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Kwon KY, Jeong H, Jang DG, Kwon T, Park TJ. Ckb and Ybx2 interact with Ribc2 and are necessary for the ciliary beating of multi-cilia. Genes Genomics 2023; 45:157-167. [PMID: 36508087 DOI: 10.1007/s13258-022-01350-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/26/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Motile cilia in a vertebrate are important to sustaining activities of life. Fluid flow on the apical surface of several tissues, including bronchial epithelium, ependymal epithelium, and fallopian tubules is generated by the ciliary beating of motile cilia. Multi-ciliated cells in ependymal tissue are responsible for the circulation of cerebrospinal fluid (CSF), which is essential for the development and homeostasis of the central nervous system, and airway tissues are protected from external contaminants by cilia-driven mucosal flow over the top of the airway epithelium. OBJECTIVE A previous study reported that reduction of Ribc2 protein leads to disruption of ciliary beating in multi-ciliated cells. However, knowledge regarding the molecular function of Ribc2 is limited, thus currently available information is also limited. Therefore, we evaluated the importance of proteins involved in the interaction with Ribc2 in the process of ciliary beating. METHODS Immunoprecipitation and mass spectrometry analysis was performed for the discovery of proteins involved in the interaction with Ribc2. Expression of the target gene was inhibited by injection of antisense morpholinos and measurement of the fluid flow on the embryonic epidermis of Xenopus was performed using fluorescent beads for examination of the ciliary beating of multi cilia. In addition, the flag-tagged protein was expressed by injection of mRNA and the changes in protein localization in the cilia were measured by immunostaining and western blot analysis for analysis of the molecular interaction between Ribc2 and Ribc2 binding proteins in multi-cilia. RESULTS The IP/MS analysis identified Ckb and Ybx2 as Ribc2 binding proteins and our results showed that localization of both Ckb and Ybx2 occurs at the axoneme of multi-cilia on the embryonic epithelium of Xenopus laevis. In addition, our findings confirmed that knock-down of Ckb or Ybx2 resulted in abnormal ciliary beating and reduction of cilia-driven fluid flow on multi-cilia of Xenopus laevis. In addition, significantly decreased localization of Ckb or Ybx2 in the ciliary axoneme was observed in Ribc2-depleted multi-cilia. CONCLUSION Ckb and Ybx2 are involved in the interaction with Ribc2 and are necessary for the ciliary beating of multi-cilia.
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Affiliation(s)
- Keun Yeong Kwon
- Department of Biological Sciences, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Hyeongsun Jeong
- Department of Biological Medical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Dong Gil Jang
- Department of Biological Sciences, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Taejoon Kwon
- Department of Biological Medical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea.
| | - Tae Joo Park
- Department of Biological Sciences, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea.
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Abstract
We report a complete 3D structural model of typical epithelial primary cilia based on structural maps of full-length primary cilia obtained by serial section electron tomography. Our data demonstrate the architecture of primary cilia differs extensively from the commonly acknowledged 9+0 paradigm. The axoneme structure is relatively stable but gradually evolves from base to tip with a decreasing number of microtubule complexes (MtCs) and a reducing diameter. The axonemal MtCs are cross-linked by previously unrecognized fibrous protein networks. Such an architecture explains why primary cilia can elastically withstand liquid flow for mechanosensing. The nine axonemal MtCs in a cilium are found to differ significantly in length indicating intraflagellar transport processes in primary cilia may be more complicated than that reported for motile cilia. The 3D maps of microtubule doublet-singlet transitions generally display longitudinal gaps at the inner junction between the A- and B-tubules, which indicates the inner junction protein is a major player in doublet-singlet transitions. In addition, vesicles releasing from kidney primary cilia were observed in the structural maps, supporting that ciliary vesicles budding may serve as ectosomes for cell-cell communication.
