable
photosynthetic vesicles with demembranated flagella. The flagellar
propulsion is coupled to the beating frequency, and dynamic ATP synthesis
in response to illumination allows us to control beating frequency
of flagella in a light-dependent manner. In addition, we verified
the functionality of light-powered synthetic vesicles in in
vitro motility assays by encapsulating microtubules assembled
with force-generating kinesin-1 motors and the energy module to investigate
the dynamics of a contractile filamentous network in cell-like compartments
by optical stimulation. Integration of this photosynthetic system
with various biological building blocks such as cytoskeletal filaments
and molecular motors may contribute to the bottom-up synthesis of
artificial cells that are able to undergo motor-driven morphological
deformations and exhibit directional motion in a light-controllable
fashion.
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Affiliation(s)
- Raheel Ahmad
- Max-Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
| | - Christin Kleineberg
- Max-Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Vahid Nasirimarekani
- Microfluidics & BIOMICS Cluster UPV/EHU, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Yu-Jung Su
- Max-Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
| | - Samira Goli Pozveh
- Max-Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
| | - Albert Bae
- Department of Biomedical Engineering, University of Rochester, Rochester, New York 14627, United States
| | - Kai Sundmacher
- Max-Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- Otto von Guericke University, Universitaetsplatz 2, 39106 Magdeburg, Germany
| | - Eberhard Bodenschatz
- Max-Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
- Institute for Dynamics of Complex Systems, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Isabella Guido
- Max-Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
| | - Tanja Vidaković-koch
- Max-Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Azam Gholami
- Max-Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
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91
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Hou Y, Zhao L, Kubo T, Cheng X, McNeill N, Oda T, Witman GB. Chlamydomonas FAP70 is a component of the previously uncharacterized ciliary central apparatus projection C2a. J Cell Sci 2021; 134:jcs258540. [PMID: 33988244 PMCID: PMC8272932 DOI: 10.1242/jcs.258540] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/23/2021] [Indexed: 12/12/2022] Open
Abstract
Cilia are essential organelles required for cell signaling and motility. Nearly all motile cilia have a '9+2' axoneme composed of nine outer doublet microtubules plus two central microtubules; the central microtubules together with their projections are termed the central apparatus (CA). In Chlamydomonas reinhardtii, a model organism for studying cilia, 30 proteins are known CA components, and ∼36 more are predicted to be CA proteins. Among the candidate CA proteins is the highly conserved FAP70 (CFAP70 in humans), which also has been reported to be associated with the doublet microtubules. Here, we determined by super-resolution structured illumination microscopy that FAP70 is located exclusively in the CA, and show by cryo-electron microscopy that its N-terminus is located at the base of the C2a projection of the CA. We also found that fap70-1 mutant axonemes lack most of the C2a projection. Mass spectrometry revealed that fap70-1 axonemes lack not only FAP70 but two other conserved candidate CA proteins, FAP65 (CFAP65 in humans) and FAP147 (MYCBPAP in humans). Finally, FAP65 and FAP147 co-immunoprecipitated with HA-tagged FAP70. Taken together, these data identify FAP70, FAP65 and FAP147 as the first defining components of the C2a projection.
