1
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Li D, Chen D, Li W, Ou G. Inhibition of a cyclic nucleotide-gated channel on neuronal cilia activates unfolded protein response in intestinal cells to promote longevity. Proc Natl Acad Sci U S A 2024; 121:e2321228121. [PMID: 38857399 PMCID: PMC11194586 DOI: 10.1073/pnas.2321228121] [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: 12/03/2023] [Accepted: 04/25/2024] [Indexed: 06/12/2024] Open
Abstract
Ciliary defects are linked to ciliopathies, but impairments in the sensory cilia of Caenorhabditis elegans neurons extend lifespan, a phenomenon with previously unclear mechanisms. Our study reveals that neuronal cilia defects trigger the unfolded protein response of the endoplasmic reticulum (UPRER) within intestinal cells, a process dependent on the insulin/insulin-like growth factor 1 (IGF-1) signaling transcription factor and the release of neuronal signaling molecules. While inhibiting UPRER doesn't alter the lifespan of wild-type worms, it normalizes the extended lifespan of ciliary mutants. Notably, deactivating the cyclic nucleotide-gated (CNG) channel TAX-4 on the ciliary membrane promotes lifespan extension through a UPRER-dependent mechanism. Conversely, constitutive activation of TAX-4 attenuates intestinal UPRER in ciliary mutants. Administering a CNG channel blocker to worm larvae activates intestinal UPRER and increases adult longevity. These findings suggest that ciliary dysfunction in sensory neurons triggers intestinal UPRER, contributing to lifespan extension and implying that transiently inhibiting ciliary channel activity may effectively prolong lifespan.
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Affiliation(s)
- Dongdong Li
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
- Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
- McGovern Institute for Brain Research, Tsinghua University, Beijing, China
- School of Life Sciences and Ministry of Education Key Laboratory for Protein Science, Tsinghua University, Beijing, China
| | - Di Chen
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Li
- School of Medicine, Tsinghua University, Beijing, China
| | - Guangshuo Ou
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
- Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
- McGovern Institute for Brain Research, Tsinghua University, Beijing, China
- School of Life Sciences and Ministry of Education Key Laboratory for Protein Science, Tsinghua University, Beijing, China
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2
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Marshall WF. Chlamydomonas as a model system to study cilia and flagella using genetics, biochemistry, and microscopy. Front Cell Dev Biol 2024; 12:1412641. [PMID: 38872931 PMCID: PMC11169674 DOI: 10.3389/fcell.2024.1412641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 05/13/2024] [Indexed: 06/15/2024] Open
Abstract
The unicellular green alga, Chlamydomonas reinhardtii, has played a central role in discovering much of what is currently known about the composition, assembly, and function of cilia and flagella. Chlamydomonas combines excellent genetics, such as the ability to grow cells as haploids or diploids and to perform tetrad analysis, with an unparalleled ability to detach and isolate flagella in a single step without cell lysis. The combination of genetics and biochemistry that is possible in Chlamydomonas has allowed many of the key components of the cilium to be identified by looking for proteins that are missing in a defined mutant. Few if any other model organisms allow such a seamless combination of genetic and biochemical approaches. Other major advantages of Chlamydomonas compared to other systems include the ability to induce flagella to regenerate in a highly synchronous manner, allowing the kinetics of flagellar growth to be measured, and the ability of Chlamydomonas flagella to adhere to glass coverslips allowing Intraflagellar Transport to be easily imaged inside the flagella of living cells, with quantitative precision and single-molecule resolution. These advantages continue to work in favor of Chlamydomonas as a model system going forward, and are now augmented by extensive genomic resources, a knockout strain collection, and efficient CRISPR gene editing. While Chlamydomonas has obvious limitations for studying ciliary functions related to animal development or organ physiology, when it comes to studying the fundamental biology of cilia and flagella, Chlamydomonas is simply unmatched in terms of speed, efficiency, cost, and the variety of approaches that can be brought to bear on a question.
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Affiliation(s)
- Wallace F. Marshall
- Department Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, United States
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3
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Penny GM, Dutcher SK. Gene dosage of independent dynein arm motor preassembly factors influences cilia assembly in Chlamydomonas reinhardtii. PLoS Genet 2024; 20:e1011038. [PMID: 38498551 PMCID: PMC11020789 DOI: 10.1371/journal.pgen.1011038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 04/16/2024] [Accepted: 02/26/2024] [Indexed: 03/20/2024] Open
Abstract
Motile cilia assembly utilizes over 800 structural and cytoplasmic proteins. Variants in approximately 58 genes cause primary ciliary dyskinesia (PCD) in humans, including the dynein arm (pre)assembly factor (DNAAF) gene DNAAF4. In humans, outer dynein arms (ODAs) and inner dynein arms (IDAs) fail to assemble motile cilia when DNAAF4 function is disrupted. In Chlamydomonas reinhardtii, a ciliated unicellular alga, the DNAAF4 ortholog is called PF23. The pf23-1 mutant assembles short cilia and lacks IDAs, but partially retains ODAs. The cilia of a new null allele (pf23-4) completely lack ODAs and IDAs and are even shorter than cilia from pf23-1. In addition, PF23 plays a role in the cytoplasmic modification of IC138, a protein of the two-headed IDA (I1/f). As most PCD variants in humans are recessive, we sought to test if heterozygosity at two genes affects ciliary function using a second-site non-complementation (SSNC) screening approach. We asked if phenotypes were observed in diploids with pairwise heterozygous combinations of 21 well-characterized ciliary mutant Chlamydomonas strains. Vegetative cultures of single and double heterozygous diploid cells did not show SSNC for motility phenotypes. When protein synthesis is inhibited, wild-type Chlamydomonas cells utilize the pool of cytoplasmic proteins to assemble half-length cilia. In this sensitized assay, 8 double heterozygous diploids with pf23 and other DNAAF mutations show SSNC; they assemble shorter cilia than wild-type. In contrast, double heterozygosity of the other 203 strains showed no effect on ciliary assembly. Immunoblots of diploids heterozygous for pf23 and wdr92 or oda8 show that PF23 is reduced by half in these strains, and that PF23 dosage affects phenotype severity. Reductions in PF23 and another DNAAF in diploids affect the ability to assemble ODAs and IDAs and impedes ciliary assembly. Thus, dosage of multiple DNAAFs is an important factor in cilia assembly and regeneration.
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Affiliation(s)
- Gervette M. Penny
- Department of Genetics, Washington University in Saint Louis, Saint Louis,Missouri, United States of America
| | - Susan K. Dutcher
- Department of Genetics, Washington University in Saint Louis, Saint Louis,Missouri, United States of America
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4
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Hwang J, Yanagisawa H, Davis KC, Hunter EL, Fox LA, Jimenez AR, Goodwin RE, Gordon SA, Stuart CDE, Bower R, Porter ME, Dutcher SK, Sale WS, Lechtreck KF, Alford LM. Assembly of FAP93 at the proximal axoneme in Chlamydomonas cilia. Cytoskeleton (Hoboken) 2024. [PMID: 38224153 DOI: 10.1002/cm.21818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 01/16/2024]
Abstract
To identify proteins specific to the proximal ciliary axoneme, we used iTRAQ to compare short (~2 μm) and full-length (~11 μm) axonemes of Chlamydomonas. Known compoents of the proximal axoneme such as minor dynein heavy chains and LF5 kinase as well as the ciliary tip proteins FAP256 (CEP104) and EB1 were enriched in short axonemes whereas proteins present along the length of the axoneme were of similar abundance in both samples. The iTRAQ analysis revealed that FAP93, a protein of unknown function, and protein phosphatase 2A (PP2A) are enriched in the short axonemes. Consistently, immunoblots show enrichment of FAP93 and PP2A in short axonemes and immunofluorescence confirms the localization of FAP93 and enrichment of PP2A at the proximal axoneme. Ciliary regeneration reveals that FAP93 assembles continuously but more slowly than other axonemal structures and terminates at 1.03 μm in steady-state axonemes. The length of FAP93 assembly correlates with ciliary length, demonstrating ciliary length-dependent assembly of FAP93. Dikaryon rescue experiments show that FAP93 can assemble independently of IFT transport. In addition, FRAP analysis of GFP-tagged FAP93 demonstrates that FAP93 is stably anchored in axoneme. FAP93 may function as a scaffold for assembly of other specific proteins at the proximal axoneme.
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Affiliation(s)
- Juyeon Hwang
- Department of Cell Biology, Emory University, Atlanta, Georgia, USA
| | | | - Keira C Davis
- Department of Cell Biology, Emory University, Atlanta, Georgia, USA
- College of Arts & Sciences, Clayton State University, Morrow, Georgia, USA
| | - Emily L Hunter
- Department of Cell Biology, Emory University, Atlanta, Georgia, USA
- Science Communication Group, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Laura A Fox
- Department of Cell Biology, Emory University, Atlanta, Georgia, USA
| | - Ariana R Jimenez
- Division of Natural Sciences, Oglethorpe University, Atlanta, Georgia, USA
| | - Reagan E Goodwin
- Division of Natural Sciences, Oglethorpe University, Atlanta, Georgia, USA
| | - Sarah A Gordon
- Division of Natural Sciences, Oglethorpe University, Atlanta, Georgia, USA
| | | | - Raqual Bower
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Mary E Porter
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Susan K Dutcher
- Department of Genetics, Washington University St. Louis, St. Louis, Missouri, USA
| | - Winfield S Sale
- Department of Cell Biology, Emory University, Atlanta, Georgia, USA
| | - Karl F Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Lea M Alford
- Division of Natural Sciences, Oglethorpe University, Atlanta, Georgia, USA
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5
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Tian Z, Li X, Yu X, Yan S, Sun J, Ma W, Zhu X, Tang Y. The role of primary cilia in thyroid diseases. Front Endocrinol (Lausanne) 2024; 14:1306550. [PMID: 38260150 PMCID: PMC10801159 DOI: 10.3389/fendo.2023.1306550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/05/2023] [Indexed: 01/24/2024] Open
Abstract
Primary cilia (PC) are non-motile and microtube-based organelles protruding from the surface of almost all thyroid follicle cells. They maintain homeostasis in thyrocytes and loss of PC can result in diverse thyroid diseases. The dysfunction of structure and function of PC are found in many patients with common thyroid diseases. The alterations are associated with the cause, development, and recovery of the diseases and are regulated by PC-mediated signals. Restoring normal PC structure and function in thyrocytes is a promising therapeutic strategy to treat thyroid diseases. This review explores the function of PC in normal thyroid glands. It summarizes the pathology caused by PC alterations in thyroid cancer (TC), autoimmune thyroid diseases (AITD), hypothyroidism, and thyroid nodules (TN) to provide comprehensive references for further study.
