1
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Wang H, He K, Zhang H, Zhang Q, Cao L, Li J, Zhong Z, Chen H, Zhou L, Lian C, Wang M, Chen K, Qian PY, Li C. Deciphering deep-sea chemosynthetic symbiosis by single-nucleus RNA-sequencing. eLife 2024; 12:RP88294. [PMID: 39102287 PMCID: PMC11299980 DOI: 10.7554/elife.88294] [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: 08/06/2024] Open
Abstract
Bathymodioline mussels dominate deep-sea methane seep and hydrothermal vent habitats and obtain nutrients and energy primarily through chemosynthetic endosymbiotic bacteria in the bacteriocytes of their gill. However, the molecular mechanisms that orchestrate mussel host-symbiont interactions remain unclear. Here, we constructed a comprehensive cell atlas of the gill in the mussel Gigantidas platifrons from the South China Sea methane seeps (1100 m depth) using single-nucleus RNA-sequencing (snRNA-seq) and whole-mount in situ hybridisation. We identified 13 types of cells, including three previously unknown ones, and uncovered unknown tissue heterogeneity. Every cell type has a designated function in supporting the gill's structure and function, creating an optimal environment for chemosynthesis, and effectively acquiring nutrients from the endosymbiotic bacteria. Analysis of snRNA-seq of in situ transplanted mussels clearly showed the shifts in cell state in response to environmental oscillations. Our findings provide insight into the principles of host-symbiont interaction and the bivalves' environmental adaption mechanisms.
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Affiliation(s)
- Hao Wang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Laoshan LaboratoryQingdaoChina
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)GuangzhouChina
- Department of Ocean Science, Hong Kong University of Science and TechnologyHong KongChina
| | - Kai He
- Key Laboratory of Conservation and Application in Biodiversity of South China, School of Life Sciences, Guangzhou UniversityGuangzhouChina
| | - Huan Zhang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Quanyong Zhang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and TechnologyKunmingJapan
| | - Lei Cao
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Jing Li
- South China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhouChina
| | - Zhaoshan Zhong
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Hao Chen
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Li Zhou
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Chao Lian
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Minxiao Wang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Kai Chen
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and TechnologyKunmingJapan
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)GuangzhouChina
- Department of Ocean Science, Hong Kong University of Science and TechnologyHong KongChina
| | - Chaolun Li
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- South China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
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2
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Deretic J, Odabasi E, Firat-Karalar EN. The multifaceted roles of microtubule-associated proteins in the primary cilium and ciliopathies. J Cell Sci 2023; 136:jcs261148. [PMID: 38095645 DOI: 10.1242/jcs.261148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023] Open
Abstract
The primary cilium is a conserved microtubule-based organelle that is critical for transducing developmental, sensory and homeostatic signaling pathways. It comprises an axoneme with nine parallel doublet microtubules extending from the basal body, surrounded by the ciliary membrane. The axoneme exhibits remarkable stability, serving as the skeleton of the cilium in order to maintain its shape and provide tracks to ciliary trafficking complexes. Although ciliary trafficking and signaling have been exhaustively characterized over the years, less is known about the unique structural and functional complexities of the axoneme. Recent work has yielded new insights into the mechanisms by which the axoneme is built with its proper length and architecture, particularly regarding the activity of microtubule-associated proteins (MAPs). In this Review, we first summarize current knowledge about the architecture, composition and specialized compartments of the primary cilium. Next, we discuss the mechanistic underpinnings of how a functional cilium is assembled, maintained and disassembled through the regulation of its axonemal microtubules. We conclude by examining the diverse localizations and functions of ciliary MAPs for the pathobiology of ciliary diseases.
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Affiliation(s)
- Jovana Deretic
- Department of Molecular Biology and Genetics, Koç University, Istanbul 34450, Turkey
| | - Ezgi Odabasi
- Department of Molecular Biology and Genetics, Koç University, Istanbul 34450, Turkey
| | - Elif Nur Firat-Karalar
- Department of Molecular Biology and Genetics, Koç University, Istanbul 34450, Turkey
- School of Medicine, Koç University, Istanbul 34450, Turkey
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3
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Legal T, Parra M, Tong M, Black CS, Joachimiak E, Valente-Paterno M, Lechtreck K, Gaertig J, Bui KH. CEP104/FAP256 and associated cap complex maintain stability of the ciliary tip. J Cell Biol 2023; 222:e202301129. [PMID: 37756660 PMCID: PMC10522465 DOI: 10.1083/jcb.202301129] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 07/13/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Cilia are essential organelles that protrude from the cell body. Cilia are made of a microtubule-based structure called the axoneme. In most types of cilia, the ciliary tip is distinct from the rest of the cilium. Here, we used cryo-electron tomography and subtomogram averaging to obtain the structure of the ciliary tip of the ciliate Tetrahymena thermophila. We show that the microtubules at the tip are highly crosslinked with each other and stabilized by luminal proteins, plugs, and cap proteins at the plus ends. In the tip region, the central pair lacks typical projections and twists significantly. By analyzing cells lacking a ciliary tip-enriched protein CEP104/FAP256 by cryo-electron tomography and proteomics, we discovered candidates for the central pair cap complex and explained the potential functions of CEP104/FAP256. These data provide new insights into the function of the ciliary tip and the mechanisms of ciliary assembly and length regulation.
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Affiliation(s)
- Thibault Legal
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
| | - Mireya Parra
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Maxwell Tong
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
| | - Corbin S. Black
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Melissa Valente-Paterno
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
| | - Karl Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Jacek Gaertig
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Khanh Huy Bui
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
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4
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Ryniawec JM, Hannaford MR, Zibrat ME, Fagerstrom CJ, Galletta BJ, Aguirre SE, Guice BA, Dean SM, Rusan NM, Rogers GC. Cep104 is a component of the centriole distal tip complex that regulates centriole growth and contributes to Drosophila spermiogenesis. Curr Biol 2023; 33:4202-4216.e9. [PMID: 37729913 PMCID: PMC10591971 DOI: 10.1016/j.cub.2023.08.075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/21/2023] [Accepted: 08/24/2023] [Indexed: 09/22/2023]
Abstract
Proper centrosome number and function relies on the accurate assembly of centrioles, barrel-shaped structures that form the core duplicating elements of the organelle. The growth of centrioles is regulated in a cell cycle-dependent manner; while new daughter centrioles elongate during the S/G2/M phase, mature mother centrioles maintain their length throughout the cell cycle. Centriole length is controlled by the synchronized growth of the microtubules that ensheathe the centriole barrel. Although proteins exist that target the growing distal tips of centrioles, such as CP110 and Cep97, these proteins are generally thought to suppress centriolar microtubule growth, suggesting that distal tips may also contain unidentified counteracting factors that facilitate microtubule polymerization. Currently, a mechanistic understanding of how distal tip proteins balance microtubule growth and shrinkage to either promote daughter centriole elongation or maintain centriole length is lacking. Using a proximity-labeling screen in Drosophila cells, we identified Cep104 as a novel component of a group of evolutionarily conserved proteins that we collectively refer to as the distal tip complex (DTC). We found that Cep104 regulates centriole growth and promotes centriole elongation through its microtubule-binding TOG domain. Furthermore, analysis of Cep104 null flies revealed that Cep104 and Cep97 cooperate during spermiogenesis to align spermatids and coordinate individualization. Lastly, we mapped the complete DTC interactome and showed that Cep97 is the central scaffolding unit required to recruit DTC components to the distal tip of centrioles.
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Affiliation(s)
- John M Ryniawec
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA
| | - Matthew R Hannaford
- Cell and Developmental Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Melanie E Zibrat
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA
| | - Carey J Fagerstrom
- Cell and Developmental Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Brian J Galletta
- Cell and Developmental Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sophia E Aguirre
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA
| | - Bethany A Guice
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA
| | - Spencer M Dean
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA
| | - Nasser M Rusan
- Cell and Developmental Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Gregory C Rogers
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA.