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Affiliation(s)
- Yuqing Hou
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, Massachusetts, 01655, USA
| | - Lei Zhao
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, Massachusetts, 01655, USA
| | - Tomohiro Kubo
- Department of Anatomy and Structural Biology, Graduate School of Medicine, University of Yamanashi, Chuo, Yamanashi 409-3898, Japan
| | - Xi Cheng
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, Massachusetts, 01655, USA
| | - Nathan McNeill
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, Massachusetts, 01655, USA
| | - Toshiyuki Oda
- Department of Anatomy and Structural Biology, Graduate School of Medicine, University of Yamanashi, Chuo, Yamanashi 409-3898, Japan
| | - George B. Witman
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, Massachusetts, 01655, USA
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92
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Salomé PA, Merchant SS. Co-expression networks in Chlamydomonas reveal significant rhythmicity in batch cultures and empower gene function discovery. THE PLANT CELL 2021; 33:1058-1082. [PMID: 33793846 PMCID: PMC8226298 DOI: 10.1093/plcell/koab042] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/25/2021] [Indexed: 05/18/2023]
Abstract
The unicellular green alga Chlamydomonas reinhardtii is a choice reference system for the study of photosynthesis and chloroplast metabolism, cilium assembly and function, lipid and starch metabolism, and metal homeostasis. Despite decades of research, the functions of thousands of genes remain largely unknown, and new approaches are needed to categorically assign genes to cellular pathways. Growing collections of transcriptome and proteome data now allow a systematic approach based on integrative co-expression analysis. We used a dataset comprising 518 deep transcriptome samples derived from 58 independent experiments to identify potential co-expression relationships between genes. We visualized co-expression potential with the R package corrplot, to easily assess co-expression and anti-correlation between genes. We extracted several hundred high-confidence genes at the intersection of multiple curated lists involved in cilia, cell division, and photosynthesis, illustrating the power of our method. Surprisingly, Chlamydomonas experiments retained a significant rhythmic component across the transcriptome, suggesting an underappreciated variable during sample collection, even in samples collected in constant light. Our results therefore document substantial residual synchronization in batch cultures, contrary to assumptions of asynchrony. We provide step-by-step protocols for the analysis of co-expression across transcriptome data sets from Chlamydomonas and other species to help foster gene function discovery.
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Affiliation(s)
- Patrice A Salomé
- Department of Chemistry and Biochemistry, University of California—Los Angeles, Los Angeles California 90095
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California—Los Angeles, Los Angeles California 90095
- Departments of Molecular and Cell Biology and Plant and Microbial Biology, University of California-Berkeley, Berkeley, California 94720 and Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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93
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Daigneault BW, Miller DJ. Transient receptor potential polycystin-2 (TRPP2) regulates motility and intracellular calcium of porcine sperm. Andrologia 2021; 53:e14124. [PMID: 34042198 DOI: 10.1111/and.14124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/01/2021] [Accepted: 05/01/2021] [Indexed: 12/17/2022] Open
Abstract
Polycystin-2, also known as transient receptor potential polycystin-2 (TRPP2), is a membrane protein that regulates calcium homeostasis in renal epithelial cells. Mutations in PKD2, the gene encoding human TRPP2, cause enlarged cystic kidneys and contribute to polycystic kidney disease (PKD). Male Drosophila melanogaster with mutations in amo, the homolog of PKD2, display a mild decrease in sperm motility but have a drastic reduction in fertility due to failed sperm migration and storage within the female tract. Although TRPP2 has critical roles for Drosophila sperm function, the protein has not been described in mammalian sperm. Herein, we report the localization of TRPP2 in porcine sperm and identify functions of TRPP2 in regulating intracellular Ca2+ and motility. Porcine sperm treated with an antibody to TRPP2 in capacitating medium had reduced average path velocity and curvilinear velocity (p < .05). Blocking TRPP2 also increased sperm tail beat-cross frequency (p < .05). After 90 min of capacitation, sperm incubated with TRPP2 antibody had decreased intracellular Ca2+ concentration compared to controls (p < .05), consistent with TRPP2 function as a plasma membrane cation channel. This is the first report that mammalian sperm contain TRPP2, which appears to regulate intracellular Ca2+ and motility patterns in porcine sperm.