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Affiliation(s)
- Zijiao Tian
- College of Traditional Chinese Medicine of Beijing University of Chinese Medicine, Beijing, China
| | - Xinlin Li
- College of Traditional Chinese Medicine of Beijing University of Chinese Medicine, Beijing, China
| | - Xue Yu
- College of Traditional Chinese Medicine of Beijing University of Chinese Medicine, Beijing, China
| | - Shuxin Yan
- College of Traditional Chinese Medicine of Beijing University of Chinese Medicine, Beijing, China
| | - Jingwei Sun
- College of Traditional Chinese Medicine of Beijing University of Chinese Medicine, Beijing, China
| | - Wenxin Ma
- College of Traditional Chinese Medicine of Beijing University of Chinese Medicine, Beijing, China
| | - Xiaoyun Zhu
- Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yang Tang
- College of Traditional Chinese Medicine of Beijing University of Chinese Medicine, Beijing, China
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6
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Dougherty LL, Avasthi P. Determinants of cytoplasmic microtubule depolymerization during ciliogenesis in Chlamydomonas. Life Sci Alliance 2024; 7:e202302287. [PMID: 37813489 PMCID: PMC10561824 DOI: 10.26508/lsa.202302287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/12/2023] Open
Abstract
At the core of cilia are microtubules which establish length and assist ciliary assembly and disassembly; however, microtubules outside of the cilium can regulate ciliogenesis. The microtubule cytoskeleton polymerizes and depolymerizes rapidly. These processes have been studied across various organisms with chemical and genetic perturbations. However, these have generated conflicting data in terms of the role of cytoplasmic microtubules (CytoMTs) and free tubulin dynamics during ciliogenesis. Here, we look at the relationship between ciliogenesis and CytoMT dynamics in Chlamydomonas reinhardtii using chemical and mechanical perturbations. We find that not only can stabilized CytoMTs allow for normal ciliary assembly, but high calcium concentrations and low pH-induced deciliation cause CytoMTs to depolymerize separately from ciliary shedding. In addition, ciliary shedding through mechanical shearing allows cilia to regenerate earlier despite intact CytoMTs. Our data suggest that CytoMTs are not a sink for a limiting pool of cytoplasmic tubulin in Chlamydomonas, depolymerization after deciliation is a consequence rather than a requirement for ciliogenesis, and intact tubulin in the cytoplasm and proximal cilium support more efficient ciliary assembly.
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Affiliation(s)
- Larissa L Dougherty
- Biochemistry and Cell Biology Department, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Prachee Avasthi
- Biochemistry and Cell Biology Department, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
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7
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Kong D, Wei M, Liu D, Zhang Z, Ma Y, Zhang Z. Morphological Observation and Transcriptome Analysis of Ciliogenesis in Urechis unicinctus (Annelida, Echiura). Int J Mol Sci 2023; 24:11537. [PMID: 37511295 PMCID: PMC10380512 DOI: 10.3390/ijms241411537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
During the early development of marine invertebrates, planktic larvae usually occur, and their body surfaces often form specific types of cilia that are involved in locomotion and feeding. The echiuran worm Urechis unicinctus sequentially undergoes the formation and disappearance of different types of body surface cilia during embryonic and larval development. The morphological characteristics and molecular mechanisms involved in the process remain unclear. In this study, we found that body surface cilia in U. unicinctus embryos and larvae can be distinguished into four types: body surface short cilia, apical tufts, circumoral cilia and telotrochs. Further, distribution and genesis of the body surface cilia were characterized using light microscope and electron microscope. To better understand the molecular mechanism during ciliogenesis, we revealed the embryonic and larval transcriptome profile of the key stages of ciliogenesis in U. unicinctus using RNA-Seq technology. A total of 29,158 differentially expressed genes (DEGs) were obtained from 24 cDNA libraries by RNA-Seq. KEGG pathway enrichment results showed that Notch, Wnt and Ca2+ signaling pathways were significantly enriched during the occurrence of apical tufts and circumoral cilia. Furthermore, all DEGs were classified according to their expression pattern, and DEGs with similar expression pattern were grouped into a module. All DEG co-expression modules were correlated with traits (body surface short cilia, apical tufts, circumoral cilia and telotrochs) by WGCNA, the results showed DEGs were divided into 13 modules by gene expression patterns and that the genes in No. 7, No. 8 and No. 10 modules were to be highly correlated with the occurrence of apical tufts, circumoral cilia and telotrochs. The top 10 hub genes in the above three modules were identified to be highly correlated with ciliogenesis, including the reported cilium-related gene Cnbd2 and unreported cilium-related candidate genes FAM181B, Capsl, Chst3, TMIE and Innexin. Notably, Innexin was included in the top10 hub genes of the two modules (No. 7 and No. 8), suggesting that Innexin may play an important role in U. unicinctus apical tufts, circumoral cilia and telotrochs genesis. This study revealed the characteristics of ciliogenesis on the body surface of U. unicinctus embryos and larvae, providing basic data for exploring the molecular mechanism of ciliogenesis on the body surface.
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Affiliation(s)
- Dexu Kong
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Maokai Wei
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Danwen Liu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Zhengrui Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yubin Ma
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Zhifeng Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
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8
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Payne ZL, Penny GM, Turner TN, Dutcher SK. A gap-free genome assembly of Chlamydomonas reinhardtii and detection of translocations induced by CRISPR-mediated mutagenesis. PLANT COMMUNICATIONS 2023; 4:100493. [PMID: 36397679 PMCID: PMC10030371 DOI: 10.1016/j.xplc.2022.100493] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/26/2022] [Accepted: 11/15/2022] [Indexed: 05/04/2023]
Abstract
Genomic assemblies of the unicellular green alga Chlamydomonas reinhardtii have provided important resources for researchers. However, assembly errors, large gaps, and unplaced scaffolds as well as strain-specific variants currently impede many types of analysis. By combining PacBio HiFi and Oxford Nanopore long-read technologies, we generated a de novo genome assembly for strain CC-5816, derived from crosses of strains CC-125 and CC-124. Multiple methods of evaluating genome completeness and base-pair error rate suggest that the final telomere-to-telomere assembly is highly accurate. The CC-5816 assembly enabled previously difficult analyses that include characterization of the 17 centromeres, rDNA arrays on three chromosomes, and 56 insertions of organellar DNA into the nuclear genome. Using Nanopore sequencing, we identified sites of cytosine (CpG) methylation, which are enriched at centromeres. We analyzed CRISPR-Cas9 insertional mutants in the PF23 gene. Two of the three alleles produced progeny that displayed patterns of meiotic inviability that suggested the presence of a chromosomal aberration. Mapping Nanopore reads from pf23-2 and pf23-3 onto the CC-5816 genome showed that these two strains each carry a translocation that was initiated at the PF23 gene locus on chromosome 11 and joined with chromosomes 5 or 3, respectively. The translocations were verified by demonstrating linkage between loci on the two translocated chromosomes in meiotic progeny. The three pf23 alleles display the expected short-cilia phenotype, and immunoblotting showed that pf23-2 lacks the PF23 protein. Our CC-5816 genome assembly will undoubtedly provide an important tool for the Chlamydomonas research community.
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Affiliation(s)
- Zachary L Payne
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Gervette M Penny
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Tychele N Turner
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Susan K Dutcher
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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9
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Zaqout S, Mannaa A, Klein O, Krajewski A, Klose J, Luise-Becker L, Elsabagh A, Ferih K, Kraemer N, Ravindran E, Makridis K, Kaindl AM. Proteome changes in autosomal recessive primary microcephaly. Ann Hum Genet 2023; 87:50-62. [PMID: 36448252 DOI: 10.1111/ahg.12489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 12/05/2022]
Abstract
BACKGROUND/AIM Autosomal recessive primary microcephaly (MCPH) is a rare and genetically heterogeneous group of disorders characterized by intellectual disability and microcephaly at birth, classically without further organ involvement. MCPH3 is caused by biallelic variants in the cyclin-dependent kinase 5 regulatory subunit-associated protein 2 gene CDK5RAP2. In the corresponding Cdk5rap2 mutant or Hertwig's anemia mouse model, congenital microcephaly as well as defects in the hematopoietic system, germ cells and eyes have been reported. The reduction in brain volume, particularly affecting gray matter, has been attributed mainly to disturbances in the proliferation and survival of early neuronal progenitors. In addition, defects in dendritic development and synaptogenesis exist that affect the excitation-inhibition balance. Here, we studied proteomic changes in cerebral cortices of Cdk5rap2 mutant mice. MATERIAL AND METHODS We used large-gel two-dimensional gel (2-DE) electrophoresis to separate cortical proteins. 2-DE gels were visualized by a trained observer on a light box. Spot changes were considered with respect to presence/absence, quantitative variation and altered mobility. RESULT We identified a reduction in more than 30 proteins that play a role in processes such as cell cytoskeleton dynamics, cell cycle progression, ciliary functions and apoptosis. These proteome changes in the MCPH3 model can be associated with various functional and morphological alterations of the developing brain. CONCLUSION Our results shed light on potential protein candidates for the disease-associated phenotype reported in MCPH3.