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Dobbelaere J, Su TY, Erdi B, Schleiffer A, Dammermann A. A phylogenetic profiling approach identifies novel ciliogenesis genes in Drosophila and C. elegans. EMBO J 2023; 42:e113616. [PMID: 37317646 PMCID: PMC10425847 DOI: 10.15252/embj.2023113616] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 05/22/2023] [Accepted: 06/01/2023] [Indexed: 06/16/2023] Open
Abstract
Cilia are cellular projections that perform sensory and motile functions in eukaryotic cells. A defining feature of cilia is that they are evolutionarily ancient, yet not universally conserved. In this study, we have used the resulting presence and absence pattern in the genomes of diverse eukaryotes to identify a set of 386 human genes associated with cilium assembly or motility. Comprehensive tissue-specific RNAi in Drosophila and mutant analysis in C. elegans revealed signature ciliary defects for 70-80% of novel genes, a percentage similar to that for known genes within the cluster. Further characterization identified different phenotypic classes, including a set of genes related to the cartwheel component Bld10/CEP135 and two highly conserved regulators of cilium biogenesis. We propose this dataset defines the core set of genes required for cilium assembly and motility across eukaryotes and presents a valuable resource for future studies of cilium biology and associated disorders.
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Affiliation(s)
- Jeroen Dobbelaere
- Max Perutz LabsUniversity of Vienna, Vienna Biocenter (VBC)ViennaAustria
| | - Tiffany Y Su
- Max Perutz LabsUniversity of Vienna, Vienna Biocenter (VBC)ViennaAustria
- Vienna BioCenter PhD ProgramDoctoral School of the University of Vienna and Medical University of ViennaViennaAustria
| | - Balazs Erdi
- Max Perutz LabsUniversity of Vienna, Vienna Biocenter (VBC)ViennaAustria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology, Vienna Biocenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC)ViennaAustria
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6
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Dong Y, Zhang K, Yao H, Jia T, Wang J, Zhu D, Xu F, Cheng M, Zhao S, Shi X. Clinical and genetic characteristics of 36 children with Joubert syndrome. Front Pediatr 2023; 11:1102639. [PMID: 37547106 PMCID: PMC10401045 DOI: 10.3389/fped.2023.1102639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/10/2023] [Indexed: 08/08/2023] Open
Abstract
Background and aims Joubert syndrome (JBTS, OMIM # 213300) is a group of ciliopathies characterized by mid-hindbrain malformation, developmental delay, hypotonia, oculomotor apraxia, and breathing abnormalities. Molar tooth sign in brain imaging is the hallmark for diagnosing JBTS. It is a clinically and genetically heterogeneous disorder involving mutations in more than 40 ciliopathy-related genes. However, long-term follow-up data are scarce, and further research is needed to determine the abundant phenotypes and genetics of this disorder. The study aimed to summarize clinical manifestations, particular appearance on cranial imaging, genetic data, and prognostic features of patients with JBTS. Methods A retrospective case review of 36 cases of JBTS from May 1986 to December 2021 was performed. Clinical data of JBTS patients with development retardation and molar tooth sign on cranial imaging as the main features were analyzed. Genetic testing was performed according to consent obtained from patients and their families. The Gesell Developmental Scale was used to evaluate the intelligence level before and after treatment. The children were divided into a purely neurological JBTS (pure JBTS) group and JBTS with multi-organ system involvement group and then followed up every 3-6 months. Results We enrolled 18 males and 18 females. Thirty-four (94.44%) cases had developmental delay, one patient (2.78%) had strabismus, and one patient (2.78%) had intermittent dizziness. There was one case co-morbid with Lesch-Nyhan syndrome. Three-quarters of cases had one or more other organ or system involvement, with a greater predilection for vision and hearing impairment. JBTS could also involve the skin. Thirty-one cases (86.11%) showed a typical molar tooth sign, and five cases showed a bat wing sign on cranial imaging. Abnormal video electroencephalogram (VEEG) result was obtained in 7.69% of cases. We found six JBTS-related novel gene loci variants: CPLANE1: c.4189 + 1G > A, c.3101T > C(p.Ile1034Thr), c.3733T > C (p.Cys1245Arg), c.4080G > A(p.Lys1360=); RPGRIP1l: c.1351-11A > G; CEP120: c.214 C > T(p.Arg72Cys). The CHD7 gene may be potentially related to the occurrence of JBTS. Analysis showed that the prognosis of pure JBTS was better than that of JBTS with neurological and non-neurological involvement after the formal rehabilitation treatment (P < 0.05). Of the three children with seizures, two cases had epilepsy with a poor prognosis, and another case had breath-holding spells. Conclusion Our findings indicate that early cranial imaging is helpful for the etiological diagnosis of children with unexplained developmental delay and multiple malformations. Patients with JBTS may have coexisting skin abnormalities. The novel gene loci of CPLANE1, RPGRIP1l, and CEP120 were associated with JBTS in our study and provided significant information to enrich the related genetic data. Future works investigating several aspects of the association between CHD7 gene and JBTS merit further investigation. The prognosis of children with pure JBTS is better than that of children with JBTS with non-neurological involvement.
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Affiliation(s)
- Yan Dong
- Department of Pediatrics, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Child Brain Injury, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ke Zhang
- Department of Pediatrics, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - He Yao
- Department of Pediatrics, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Tianming Jia
- Department of Pediatrics, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jun Wang
- Department of Children Rehabilitation, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dengna Zhu
- Department of Children Rehabilitation, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Falin Xu
- Department of Pediatrics, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Meiying Cheng
- Department of Radiology, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shichao Zhao
- Department of Pediatrics, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoyi Shi
- Department of Pediatric Development and Behavior, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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7
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Konjikusic MJ, Lee C, Yue Y, Shrestha BD, Nguimtsop AM, Horani A, Brody S, Prakash VN, Gray RS, Verhey KJ, Wallingford JB. Kif9 is an active kinesin motor required for ciliary beating and proximodistal patterning of motile axonemes. J Cell Sci 2023; 136:jcs259535. [PMID: 35531639 PMCID: PMC9357393 DOI: 10.1242/jcs.259535] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 04/27/2022] [Indexed: 03/19/2024] Open
Abstract
Most motile cilia have a stereotyped structure of nine microtubule outer doublets and a single central pair of microtubules. The central pair of microtubules are surrounded by a set of proteins, termed the central pair apparatus. A specific kinesin, Klp1 projects from the central pair and contributes to ciliary motility in Chlamydomonas. The vertebrate ortholog, Kif9, is required for beating in mouse sperm flagella, but the mechanism of Kif9/Klp1 function remains poorly defined. Here, using Xenopus epidermal multiciliated cells, we show that Kif9 is necessary for ciliary motility and the proper distal localization of not only central pair proteins, but also radial spokes and dynein arms. In addition, single-molecule assays in vitro reveal that Xenopus Kif9 is a long-range processive motor, although it does not mediate long-range movement in ciliary axonemes in vivo. Together, our data suggest that Kif9 is integral for ciliary beating and is necessary for proper axonemal distal end integrity.