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Tessier L, Côté O, Bienzle D. Sequence variant analysis of RNA sequences in severe equine asthma. PeerJ 2018; 6:e5759. [PMID: 30324028 PMCID: PMC6186407 DOI: 10.7717/peerj.5759] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 09/15/2018] [Indexed: 12/13/2022] Open
Abstract
Background Severe equine asthma is a chronic inflammatory disease of the lung in horses similar to low-Th2 late-onset asthma in humans. This study aimed to determine the utility of RNA-Seq to call gene sequence variants, and to identify sequence variants of potential relevance to the pathogenesis of asthma. Methods RNA-Seq data were generated from endobronchial biopsies collected from six asthmatic and seven non-asthmatic horses before and after challenge (26 samples total). Sequences were aligned to the equine genome with Spliced Transcripts Alignment to Reference software. Read preparation for sequence variant calling was performed with Picard tools and Genome Analysis Toolkit (GATK). Sequence variants were called and filtered using GATK and Ensembl Variant Effect Predictor (VEP) tools, and two RNA-Seq predicted sequence variants were investigated with both PCR and Sanger sequencing. Supplementary analysis of novel sequence variant selection with VEP was based on a score of <0.01 predicted with Sorting Intolerant from Tolerant software, missense nature, location within the protein coding sequence and presence in all asthmatic individuals. For select variants, effect on protein function was assessed with Polymorphism Phenotyping 2 and screening for non-acceptable polymorphism 2 software. Sequences were aligned and 3D protein structures predicted with Geneious software. Difference in allele frequency between the groups was assessed using a Pearson’s Chi-squared test with Yates’ continuity correction, and difference in genotype frequency was calculated using the Fisher’s exact test for count data. Results RNA-Seq variant calling and filtering correctly identified substitution variants in PACRG and RTTN. Sanger sequencing confirmed that the PACRG substitution was appropriately identified in all 26 samples while the RTTN substitution was identified correctly in 24 of 26 samples. These variants of uncertain significance had substitutions that were predicted to result in loss of function and to be non-neutral. Amino acid substitutions projected no change of hydrophobicity and isoelectric point in PACRG, and a change in both for RTTN. For PACRG, no difference in allele frequency between the two groups was detected but a higher proportion of asthmatic horses had the altered RTTN allele compared to non-asthmatic animals. Discussion RNA-Seq was sensitive and specific for calling gene sequence variants in this disease model. Even moderate coverage (<10–20 counts per million) yielded correct identification in 92% of samples, suggesting RNA-Seq may be suitable to detect sequence variants in low coverage samples. The impact of amino acid alterations in PACRG and RTTN proteins, and possible association of the sequence variants with asthma, is of uncertain significance, but their role in ciliary function may be of future interest.
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Affiliation(s)
- Laurence Tessier
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada.,BenchSci, Toronto, ON, Canada
| | - Olivier Côté
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada.,BioAssay Works, Ijamsville, MD, USA
| | - Dorothee Bienzle
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
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Loucks CM, Bialas NJ, Dekkers MPJ, Walker DS, Grundy LJ, Li C, Inglis PN, Kida K, Schafer WR, Blacque OE, Jansen G, Leroux MR. PACRG, a protein linked to ciliary motility, mediates cellular signaling. Mol Biol Cell 2016; 27:2133-44. [PMID: 27193298 PMCID: PMC4927285 DOI: 10.1091/mbc.e15-07-0490] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 05/09/2016] [Indexed: 01/15/2023] Open
Abstract
Cilia are cellular projections that can be motile to generate fluid flow or nonmotile to enable signaling. Both forms are based on shared components, and proteins involved in ciliary motility, like PACRG, may also function in ciliary signaling. Caenorhabditis elegans PACRG acts in a subset of nonmotile cilia to influence a learning behavior and promote longevity. Cilia are microtubule-based organelles that project from nearly all mammalian cell types. Motile cilia generate fluid flow, whereas nonmotile (primary) cilia are required for sensory physiology and modulate various signal transduction pathways. Here we investigate the nonmotile ciliary signaling roles of parkin coregulated gene (PACRG), a protein linked to ciliary motility. PACRG is associated with the protofilament ribbon, a structure believed to dictate the regular arrangement of motility-associated ciliary components. Roles for protofilament ribbon–associated proteins in nonmotile cilia and cellular signaling have not been investigated. We show that PACRG localizes to a small subset of nonmotile cilia in Caenorhabditis elegans, suggesting an evolutionary adaptation for mediating specific sensory/signaling functions. We find that it influences a learning behavior known as gustatory plasticity, in which it is functionally coupled to heterotrimeric G-protein signaling. We also demonstrate that PACRG promotes longevity in C. elegans by acting upstream of the lifespan-promoting FOXO transcription factor DAF-16 and likely upstream of insulin/IGF signaling. Our findings establish previously unrecognized sensory/signaling functions for PACRG and point to a role for this protein in promoting longevity. Furthermore, our work suggests additional ciliary motility-signaling connections, since EFHC1 (EF-hand containing 1), a potential PACRG interaction partner similarly associated with the protofilament ribbon and ciliary motility, also positively regulates lifespan.