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Affiliation(s)
- Sami Zaqout
- Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Atef Mannaa
- Higher Institute of Engineering and Technology, New Borg AlArab City, Alexandria, Egypt.,Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire & Spectrométrie de Masse (PRISM), Université de Lille, Lille, France
| | - Oliver Klein
- BIH Center for Regenerative Therapies BCRT, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Charité-Universitätsmedizin Berlin (BIH), Berlin, Germany
| | - Angelika Krajewski
- BIH Center for Regenerative Therapies BCRT, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Charité-Universitätsmedizin Berlin (BIH), Berlin, Germany
| | - Joachim Klose
- Charité-Universitätsmedizin, Institute of Human Genetics, Berlin, Germany
| | - Lena Luise-Becker
- Charité-Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Center for Chronically Sick Children (Sozialpädiatrisches Zentrum, SPZ), Berlin, Germany.,Department of Pediatric Neurology, Charité-Universitätsmedizin, Berlin, Germany
| | - Ahmed Elsabagh
- Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Khaled Ferih
- Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Nadine Kraemer
- Charité-Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Center for Chronically Sick Children (Sozialpädiatrisches Zentrum, SPZ), Berlin, Germany.,Department of Pediatric Neurology, Charité-Universitätsmedizin, Berlin, Germany
| | - Ethiraj Ravindran
- Charité-Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Center for Chronically Sick Children (Sozialpädiatrisches Zentrum, SPZ), Berlin, Germany.,Department of Pediatric Neurology, Charité-Universitätsmedizin, Berlin, Germany
| | - Konstantin Makridis
- Charité-Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Center for Chronically Sick Children (Sozialpädiatrisches Zentrum, SPZ), Berlin, Germany.,Department of Pediatric Neurology, Charité-Universitätsmedizin, Berlin, Germany
| | - Angela M Kaindl
- Charité-Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Center for Chronically Sick Children (Sozialpädiatrisches Zentrum, SPZ), Berlin, Germany.,Department of Pediatric Neurology, Charité-Universitätsmedizin, Berlin, Germany
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10
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Wang L, Li X, Liu G, Pan J. FBB18 participates in preassembly of almost all axonemal dyneins independent of R2TP complex. PLoS Genet 2022; 18:e1010374. [PMID: 36026524 PMCID: PMC9455862 DOI: 10.1371/journal.pgen.1010374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 09/08/2022] [Accepted: 08/04/2022] [Indexed: 11/19/2022] Open
Abstract
Assembly of dynein arms requires cytoplasmic processes which are mediated by dynein preassembly factors (DNAAFs). CFAP298, which is conserved in organisms with motile cilia, is required for assembly of dynein arms but with obscure mechanisms. Here, we show that FBB18, a Chlamydomonas homologue of CFAP298, localizes to the cytoplasm and functions in folding/stabilization of almost all axonemal dyneins at the early steps of dynein preassembly. Mutation of FBB18 causes no or short cilia accompanied with partial loss of both outer and inner dynein arms. Comparative proteomics using 15N labeling suggests partial degradation of almost all axonemal dynein heavy chains (DHCs). A mutant mimicking a patient variant induces particular loss of DHCα. FBB18 associates with 9 DNAAFs and 14 out of 15 dynein HCs but not with IC1/IC2. FBB18 interacts with RuvBL1/2, components of the HSP90 co-chaperone R2TP complex but not the holo-R2TP complex. Further analysis suggests simultaneous formation of multiple DNAAF complexes involves dynein folding/stability and thus provides new insights into axonemal dynein preassembly. Motile cilia are important for human physiology and defects in cilia motility may cause human disorders such as male infertility and primary ciliary dyskinesia. The motility of cilia requires preassembly of axonemal dyneins. Using a combination of genetic and other approaches, we have studied the working mechanism of FBB18, a Chlamydomonas homologue of CFAP298, defects in which result in primary ciliary dyskinesia. We found that FBB18 participates in dynein folding/stability in the cytoplasm, which is distinct from its proposed function in ciliary targeting of dynein complexes or stabilization of dynein arms within cilia. In addition, we have provided evidence that multiple distinct complexes are simultaneously formed to participate in dynein folding, thus providing new insights into dynein preassembly. Last but not least, we showed that RuvBL1/2 of the HSP90 co-chaperone R2TP complex may function independently of the R2TP complex in dynein disassembly. This work has both scientific and medical significance and will be of general interest to the fields of ciliary biology and protein folding/stability.
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Affiliation(s)
- Limei Wang
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xuecheng Li
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Guang Liu
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Junmin Pan
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province, China
- * E-mail:
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11
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Sood P, Lin A, Yan C, McGillivary R, Diaz U, Makushok T, Nadkarni A, Tang SKY, Marshall WF. Modular, cascade-like transcriptional program of regeneration in Stentor. eLife 2022; 11:80778. [PMID: 35924891 PMCID: PMC9371601 DOI: 10.7554/elife.80778] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 08/04/2022] [Indexed: 11/15/2022] Open
Abstract
The giant ciliate Stentor coeruleus is a classical model system for studying regeneration and morphogenesis in a single cell. The anterior of the cell is marked by an array of cilia, known as the oral apparatus, which can be induced to shed and regenerate in a series of reproducible morphological steps, previously shown to require transcription. If a cell is cut in half, each half regenerates an intact cell. We used RNA sequencing (RNAseq) to assay the dynamic changes in Stentor’s transcriptome during regeneration, after both oral apparatus shedding and bisection, allowing us to identify distinct temporal waves of gene expression including kinases, RNA -binding proteins, centriole biogenesis factors, and orthologs of human ciliopathy genes. By comparing transcriptional profiles of different regeneration events, we identified distinct modules of gene expression corresponding to oral apparatus regeneration, posterior holdfast regeneration, and recovery after wounding. By measuring gene expression after blocking translation, we show that the sequential waves of gene expression involve a cascade mechanism in which later waves of expression are triggered by translation products of early-expressed genes. Among the early-expressed genes, we identified an E2F transcription factor and the RNA-binding protein Pumilio as potential regulators of regeneration based on the expression pattern of their predicted target genes. RNAi-mediated knockdown experiments indicate that Pumilio is required for regenerating oral structures of the correct size. E2F is involved in the completion of regeneration but is dispensable for earlier steps. This work allows us to classify regeneration genes into groups based on their potential role for regeneration in distinct cell regeneration paradigms, and provides insight into how a single cell can coordinate complex morphogenetic pathways to regenerate missing structures.
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Affiliation(s)
- Pranidhi Sood
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Athena Lin
- Department of Biochemistry and BioPhysics, University of California, San Francisco, San Francisco, United States
| | - Connie Yan
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Rebecca McGillivary
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Ulises Diaz
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Tatyana Makushok
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Ambika Nadkarni
- Department of Mechanical Engineering, Stanford University, palo alto, United States
| | - Sindy K Y Tang
- Department of Mechanical Engineering, Stanford University, Palo Alto, United States
| | - Wallace F Marshall
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
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12
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Abstract
Cilium formation and regeneration requires new protein synthesis, but the underlying cytosolic translational reprogramming remains largely unknown. Using ribosome footprinting, we performed global translatome profiling during cilia regeneration in Chlamydomonas and uncovered that flagellar genes undergo an early transcriptional activation but late translational repression. This pattern guided our identification of sphingolipid metabolism enzymes, including serine palmitoyltransferase (SPT), as essential regulators for ciliogenesis. Cryo-electron tomography showed that ceramide loss abnormally increased the membrane-axoneme distance and generated bulged cilia. We found that ceramides interact with intraflagellar transport (IFT) particle proteins that IFT motors transport along axoneme microtubules (MTs), suggesting that ceramide-IFT particle-IFT motor-MT interactions connect the ciliary membrane with the axoneme to form rod-shaped cilia. SPT-deficient vertebrate cells were defective in ciliogenesis, and SPT mutations from patients with hereditary sensory neuropathy disrupted cilia, which could be restored by sphingolipid supplementation. These results reveal a conserved role of sphingolipid in cilium formation and link compromised sphingolipid production with ciliopathies.
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13
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Lechtreck KF, Liu Y, Dai J, Alkhofash RA, Butler J, Alford L, Yang P. Chlamydomonas ARMC2/PF27 is an obligate cargo adapter for intraflagellar transport of radial spokes. eLife 2022; 11:74993. [PMID: 34982025 PMCID: PMC8789290 DOI: 10.7554/elife.74993] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/03/2022] [Indexed: 12/19/2022] Open
Abstract
Intraflagellar transport (IFT) carries proteins into flagella but how IFT trains interact with the large number of diverse proteins required to assemble flagella remains largely unknown. Here, we show that IFT of radial spokes in Chlamydomonas requires ARMC2/PF27, a conserved armadillo repeat protein associated with male infertility and reduced lung function. Chlamydomonas ARMC2 was highly enriched in growing flagella and tagged ARMC2 and the spoke protein RSP3 co-migrated on anterograde trains. In contrast, a cargo and an adapter of inner and outer dynein arms moved independently of ARMC2, indicating that unrelated cargoes distribute stochastically onto the IFT trains. After concomitant unloading at the flagellar tip, RSP3 attached to the axoneme whereas ARMC2 diffused back to the cell body. In armc2/pf27 mutants, IFT of radial spokes was abolished and the presence of radial spokes was limited to the proximal region of flagella. We conclude that ARMC2 is a cargo adapter required for IFT of radial spokes to ensure their assembly along flagella. ARMC2 belongs to a growing class of cargo-specific adapters that enable flagellar transport of preassembled axonemal substructures by IFT.
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Affiliation(s)
- Karl F Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, United States
| | - Yi Liu
- Department of Biological Sciences, Marquette University, Milwaukee, United States
| | - Jin Dai
- Department of Cellular Biology, University of Georgia, Athens, United States
| | - Rama A Alkhofash
- Department of Cellular Biology, University of Georgia, Athens, United States
| | - Jack Butler
- Department of Cellular Biology, University of Georgia, Athens, United States
| | - Lea Alford
- Division of Natural Sciences,, Oglethorpe University, Atlanta, United States
| | - Pinfen Yang
- Department of Biological Sciences, Marquette University, Milwaukee, United States
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14
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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: 2] [Impact Index Per Article: 0.7] [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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15
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Bauerly E, Akiyama T, Staber C, Yi K, Gibson MC. Impact of cilia-related genes on mitochondrial dynamics during Drosophila spermatogenesis. Dev Biol 2021; 482:17-27. [PMID: 34822845 DOI: 10.1016/j.ydbio.2021.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/29/2021] [Accepted: 11/09/2021] [Indexed: 11/28/2022]
Abstract
Spermatogenesis is a dynamic process of cellular differentiation that generates the mature spermatozoa required for reproduction. Errors that arise during this process can lead to sterility due to low sperm counts and malformed or immotile sperm. While it is estimated that 1 out of 7 human couples encounter infertility, the underlying cause of male infertility can only be identified in 50% of cases. Here, we describe and examine the genetic requirements for missing minor mitochondria (mmm), sterile affecting ciliogenesis (sac), and testes of unusual size (tous), three previously uncharacterized genes in Drosophila that are predicted to be components of the flagellar axoneme. Using Drosophila, we demonstrate that these genes are essential for male fertility and that loss of mmm, sac, or tous results in complete immotility of the sperm flagellum. Cytological examination uncovered additional roles for sac and tous during cytokinesis and transmission electron microscopy of developing spermatids in mmm, sac, and tous mutant animals revealed defects associated with mitochondria and the accessory microtubules required for the proper elongation of the mitochondria and flagella during ciliogenesis. This study highlights the complex interactions of cilia-related proteins within the cell body and advances our understanding of male infertility by uncovering novel mitochondrial defects during spermatogenesis.
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Affiliation(s)
| | - Takuya Akiyama
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Cynthia Staber
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Kexi Yi
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Matthew C Gibson
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA; Department of Anatomy and Cell Biology, The University of Kansas School of Medicine, Kansas City, KS, 66160, USA.