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Affiliation(s)
- Mia J. Konjikusic
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
- Department of Pediatrics, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd, The University of Texas at Austin, Dell Medical School, Austin, TX 78712, USA
- Department of Nutritional Sciences, 200 W 24th Street, The University of Texas at Austin, Austin, TX 78712, USA
| | - Chanjae Lee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Yang Yue
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Ange M. Nguimtsop
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Amjad Horani
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63130, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Steven Brody
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Vivek N. Prakash
- Department of Physics, University of Miami, Coral Gables, FL 33146, USA
- Department of Biology and Department of Marine Biology and Ecology, University of Miami, Coral Gables, FL 33146,USA
| | - Ryan S. Gray
- Department of Pediatrics, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd, The University of Texas at Austin, Dell Medical School, Austin, TX 78712, USA
- Department of Nutritional Sciences, 200 W 24th Street, The University of Texas at Austin, Austin, TX 78712, USA
| | - Kristen J. Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - John B. Wallingford
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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8
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Liu P, Liu Y, Zhou J. Ciliary mechanosensation - roles of polycystins and mastigonemes. J Cell Sci 2023; 136:286945. [PMID: 36752106 DOI: 10.1242/jcs.260565] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Cilia are surface-exposed organelles that provide motility and sensory functions for cells, and it is widely believed that mechanosensation can be mediated through cilia. Polycystin-1 and -2 (PC-1 and PC-2, respectively) are transmembrane proteins that can localize to cilia; however, the molecular mechanisms by which polycystins contribute to mechanosensation are still controversial. Studies detail two prevailing models for the molecular roles of polycystins on cilia; one stresses the mechanosensation capabilities and the other unveils their ligand-receptor nature. The discovery that polycystins interact with mastigonemes, the 'hair-like' protrusions of flagella, is a novel finding in identifying the interactors of polycystins in cilia. While the functions of polycystins proposed by both models may coexist in cilia, it is hoped that a precise understanding of the mechanism of action of polycystins can be achieved by uncovering their distribution and interacting factors inside cilia. This will hopefully provide a satisfying answer to the pathogenesis of autosomal dominant polycystic kidney disease (ADPKD), which is caused by mutations in PC-1 and PC-2. In this Review, we discuss the characteristics of polycystins in the context of cilia and summarize the functions of mastigonemes in unicellular ciliates. Finally, we compare flagella and molecular features of PC-2 between unicellular and multicellular organisms, with the aim of providing new insights into the ciliary roles of polycystins in general.
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Affiliation(s)
- Peiwei Liu
- Shandong Provincial Key Laboratory of Animal Resistance Biology , College of Life Sciences in Shandong Normal University, Jinan 250358, China
| | - Ying Liu
- Shandong Provincial Key Laboratory of Animal Resistance Biology , College of Life Sciences in Shandong Normal University, Jinan 250358, China
| | - Jun Zhou
- Shandong Provincial Key Laboratory of Animal Resistance Biology , College of Life Sciences in Shandong Normal University, Jinan 250358, China.,College of Life Sciences, Nankai University, Tianjin 300071, China
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9
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Legal T, Tong M, Black C, Valente Paterno M, Gaertig J, Bui KH. Molecular architecture of the ciliary tip revealed by cryo-electron tomography. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.522627. [PMID: 36711791 PMCID: PMC9881849 DOI: 10.1101/2023.01.03.522627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Cilia are essential organelles that protrude from the cell body. Cilia are made of a microtubule-based structure called the axoneme. In most types of cilia, the ciliary tip is distinct from the rest of the cilium. Here, we used cryo-electron tomography and subtomogram averaging to obtain the structure of the ciliary tip of the ciliate Tetrahymena thermophila. We show the microtubules in the tip are highly cross-linked with each other and stabilised by luminal proteins, plugs and cap proteins at the plus ends. In the tip region, the central pair lacks the typical projections and twists significantly. By analysing cells lacking a ciliary tip-enriched protein CEP104/FAP256 by cryo-electron tomography and proteomics, we discovered candidates for the central pair cap complex and explain potential functions of CEP104/FAP256. These data provide new insights into the function of the ciliary tip and inform about the mechanisms of ciliary assembly and length regulation.
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Affiliation(s)
- T Legal
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
| | - M Tong
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
| | - C Black
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
| | - M Valente Paterno
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
| | - J Gaertig
- Department of Cellular Biology, University of Georgia, Athens, GA, United States of America
| | - K H Bui
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
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10
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De Ita M, Gaytán-Cervantes J, Cisneros B, Araujo MA, Huicochea-Montiel JC, Cárdenas-Conejo A, Lazo-Cárdenas CC, Ramírez-Portillo CI, Feria-Kaiser C, Peregrino-Bejarano L, Yáñez-Gutiérrez L, González-Torres C, Rosas-Vargas H. Clustering of Genetic Anomalies of Cilia Outer Dynein Arm and Central Apparatus in Patients with Transposition of the Great Arteries. Genes (Basel) 2022; 13:genes13091662. [PMID: 36140829 PMCID: PMC9498580 DOI: 10.3390/genes13091662] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/10/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022] Open
Abstract
Transposition of the great arteries (TGA) is a congenital heart defect with a complex pathogenesis that has not been fully elucidated. In this study, we performed whole-exome sequencing (WES) in isolated TGA-diagnosed patients and analyzed genes of motile and non-motile cilia ciliogenesis and ciliary trafficking, as well as genes previously associated with this heart malformation. Deleterious missense and splicing variants of genes DNAH9, DNAH11, and ODAD4 of cilia outer dynein arm and central apparatus, HYDIN, were found in our TGA patients. Remarkable, there is a clustering of deleterious genetic variants in cilia genes, suggesting it could be an oligogenic disease. Our data evidence the genetic diversity and etiological complexity of TGA and point out that population allele determination and genetic aggregation studies are required to improve genetic counseling.
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Affiliation(s)
- Marlon De Ita
- Unidad de Investigación Médica en Genética Humana, UMAE Hospital de Pediatría, Centro Médico Nacional Siglo XXI, IMSS, Ciudad de México 06720, Mexico
- Dpto de Genética y Biología Molecular, CINVESTAV Zacatenco IPN, Ciudad de México 07360, Mexico
| | - Javier Gaytán-Cervantes
- Laboratorio de Secuenciación, División de Desarrollo de la Investigación, IMSS, Ciudad de México 06720, Mexico
| | - Bulmaro Cisneros
- Dpto de Genética y Biología Molecular, CINVESTAV Zacatenco IPN, Ciudad de México 07360, Mexico
| | - María Antonieta Araujo
- Departamento clínico de Genética Médica, UMAE Hospital de Pediatría, Centro Médico Nacional Siglo XXI, IMSS, Ciudad de México 06720, Mexico
| | - Juan Carlos Huicochea-Montiel
- Departamento clínico de Genética Médica, UMAE Hospital de Pediatría, Centro Médico Nacional Siglo XXI, IMSS, Ciudad de México 06720, Mexico
| | - Alan Cárdenas-Conejo
- Departamento clínico de Genética Médica, UMAE Hospital de Pediatría, Centro Médico Nacional Siglo XXI, IMSS, Ciudad de México 06720, Mexico
| | - Charles César Lazo-Cárdenas
- Departamento clínico de Cardiología, UMAE Hospital de Pediatría, Centro Médico Nacional Siglo XXI, IMSS, Ciudad de México 06720, Mexico
| | - César Iván Ramírez-Portillo
- Departamento clínico de Cardiología, UMAE Hospital de Pediatría, Centro Médico Nacional Siglo XXI, IMSS, Ciudad de México 06720, Mexico
| | - Carina Feria-Kaiser
- Unidad de Cuidados Intensivos Neonatales, UMAE Hospital de Pediatría, Centro Médico Nacional Siglo XXI, IMSS, Ciudad de México 06720, Mexico
| | | | - Lucelli Yáñez-Gutiérrez
- Clínica de Cardiopatías Congénitas, UMAE Hospital de Cardiología, CMN Siglo XXI, Ciudad de México 06720, Mexico
| | - Carolina González-Torres
- Laboratorio de Secuenciación, División de Desarrollo de la Investigación, IMSS, Ciudad de México 06720, Mexico
- Correspondence: (C.G.-T.); (H.R.-V.)
| | - Haydeé Rosas-Vargas
- Unidad de Investigación Médica en Genética Humana, UMAE Hospital de Pediatría, Centro Médico Nacional Siglo XXI, IMSS, Ciudad de México 06720, Mexico
- Correspondence: (C.G.-T.); (H.R.-V.)