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Affiliation(s)
- Bradford W Daigneault
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA.,Department of Animal Sciences, University of Illinois, Urbana-Champaign, IL, USA
| | - David J Miller
- Department of Animal Sciences, University of Illinois, Urbana-Champaign, IL, USA
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94
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Mohieldin AM, Pala R, Beuttler R, Moresco JJ, Yates JR, Nauli SM. Ciliary extracellular vesicles are distinct from the cytosolic extracellular vesicles. J Extracell Vesicles 2021; 10:e12086. [PMID: 33936569 PMCID: PMC8077156 DOI: 10.1002/jev2.12086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 03/25/2021] [Accepted: 04/06/2021] [Indexed: 12/28/2022] Open
Abstract
Extracellular vesicles (EVs) are cell‐derived membrane vesicles that are released into the extracellular space. EVs encapsulate key proteins and mediate intercellular signalling pathways. Recently, primary cilia have been shown to release EVs under fluid‐shear flow, but many proteins encapsulated in these vesicles have never been identified. Primary cilia are ubiquitous mechanosensory organelles that protrude from the apical surface of almost all human cells. Primary cilia also serve as compartments for signalling pathways, and their defects have been associated with a wide range of human genetic diseases called ciliopathies. To better understand the mechanism of ciliopathies, it is imperative to know the distinctive protein profiles of the differently sourced EVs (cilia vs cytosol). Here, we isolated EVs from ciliated wild‐type (WT) and non‐ciliated IFT88 knockout (KO) mouse endothelial cells using fluid‐shear flow followed by a conventional method of EV isolation. EVs isolated from WT and KO exhibited distinctive sizes. Differences in EV protein contents were studied using liquid chromatography with tandem mass spectrometry (LC‐MS‐MS) and proteomic comparative analysis, which allowed us to classify proteins between ciliary EVs and cytosolic EVs derived from WT and KO, respectively. A total of 79 proteins were exclusively expressed in WT EVs, 145 solely in KO EVs, and 524 in both EVs. Our bioinformatics analyses revealed 29% distinct protein classes and 75% distinct signalling pathways between WT and KO EVs. Based on our statistical analyses and in vitro studies, we identified NADPH‐cytochrome P450 reductase (POR), and CD166 antigen (CD166) as potential biomarkers for ciliary and cytosolic EVs, respectively. Our protein‐protein interaction network analysis revealed that POR, but not CD166, interacted with either established or strong ciliopathy gene candidates. This report shows the unique differences between EVs secreted from cilia and the cytosol. These results will be important in advancing our understanding of human genetic diseases.
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Affiliation(s)
- Ashraf M Mohieldin
- Department of Biomedical & Pharmaceutical Sciences Chapman University Irvine California USA.,Department of Medicine University of California Irvine Irvine California USA
| | - Rajasekharreddy Pala
- Department of Biomedical & Pharmaceutical Sciences Chapman University Irvine California USA
| | - Richard Beuttler
- Department of Biomedical & Pharmaceutical Sciences Chapman University Irvine California USA
| | - James J Moresco
- Department of Molecular Medicine The Scripps Research Institute La Jolla California USA
| | - John R Yates
- Department of Molecular Medicine The Scripps Research Institute La Jolla California USA
| | - Surya M Nauli
- Department of Biomedical & Pharmaceutical Sciences Chapman University Irvine California USA.,Department of Medicine University of California Irvine Irvine California USA
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95
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Heme-binding protein CYB5D1 is a radial spoke component required for coordinated ciliary beating. Proc Natl Acad Sci U S A 2021; 118:2015689118. [PMID: 33875586 DOI: 10.1073/pnas.2015689118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Coordinated beating is crucial for the function of multiple cilia. However, the molecular mechanism is poorly understood. Here, we characterize a conserved ciliary protein CYB5D1 with a heme-binding domain and a cordon-bleu ubiquitin-like domain. Mutation or knockdown of Cyb5d1 in zebrafish impaired coordinated ciliary beating in the otic vesicle and olfactory epithelium. Similarly, the two flagella of an insertional mutant of the CYB5D1 ortholog in Chlamydomonas (Crcyb5d1) showed an uncoordinated pattern due to a defect in the cis-flagellum. Biochemical analyses revealed that CrCYB5D1 is a radial spoke stalk protein that binds heme only under oxidizing conditions. Lack of CrCYB5D1 resulted in a reductive shift in flagellar redox state and slowing down of the phototactic response. Treatment of Crcyb5d1 with oxidants restored coordinated flagellar beating. Taken together, these data suggest that CrCYB5D1 may integrate environmental and intraciliary signals and regulate the redox state of cilia, which is crucial for the coordinated beating of multiple cilia.