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16
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Li D, Liu Y, Yi P, Zhu Z, Li W, Zhang QC, Li JB, Ou G. RNA editing restricts hyperactive ciliary kinases. Science 2021; 373:984-991. [PMID: 34446600 DOI: 10.1126/science.abd8971] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 04/01/2021] [Accepted: 07/16/2021] [Indexed: 12/17/2022]
Abstract
Protein kinase activity must be precisely regulated, but how a cell governs hyperactive kinases remains unclear. In this study, we generated a constitutively active mitogen-activated protein kinase DYF-5 (DYF-5CA) in Caenorhabditis elegans that disrupted sensory cilia. Genetic suppressor screens identified that mutations of ADR-2, an RNA adenosine deaminase, rescued ciliary phenotypes of dyf-5CA We found that dyf-5CA animals abnormally transcribed antisense RNAs that pair with dyf-5CA messenger RNA (mRNA) to form double-stranded RNA, recruiting ADR-2 to edit the region ectopically. RNA editing impaired dyf-5CA mRNA splicing, and the resultant intron retentions blocked DYF-5CA protein translation and activated nonsense-mediated dyf-5CA mRNA decay. The kinase RNA editing requires kinase hyperactivity. The similar RNA editing-dependent feedback regulation restricted the other ciliary kinases NEKL-4/NEK10 and DYF-18/CCRK, which suggests a widespread mechanism that underlies kinase regulation.
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Affiliation(s)
- Dongdong Li
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
| | - Yufan Liu
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
| | - Peishan Yi
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
| | - Zhiwen Zhu
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
| | - Wei Li
- School of Medicine, Tsinghua University, Beijing, China
| | - Qiangfeng Cliff Zhang
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China
| | - Jin Billy Li
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Guangshuo Ou
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China. .,Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
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17
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Rao VG, Kulkarni SS. Xenopus to the rescue: A model to validate and characterize candidate ciliopathy genes. Genesis 2021; 59:e23414. [PMID: 33576572 DOI: 10.1002/dvg.23414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 12/14/2022]
Abstract
Cilia are present on most vertebrate cells and play a central role in development, growth, and homeostasis. Thus, cilia dysfunction can manifest into an array of diseases, collectively termed ciliopathies, affecting millions of lives worldwide. Yet, our understanding of the gene regulatory networks that control cilia assembly and functions remain incomplete. With the advances in next-generation sequencing technologies, we can now rapidly predict pathogenic variants from hundreds of ciliopathy patients. While the pace of candidate gene discovery is exciting, most of these genes have never been previously implicated in cilia assembly or function. This makes assigning the disease causality difficult. This review discusses how Xenopus, a genetically tractable and high-throughput vertebrate model, has played a central role in identifying, validating, and characterizing candidate ciliopathy genes. The review is focused on multiciliated cells (MCCs) and diseases associated with MCC dysfunction. MCCs harbor multiple motile cilia on their apical surface to generate extracellular fluid flow inside the airway, the brain ventricles, and the oviduct. In Xenopus, these cells are external and present on the embryonic epidermal epithelia, facilitating candidate genes analysis in MCC development in vivo. The ability to introduce patient variants to study their effects on disease progression makes Xenopus a powerful model to improve our understanding of the underlying disease mechanisms and explain the patient phenotype.
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Affiliation(s)
- Venkatramanan G Rao
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Saurabh S Kulkarni
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia, USA.,Department of Biology, University of Virginia, Charlottesville, Virginia, USA
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18
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Ma CX, Ma XN, Li YD, Fu SB. The Role of Primary Cilia in Thyroid Cancer: From Basic Research to Clinical Applications. Front Endocrinol (Lausanne) 2021; 12:685228. [PMID: 34168619 PMCID: PMC8218906 DOI: 10.3389/fendo.2021.685228] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/24/2021] [Indexed: 12/07/2022] Open
Abstract
Primary cilia (PC) are microtubule-based organelles that are present on nearly all thyroid follicle cells and play an important role in physiological development and in maintaining the dynamic homeostasis of thyroid follicles. PC are generally lost in many thyroid cancers (TCs), and this loss has been linked to the malignant transformation of thyrocytes, which is regulated by PC-mediated signaling reciprocity between the stroma and cancer cells. Restoring PC on TC cells is a possible promising therapeutic strategy, and the therapeutic response and prognosis of TC are associated with the presence or absence of PC. This review mainly discusses the role of PC in the normal thyroid and TC as well as their potential clinical utility.
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Affiliation(s)
- Cheng-Xu Ma
- Department of Endocrinology, The First Hospital of Lanzhou University, Lanzhou, China
- The First Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Xiao-Ni Ma
- Department of Endocrinology, The First Hospital of Lanzhou University, Lanzhou, China
- The First Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Ying-Dong Li
- College of Integrated Traditional Chinese and Western Medicine, Gansu University of Chinese Medicine, Lanzhou, China
| | - Song-Bo Fu
- Department of Endocrinology, The First Hospital of Lanzhou University, Lanzhou, China
- The First Clinical Medical College of Lanzhou University, Lanzhou, China
- *Correspondence: Song-Bo Fu,
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19
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Huang S, Dougherty LL, Avasthi P. Separable roles for RanGTP in nuclear and ciliary trafficking of a kinesin-2 subunit. J Biol Chem 2021; 296:100117. [PMID: 33234597 PMCID: PMC7948393 DOI: 10.1074/jbc.ra119.010936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 11/16/2020] [Accepted: 11/24/2020] [Indexed: 01/05/2023] Open
Abstract
Kinesin is part of the microtubule-binding motor protein superfamily, which serves important roles in cell division and intraorganellar transport. The heterotrimeric kinesin-2, consisting of the heterodimeric motor subunits, kinesin family member 3A/3B (KIF3A/3B), and kinesin-associated protein 3 (KAP3), is highly conserved across species from the unicellular eukaryote Chlamydomonas to humans. It plays diverse roles in cargo transport including anterograde (base to tip) trafficking in cilia. However, the molecular determinants mediating trafficking of heterotrimeric kinesin-2 itself are poorly understood. It has been previously suggested that ciliary transport is analogous to nuclear transport mechanisms. Using Chlamydomonas and human telomerase reverse transcriptase-retinal pigment epithelial cell line, we show that RanGTP, a small GTPase that dictates nuclear transport, regulates ciliary trafficking of KAP3, a key component for functional kinesin-2. We found that the armadillo-repeat region 6 to 9 (ARM6-9) of KAP3, required for its nuclear translocation, is also necessary and sufficient for its targeting to the ciliary base. Given that KAP3 is essential for cilium formation and there are the emerging roles for RanGTP/importin β in ciliary protein targeting, we further investigated the effect of RanGTP in cilium formation and maintenance. We found that precise control of RanGTP levels, revealed by different Ran mutants, is crucial for cilium formation and maintenance. Most importantly, we were able to provide orthogonal support in an algal model system that segregates RanGTP regulation of ciliary protein trafficking from its nuclear roles. Our work provides important support for the model that nuclear import mechanisms have been co-opted for independent roles in ciliary import.
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Affiliation(s)
- Shengping Huang
- Department of Ophthalmology, University of Kansas Medical Center, Kansas City, Kansas, USA.
| | - Larissa L Dougherty
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas, USA; Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, USA
| | - Prachee Avasthi
- Department of Ophthalmology, University of Kansas Medical Center, Kansas City, Kansas, USA; Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas, USA; Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, USA.
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20
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Abstract
Genome-wide analysis of transcriptome data in Chlamydomonas reinhardtii shows periodic patterns in gene expression levels when cultures are grown under alternating light and dark cycles so that G1 of the cell cycle occurs in the light phase and S/M/G0 occurs during the dark phase. However, alternative splicing, a process that enables a greater protein diversity from a limited set of genes, remains largely unexplored by previous transcriptome based studies in C. reinhardtii. In this study, we used existing longitudinal RNA-seq data obtained during the light-dark cycle to investigate the changes in the alternative splicing pattern and found that 3277 genes (19.75% of 17,746 genes) undergo alternative splicing. These splicing events include Alternative 5′ (Alt 5′), Alternative 3′ (Alt 3′) and Exon skipping (ES) events that are referred as alternative site selection (ASS) events and Intron retention (IR) events. By clustering analysis, we identified a subset of events (26 ASS events and 10 IR events) that show periodic changes in the splicing pattern during the cell cycle. About two-thirds of these 36 genes either introduce a pre-termination codon (PTC) or introduce insertions or deletions into functional domains of the proteins, which implicate splicing in altering gene function. These findings suggest that alternative splicing is also regulated during the Chlamydomonas cell cycle, although not as extensively as changes in gene expression. The longitudinal changes in the alternative splicing pattern during the cell cycle captured by this study provides an important resource to investigate alternative splicing in genes of interest during the cell cycle in Chlamydomonas reinhardtii and other eukaryotes.
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21
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Petriman NA, Lorentzen E. Structural insights into the architecture and assembly of eukaryotic flagella. MICROBIAL CELL (GRAZ, AUSTRIA) 2020; 7:289-299. [PMID: 33150161 PMCID: PMC7590530 DOI: 10.15698/mic2020.11.734] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/07/2020] [Accepted: 09/14/2020] [Indexed: 12/16/2022]
Abstract
Cilia and flagella are slender projections found on most eukaryotic cells including unicellular organisms such as Chlamydomonas, Trypanosoma and Tetrahymena, where they serve motility and signaling functions. The cilium is a large molecular machine consisting of hundreds of different proteins that are trafficked into the organelle to organize a repetitive microtubule-based axoneme. Several recent studies took advantage of improved cryo-EM methodology to unravel the high-resolution structures of ciliary complexes. These include the recently reported purification and structure determination of axonemal doublet microtubules from the green algae Chlamydomonas reinhardtii, which allows for the modeling of more than 30 associated protein factors to provide deep molecular insight into the architecture and repetitive nature of doublet microtubules. In addition, we will review several recent contributions that dissect the structure and function of ciliary trafficking complexes that ferry structural and signaling components between the cell body and the cilium organelle.