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11
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Ge R, Cao M, Chen M, Liu M, Xie S. Cytoskeletal networks in primary cilia: Current knowledge and perspectives. J Cell Physiol 2022; 237:3975-3983. [PMID: 36000703 DOI: 10.1002/jcp.30865] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/08/2022] [Accepted: 08/11/2022] [Indexed: 11/12/2022]
Abstract
Primary cilia, microtubule-based protrusions present on the surface of most mammalian cells, function as sensory organelles that monitor extracellular signals and transduce them into intracellular biochemical responses. There is renewed research interest in primary cilia due to their essential roles in development, tissue homeostasis, and human diseases. Primary cilia dysfunction causes a large spectrum of human diseases, collectively known as ciliopathies. Despite significant advances in our understanding of primary cilia, there are still no effective agents for treating ciliopathies. Primary ciliogenesis is a highly ordered process involving membrane trafficking, basal body maturation, vesicle docking and fusion, transition zone assembly, and axoneme extension, in which actin and microtubule networks play critical and multiple roles. Actin and microtubule network architecture, isotropy, and dynamics are tightly controlled by cytoskeleton-associated proteins, a growing number of which are now recognized as responsible for cilium formation and maintenance. Here we summarize the roles of actin and microtubules and their associated proteins in primary ciliogenesis and maintenance. In doing so, we highlight that targeting cytoskeleton-associated proteins may be a promising therapeutic strategy for the treatment of ciliopathies.
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Affiliation(s)
- Ruixin Ge
- Department of Cell Biology, College of Life Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Institute of Biomedical Sciences, Shandong Normal University, Jinan, China
| | - Minghui Cao
- Department of Cell Biology, College of Life Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Institute of Biomedical Sciences, Shandong Normal University, Jinan, China
| | - Miao Chen
- Department of Bioscience, School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Min Liu
- Department of Cell Biology, College of Life Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Institute of Biomedical Sciences, Shandong Normal University, Jinan, China
| | - Songbo Xie
- Department of Cell Biology, College of Life Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Institute of Biomedical Sciences, Shandong Normal University, Jinan, China.,Department of Bioscience, School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
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12
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Tiryaki F, Deretic J, Firat-Karalar EN. ENKD1 is a centrosomal and ciliary microtubule-associated protein important for primary cilium content regulation. FEBS J 2022; 289:3789-3812. [PMID: 35072334 DOI: 10.1111/febs.16367] [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: 09/16/2021] [Revised: 12/08/2021] [Accepted: 01/20/2022] [Indexed: 12/19/2022]
Abstract
Centrioles and cilia are conserved, microtubule-based structures critical for cell function and development. Their dysfunction causes cancer and developmental disorders. How microtubules are organized into ordered structures by microtubule-associated proteins (MAPs) and tubulin modifications is best understood during mitosis but is largely unexplored for the centrioles and the ciliary axoneme, which are composed of stable microtubules that maintain their length at a steady-state. In particular, we know little about the identity of the centriolar and ciliary MAPs and how they work together during the assembly and maintenance of the cilium and centriole. Here, we identified the Enkurin domain containing 1 (ENKD1) as a component of the centriole wall and the axoneme in mammalian cells and showed that it has extensive proximity interactions with these compartments and MAPs. Using in vitro and cellular assays, we found that ENKD1 is a new MAP that regulates microtubule organization and stability. Consistently, we observed an increase in tubulin polymerization and microtubule stability, as well as disrupted microtubule organization in ENKD1 overexpression. Cells depleted for ENKD1 were defective in ciliary length and content regulation and failed to respond to Hedgehog pathway activation. Together, our results advance our understanding of the functional and regulatory relationship between MAPs and the primary cilium.
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Affiliation(s)
- Fatmanur Tiryaki
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | - Jovana Deretic
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | - Elif Nur Firat-Karalar
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey.,Koç University School of Medicine, Istanbul, Turkey
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13
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Wang H, Luo G, Hu W, Mei J, Shen Y, Wang M, Tan Y, Yang Y, Lu C, Zhao Y, Qi M. Whole Exome Sequencing Identified Novel ARMC9 Variations in Two Cases With Joubert Syndrome. Front Genet 2022; 13:817153. [PMID: 35186037 PMCID: PMC8855066 DOI: 10.3389/fgene.2022.817153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/10/2022] [Indexed: 11/23/2022] Open
Abstract
Background: Biallelic variations in the armadillo repeat-containing 9 (ARMC9) gene were recently defined to cause Joubert syndrome (JS) type thirty. In this study, two unrelated families with probands displaying typical indications of JS were enrolled and underwent a series of clinical and genetic investigations. Methods: Routine evaluation including magnetic resonance imaging (MRI) was carried out. Whole-exome sequencing (WES) was performed on the probands to detect causative variants. Next, in silico structural and molecular dynamic (MD) analysis was conducted on the missense variant for analyzing its intramolecular impact. Meanwhile, an in vitro study with the minigene system was performed to explore the specific impact on mRNA splicing of another variant. Results: Two unrelated patients from two different families came to our hospital exhibiting typical JS presentations, such as the “molar tooth sign.” Using WES, we identified that both probands carried the compound heterogeneous variants in ARMC9 (NM_025139.6), with c.1878+1G > A and c.895C > T (p.Arg299Ter) in family 1 and c.1878+1G > A and c.1027C > T (p.Arg343Cys) in family 2. These variants were inherited from their unaffected parents by Sanger sequencing, respectively, and ARMC9 c.895C > T (p.Arg299Ter) and c.1878+1G > A were novel variants. In silico analysis indicated the c.1027C > T (p.Arg343Cys) would likely affect the secondary structure of the ARMC9 protein. The minigene study demonstrated that the splice site variant c.1878+1G > A abolished the canonical donor site, resulting in an 18bp intronic retention of intron 20. Conclusion: The findings in this study expanded the mutation spectrum of ARMC9-associated JS, and we suggested that the function of ARMC9 in the pathogenesis of JS might involve the development of primary cilia, after discussing the function of the ARMC9 protein.
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Affiliation(s)
- Hao Wang
- Department of Cell Biology and Medical Genetics, School of Medicine, Zhejiang University, Hangzhou, China
- Prenatal Diagnosis Center, Hangzhou Women’s Hospital, Hangzhou, China
| | - Guanjun Luo
- Child Rehabilitation Department, Nanhai Affiliated Maternity and Children’s Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Wensheng Hu
- Prenatal Diagnosis Center, Hangzhou Women’s Hospital, Hangzhou, China
- Department of Obstetrics and Gynecology, Hangzhou Women’s Hospital Hangzhou, Hangzhou, China
| | - Jin Mei
- Prenatal Diagnosis Center, Hangzhou Women’s Hospital, Hangzhou, China
| | - Yue Shen
- National Research Institute for Family Planning, Beijing, China
| | - Min Wang
- Prenatal Diagnosis Center, Hangzhou Women’s Hospital, Hangzhou, China
| | - Yuan Tan
- Child Rehabilitation Department, Nanhai Affiliated Maternity and Children’s Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Yang Yang
- Prenatal Diagnosis Center, Hangzhou Women’s Hospital, Hangzhou, China
| | - Chao Lu
- National Research Institute for Family Planning, Beijing, China
| | - Yong Zhao
- Child Rehabilitation Department, Nanhai Affiliated Maternity and Children’s Hospital of Guangzhou University of Chinese Medicine, Foshan, China
- *Correspondence: Ming Qi, ; Yong Zhao,
| | - Ming Qi
- Department of Cell Biology and Medical Genetics, School of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Ming Qi, ; Yong Zhao,
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14
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Huang Y, Jiang Z, Gao X, Luo P, Jiang X. ARMC Subfamily: Structures, Functions, Evolutions, Interactions, and Diseases. Front Mol Biosci 2021; 8:791597. [PMID: 34912852 PMCID: PMC8666550 DOI: 10.3389/fmolb.2021.791597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/15/2021] [Indexed: 12/29/2022] Open
Abstract
Armadillo repeat-containing proteins (ARMCs) are widely distributed in eukaryotes and have important influences on cell adhesion, signal transduction, mitochondrial function regulation, tumorigenesis, and other processes. These proteins share a similar domain consisting of tandem repeats approximately 42 amino acids in length, and this domain constitutes a substantial platform for the binding between ARMCs and other proteins. An ARMC subfamily, including ARMC1∼10, ARMC12, and ARMCX1∼6, has received increasing attention. These proteins may have many terminal regions and play a critical role in various diseases. On the one hand, based on their similar central domain of tandem repeats, this ARMC subfamily may function similarly to other ARMCs. On the other hand, the unique domains on their terminals may cause these proteins to have different functions. Here, we focus on the ARMC subfamily (ARMC1∼10, ARMC12, and ARMCX1∼6), which is relatively conserved in vertebrates and highly conserved in mammals, particularly primates. We review the structures, biological functions, evolutions, interactions, and related diseases of the ARMC subfamily, which involve more than 30 diseases and 40 bypasses, including interactions and relationships between more than 100 proteins and signaling molecules. We look forward to obtaining a clearer understanding of the ARMC subfamily to facilitate further in-depth research and treatment of related diseases.