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Affiliation(s)
- Catrina M Loucks
- Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Nathan J Bialas
- Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | | | - Denise S Walker
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Laura J Grundy
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Chunmei Li
- Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - P Nick Inglis
- Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Katarzyna Kida
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - William R Schafer
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Gert Jansen
- Department of Cell Biology, Erasmus MC, 3000 CA, Rotterdam, The Netherlands
| | - Michel R Leroux
- Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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Lin H, Zhang Z, Guo S, Chen F, Kessler JM, Wang YM, Dutcher SK. A NIMA-Related Kinase Suppresses the Flagellar Instability Associated with the Loss of Multiple Axonemal Structures. PLoS Genet 2015; 11:e1005508. [PMID: 26348919 PMCID: PMC4562644 DOI: 10.1371/journal.pgen.1005508] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 08/17/2015] [Indexed: 11/18/2022] Open
Abstract
CCDC39 and CCDC40 were first identified as causative mutations in primary ciliary dyskinesia patients; cilia from patients show disorganized microtubules, and they are missing both N-DRC and inner dynein arms proteins. In Chlamydomonas, we used immunoblots and microtubule sliding assays to show that mutants in CCDC40 (PF7) and CCDC39 (PF8) fail to assemble N-DRC, several inner dynein arms, tektin, and CCDC39. Enrichment screens for suppression of pf7; pf8 cells led to the isolation of five independent extragenic suppressors defined by four different mutations in a NIMA-related kinase, CNK11. These alleles partially rescue the flagellar length defect, but not the motility defect. The suppressor does not restore the missing N-DRC and inner dynein arm proteins. In addition, the cnk11 mutations partially suppress the short flagella phenotype of N-DRC and axonemal dynein mutants, but do not suppress the motility defects. The tpg1 mutation in TTLL9, a tubulin polyglutamylase, partially suppresses the length phenotype in the same axonemal dynein mutants. In contrast to cnk11, tpg1 does not suppress the short flagella phenotype of pf7. The polyglutamylated tubulin in the proximal region that remains in the tpg1 mutant is reduced further in the pf7; tpg1 double mutant by immunofluorescence. CCDC40, which is needed for docking multiple other axonemal complexes, is needed for tubulin polyglutamylation in the proximal end of the flagella. The CCDC39 and CCDC40 proteins are likely to be involved in recruiting another tubulin glutamylase(s) to the flagella. Another difference between cnk11-1 and tpg1 mutants is that cnk11-1 cells show a faster turnover rate of tubulin at the flagellar tip than in wild-type flagella and tpg1 flagella show a slower rate. The double mutant shows a turnover rate similar to tpg1, which suggests the faster turnover rate in cnk11-1 flagella requires polyglutamylation. Thus, we hypothesize that many short flagella mutants in Chlamydomonas have increased instability of axonemal microtubules. Both CNK11 and tubulin polyglutamylation play roles in regulating the stability of axonemal microtubules.