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Affiliation(s)
- Narcis-Adrian Petriman
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, DK-8000 Aarhus C, Denmark
| | - Esben Lorentzen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, DK-8000 Aarhus C, Denmark
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22
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Ma M, Stoyanova M, Rademacher G, Dutcher SK, Brown A, Zhang R. Structure of the Decorated Ciliary Doublet Microtubule. Cell 2019; 179:909-922.e12. [PMID: 31668805 PMCID: PMC6936269 DOI: 10.1016/j.cell.2019.09.030] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/29/2019] [Accepted: 09/23/2019] [Indexed: 02/02/2023]
Abstract
The axoneme of motile cilia is the largest macromolecular machine of eukaryotic cells. In humans, impaired axoneme function causes a range of ciliopathies. Axoneme assembly, structure, and motility require a radially arranged set of doublet microtubules, each decorated in repeating patterns with non-tubulin components. We use single-particle cryo-electron microscopy to visualize and build an atomic model of the repeating structure of a native axonemal doublet microtubule, which reveals the identities, positions, repeat lengths, and interactions of 38 associated proteins, including 33 microtubule inner proteins (MIPs). The structure demonstrates how these proteins establish the unique architecture of doublet microtubules, maintain coherent periodicities along the axoneme, and stabilize the microtubules against the repeated mechanical stress induced by ciliary motility. Our work elucidates the architectural principles that underpin the assembly of this large, repetitive eukaryotic structure and provides a molecular basis for understanding the etiology of human ciliopathies.
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Affiliation(s)
- Meisheng Ma
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Mihaela Stoyanova
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
| | - Griffin Rademacher
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Susan K Dutcher
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
| | - Alan Brown
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| | - Rui Zhang
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA.
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23
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Characterization of GLOD4 in Leydig Cells of Tibetan Sheep During Different Stages of Maturity. Genes (Basel) 2019; 10:genes10100796. [PMID: 31614839 PMCID: PMC6826996 DOI: 10.3390/genes10100796] [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: 09/17/2019] [Revised: 10/10/2019] [Accepted: 10/10/2019] [Indexed: 12/19/2022] Open
Abstract
We have previously reported that glyoxalase domain-containing protein 4 (GLOD4) is expressed in sheep testes by proteome analysis, but its roles during testicular development remain unclear. The aim of this study was to understand the expression characteristics and biological functions of the GLOD4 gene in developmental Tibetan sheep testes. The cDNA sequence of the Tibetan sheep GLOD4 gene was cloned by the RT-PCR method, and the structural characteristics of the GLOD4 protein were analyzed using relevant bioinformatics software, including ProtParam, TMHMM, Signal P 4.1, SOPMA, and phyre2. The expression patterns and immunolocalization of GLOD4 were examined in developmental testes derived from three-month-old (3M), one-year-old (1Y), and three-year-old (3Y) Tibetan sheep using quantitative real-time PCR (qRT-PCR), Western blot, immunohistochemistry, and immunofluorescence staining. The sequence analysis showed that the coding sequence (CDS) region of the GLOD4 gene was 729 bp in length and encoded 242 amino acids. Bioinformatics analysis found that the nucleotide and amino acid sequence of Tibetan sheep GLOD4 exhibited the highest sequence similarity with goat and chiru, and the least with zig-zag eel, of the species compared. GLOD4 expressions at both the mRNA and protein levels were significantly higher in the testes of the 1Y and 3Y groups than those in the 3M group (p < 0.01). Immunohistochemistry and immunofluorescence results indicated that the GLOD4 protein was mainly localized in the cytoplasm of Leydig cells from Tibetan sheep testes throughout the development stages. These results taken together suggest that the GLOD4 gene may be implicated in the development of the Leydig cells of Tibetan sheep during different stages of maturity.
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Lin J, Le TV, Augspurger K, Tritschler D, Bower R, Fu G, Perrone C, O’Toole ET, Mills KV, Dymek E, Smith E, Nicastro D, Porter ME. FAP57/WDR65 targets assembly of a subset of inner arm dyneins and connects to regulatory hubs in cilia. Mol Biol Cell 2019; 30:2659-2680. [PMID: 31483737 PMCID: PMC6761771 DOI: 10.1091/mbc.e19-07-0367] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/22/2019] [Accepted: 08/29/2019] [Indexed: 01/19/2023] Open
Abstract
Ciliary motility depends on both the precise spatial organization of multiple dynein motors within the 96 nm axonemal repeat and the highly coordinated interactions between different dyneins and regulatory complexes located at the base of the radial spokes. Mutations in genes encoding cytoplasmic assembly factors, intraflagellar transport factors, docking proteins, dynein subunits, and associated regulatory proteins can all lead to defects in dynein assembly and ciliary motility. Significant progress has been made in the identification of dynein subunits and extrinsic factors required for preassembly of dynein complexes in the cytoplasm, but less is known about the docking factors that specify the unique binding sites for the different dynein isoforms on the surface of the doublet microtubules. We have used insertional mutagenesis to identify a new locus, IDA8/BOP2, required for targeting the assembly of a subset of inner dynein arms (IDAs) to a specific location in the 96 nm repeat. IDA8 encodes flagellar-associated polypeptide (FAP)57/WDR65, a highly conserved WD repeat, coiled coil domain protein. Using high resolution proteomic and structural approaches, we find that FAP57 forms a discrete complex. Cryo-electron tomography coupled with epitope tagging and gold labeling reveal that FAP57 forms an extended structure that interconnects multiple IDAs and regulatory complexes.
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Affiliation(s)
- Jianfeng Lin
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Thuc Vy Le
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455
| | - Katherine Augspurger
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455
| | - Douglas Tritschler
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455
| | - Raqual Bower
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455
| | - Gang Fu
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Catherine Perrone
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455
| | - Eileen T. O’Toole
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309
| | - Kristyn VanderWaal Mills
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455
| | - Erin Dymek
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755
| | - Elizabeth Smith
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755
| | - Daniela Nicastro
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Mary E. Porter
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455
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Lin H, Zhang Z, Iomini C, Dutcher SK. Identifying RNA splicing factors using IFT genes in Chlamydomonas reinhardtii. Open Biol 2019. [PMID: 29514868 PMCID: PMC5881031 DOI: 10.1098/rsob.170211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Intraflagellar transport moves proteins in and out of flagella/cilia and it is essential for the assembly of these organelles. Using whole-genome sequencing, we identified splice site mutations in two IFT genes, IFT81 (fla9) and IFT121 (ift121-2), which lead to flagellar assembly defects in the unicellular green alga Chlamydomonas reinhardtii. The splicing defects in these ift mutants are partially corrected by mutations in two conserved spliceosome proteins, DGR14 and FRA10. We identified a dgr14 deletion mutant, which suppresses the 3′ splice site mutation in IFT81, and a frameshift mutant of FRA10, which suppresses the 5′ splice site mutation in IFT121. Surprisingly, we found dgr14-1 and fra10 mutations suppress both splice site mutations. We suggest these two proteins are involved in facilitating splice site recognition/interaction; in their absence some splice site mutations are tolerated. Nonsense mutations in SMG1, which is involved in nonsense-mediated decay, lead to accumulation of aberrant transcripts and partial restoration of flagellar assembly in the ift mutants. The high density of introns and the conservation of noncore splicing factors, together with the ease of scoring the ift mutant phenotype, make Chlamydomonas an attractive organism to identify new proteins involved in splicing through suppressor screening.
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Affiliation(s)
- Huawen Lin
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, St Louis, MO 63110, USA
| | - Zhengyan Zhang
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, St Louis, MO 63110, USA
| | - Carlo Iomini
- Department of Ophthalmology, Mount Sinai School of Medicine, New York, NY, USA
| | - Susan K Dutcher
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, St Louis, MO 63110, USA
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C11orf70 Mutations Disrupting the Intraflagellar Transport-Dependent Assembly of Multiple Axonemal Dyneins Cause Primary Ciliary Dyskinesia. Am J Hum Genet 2018; 102:956-972. [PMID: 29727692 DOI: 10.1016/j.ajhg.2018.03.024] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 03/23/2018] [Indexed: 01/05/2023] Open
Abstract
Primary ciliary dyskinesia (PCD) is a genetically and phenotypically heterogeneous disorder characterized by destructive respiratory disease and laterality abnormalities due to randomized left-right body asymmetry. PCD is mostly caused by mutations affecting the core axoneme structure of motile cilia that is essential for movement. Genes that cause PCD when mutated include a group that encode proteins essential for the assembly of the ciliary dynein motors and the active transport process that delivers them from their cytoplasmic assembly site into the axoneme. We screened a cohort of affected individuals for disease-causing mutations using a targeted next generation sequencing panel and identified two unrelated families (three affected children) with mutations in the uncharacterized C11orf70 gene (official gene name CFAP300). The affected children share a consistent PCD phenotype from early life with laterality defects and immotile respiratory cilia displaying combined loss of inner and outer dynein arms (IDA+ODA). Phylogenetic analysis shows C11orf70 is highly conserved, distributed across species similarly to proteins involved in the intraflagellar transport (IFT)-dependant assembly of axonemal dyneins. Paramecium C11orf70 RNAi knockdown led to combined loss of ciliary IDA+ODA with reduced cilia beating and swim velocity. Tagged C11orf70 in Paramecium and Chlamydomonas localizes mainly in the cytoplasm with a small amount in the ciliary component. IFT139/TTC21B (IFT-A protein) and FLA10 (IFT kinesin) depletion experiments show that its transport within cilia is IFT dependent. During ciliogenesis, C11orf70 accumulates at the ciliary tips in a similar distribution to the IFT-B protein IFT46. In summary, C11orf70 is essential for assembly of dynein arms and C11orf70 mutations cause defective cilia motility and PCD.
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27
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Hua K, Ferland RJ. Primary cilia proteins: ciliary and extraciliary sites and functions. Cell Mol Life Sci 2018; 75:1521-1540. [PMID: 29305615 PMCID: PMC5899021 DOI: 10.1007/s00018-017-2740-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 12/21/2017] [Accepted: 12/27/2017] [Indexed: 02/07/2023]
Abstract
Primary cilia are immotile organelles known for their roles in development and cell signaling. Defects in primary cilia result in a range of disorders named ciliopathies. Because this organelle can be found singularly on almost all cell types, its importance extends to most organ systems. As such, elucidating the importance of the primary cilium has attracted researchers from all biological disciplines. As the primary cilia field expands, caution is warranted in attributing biological defects solely to the function of this organelle, since many of these "ciliary" proteins are found at other sites in cells and likely have non-ciliary functions. Indeed, many, if not all, cilia proteins have locations and functions outside the primary cilium. Extraciliary functions are known to include cell cycle regulation, cytoskeletal regulation, and trafficking. Cilia proteins have been observed in the nucleus, at the Golgi apparatus, and even in immune synapses of T cells (interestingly, a non-ciliated cell). Given the abundance of extraciliary sites and functions, it can be difficult to definitively attribute an observed phenotype solely to defective cilia rather than to some defective extraciliary function or a combination of both. Thus, extraciliary sites and functions of cilia proteins need to be considered, as well as experimentally determined. Through such consideration, we will understand the true role of the primary cilium in disease as compared to other cellular processes' influences in mediating disease (or through a combination of both). Here, we review a compilation of known extraciliary sites and functions of "cilia" proteins as a means to demonstrate the potential non-ciliary roles for these proteins.