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Affiliation(s)
- Yutao Huang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,Institue of Neurosurgery of People's Liberation Army of China (PLA), PLA's Key Laboratory of Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Zijian Jiang
- Department of Hepato-biliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiangyu Gao
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, China
| | - Peng Luo
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,Institue of Neurosurgery of People's Liberation Army of China (PLA), PLA's Key Laboratory of Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiaofan Jiang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,Institue of Neurosurgery of People's Liberation Army of China (PLA), PLA's Key Laboratory of Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
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15
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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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16
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Wingfield JL, Mekonnen B, Mengoni I, Liu P, Jordan M, Diener D, Pigino G, Lechtreck K. In vivo imaging shows continued association of several IFT-A, IFT-B and dynein complexes while IFT trains U-turn at the tip. J Cell Sci 2021; 134:271904. [PMID: 34415027 DOI: 10.1242/jcs.259010] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/12/2021] [Indexed: 01/05/2023] Open
Abstract
Flagellar assembly depends on intraflagellar transport (IFT), a bidirectional motility of protein carriers, the IFT trains. The trains are periodic assemblies of IFT-A and IFT-B subcomplexes and the motors kinesin-2 and IFT dynein. At the tip, anterograde trains are remodeled for retrograde IFT, a process that in Chlamydomonas involves kinesin-2 release and train fragmentation. However, the degree of train disassembly at the tip remains unknown. Here, we performed two-color imaging of fluorescent protein-tagged IFT components, which indicates that IFT-A and IFT-B proteins from a given anterograde train usually return in the same set of retrograde trains. Similarly, concurrent turnaround was typical for IFT-B proteins and the IFT dynein subunit D1bLIC-GFP but severance was observed as well. Our data support a simple model of IFT turnaround, in which IFT-A, IFT-B and IFT dynein typically remain associated at the tip and segments of the anterograde trains convert directly into retrograde trains. Continuous association of IFT-A, IFT-B and IFT dynein during tip remodeling could balance protein entry and exit, preventing the build-up of IFT material in flagella.
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Affiliation(s)
- Jenna L Wingfield
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Betlehem Mekonnen
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Ilaria Mengoni
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Peiwei Liu
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Mareike Jordan
- Max Planck Institute of Molecular Cell Biology and Genetics, D-01307 Dresden, Germany
| | - Dennis Diener
- Max Planck Institute of Molecular Cell Biology and Genetics, D-01307 Dresden, Germany
| | - Gaia Pigino
- Max Planck Institute of Molecular Cell Biology and Genetics, D-01307 Dresden, Germany.,Human Technopole, Via Cristina Belgioioso 171, 20157 Milan, Italy
| | - Karl Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
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17
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Park K, Li C, Tsiropoulou S, Gonçalves J, Kondratev C, Pelletier L, Blacque OE, Leroux MR. CDKL kinase regulates the length of the ciliary proximal segment. Curr Biol 2021; 31:2359-2373.e7. [PMID: 33857430 DOI: 10.1016/j.cub.2021.03.068] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/25/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022]
Abstract
Cilia are organelles found throughout most unicellular eukaryotes and different metazoan cell types. To accomplish their essential roles in cell motility, fluid flow, and signaling, cilia are divided into subcompartments with variable structures, compositions, and functions. How these specific subcompartments are built remains almost completely unexplored. Here, we show that C. elegans CDKL-1, related to the human CDKL kinase family (CDKL1/CDKL2/CDKL3/CDKL4/CDKL5), specifically controls the length of the proximal segment, a ciliary subdomain conserved in evolution from Tetrahymena motile cilia to C. elegans chemosensory, mammalian olfactory, and photoreceptor non-motile cilia. CDKL-1 associates with intraflagellar transport (IFT), influences the distribution of the IFT anterograde motors heterotrimeric kinesin-II and homodimeric OSM-3-kinesin/KIF17 in the proximal segment, and shifts the boundary between the proximal and distal segments (PS/DS boundary). CDKL-1 appears to function independently from several factors that influence cilium length, namely the kinases DYF-5 (mammalian CILK1/MAK) and NEKL-1 (NEK9), as well as the depolymerizing kinesins KLP-13 (KIF19) and KLP-7 (KIF2). However, a different kinase, DYF-18 (CCRK), is needed for the correct localization and function of CDKL-1 and similarly influences the length of the proximal segment. Loss of CDKL-1, which affects proximal segment length without impairing overall ciliary microtubule structural integrity, also impairs cilium-dependent processes, namely cGMP-signaling-dependent body length control and CO2 avoidance. Collectively, our findings suggest that cilium length is regulated by various pathways and that the IFT-associated kinase CDKL-1 is essential for the construction of a specific ciliary compartment and contributes to development and sensory physiology.
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Affiliation(s)
- Kwangjin Park
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada; Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Chunmei Li
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada; Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Sofia Tsiropoulou
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - João Gonçalves
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Christine Kondratev
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada; Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Laurence Pelletier
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Michel R Leroux
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada; Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.
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18
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Akella JS, Barr MM. The tubulin code specializes neuronal cilia for extracellular vesicle release. Dev Neurobiol 2021; 81:231-252. [PMID: 33068333 PMCID: PMC8052387 DOI: 10.1002/dneu.22787] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 09/07/2020] [Accepted: 09/23/2020] [Indexed: 12/17/2022]
Abstract
Cilia are microtubule-based organelles that display diversity in morphology, ultrastructure, protein composition, and function. The ciliary microtubules of C. elegans sensory neurons exemplify this diversity and provide a paradigm to understand mechanisms driving ciliary specialization. Only a subset of ciliated neurons in C. elegans are specialized to make and release bioactive extracellular vesicles (EVs) into the environment. The cilia of extracellular vesicle releasing neurons have distinct axonemal features and specialized intraflagellar transport that are important for releasing EVs. In this review, we discuss the role of the tubulin code in the specialization of microtubules in cilia of EV releasing neurons.
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Affiliation(s)
- Jyothi S Akella
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Maureen M Barr
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
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19
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Nabeel-Shah S, Garg J, Kougnassoukou Tchara PE, Pearlman RE, Lambert JP, Fillingham J. Functional proteomics protocol for the identification of interaction partners in Tetrahymena thermophila. STAR Protoc 2021; 2:100362. [PMID: 33786459 PMCID: PMC7988224 DOI: 10.1016/j.xpro.2021.100362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
We describe an optimized protocol for one-step affinity purification of FZZ-tagged proteins followed by mass spectrometry analysis for the identification of protein-protein interactions in the ciliate protozoan Tetrahymena thermophila. The FZZ epitope tag contains 2 protein A moieties (ZZ) and a 3xFLAG separated by a TEV cleavage site, which can also be employed in tandem affinity purification. This protocol is versatile and is suitable to use for other common epitope tags and can be adapted for other ciliates. For complete details on the use and execution of this protocol, please refer to Garg et al. (2019).