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Affiliation(s)
- Huawen Lin
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Zhengyan Zhang
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Suyang Guo
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Fan Chen
- Department of Physics, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Jonathan M. Kessler
- Department of Physics, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Yan Mei Wang
- Department of Physics, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Susan K. Dutcher
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
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Chung MI, Kwon T, Tu F, Brooks ER, Gupta R, Meyer M, Baker JC, Marcotte EM, Wallingford JB. Coordinated genomic control of ciliogenesis and cell movement by RFX2. eLife 2014; 3:e01439. [PMID: 24424412 PMCID: PMC3889689 DOI: 10.7554/elife.01439] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 11/27/2013] [Indexed: 12/16/2022] Open
Abstract
The mechanisms linking systems-level programs of gene expression to discrete cell biological processes in vivo remain poorly understood. In this study, we have defined such a program for multi-ciliated epithelial cells (MCCs), a cell type critical for proper development and homeostasis of the airway, brain and reproductive tracts. Starting from genomic analysis of the cilia-associated transcription factor Rfx2, we used bioinformatics and in vivo cell biological approaches to gain insights into the molecular basis of cilia assembly and function. Moreover, we discovered a previously un-recognized role for an Rfx factor in cell movement, finding that Rfx2 cell-autonomously controls apical surface expansion in nascent MCCs. Thus, Rfx2 coordinates multiple, distinct gene expression programs in MCCs, regulating genes that control cell movement, ciliogenesis, and cilia function. As such, the work serves as a paradigm for understanding genomic control of cell biological processes that span from early cell morphogenetic events to terminally differentiated cellular functions. DOI: http://dx.doi.org/10.7554/eLife.01439.001.
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Affiliation(s)
- Mei-I Chung
- Department of Molecular Biosciences, University of Texas at Austin, Austin, United States
| | - Taejoon Kwon
- Department of Molecular Biosciences, University of Texas at Austin, Austin, United States
| | - Fan Tu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, United States
| | - Eric R Brooks
- Department of Molecular Biosciences, University of Texas at Austin, Austin, United States
| | - Rakhi Gupta
- Department of Genetics, Stanford University, Stanford, United States
| | - Matthew Meyer
- Department of Molecular Biosciences, University of Texas at Austin, Austin, United States
| | - Julie C Baker
- Department of Genetics, Stanford University, Stanford, United States
| | - Edward M Marcotte
- Department of Molecular Biosciences, University of Texas at Austin, Austin, United States
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, United States
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, United States
| | - John B Wallingford
- Department of Molecular Biosciences, University of Texas at Austin, Austin, United States
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, United States
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, United States
- Howard Hughes Medical Institute, University of Texas at Austin, Austin, United States
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7
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Nguyen HT, Sandhu J, Langousis G, Hill KL. CMF22 is a broadly conserved axonemal protein and is required for propulsive motility in Trypanosoma brucei. EUKARYOTIC CELL 2013; 12:1202-13. [PMID: 23851336 PMCID: PMC3811564 DOI: 10.1128/ec.00068-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 07/02/2013] [Indexed: 12/23/2022]
Abstract
The eukaryotic flagellum (or cilium) is a broadly conserved organelle that provides motility for many pathogenic protozoa and is critical for normal development and physiology in humans. Therefore, defining core components of motile axonemes enhances understanding of eukaryotic biology and provides insight into mechanisms of inherited and infectious diseases in humans. In this study, we show that component of motile flagella 22 (CMF22) is tightly associated with the flagellar axoneme and is likely to have been present in the last eukaryotic common ancestor. The CMF22 amino acid sequence contains predicted IQ and ATPase associated with a variety of cellular activities (AAA) motifs that are conserved among CMF22 orthologues in diverse organisms, hinting at the importance of these domains in CMF22 function. Knockdown by RNA interference (RNAi) and rescue with an RNAi-immune mRNA demonstrated that CMF22 is required for propulsive cell motility in Trypanosoma brucei. Loss of propulsive motility in CMF22-knockdown cells was due to altered flagellar beating patterns, rather than flagellar paralysis, indicating that CMF22 is essential for motility regulation and likely functions as a fundamental regulatory component of motile axonemes. CMF22 association with the axoneme is weakened in mutants that disrupt the nexin-dynein regulatory complex, suggesting potential interaction with this complex. Our results provide insight into the core machinery required for motility of eukaryotic flagella.