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Affiliation(s)
- Kiet Hua
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, 47 New Scotland Avenue, MC-136, Albany, NY, 12208, USA.
| | - Russell J Ferland
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, 47 New Scotland Avenue, MC-136, Albany, NY, 12208, USA.
- Department of Neurology, Albany Medical College, Albany, NY, 12208, USA.
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28
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Cell-Type Transcriptomes of the Multicellular Green Alga Volvox carteri Yield Insights into the Evolutionary Origins of Germ and Somatic Differentiation Programs. G3-GENES GENOMES GENETICS 2018; 8:531-550. [PMID: 29208647 PMCID: PMC5919742 DOI: 10.1534/g3.117.300253] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Germ-soma differentiation is a hallmark of complex multicellular organisms, yet its origins are not well understood. Volvox carteri is a simple multicellular green alga that has recently evolved a simple germ-soma dichotomy with only two cell-types: large germ cells called gonidia and small terminally differentiated somatic cells. Here, we provide a comprehensive characterization of the gonidial and somatic transcriptomes of V. carteri to uncover fundamental differences between the molecular and metabolic programming of these cell-types. We found extensive transcriptome differentiation between cell-types, with somatic cells expressing a more specialized program overrepresented in younger, lineage-specific genes, and gonidial cells expressing a more generalist program overrepresented in more ancient genes that shared striking overlap with stem cell-specific genes from animals and land plants. Directed analyses of different pathways revealed a strong dichotomy between cell-types with gonidial cells expressing growth-related genes and somatic cells expressing an altruistic metabolic program geared toward the assembly of flagella, which support organismal motility, and the conversion of storage carbon to sugars, which act as donors for production of extracellular matrix (ECM) glycoproteins whose secretion enables massive organismal expansion. V. carteri orthologs of diurnally controlled genes from C. reinhardtii, a single-celled relative, were analyzed for cell-type distribution and found to be strongly partitioned, with expression of dark-phase genes overrepresented in somatic cells and light-phase genes overrepresented in gonidial cells- a result that is consistent with cell-type programs in V. carteri arising by cooption of temporal regulons in a unicellular ancestor. Together, our findings reveal fundamental molecular, metabolic, and evolutionary mechanisms that underlie the origins of germ-soma differentiation in V. carteri and provide a template for understanding the acquisition of germ-soma differentiation in other multicellular lineages.
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29
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Chien A, Shih SM, Bower R, Tritschler D, Porter ME, Yildiz A. Dynamics of the IFT machinery at the ciliary tip. eLife 2017; 6:28606. [PMID: 28930071 PMCID: PMC5662288 DOI: 10.7554/elife.28606] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 09/12/2017] [Indexed: 12/15/2022] Open
Abstract
Intraflagellar transport (IFT) is essential for the elongation and maintenance of eukaryotic cilia and flagella. Due to the traffic jam of multiple trains at the ciliary tip, how IFT trains are remodeled in these turnaround zones cannot be determined by conventional imaging. Using PhotoGate, we visualized the full range of movement of single IFT trains and motors in Chlamydomonas flagella. Anterograde trains split apart and IFT complexes mix with each other at the tip to assemble retrograde trains. Dynein-1b is carried to the tip by kinesin-II as inactive cargo on anterograde trains. Unlike dynein-1b, kinesin-II detaches from IFT trains at the tip and diffuses in flagella. As the flagellum grows longer, diffusion delays return of kinesin-II to the basal body, depleting kinesin-II available for anterograde transport. Our results suggest that dissociation of kinesin-II from IFT trains serves as a negative feedback mechanism that facilitates flagellar length control in Chlamydomonas.
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Affiliation(s)
- Alexander Chien
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States
| | - Sheng Min Shih
- Physics Department, University of California, Berkeley, Berkeley, United States
| | - Raqual Bower
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, United States
| | - Douglas Tritschler
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, United States
| | - Mary E Porter
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, United States
| | - Ahmet Yildiz
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States.,Physics Department, University of California, Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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30
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Whole-Organism Developmental Expression Profiling Identifies RAB-28 as a Novel Ciliary GTPase Associated with the BBSome and Intraflagellar Transport. PLoS Genet 2016; 12:e1006469. [PMID: 27930654 PMCID: PMC5145144 DOI: 10.1371/journal.pgen.1006469] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 11/08/2016] [Indexed: 01/18/2023] Open
Abstract
Primary cilia are specialised sensory and developmental signalling devices extending from the surface of most eukaryotic cells. Defects in these organelles cause inherited human disorders (ciliopathies) such as retinitis pigmentosa and Bardet-Biedl syndrome (BBS), frequently affecting many physiological and developmental processes across multiple organs. Cilium formation, maintenance and function depend on intracellular transport systems such as intraflagellar transport (IFT), which is driven by kinesin-2 and IFT-dynein motors and regulated by the Bardet-Biedl syndrome (BBS) cargo-adaptor protein complex, or BBSome. To identify new cilium-associated genes, we employed the nematode C. elegans, where ciliogenesis occurs within a short timespan during late embryogenesis when most sensory neurons differentiate. Using whole-organism RNA-Seq libraries, we discovered a signature expression profile highly enriched for transcripts of known ciliary proteins, including FAM-161 (FAM161A orthologue), CCDC-104 (CCDC104), and RPI-1 (RP1/RP1L1), which we confirm are cilium-localised in worms. From a list of 185 candidate ciliary genes, we uncover orthologues of human MAP9, YAP, CCDC149, and RAB28 as conserved cilium-associated components. Further analyses of C. elegans RAB-28, recently associated with autosomal-recessive cone-rod dystrophy, reveal that this small GTPase is exclusively expressed in ciliated neurons where it dynamically associates with IFT trains. Whereas inactive GDP-bound RAB-28 displays no IFT movement and diffuse localisation, GTP-bound (activated) RAB-28 concentrates at the periciliary membrane in a BBSome-dependent manner and undergoes bidirectional IFT. Functional analyses reveal that whilst cilium structure, sensory function and IFT are seemingly normal in a rab-28 null allele, overexpression of predicted GDP or GTP locked variants of RAB-28 perturbs cilium and sensory pore morphogenesis and function. Collectively, our findings present a new approach for identifying ciliary proteins, and unveil RAB28, a GTPase most closely related to the BBS protein RABL4/IFT27, as an IFT-associated cargo with BBSome-dependent cell autonomous and non-autonomous functions at the ciliary base. Ciliopathies are genetic disorders that arise from loss or mutation of genes that encode proteins which play roles in the biology of cilia, organelles found on most of the cells in the human body. Ciliopathy-associated ailments include–but are not limited to–kidney dysfunction, blindness, skeletal abnormalities, as well as brain disorders. Although a great number of cilium-targeted proteins are known, it is thought that a large proportion remain unidentified. Here, we use a developmental gene expression series to discover novel cilia genes in the nematode Caenorhabditis elegans. We present several cilium-localised proteins resulting from our analysis, including RAB-28, a GTPase previously implicated in the degenerative eye disease known as cone-rod dystrophy. Through live videomicroscopy, we show that RAB-28 undergoes bidirectional transport within the cilium. A RAB-28 inactivating mutation results in loss of transport, while an activating mutation results in stronger localisation at the ciliary base and robust transport, although overexpression results in a variety of cilia-related defects. Both the wild type and activating mutant proteins require the Bardet-Biedl Syndrome-related complex of proteins for their transport, linking RAB-28 to an established ciliary transport machinery.
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31
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Abedalthagafi MS, Wu MP, Merrill PH, Du Z, Woo T, Sheu SH, Hurwitz S, Ligon KL, Santagata S. Decreased FOXJ1 expression and its ciliogenesis programme in aggressive ependymoma and choroid plexus tumours. J Pathol 2016; 238:584-97. [PMID: 26690880 DOI: 10.1002/path.4682] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 11/12/2015] [Accepted: 12/10/2015] [Indexed: 12/21/2022]
Abstract
Well-differentiated human cancers share transcriptional programmes with the normal tissue counterparts from which they arise. These programmes broadly influence cell behaviour and function and are integral modulators of malignancy. Here, we show that the master regulator of motile ciliogenesis, FOXJ1, is highly expressed in cells along the ventricular surface of the human brain. Strong expression is present in cells of the ependyma and the choroid plexus as well as in a subset of cells residing in the subventricular zone. Expression of FOXJ1 and its transcriptional programme is maintained in many well-differentiated human tumours that arise along the ventricle, including low-grade ependymal tumours and choroid plexus papillomas. Anaplastic ependymomas as well as choroid plexus carcinomas show decreased FOXJ1 expression and its associated ciliogenesis programme genes. In ependymomas and choroid plexus tumours, reduced expression of FOXJ1 and its ciliogenesis programme are markers of poor outcome and are therefore useful biomarkers for assessing these tumours. Transitions in ciliogenesis define distinct differentiation states in ependymal and choroid plexus tumours with important implications for patient care. Copyright © 2015 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Malak S Abedalthagafi
- Department of Pathology, Division of Neuropathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pathology, King Fahad Medical City, Riyadh, Saudi Arabia.,King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.,Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael P Wu
- Department of Pathology, Division of Neuropathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Parker H Merrill
- Department of Pathology, Division of Neuropathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ziming Du
- Department of Pathology, Division of Neuropathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Terri Woo
- Department of Pathology, Division of Neuropathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shu-Hsien Sheu
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shelley Hurwitz
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Keith L Ligon
- Department of Pathology, Division of Neuropathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sandro Santagata
- Department of Pathology, Division of Neuropathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
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32
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Abstract
PURPOSE OF REVIEW Research on the biology of cilia, complex hair-like cellular organelles, has greatly informed our understanding of its crucial role in respiratory health and the pathogenesis of primary ciliary dyskinesia (PCD), including the genetics behind this condition. This review will summarize the current state of the art in the field highlighting its clinical implications. RECENT FINDINGS The genetics of PCD have exploded over the past few years as knowledge acquired from model systems has permitted the identification of genes that are key components of the ciliary apparatus and its function. In addition, clinical criteria and diagnostic tools have emerged that permit more clear identification of affected individuals. SUMMARY The rate of progress in the field continues to accelerate through international collaborative efforts and standardization of methods. Although the genetics behind PCD are complex, given the large number of genes associated with disease, as well as the large number of possible mutations even at the individual gene level, this knowledge is rapidly translating in improved diagnostics and hopefully in the near future in the identification of potential therapeutics.