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96
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May EA, Sroka TJ, Mick DU. Phosphorylation and Ubiquitylation Regulate Protein Trafficking, Signaling, and the Biogenesis of Primary Cilia. Front Cell Dev Biol 2021; 9:664279. [PMID: 33912570 PMCID: PMC8075051 DOI: 10.3389/fcell.2021.664279] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/09/2021] [Indexed: 12/30/2022] Open
Abstract
The primary cilium is a solitary, microtubule-based membrane protrusion extending from the surface of quiescent cells that senses the cellular environment and triggers specific cellular responses. The functions of primary cilia require not only numerous different components but also their regulated interplay. The cilium performs highly dynamic processes, such as cell cycle-dependent assembly and disassembly as well as delivery, modification, and removal of signaling components to perceive and process external signals. On a molecular level, these processes often rely on a stringent control of key modulatory proteins, of which the activity, localization, and stability are regulated by post-translational modifications (PTMs). While an increasing number of PTMs on ciliary components are being revealed, our knowledge on the identity of the modifying enzymes and their modulation is still limited. Here, we highlight recent findings on cilia-specific phosphorylation and ubiquitylation events. Shedding new light onto the molecular mechanisms that regulate the sensitive equilibrium required to maintain and remodel primary cilia functions, we discuss their implications for cilia biogenesis, protein trafficking, and cilia signaling processes.
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Affiliation(s)
- Elena A May
- Center of Human and Molecular Biology (ZHMB), Saarland University School of Medicine, Homburg, Germany.,Center for Molecular Signaling (PZMS), Department of Medical Biochemistry and Molecular Biology, Saarland University School of Medicine, Homburg, Germany
| | - Tommy J Sroka
- Center of Human and Molecular Biology (ZHMB), Saarland University School of Medicine, Homburg, Germany.,Center for Molecular Signaling (PZMS), Department of Medical Biochemistry and Molecular Biology, Saarland University School of Medicine, Homburg, Germany
| | - David U Mick
- Center of Human and Molecular Biology (ZHMB), Saarland University School of Medicine, Homburg, Germany.,Center for Molecular Signaling (PZMS), Department of Medical Biochemistry and Molecular Biology, Saarland University School of Medicine, Homburg, Germany
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97
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Hazime KS, Zhou Z, Joachimiak E, Bulgakova NA, Wloga D, Malicki JJ. STORM imaging reveals the spatial arrangement of transition zone components and IFT particles at the ciliary base in Tetrahymena. Sci Rep 2021; 11:7899. [PMID: 33846423 PMCID: PMC8041816 DOI: 10.1038/s41598-021-86909-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 03/22/2021] [Indexed: 11/17/2022] Open
Abstract
The base of the cilium comprising the transition zone (TZ) and transition fibers (TF) acts as a selecting gate to regulate the intraflagellar transport (IFT)-dependent trafficking of proteins to and from cilia. Before entering the ciliary compartment, IFT complexes and transported cargoes accumulate at or near the base of the cilium. The spatial organization of IFT proteins at the cilia base is key for understanding cilia formation and function. Using stochastic optical reconstruction microscopy (STORM) and computational averaging, we show that seven TZ, nine IFT, three Bardet–Biedl syndrome (BBS), and one centrosomal protein, form 9-clustered rings at the cilium base of a ciliate Tetrahymena thermophila. In the axial dimension, analyzed TZ proteins localize to a narrow region of about 30 nm while IFT proteins dock approximately 80 nm proximal to TZ. Moreover, the IFT-A subcomplex is positioned peripheral to the IFT-B subcomplex and the investigated BBS proteins localize near the ciliary membrane. The positioning of the HA-tagged N- and C-termini of the selected proteins enabled the prediction of the spatial orientation of protein particles and likely cargo interaction sites. Based on the obtained data, we built a comprehensive 3D-model showing the arrangement of the investigated ciliary proteins.
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Affiliation(s)
- Khodor S Hazime
- Bateson Centre and the Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
| | - Zhu Zhou
- Bateson Centre and the Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, 3 Pasteur Street, 02-093, Warsaw, Poland
| | - Natalia A Bulgakova
- Bateson Centre and the Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
| | - Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, 3 Pasteur Street, 02-093, Warsaw, Poland.