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Affiliation(s)
- HoangKim T. Nguyen
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California, USA
| | - Jaspreet Sandhu
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California, USA
| | - Gerasimos Langousis
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California, USA
| | - Kent L. Hill
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California, USA
- Molecular Biology Institute, University of California, Los Angeles, California, USA
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8
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Dacheux D, Landrein N, Thonnus M, Gilbert G, Sahin A, Wodrich H, Robinson DR, Bonhivers M. A MAP6-related protein is present in protozoa and is involved in flagellum motility. PLoS One 2012; 7:e31344. [PMID: 22355359 PMCID: PMC3280300 DOI: 10.1371/journal.pone.0031344] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 01/06/2012] [Indexed: 12/25/2022] Open
Abstract
In vertebrates the microtubule-associated proteins MAP6 and MAP6d1 stabilize cold-resistant microtubules. Cilia and flagella have cold-stable microtubules but MAP6 proteins have not been identified in these organelles. Here, we describe TbSAXO as the first MAP6-related protein to be identified in a protozoan, Trypanosoma brucei. Using a heterologous expression system, we show that TbSAXO is a microtubule stabilizing protein. Furthermore we identify the domains of the protein responsible for microtubule binding and stabilizing and show that they share homologies with the microtubule-stabilizing Mn domains of the MAP6 proteins. We demonstrate, in the flagellated parasite, that TbSAXO is an axonemal protein that plays a role in flagellum motility. Lastly we provide evidence that TbSAXO belongs to a group of MAP6-related proteins (SAXO proteins) present only in ciliated or flagellated organisms ranging from protozoa to mammals. We discuss the potential roles of the SAXO proteins in cilia and flagella function.
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Affiliation(s)
- Denis Dacheux
- Microbiologie Fondamentale et Pathogénicité, Université de Bordeaux, UMR 5234, Bordeaux, France
- Microbiologie Fondamentale et Pathogénicité, CNRS, UMR 5234, Bordeaux, France
- Microbiologie Fondamentale et Pathogénicité, Institut Polytechnique de Bordeaux, UMR 5234, Bordeaux, France
| | - Nicolas Landrein
- Microbiologie Fondamentale et Pathogénicité, Université de Bordeaux, UMR 5234, Bordeaux, France
- Microbiologie Fondamentale et Pathogénicité, CNRS, UMR 5234, Bordeaux, France
| | - Magali Thonnus
- Microbiologie Fondamentale et Pathogénicité, Université de Bordeaux, UMR 5234, Bordeaux, France
- Microbiologie Fondamentale et Pathogénicité, CNRS, UMR 5234, Bordeaux, France
| | - Guillaume Gilbert
- Microbiologie Fondamentale et Pathogénicité, Université de Bordeaux, UMR 5234, Bordeaux, France
- Microbiologie Fondamentale et Pathogénicité, CNRS, UMR 5234, Bordeaux, France
| | - Annelise Sahin
- Microbiologie Fondamentale et Pathogénicité, Université de Bordeaux, UMR 5234, Bordeaux, France
- Microbiologie Fondamentale et Pathogénicité, CNRS, UMR 5234, Bordeaux, France
| | - Harald Wodrich
- Microbiologie Fondamentale et Pathogénicité, Université de Bordeaux, UMR 5234, Bordeaux, France
- Microbiologie Fondamentale et Pathogénicité, CNRS, UMR 5234, Bordeaux, France
| | - Derrick R. Robinson
- Microbiologie Fondamentale et Pathogénicité, Université de Bordeaux, UMR 5234, Bordeaux, France
- Microbiologie Fondamentale et Pathogénicité, CNRS, UMR 5234, Bordeaux, France
| | - Mélanie Bonhivers
- Microbiologie Fondamentale et Pathogénicité, Université de Bordeaux, UMR 5234, Bordeaux, France
- Microbiologie Fondamentale et Pathogénicité, CNRS, UMR 5234, Bordeaux, France
- * E-mail:
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9
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Proteomic analysis of mammalian primary cilia. Curr Biol 2012; 22:414-9. [PMID: 22326026 DOI: 10.1016/j.cub.2012.01.031] [Citation(s) in RCA: 207] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 12/16/2011] [Accepted: 01/16/2012] [Indexed: 11/23/2022]
Abstract
The primary cilium is a microtubule-based organelle that senses extracellular signals as a cellular antenna. Primary cilia are found on many types of cells in our body and play important roles in development and physiology. Defects of primary cilia cause a broad class of human genetic diseases called ciliopathies. To gain new insights into ciliary functions and better understand the molecular mechanisms underlying ciliopathies, it is of high importance to generate a catalog of primary cilia proteins. In this study, we isolated primary cilia from mouse kidney cells by using a calcium-shock method and identified 195 candidate primary cilia proteins by MudPIT (multidimensional protein identification technology), protein correlation profiling, and subtractive proteomic analysis. Based on comparisons with other proteomic studies of cilia, around 75% of our candidate primary cilia proteins are shared components with motile or specialized sensory cilia. The remaining 25% of the candidate proteins are possible primary cilia-specific proteins. These possible primary cilia-specific proteins include EVC2, INPP5E, and inversin, several of which have been linked to known ciliopathies. We have performed the first reported proteomic analysis of primary cilia from mammalian cells. These results provide new insights into primary cilia structure and function.