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Affiliation(s)
- Carlos E. Milla
- The Stanford Cystic Fibrosis Center, Center for Excellence in Pulmonary Biology, Stanford University School of Medicine, 770 Welch Rd., Ste. 350, Palo Alto, CA 94304, P. +1-650-736-9824, F. +1-650-723-5201,
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33
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Li X, Zhang R, Patena W, Gang SS, Blum SR, Ivanova N, Yue R, Robertson JM, Lefebvre PA, Fitz-Gibbon ST, Grossman AR, Jonikas MC. An Indexed, Mapped Mutant Library Enables Reverse Genetics Studies of Biological Processes in Chlamydomonas reinhardtii. THE PLANT CELL 2016; 28:367-87. [PMID: 26764374 PMCID: PMC4790863 DOI: 10.1105/tpc.15.00465] [Citation(s) in RCA: 236] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 11/30/2015] [Accepted: 01/11/2016] [Indexed: 05/18/2023]
Abstract
The green alga Chlamydomonas reinhardtii is a leading unicellular model for dissecting biological processes in photosynthetic eukaryotes. However, its usefulness has been limited by difficulties in obtaining mutants in specific genes of interest. To allow generation of large numbers of mapped mutants, we developed high-throughput methods that (1) enable easy maintenance of tens of thousands of Chlamydomonas strains by propagation on agar media and by cryogenic storage, (2) identify mutagenic insertion sites and physical coordinates in these collections, and (3) validate the insertion sites in pools of mutants by obtaining >500 bp of flanking genomic sequences. We used these approaches to construct a stably maintained library of 1935 mapped mutants, representing disruptions in 1562 genes. We further characterized randomly selected mutants and found that 33 out of 44 insertion sites (75%) could be confirmed by PCR, and 17 out of 23 mutants (74%) contained a single insertion. To demonstrate the power of this library for elucidating biological processes, we analyzed the lipid content of mutants disrupted in genes encoding proteins of the algal lipid droplet proteome. This study revealed a central role of the long-chain acyl-CoA synthetase LCS2 in the production of triacylglycerol from de novo-synthesized fatty acids.
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Affiliation(s)
- Xiaobo Li
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Ru Zhang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Weronika Patena
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Spencer S Gang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Sean R Blum
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Nina Ivanova
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Rebecca Yue
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Jacob M Robertson
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Paul A Lefebvre
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Sorel T Fitz-Gibbon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Martin C Jonikas
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
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34
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Lopez D, Hamaji T, Kropat J, De Hoff P, Morselli M, Rubbi L, Fitz-Gibbon S, Gallaher SD, Merchant SS, Umen J, Pellegrini M. Dynamic Changes in the Transcriptome and Methylome of Chlamydomonas reinhardtii throughout Its Life Cycle. PLANT PHYSIOLOGY 2015; 169:2730-43. [PMID: 26450704 PMCID: PMC4677889 DOI: 10.1104/pp.15.00861] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 10/07/2015] [Indexed: 05/02/2023]
Abstract
The green alga Chlamydomonas reinhardtii undergoes gametogenesis and mating upon nitrogen starvation. While the steps involved in its sexual reproductive cycle have been extensively characterized, the genome-wide transcriptional and epigenetic changes underlying different life cycle stages have yet to be fully described. Here, we performed transcriptome and methylome sequencing to quantify expression and DNA methylation from vegetative and gametic cells of each mating type and from zygotes. We identified 361 gametic genes with mating type-specific expression patterns and 627 genes that are specifically induced in zygotes; furthermore, these sex-related gene sets were enriched for secretory pathway and alga-specific genes. We also examined the C. reinhardtii nuclear methylation map with base-level resolution at different life cycle stages. Despite having low global levels of nuclear methylation, we detected 23 hypermethylated loci in gene-poor, repeat-rich regions. We observed mating type-specific differences in chloroplast DNA methylation levels in plus versus minus mating type gametes followed by chloroplast DNA hypermethylation in zygotes. Lastly, we examined the expression of candidate DNA methyltransferases and found three, DMT1a, DMT1b, and DMT4, that are differentially expressed during the life cycle and are candidate DNA methylases. The expression and methylation data we present provide insight into cell type-specific transcriptional and epigenetic programs during key stages of the C. reinhardtii life cycle.
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Affiliation(s)
- David Lopez
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Takashi Hamaji
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Janette Kropat
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Peter De Hoff
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Marco Morselli
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Liudmilla Rubbi
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Sorel Fitz-Gibbon
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Sean D Gallaher
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Sabeeha S Merchant
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - James Umen
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Matteo Pellegrini
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
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Zones JM, Blaby IK, Merchant SS, Umen JG. High-Resolution Profiling of a Synchronized Diurnal Transcriptome from Chlamydomonas reinhardtii Reveals Continuous Cell and Metabolic Differentiation. THE PLANT CELL 2015; 27:2743-69. [PMID: 26432862 PMCID: PMC4682324 DOI: 10.1105/tpc.15.00498] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/27/2015] [Accepted: 09/14/2015] [Indexed: 05/18/2023]
Abstract
The green alga Chlamydomonas reinhardtii is a useful model organism for investigating diverse biological processes, such as photosynthesis and chloroplast biogenesis, flagella and basal body structure/function, cell growth and division, and many others. We combined a highly synchronous photobioreactor culture system with frequent temporal sampling to characterize genome-wide diurnal gene expression in Chlamydomonas. Over 80% of the measured transcriptome was expressed with strong periodicity, forming 18 major clusters. Genes associated with complex structures and processes, including cell cycle control, flagella and basal bodies, ribosome biogenesis, and energy metabolism, all had distinct signatures of coexpression with strong predictive value for assigning and temporally ordering function. Importantly, the frequent sampling regime allowed us to discern meaningful fine-scale phase differences between and within subgroups of genes and enabled the identification of a transiently expressed cluster of light stress genes. Coexpression was further used both as a data-mining tool to classify and/or validate genes from other data sets related to the cell cycle and to flagella and basal bodies and to assign isoforms of duplicated enzymes to their cognate pathways of central carbon metabolism. Our diurnal coexpression data capture functional relationships established by dozens of prior studies and are a valuable new resource for investigating a variety of biological processes in Chlamydomonas and other eukaryotes.
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Affiliation(s)
- James Matt Zones
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132 Division of Biological Sciences, University of California San Diego, La Jolla, California 92093
| | - Ian K Blaby
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095 Institute of Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - James G Umen
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
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Tulin F, Cross FR. Cyclin-Dependent Kinase Regulation of Diurnal Transcription in Chlamydomonas. THE PLANT CELL 2015; 27:2727-42. [PMID: 26475866 PMCID: PMC4682320 DOI: 10.1105/tpc.15.00400] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 08/01/2015] [Accepted: 09/18/2015] [Indexed: 05/18/2023]
Abstract
We analyzed global transcriptome changes during synchronized cell division in the green alga Chlamydomonas reinhardtii. The Chlamydomonas cell cycle consists of a long G1 phase, followed by an S/M phase with multiple rapid, alternating rounds of DNA replication and segregation. We found that the S/M period is associated with strong induction of ∼2300 genes, many with conserved roles in DNA replication or cell division. Other genes, including many involved in photosynthesis, are reciprocally downregulated in S/M, suggesting a gene expression split correlating with the temporal separation between G1 and S/M. The Chlamydomonas cell cycle is synchronized by light-dark cycles, so in principle, these transcriptional changes could be directly responsive to light or to metabolic cues. Alternatively, cell-cycle-periodic transcription may be directly regulated by cyclin-dependent kinases. To distinguish between these possibilities, we analyzed transcriptional profiles of mutants in the kinases CDKA and CDKB, as well as other mutants with distinct cell cycle blocks. Initial cell-cycle-periodic expression changes are largely CDK independent, but later regulation (induction and repression) is under differential control by CDKA and CDKB. Deviation from the wild-type transcriptional program in diverse cell cycle mutants will be an informative phenotype for further characterization of the Chlamydomonas cell cycle.
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Affiliation(s)
- Frej Tulin
- The Rockefeller University, New York, NY
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Abstract
All of the same conceptual questions about size in organisms apply equally at the level of single cells. What determines the size, not only of the whole cell, but of all of its parts? What ensures that subcellular components are properly proportioned relative to the whole cell? How does alteration in organelle size affect biochemical function? Answering such fundamental questions requires us to understand how the size of individual organelles and other cellular structures is determined. Knowledge of organelle biogenesis and dynamics has advanced rapidly in recent years. Does this knowledge give us enough information to formulate reasonable models for organelle size control, or are we still missing something?
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Affiliation(s)
- Wallace F Marshall
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, California 94158
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Lin H, Dutcher SK. Genetic and genomic approaches to identify genes involved in flagellar assembly in Chlamydomonas reinhardtii. Methods Cell Biol 2015; 127:349-86. [PMID: 25837400 DOI: 10.1016/bs.mcb.2014.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Flagellar assembly requires intraflagellar transport of components from the cell body to the flagellar tip for assembly. The understanding of flagellar assembly has been aided by the ease of biochemistry and the availability of mutants in the unicellular green alga, Chlamydomonas reinhardtii. In this chapter, we discuss means to identify genes involved in these processes using forward and reverse genetics. In particular, the ease and low cost of whole genome sequencing (WGS) will help to make gene identification easier and promote the understanding of this important process.
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Affiliation(s)
- Huawen Lin
- Department of Genetics, Washington University, St. Louis, MO, USA
| | - Susan K Dutcher
- Department of Genetics, Washington University, St. Louis, MO, USA.