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Affiliation(s)
- Syed Nabeel-Shah
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Jyoti Garg
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Pata-Eting Kougnassoukou Tchara
- Department of Molecular Medicine, Cancer Research Center, Big Data Research Center, Université Laval, Quebec City, QC, Canada
- CHU de Québec Research Center, CHUL, 2705 Laurier Boulevard, Quebec City, QC, G1V 4G2, Canada
| | - Ronald E. Pearlman
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Jean-Philippe Lambert
- Department of Molecular Medicine, Cancer Research Center, Big Data Research Center, Université Laval, Quebec City, QC, Canada
- CHU de Québec Research Center, CHUL, 2705 Laurier Boulevard, Quebec City, QC, G1V 4G2, Canada
| | - Jeffrey Fillingham
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
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20
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Latour BL, Van De Weghe JC, Rusterholz TD, Letteboer SJ, Gomez A, Shaheen R, Gesemann M, Karamzade A, Asadollahi M, Barroso-Gil M, Chitre M, Grout ME, van Reeuwijk J, van Beersum SE, Miller CV, Dempsey JC, Morsy H, Bamshad MJ, Nickerson DA, Neuhauss SC, Boldt K, Ueffing M, Keramatipour M, Sayer JA, Alkuraya FS, Bachmann-Gagescu R, Roepman R, Doherty D. Dysfunction of the ciliary ARMC9/TOGARAM1 protein module causes Joubert syndrome. J Clin Invest 2021; 130:4423-4439. [PMID: 32453716 DOI: 10.1172/jci131656] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 05/14/2020] [Indexed: 02/06/2023] Open
Abstract
Joubert syndrome (JBTS) is a recessive neurodevelopmental ciliopathy characterized by a pathognomonic hindbrain malformation. All known JBTS genes encode proteins involved in the structure or function of primary cilia, ubiquitous antenna-like organelles essential for cellular signal transduction. Here, we used the recently identified JBTS-associated protein armadillo repeat motif-containing 9 (ARMC9) in tandem-affinity purification and yeast 2-hybrid screens to identify a ciliary module whose dysfunction underlies JBTS. In addition to the known JBTS-associated proteins CEP104 and CSPP1, we identified coiled-coil domain containing 66 (CCDC66) and TOG array regulator of axonemal microtubules 1 (TOGARAM1) as ARMC9 interaction partners. We found that TOGARAM1 variants cause JBTS and disrupt TOGARAM1 interaction with ARMC9. Using a combination of protein interaction analyses, characterization of patient-derived fibroblasts, and analysis of CRISPR/Cas9-engineered zebrafish and hTERT-RPE1 cells, we demonstrated that dysfunction of ARMC9 or TOGARAM1 resulted in short cilia with decreased axonemal acetylation and polyglutamylation, but relatively intact transition zone function. Aberrant serum-induced ciliary resorption and cold-induced depolymerization in ARMC9 and TOGARAM1 patient cell lines suggest a role for this new JBTS-associated protein module in ciliary stability.
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Affiliation(s)
- Brooke L Latour
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Tamara Ds Rusterholz
- Institute of Medical Genetics, and.,Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
| | - Stef Jf Letteboer
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Arianna Gomez
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Matthias Gesemann
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
| | - Arezou Karamzade
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mostafa Asadollahi
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Miguel Barroso-Gil
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Manali Chitre
- Department of Paediatric Neurology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Megan E Grout
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Jeroen van Reeuwijk
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Sylvia Ec van Beersum
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Caitlin V Miller
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Jennifer C Dempsey
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Heba Morsy
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | | | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, Washington, USA.,The University of Washington Center for Mendelian Genomics is detailed in Supplemental Acknowledgments.,University of Washington Center for Mendelian Genomics, Seattle, Washington, USA.,Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | | | - Deborah A Nickerson
- The University of Washington Center for Mendelian Genomics is detailed in Supplemental Acknowledgments.,University of Washington Center for Mendelian Genomics, Seattle, Washington, USA
| | - Stephan Cf Neuhauss
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
| | - Karsten Boldt
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Marius Ueffing
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Mohammad Keramatipour
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - John A Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Ruxandra Bachmann-Gagescu
- Institute of Medical Genetics, and.,Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
| | - Ronald Roepman
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, Washington, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
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21
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Yamazoe T, Nagai T, Umeda S, Sugaya Y, Mizuno K. Roles of TOG and jelly-roll domains of centrosomal protein CEP104 in its functions in cilium elongation and Hedgehog signaling. J Biol Chem 2020; 295:14723-14736. [PMID: 32820051 DOI: 10.1074/jbc.ra120.013334] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 08/11/2020] [Indexed: 12/26/2022] Open
Abstract
Primary cilia are generated through the extension of the microtubule-based axoneme. Centrosomal protein 104 (CEP104) localizes to the tip of the elongating axoneme, and CEP104 mutations are linked to a ciliopathy, Joubert syndrome. Thus, CEP104 has been implicated in ciliogenesis. However, the mechanism by which CEP104 regulates ciliogenesis remains elusive. We report here that CEP104 is critical for cilium elongation but not for initiating ciliogenesis. We also demonstrated that the tumor-overexpressed gene (TOG) domain of CEP104 exhibits microtubule-polymerizing activity and that this activity is essential for the cilium-elongating activity of CEP104. Knockdown/rescue experiments showed that the N-terminal jelly-roll (JR) fold partially contributes to cilium-elongating activity of CEP104, but neither the zinc-finger region nor the SXIP motif is required for this activity. CEP104 binds to a centriole-capping protein, CP110, through the zinc-finger region and to a microtubule plus-end-binding protein, EB1, through the SXIP motif, indicating that the binding of CP110 and EB1 is dispensable for the cilium-elongating activity of CEP104. Moreover, CEP104 depletion does not affect CP110 removal from the mother centriole, which suggests that CEP104 functions after the removal of CP110. Last, we also showed that CEP104 is required for the ciliary entry of Smoothened and export of GPR161 upon Hedgehog signal activation and that the TOG domain plays a critical role in this activity. Our results define the roles of the individual domains of CEP104 in its functions in cilium elongation and Hedgehog signaling and should enhance our understanding of the mechanism underlying CEP104 mutation-associated ciliopathies.
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Affiliation(s)
- Takashi Yamazoe
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Tomoaki Nagai
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan; Department of Biochemistry, Fukushima Medical University School of Medicine, Fukushima, Japan.
| | - Shinya Umeda
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Yuko Sugaya
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Kensaku Mizuno
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan; Institute of Liberal Arts and Sciences, Tohoku University, Kawauchi, Sendai, Miyagi, Japan.