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Abstract
The cilium is a complex organelle, the assembly of which requires the coordination of motor-driven intraflagellar transport (IFT), membrane trafficking and selective import of cilium-specific proteins through a barrier at the ciliary transition zone. Recent findings provide insights into how cilia assemble and disassemble in synchrony with the cell cycle and how the balance of ciliary assembly and disassembly determines the steady-state ciliary length, with the inherent length-dependence of IFT rendering the ciliary assembly rate a decreasing function of length. As cilia are important in sensing and processing developmental signals and directing the flow of fluids such as mucus, defects in ciliogenesis and length control are likely to underlie a range of cilium-related human diseases.
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Abstract
Tektins are insoluble a-helical proteins essential for the construction of cilia and flagella and are found throughout the eukaryotes apart from higher plants.
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Affiliation(s)
- Linda A Amos
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK.
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Caspary T, Larkins CE, Anderson KV. The Graded Response to Sonic Hedgehog Depends on Cilia Architecture. Dev Cell 2007; 12:767-78. [PMID: 17488627 DOI: 10.1016/j.devcel.2007.03.004] [Citation(s) in RCA: 577] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2006] [Revised: 02/28/2007] [Accepted: 03/05/2007] [Indexed: 10/23/2022]
Abstract
Several studies have linked cilia and Hedgehog signaling, but the precise roles of ciliary proteins in signal transduction remain enigmatic. Here we describe a mouse mutation, hennin (hnn), that causes coupled defects in cilia structure and Sonic hedgehog (Shh) signaling. The hnn mutant cilia are short with a specific defect in the structure of the ciliary axoneme, and the hnn neural tube shows a Shh-independent expansion of the domain of motor neuron progenitors. The hnn mutation is a null allele of Arl13b, a small GTPase of the Arf/Arl family, and the Arl13b protein is localized to cilia. Double mutant analysis indicates that Gli3 repressor activity is normal in hnn embryos, but Gli activators are constitutively active at low levels. Thus, normal structure of the ciliary axoneme is required for the cell to translate different levels of Shh ligand into differential regulation of the Gli transcription factors that implement Hedgehog signals.
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Affiliation(s)
- Tamara Caspary
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, New York, NY 10021, USA
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Downing KH, Sui H. Structural insights into microtubule doublet interactions in axonemes. Curr Opin Struct Biol 2007; 17:253-9. [PMID: 17387011 DOI: 10.1016/j.sbi.2007.03.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Revised: 02/06/2007] [Accepted: 03/16/2007] [Indexed: 11/28/2022]
Abstract
Coordinated sliding of microtubule doublets, driven by dynein motors, produces periodic beating of eukaryotic cilia and flagella. Recent structural studies of the axoneme, which forms the core of cilia and flagella, have used cryo-electron tomography to reveal new details of the interactions between some of the multitude of proteins that form the axoneme and regulate its movement. Connections between the several types of dyneins, in particular, suggest ways in which their action might be coordinated. Study of the molecular architecture of isolated doublets has provided a structural basis for understanding mechanical properties related to the bending of the axoneme, and has also offered insight into the potential role of doublets in the mechanism of dynein activity regulation.