| | - Jarema J Malicki
- Bateson Centre and the Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
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98
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Liu P, Lou X, Wingfield JL, Lin J, Nicastro D, Lechtreck K. Chlamydomonas PKD2 organizes mastigonemes, hair-like glycoprotein polymers on cilia. J Cell Biol 2021; 219:151720. [PMID: 32348466 PMCID: PMC7265326 DOI: 10.1083/jcb.202001122] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/10/2020] [Accepted: 03/16/2020] [Indexed: 12/20/2022] Open
Abstract
Mutations in the channel protein PKD2 cause autosomal dominant polycystic kidney disease, but the function of PKD2 in cilia remains unclear. Here, we show that PKD2 targets and anchors mastigonemes, filamentous polymers of the glycoprotein MST1, to the extracellular surface of Chlamydomonas cilia. PKD2–mastigoneme complexes physically connect to the axonemal doublets 4 and 8, positioning them perpendicular to the plane of ciliary beating. pkd2 mutant cilia lack mastigonemes, and mutant cells swim with reduced velocity, indicating a motility-related function of the PKD2–mastigoneme complex. Association with both the axoneme and extracellular structures supports a mechanosensory role of Chlamydomonas PKD2. We propose that PKD2–mastigoneme arrays, on opposing sides of the cilium, could perceive forces during ciliary beating and transfer these signals to locally regulate the response of the axoneme.
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Affiliation(s)
- Peiwei Liu
- Department of Cellular Biology, University of Georgia, Athens, GA
| | - Xiaochu Lou
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX
| | | | - Jianfeng Lin
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Daniela Nicastro
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Karl Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, GA
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99
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Desai PB, Stuck MW, Lv B, Pazour GJ. Ubiquitin links smoothened to intraflagellar transport to regulate Hedgehog signaling. J Cell Biol 2021; 219:151798. [PMID: 32435793 PMCID: PMC7337509 DOI: 10.1083/jcb.201912104] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/17/2020] [Accepted: 04/19/2020] [Indexed: 12/17/2022] Open
Abstract
In the absence of Hedgehog ligand, patched-1 (Ptch1) localizes to cilia and prevents ciliary accumulation and activation of smoothened (Smo). Upon ligand binding, Ptch1 is removed from cilia, and Smo is derepressed and accumulates in cilia where it activates signaling. The mechanisms regulating these dynamic movements are not well understood, but defects in intraflagellar transport components, including Ift27 and the BBSome, cause Smo to accumulate in cilia without pathway activation. We find that in the absence of ligand-induced pathway activation, Smo is ubiquitinated and removed from cilia, and this process is dependent on Ift27 and BBSome components. Activation of Hedgehog signaling decreases Smo ubiquitination and ciliary removal, resulting in its accumulation. Blocking ubiquitination of Smo by an E1 ligase inhibitor or by mutating two lysine residues in intracellular loop three causes Smo to aberrantly accumulate in cilia without pathway activation. These data provide a mechanism to control Smo's ciliary level during Hedgehog signaling by regulating the ubiquitination state of the receptor.
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Affiliation(s)
- Paurav B Desai
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Michael W Stuck
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Bo Lv
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA
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100
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The novel testicular enrichment protein Cfap58 is required for Notch-associated ciliogenesis. Biosci Rep 2021; 40:221781. [PMID: 31904090 PMCID: PMC6970087 DOI: 10.1042/bsr20192666] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/28/2019] [Accepted: 01/03/2020] [Indexed: 02/06/2023] Open
Abstract
Cilia and flagella are critical organelles with conserved internal structures and diverse developmental and physiological processes according to cell type. Although the core components of structures are shared with thousands of associated proteins involved in cilia or flagella formation, we hypothesized that some unknown proteins, such as outer dense fiber 2 (Odf2/Cenexin) perform distinct functions in these organelles. In the present study, we identified several uncharacterized proteins through mass spectrometry interactome analysis of Odf2/Cenexin proteins. We further examined the expression patterns and functions of a protein named cilia and flagella associated protein 58 (Cfap58) in cultured astrocytes and sperm flagella. The results of a combination of biochemical analyses and drug administration studies reveal that Cfap58 is a testis-enrichment protein that exhibits similar localization to Odf2/Cenexin proteins and is required for the elongation of the primary cilium and sperm midpiece via modulation of the Notch signaling pathway. However, the cell cycle-related functions and localization of Odf2/Cenexin in the mother centriole were not altered in Cfap58 knockdown cells. These findings indicate that Cfap58 may be partially recruited by Odf2/Cenexin proteins and is indispensable for the cilia and flagellar assembly. These data provide us with a better understanding of ciliogenesis and flagellar elongation and may aid in identifying new targets for diseases caused by Notch-mediated ciliopathies and flagellar abnormalities.
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