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22
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A CEP104-CSPP1 Complex Is Required for Formation of Primary Cilia Competent in Hedgehog Signaling. Cell Rep 2020; 28:1907-1922.e6. [PMID: 31412255 PMCID: PMC6702141 DOI: 10.1016/j.celrep.2019.07.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 05/21/2019] [Accepted: 07/10/2019] [Indexed: 12/25/2022] Open
Abstract
CEP104 is an evolutionarily conserved centrosomal and ciliary tip protein. CEP104 loss-of-function mutations are reported in patients with Joubert syndrome, but their function in the etiology of ciliopathies is poorly understood. Here, we show that cep104 silencing in zebrafish causes cilia-related manifestations: shortened cilia in Kupffer’s vesicle, heart laterality, and cranial nerve development defects. We show that another Joubert syndrome-associated cilia tip protein, CSPP1, interacts with CEP104 at microtubules for the regulation of axoneme length. We demonstrate in human telomerase reverse transcriptase-immortalized retinal pigmented epithelium (hTERT-RPE1) cells that ciliary translocation of Smoothened in response to Hedgehog pathway stimulation is both CEP104 and CSPP1 dependent. However, CEP104 is not required for the ciliary recruitment of CSPP1, indicating that an intra-ciliary CEP104-CSPP1 complex controls axoneme length and Hedgehog signaling competence. Our in vivo and in vitro analyses of CEP104 define its interaction with CSPP1 as a requirement for the formation of Hedgehog signaling-competent cilia, defects that underlie Joubert syndrome. cep104-depleted zebrafish display shortened KV cilia and defective brain development CEP104 interacts with CSPP1 at the tip of the primary cilium to regulate cilia length CEP104 or CSPP1 loss in human cells leads to defective Hedgehog signaling Impaired signaling is linked to reduction of ciliary SMO but not ARL13B or INPP5E
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23
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Conkar D, Firat-Karalar EN. Microtubule-associated proteins and emerging links to primary cilium structure, assembly, maintenance, and disassembly. FEBS J 2020; 288:786-798. [PMID: 32627332 DOI: 10.1111/febs.15473] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/23/2020] [Accepted: 06/30/2020] [Indexed: 12/22/2022]
Abstract
The primary cilium is a microtubule-based structure that protrudes from the cell surface in diverse eukaryotic organisms. It functions as a key signaling center that decodes a variety of mechanical and chemical stimuli and plays fundamental roles in development and homeostasis. Accordingly, structural and functional defects of the primary cilium have profound effects on the physiology of multiple organ systems including kidney, retina, and central nervous system. At the core of the primary cilium is the microtubule-based axoneme, which supports the cilium shape and acts as the scaffold for bidirectional transport of cargoes into and out of cilium. Advances in imaging, proteomics, and structural biology have revealed new insights into the ultrastructural organization and composition of the primary cilium, the mechanisms that underlie its biogenesis and functions, and the pathologies that result from their deregulation termed ciliopathies. In this viewpoint, we first discuss the recent studies that identified the three-dimensional native architecture of the ciliary axoneme and revealed that it is considerably different from the well-known '9 + 0' paradigm. Moving forward, we explore emerging themes in the assembly and maintenance of the axoneme, with a focus on how microtubule-associated proteins regulate its structure, length, and stability. This far more complex picture of the primary cilium structure and composition, as well as the recent technological advances, open up new avenues for future research.
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Affiliation(s)
- Deniz Conkar
- Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey
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24
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Bayless BA, Navarro FM, Winey M. Motile Cilia: Innovation and Insight From Ciliate Model Organisms. Front Cell Dev Biol 2019; 7:265. [PMID: 31737631 PMCID: PMC6838636 DOI: 10.3389/fcell.2019.00265] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 10/18/2019] [Indexed: 12/15/2022] Open
Abstract
Ciliates are a powerful model organism for the study of basal bodies and motile cilia. These single-celled protists contain hundreds of cilia organized in an array making them an ideal system for both light and electron microscopy studies. Isolation and subsequent proteomic analysis of both cilia and basal bodies have been carried out to great success in ciliates. These studies reveal that ciliates share remarkable protein conservation with metazoans and have identified a number of essential basal body/ciliary proteins. Ciliates also boast a genetic and molecular toolbox that allows for facile manipulation of ciliary genes. Reverse genetics studies in ciliates have expanded our understanding of how cilia are positioned within an array, assembled, stabilized, and function at a molecular level. The advantages of cilia number coupled with a robust genetic and molecular toolbox have established ciliates as an ideal system for motile cilia and basal body research and prove a promising system for future research.
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Affiliation(s)
- Brian A Bayless
- Department of Biology, Santa Clara University, Santa Clara, CA, United States
| | - Francesca M Navarro
- Department of Biology, Santa Clara University, Santa Clara, CA, United States
| | - Mark Winey
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
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25
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Luo M, Cao L, Cao Z, Ma S, Shen Y, Yang D, Lu C, Lin Z, Liu Z, Yu Y, Cai R, Chen C, Gao H, Wang X, Cao M, Ma X. Whole exome sequencing reveals novel CEP104 mutations in a Chinese patient with Joubert syndrome. Mol Genet Genomic Med 2019; 7:e1004. [PMID: 31625690 PMCID: PMC6900356 DOI: 10.1002/mgg3.1004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 12/22/2022] Open
Abstract
Background Joubert syndrome (JS, OMIM: 213300) is a recessive developmental disorder characterized by cerebellar vermis hypoplasia and a distinctive mid‐hindbrain malformation called the “molar tooth sign” on axial magnetic resonance imaging. To date, more than 35 ciliary genes have been identified as the causative genes of JS. Methods Whole exome sequencing was performed to detect the causative gene mutations in a Chinese patient with JS followed by Sanger sequencing. RT‐PCR and Sanger sequencing were used to confirm the abnormal transcript of centrosomal protein 104 (CEP104, OMIM: 616690). Results We identified two novel heterozygous mutations of CEP104 in the proband, which were c.2364+1G>A and c.414delC (p.Asn138Lysfs*11) (GenBank: NM_014704.3) and consistent with the autosomal recessive inheritance mode. Conclusion Our study reported the fourth case of JS patients with CEP104 mutations, which expands the mutation spectrum of CEP104 and elucidates the clinical heterogeneity of JS.
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Affiliation(s)
- Minna Luo
- National Research Institute for Family Planning, Beijing, China.,National Human Genetic Resources Center, Beijing, China
| | - Li Cao
- Child Healthcare Department (Child Early Development Center), Sichuan Provincial Hospital for Women and Children, Chengdu, China
| | - Zongfu Cao
- National Research Institute for Family Planning, Beijing, China.,National Human Genetic Resources Center, Beijing, China
| | - Siyu Ma
- National Research Institute for Family Planning, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China
| | - Yue Shen
- National Research Institute for Family Planning, Beijing, China.,National Human Genetic Resources Center, Beijing, China
| | - Di Yang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chao Lu
- National Research Institute for Family Planning, Beijing, China.,National Human Genetic Resources Center, 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, Shanghai, China
| | - Zhimin Liu
- Department of Radiology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yufei Yu
- National Research Institute for Family Planning, Beijing, China.,National Human Genetic Resources Center, Beijing, China
| | - Ruikun Cai
- National Research Institute for Family Planning, Beijing, China.,National Human Genetic Resources Center, Beijing, China
| | - Cuixia Chen
- National Research Institute for Family Planning, Beijing, China.,National Human Genetic Resources Center, Beijing, China
| | - Huafang Gao
- National Research Institute for Family Planning, Beijing, China.,National Human Genetic Resources Center, Beijing, China
| | - Xueyan Wang
- Department of Prenatal Diagnosis, Sichuan Provincial Hospital for Women and Children, Chengdu, 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, Shanghai, China
| | - Xu Ma
- National Research Institute for Family Planning, Beijing, China.,National Human Genetic Resources Center, Beijing, China
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26
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Structures of TOG1 and TOG2 from the human microtubule dynamics regulator CLASP1. PLoS One 2019; 14:e0219823. [PMID: 31323070 PMCID: PMC6641166 DOI: 10.1371/journal.pone.0219823] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 07/03/2019] [Indexed: 12/16/2022] Open
Abstract
Tubulin-binding TOG domains are found arrayed in a number of proteins that regulate microtubule dynamics. While much is known about the structure and function of TOG domains from the XMAP215 microtubule polymerase family, less in known about the TOG domain array found in animal CLASP family members. The animal CLASP TOG array promotes microtubule pause, potentiates rescue, and limits catastrophe. How structurally distinct the TOG domains of animal CLASP are from one another, from XMAP215 family TOG domains, and whether a specific order of structurally distinct TOG domains in the TOG array is conserved across animal CLASP family members is poorly understood. We present the x-ray crystal structures of Homo sapiens (H.s.) CLASP1 TOG1 and TOG2. The structures of H.s. CLASP1 TOG1 and TOG2 are distinct from each other and from the previously determined structure of Mus musculus (M.m.) CLASP2 TOG3. Comparative analyses of CLASP family TOG domain structures determined to date across species and paralogs supports a conserved CLASP TOG array paradigm in which structurally distinct TOG domains are arrayed in a specific order. H.s. CLASP1 TOG1 bears structural similarity to the free-tubulin binding TOG domains of the XMAP215 family but lacks many of the key tubulin-binding determinants found in XMAP215 family TOG domains. This aligns with studies that report that animal CLASP family TOG1 domains cannot bind free tubulin or microtubules. In contrast, animal CLASP family TOG2 and TOG3 domains have reported microtubule-binding activity but are structurally distinct from the free-tubulin binding TOG domains of the XMAP215 family. H.s. CLASP1 TOG2 has a convex architecture, predicted to engage a hyper-curved tubulin state that may underlie its ability to limit microtubule catastrophe and promote rescue. M.m. CLASP2 TOG3 has unique structural elements in the C-terminal half of its α-solenoid domain that our modeling studies implicate in binding to laterally-associated tubulin subunits in the microtubule lattice in a mode similar to, yet distinct from those predicted for the XMAP215 family TOG4 domain. The potential ability of the animal CLASP family TOG3 domain to engage lateral tubulin subunits may underlie the microtubule rescue activity ascribed to the domain. These findings highlight the structural diversity of TOG domains within the CLASP family TOG array and provide a molecular foundation for understanding CLASP-dependent effects on microtubule dynamics.