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Affiliation(s)
- Kenneth H Downing
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Abstract
The origin of cilia, a fundamental eukaryotic organelle, not present in prokaryotes, poses many problems, including the origins of motility and sensory function, the origins of nine-fold symmetry, of basal bodies, and of transport and selective mechanisms involved in ciliogenesis. We propose the basis of ciliary origin to be a self-assembly RNA enveloped virus that contains unique tubulin and tektin precursors. The virus becomes the centriole and basal body, which would account for the self-assembly and self-replicative properties of these organelles, in contrast to previous proposals of spirochaete origin or endogenous differentiation, which do not readily account for the centriole or its properties. The viral envelope evolves into a sensory bud. The host cell supplies the transport machinery and molecular motors to construct the axoneme. Polymerization of cytoplasmic microtubules in the 9+0 axoneme completes the 9+2 pattern.
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Affiliation(s)
- Peter Satir
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
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15
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Setter PW, Malvey-Dorn E, Steffen W, Stephens RE, Linck RW. Tektin interactions and a model for molecular functions. Exp Cell Res 2006; 312:2880-96. [PMID: 16831421 DOI: 10.1016/j.yexcr.2006.05.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2006] [Revised: 05/25/2006] [Accepted: 05/28/2006] [Indexed: 10/24/2022]
Abstract
Tektins from echinoderm flagella were analyzed for microheterogeneity, self-associations and association with tubulin, resulting in a general model of tektin filament structure and function applicable to most eukaryotic cilia and flagella. Using a new antibody to tektin consensus peptide RPNVELCRD, well-characterized chain-specific antibodies and quantitative gel densitometry, tektins A, B and C were found to be present in equimolar amounts in Sarkosyl-urea-stable filaments. In addition, two isoforms of tektin A are present in half-molar ratios to tektins B and C. Cross-linking of AB filaments indicates in situ nearest neighbor associations of tektin A1B and A2B heterodimers, -trimers, -tetramers and higher oligomers. Soluble purified tektin C is cross-linked as homodimers, trimers and tetramers, but not higher oligomers. Tektin filaments associate with both loosely bound and tightly bound tubulin, and with the latter in a 1:1 molar ratio, implying a specific, periodic association of tightly bound tubulin along the tektin axis. Similarly, in tektin-containing Sarkosyl-stable protofilament ribbons, two polypeptides ( approximately 67/73 kDa, homologues of rib72, efhc1 and efhc2) are present in equimolar ratios to each other and to individual tektins, co-fractionating with loosely bound tubulin. These results suggest a super-coiled arrangement of tektin filaments, the organization of which has important implications for the evolution, assembly and functions of cilia and flagella.
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Affiliation(s)
- Peter W Setter
- Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church St., Minneapolis, MN 55455, USA
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16
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King SM. Axonemal protofilament ribbons, DM10 domains, and the link to juvenile myoclonic epilepsy. ACTA ACUST UNITED AC 2006; 63:245-53. [PMID: 16572395 DOI: 10.1002/cm.20129] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Juvenile myoclonic epilepsy (JME) is a common neurological disorder that results in short uncontrolled muscle contractions and sometimes more severe seizures. Genetic studies have suggested that JME may be caused by mutations in EFHC1. The Efhc1 protein consists of three DM10 domains and a C-terminal region containing a potential Ca2+ -binding motif. In Chlamydomonas, a protein (Rib72) of almost identical domain structure is a component of the protofilament ribbons within the doublet microtubules of the flagellar axoneme. Here I discuss recent work that supports assignment of human Efhc1 as a ciliary component and the resulting implications for the mechanism of disease causation.
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Affiliation(s)
- Stephen M King
- Department of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, Farmington, Connecticut, USA.
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17
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Sui H, Downing KH. Molecular architecture of axonemal microtubule doublets revealed by cryo-electron tomography. Nature 2006; 442:475-8. [PMID: 16738547 DOI: 10.1038/nature04816] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2006] [Accepted: 04/21/2006] [Indexed: 11/09/2022]
Abstract
The axoneme, which forms the core of eukaryotic flagella and cilia, is one of the largest macromolecular machines, with a structure that is largely conserved from protists to mammals. Microtubule doublets are structural components of axonemes that contain a number of proteins besides tubulin, and are usually found in arrays of nine doublets arranged around two singlet microtubules. Coordinated sliding of adjacent doublets, which involves a host of other proteins in the axoneme, produces periodic beating movements of the axoneme. We have obtained a three-dimensional density map of intact microtubule doublets using cryo-electron tomography and image averaging. Our map, with a resolution of about 3 nm, provides insights into locations of particular proteins within the doublets and the structural features of the doublets that define their mechanical properties. We identify likely candidates for several of these non-tubulin components of the doublets. This work offers insight on how tubulin protofilaments and accessory proteins attach together to form the doublets and provides a structural basis for understanding doublet function in axonemes.
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Affiliation(s)
- Haixin Sui
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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18
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Smith JC, Northey JGB, Garg J, Pearlman RE, Siu KWM. Robust method for proteome analysis by MS/MS using an entire translated genome: demonstration on the ciliome of Tetrahymena thermophila. J Proteome Res 2005; 4:909-19. [PMID: 15952738 DOI: 10.1021/pr050013h] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To improve the utility of increasingly large numbers of available unannotated and initially poorly annotated genomic sequences for proteome analysis, we demonstrate that effective protein identification can be made on a large and unannotated genome. The strategy developed is to translate the unannotated genome sequence into amino acid sequence encoding putative proteins in all six reading frames, to identify peptides by tandem mass spectrometry (MS/MS), to localize them on the genome sequence, and to preliminarily annotate the protein via a similarity search by BLAST. These tasks have been optimized and automated. Optimization to obtain multiple peptide matches in effect extends the searchable region and results in more robust protein identification. The viability of this strategy is demonstrated with the identification of 223 cilia proteins in the unicellular eukaryotic model organism Tetrahymena thermophila, whose initial genomic sequence draft was released in November 2003. To the best of our knowledge, this is the first demonstration of large-scale protein identification based on such a large, unannotated genome. Of the 223 cilia proteins, 84 have no similarity to proteins in NCBI's nonredundant (nr) database. This methodology allows identifying the locations of the genes encoding these novel proteins, which is a necessary first step to downstream functional genomic experimentation.
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Affiliation(s)
- Jeffrey C Smith
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
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19
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Tanaka H, Iguchi N, Toyama Y, Kitamura K, Takahashi T, Kaseda K, Maekawa M, Nishimune Y. Mice deficient in the axonemal protein Tektin-t exhibit male infertility and immotile-cilium syndrome due to impaired inner arm dynein function. Mol Cell Biol 2004; 24:7958-64. [PMID: 15340058 PMCID: PMC515054 DOI: 10.1128/mcb.24.18.7958-7964.2004] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The haploid germ cell-specific Tektin-t protein is a member of the Tektin family of proteins that form filaments in flagellar, ciliary, and axonemal microtubules. To investigate the physiological role of Tektin-t, we generated mice with a mutation in the tektin-t gene. The homozygous mutant males were infertile, while the females were fully fertile. Sperm morphology and function were abnormal, with frequent bending of the sperm flagella and marked defects in motility. In vitro fertilization assays showed that the defective spermatozoa were able to fertilize eggs. Electron microscopic examination showed that the dynein inner arm structure was disrupted in the sperm flagella of tektin-t-deficient mice. Furthermore, homozygous mutant mice had functionally defective tracheal cilia, as evidenced by altered dynein arm morphology. These results indicate that Tektin-t participates in dynein inner arm formation or attachment and that the loss of Tektin-t results in impaired motility of both flagella and cilia. Therefore, the tektin-t gene is one of the causal genes for immotile-cilium syndrome/primary ciliary dyskinesia.
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Affiliation(s)
- Hiromitsu Tanaka
- Department of Science for Laboratory Animal Experimentation, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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