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27
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Osinka A, Poprzeczko M, Zielinska MM, Fabczak H, Joachimiak E, Wloga D. Ciliary Proteins: Filling the Gaps. Recent Advances in Deciphering the Protein Composition of Motile Ciliary Complexes. Cells 2019; 8:cells8070730. [PMID: 31319499 PMCID: PMC6678824 DOI: 10.3390/cells8070730] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/12/2019] [Accepted: 07/16/2019] [Indexed: 12/15/2022] Open
Abstract
Cilia are highly evolutionarily conserved, microtubule-based cell protrusions present in eukaryotic organisms from protists to humans, with the exception of fungi and higher plants. Cilia can be broadly divided into non-motile sensory cilia, called primary cilia, and motile cilia, which are locomotory organelles. The skeleton (axoneme) of primary cilia is formed by nine outer doublet microtubules distributed on the cilium circumference. In contrast, the skeleton of motile cilia is more complex: in addition to outer doublets, it is composed of two central microtubules and several diverse multi-protein complexes that are distributed periodically along both types of microtubules. For many years, researchers have endeavored to fully characterize the protein composition of ciliary macro-complexes and the molecular basis of signal transduction between these complexes. Genetic and biochemical analyses have suggested that several hundreds of proteins could be involved in the assembly and function of motile cilia. Within the last several years, the combined efforts of researchers using cryo-electron tomography, genetic and biochemical approaches, and diverse model organisms have significantly advanced our knowledge of the ciliary structure and protein composition. Here, we summarize the recent progress in the identification of the subunits of ciliary complexes, their precise intraciliary localization determined by cryo-electron tomography data, and the role of newly identified proteins in cilia.
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Affiliation(s)
- Anna Osinka
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Martyna Poprzeczko
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Magdalena M Zielinska
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Hanna Fabczak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland.
| | - Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland.
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28
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Saettone A, Nabeel-Shah S, Garg J, Lambert JP, Pearlman RE, Fillingham J. Functional Proteomics of Nuclear Proteins in Tetrahymena thermophila: A Review. Genes (Basel) 2019; 10:E333. [PMID: 31052454 PMCID: PMC6562869 DOI: 10.3390/genes10050333] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/23/2019] [Accepted: 04/25/2019] [Indexed: 12/14/2022] Open
Abstract
Identification and characterization of protein complexes and interactomes has been essential to the understanding of fundamental nuclear processes including transcription, replication, recombination, and maintenance of genome stability. Despite significant progress in elucidation of nuclear proteomes and interactomes of organisms such as yeast and mammalian systems, progress in other models has lagged. Protists, including the alveolate ciliate protozoa with Tetrahymena thermophila as one of the most studied members of this group, have a unique nuclear biology, and nuclear dimorphism, with structurally and functionally distinct nuclei in a common cytoplasm. These features have been important in providing important insights about numerous fundamental nuclear processes. Here, we review the proteomic approaches that were historically used as well as those currently employed to take advantage of the unique biology of the ciliates, focusing on Tetrahymena, to address important questions and better understand nuclear processes including chromatin biology of eukaryotes.
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Affiliation(s)
- Alejandro Saettone
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada.
| | - Syed Nabeel-Shah
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
| | - Jyoti Garg
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada.
| | - Jean-Philippe Lambert
- Department of Molecular Medicine and Cancer Research Centre, Université Laval, Quebec, QC, G1V 0A6, Canada.
- CHU de Québec Research Center, CHUL, 2705 Boulevard Laurier, Quebec, QC, G1V 4G2, Canada
| | - Ronald E Pearlman
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada.
| | - Jeffrey Fillingham
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada.
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29
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Cilia Distal Domain: Diversity in Evolutionarily Conserved Structures. Cells 2019; 8:cells8020160. [PMID: 30769894 PMCID: PMC6406257 DOI: 10.3390/cells8020160] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 01/25/2019] [Accepted: 02/13/2019] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic cilia are microtubule-based organelles that protrude from the cell surface to fulfill sensory and motility functions. Their basic structure consists of an axoneme templated by a centriole/basal body. Striking differences in ciliary ultra-structures can be found at the ciliary base, the axoneme and the tip, not only throughout the eukaryotic tree of life, but within a single organism. Defects in cilia biogenesis and function are at the origin of human ciliopathies. This structural/functional diversity and its relationship with the etiology of these diseases is poorly understood. Some of the important events in cilia function occur at their distal domain, including cilia assembly/disassembly, IFT (intraflagellar transport) complexes' remodeling, and signal detection/transduction. How axonemal microtubules end at this domain varies with distinct cilia types, originating different tip architectures. Additionally, they show a high degree of dynamic behavior and are able to respond to different stimuli. The existence of microtubule-capping structures (caps) in certain types of cilia contributes to this diversity. It has been proposed that caps play a role in axoneme length control and stabilization, but their roles are still poorly understood. Here, we review the current knowledge on cilia structure diversity with a focus on the cilia distal domain and caps and discuss how they affect cilia structure and function.
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30
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Abstract
Imagine that in 1678 you are Christiaan Huygens or Antonie van Leeuwenhoek seeing paramecia swim gracefully across the field of view of your new microscope. These unicellular, free-living, and swimming cells might have remained a curiosity if not for the ability of H.S. Jennings (Behavior of the lower organisms. Indiana University Press, Bloomington, 1906) and T.M. Sonneborn (Proc Natl Acad Sci USA 23:378-385, 1937) to recognize them for their behavior and genetics, both Mendelian and non-Mendelian. Following many years of painstaking work by Sonneborn and other researchers, Paramecium now serves as a modern model organism that has made specific contributions to cell and molecular biology and development. We will review the continuing usefulness and contributions of Paramecium species in this chapter.Even without a microscope, Paramecium species is visible to the naked eye because of their size (50-300 μ long). Paramecia are holotrichous ciliates, that is, unicellular organisms in the phylum Ciliophora that are covered with cilia. It was the beating of these cilia that propelled them across the slides of the first microscopes and continue to fascinate us today. Over time, Paramecium became a favorite model organism for a large variety of studies. Denis Lyn has called Paramecium the "white rat" of the Ciliophora for their manipulability and amenity to research. We will touch upon the use of Paramecium species to examine swimming behavior, ciliary structure and function, ion channel function, basal body duplication and patterning, non-Mendelian cortical inheritance, programmed DNA rearrangements, regulated secretion and exocytosis, and cell trafficking. In particular, we will focus on the use of P. tetraurelia and P. caudatum.
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