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The path to triacylglyceride obesity in the sta6 strain of Chlamydomonas reinhardtii. EUKARYOTIC CELL 2014; 13:591-613. [PMID: 24585881 DOI: 10.1128/ec.00013-14] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
When the sta6 (starch-null) strain of the green microalga Chlamydomonas reinhardtii is nitrogen starved in acetate and then "boosted" after 2 days with additional acetate, the cells become "obese" after 8 days, with triacylglyceride (TAG)-filled lipid bodies filling their cytoplasm and chloroplasts. To assess the transcriptional correlates of this response, the sta6 strain and the starch-forming cw15 strain were subjected to RNA-Seq analysis during the 2 days prior and 2 days after the boost, and the data were compared with published reports using other strains and growth conditions. During the 2 h after the boost, ∼425 genes are upregulated ≥2-fold and ∼875 genes are downregulated ≥2-fold in each strain. Expression of a small subset of "sensitive" genes, encoding enzymes involved in the glyoxylate and Calvin-Benson cycles, gluconeogenesis, and the pentose phosphate pathway, is responsive to culture conditions and genetic background as well as to boosting. Four genes-encoding a diacylglycerol acyltransferase (DGTT2), a glycerol-3-P dehydrogenase (GPD3), and two candidate lipases (Cre03.g155250 and Cre17.g735600)-are selectively upregulated in the sta6 strain. Although the bulk rate of acetate depletion from the medium is not boost enhanced, three candidate acetate permease-encoding genes in the GPR1/FUN34/YaaH superfamily are boost upregulated, and 13 of the "sensitive" genes are strongly responsive to the cell's acetate status. A cohort of 64 autophagy-related genes is downregulated by the boost. Our results indicate that the boost serves both to avert an autophagy program and to prolong the operation of key pathways that shuttle carbon from acetate into storage lipid, the combined outcome being enhanced TAG accumulation, notably in the sta6 strain.
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40
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Wren KN, Craft JM, Tritschler D, Schauer A, Patel DK, Smith EF, Porter ME, Kner P, Lechtreck KF. A differential cargo-loading model of ciliary length regulation by IFT. Curr Biol 2013; 23:2463-71. [PMID: 24316207 DOI: 10.1016/j.cub.2013.10.044] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 09/23/2013] [Accepted: 10/14/2013] [Indexed: 01/07/2023]
Abstract
BACKGROUND During the assembly and maintenance of cilia, precursor proteins need to be transported from the cell body into the organelle. Intraflagellar transport (IFT) is assumed to be the predominant protein transport pathway in cilia, but it remains largely unknown how ciliary proteins use IFT to reach their destination sites in the cilium and whether the amount of cargo transported by IFT is regulated. RESULTS Single-particle imaging showed that DRC4, a structural protein of the axoneme, moves in association with IFT particles inside Chlamydomonas reinhardtii cilia. IFT is required for DRC4 transport both into and within the cilium. DRC4 cargoes dissociate from IFT trains at the tip as well as at various sites along the length of the cilium. Unloaded DRC4 diffuses before docking at its axonemal assembly site. In growing cilia, DRC4 transport by IFT was strongly increased over the steady-state level, and the frequency decreased linearly with the increasing ciliary length. The frequency of DRC4 transport was similarly elevated in short growth-arrested cilia and remained high even when the amount of DRC4 available in the cell body was reduced. CONCLUSIONS DRC4 is a bona fide cargo of IFT. Incompletely assembled cilia trigger an increase in the amount of DRC4 cargo transported by IFT particles, and DRC4 transport is downregulated as cilia approach their steady-state length. We propose a model in which ciliary length is controlled by regulating the amount of cargo transported by IFT particles.
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Affiliation(s)
- Kathryne N Wren
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Julie M Craft
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Douglas Tritschler
- Department of Genetics, Cell Biology and Development, University of Minnesota, MN 55455, USA
| | - Alexandria Schauer
- Department of Genetics, Cell Biology and Development, University of Minnesota, MN 55455, USA
| | - Deep K Patel
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Elizabeth F Smith
- Department of Biological Science, Dartmouth College, Hanover, NH 03755, USA
| | - Mary E Porter
- Department of Genetics, Cell Biology and Development, University of Minnesota, MN 55455, USA
| | - Peter Kner
- College of Engineering, University of Georgia, Athens, GA 30602, USA
| | - Karl F Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA.
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Lin H, Nauman NP, Albee AJ, Hsu S, Dutcher SK. New mutations in flagellar motors identified by whole genome sequencing in Chlamydomonas. Cilia 2013; 2:14. [PMID: 24229452 PMCID: PMC4132587 DOI: 10.1186/2046-2530-2-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 10/02/2013] [Indexed: 02/01/2023] Open
Abstract
Background The building of a cilium or flagellum requires molecular motors and associated
proteins that allow the relocation of proteins from the cell body to the distal
end and the return of proteins to the cell body in a process termed intraflagellar
transport (IFT). IFT trains are carried out by kinesin and back to the cell body
by dynein. Methods We used whole genome sequencing to identify the causative mutations for two
temperature-sensitive flagellar assembly mutants in Chlamydomonas and
validated the changes using reversion analysis. We examined the effect of these
mutations on the localization of IFT81, an IFT complex B protein, the cytoplasmic
dynein heavy chain (DHC1b), and the dynein light intermediate chain (D1bLIC). Results The strains, fla18 and fla24, have mutations in kinesin-2 and
cytoplasmic dynein, respectively. The fla18 mutation alters the same
glutamic acid (E24G) mutated in the fla10-14 allele
(E24K). The fla18 strain loses flagella at 32?C more
rapidly than the E24K allele but less rapidly than the fla10-1
allele. The fla18 mutant loses its flagella by detachment rather than by
shortening. The fla24 mutation falls in cytoplasmic dynein and changes a
completely conserved amino acid (L3243P) in an alpha helix in the AAA5
domain. The fla24 mutant loses its flagella by shortening within 6 hours
at 32?C. DHC1b protein is reduced by 18-fold and D1bLIC is reduced by 16-fold at
21?C compared to wild-type cells. We identified two pseudorevertants
(L3243S and L3243R), which remain flagellated at 32?C.
Although fla24 cells assemble full-length flagella at 21?C, IFT81 protein
localization is dramatically altered. Instead of localizing at the basal body and
along the flagella, IFT81 is concentrated at the proximal end of the flagella. The
pseudorevertants show wild-type IFT81 localization at 21?C, but proximal end
localization of IFT81 at 32?C. Conclusions The change in the AAA5 domain of the cytoplasmic dynein in fla24 may
block the recycling of IFT trains after retrograde transport. It is clear that
different alleles in the flagellar motors reveal different functions and roles.
Multiple alleles will be important for understanding structure-function
relationships.
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Affiliation(s)
- Huawen Lin
- Department of Genetics, Washington University, 660 South Euclid Avenue, St Louis, MO 63110, USA.
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Lin H, Miller ML, Granas DM, Dutcher SK. Whole genome sequencing identifies a deletion in protein phosphatase 2A that affects its stability and localization in Chlamydomonas reinhardtii. PLoS Genet 2013; 9:e1003841. [PMID: 24086163 PMCID: PMC3784568 DOI: 10.1371/journal.pgen.1003841] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/13/2013] [Indexed: 11/19/2022] Open
Abstract
Whole genome sequencing is a powerful tool in the discovery of single nucleotide polymorphisms (SNPs) and small insertions/deletions (indels) among mutant strains, which simplifies forward genetics approaches. However, identification of the causative mutation among a large number of non-causative SNPs in a mutant strain remains a big challenge. In the unicellular biflagellate green alga Chlamydomonas reinhardtii, we generated a SNP/indel library that contains over 2 million polymorphisms from four wild-type strains, one highly polymorphic strain that is frequently used in meiotic mapping, ten mutant strains that have flagellar assembly or motility defects, and one mutant strain, imp3, which has a mating defect. A comparison of polymorphisms in the imp3 strain and the other 15 strains allowed us to identify a deletion of the last three amino acids, Y313F314L315, in a protein phosphatase 2A catalytic subunit (PP2A3) in the imp3 strain. Introduction of a wild-type HA-tagged PP2A3 rescues the mutant phenotype, but mutant HA-PP2A3 at Y313 or L315 fail to rescue. Our immunoprecipitation results indicate that the Y313, L315, or YFLΔ mutations do not affect the binding of PP2A3 to the scaffold subunit, PP2A-2r. In contrast, the Y313, L315, or YFLΔ mutations affect both the stability and the localization of PP2A3. The PP2A3 protein is less abundant in these mutants and fails to accumulate in the basal body area as observed in transformants with either wild-type HA-PP2A3 or a HA-PP2A3 with a V310T change. The accumulation of HA-PP2A3 in the basal body region disappears in mated dikaryons, which suggests that the localization of PP2A3 may be essential to the mating process. Overall, our results demonstrate that the terminal YFL tail of PP2A3 is important in the regulation on Chlamydomonas mating.
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Affiliation(s)
- Huawen Lin
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Michelle L. Miller
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - David M. Granas
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Center for Genomic Sciences and System Biology, Washington University School of Medicine, 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
- * E-mail:
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Zariwala M, Gee H, Kurkowiak M, Al-Mutairi D, Leigh M, Hurd T, Hjeij R, Dell S, Chaki M, Dougherty G, Adan M, Spear P, Esteve-Rudd J, Loges N, Rosenfeld M, Diaz KA, Olbrich H, Wolf W, Sheridan E, Batten T, Halbritter J, Porath J, Kohl S, Lovric S, Hwang DY, Pittman J, Burns K, Ferkol T, Sagel S, Olivier K, Morgan L, Werner C, Raidt J, Pennekamp P, Sun Z, Zhou W, Airik R, Natarajan S, Allen S, Amirav I, Wieczorek D, Landwehr K, Nielsen K, Schwerk N, Sertic J, Köhler G, Washburn J, Levy S, Fan S, Koerner-Rettberg C, Amselem S, Williams D, Mitchell B, Drummond I, Otto E, Omran H, Knowles M, Hildebrandt F. ZMYND10 is mutated in primary ciliary dyskinesia and interacts with LRRC6. Am J Hum Genet 2013; 93:336-45. [PMID: 23891469 DOI: 10.1016/j.ajhg.2013.06.007] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 05/21/2013] [Accepted: 06/06/2013] [Indexed: 11/27/2022] Open
Abstract
Defects of motile cilia cause primary ciliary dyskinesia (PCD), characterized by recurrent respiratory infections and male infertility. Using whole-exome resequencing and high-throughput mutation analysis, we identified recessive biallelic mutations in ZMYND10 in 14 families and mutations in the recently identified LRRC6 in 13 families. We show that ZMYND10 and LRRC6 interact and that certain ZMYND10 and LRRC6 mutations abrogate the interaction between the LRRC6 CS domain and the ZMYND10 C-terminal domain. Additionally, ZMYND10 and LRRC6 colocalize with the centriole markers SAS6 and PCM1. Mutations in ZMYND10 result in the absence of the axonemal protein components DNAH5 and DNALI1 from respiratory cilia. Animal models support the association between ZMYND10 and human PCD, given that zmynd10 knockdown in zebrafish caused ciliary paralysis leading to cystic kidneys and otolith defects and that knockdown in Xenopus interfered with ciliogenesis. Our findings suggest that a cytoplasmic protein complex containing ZMYND10 and LRRC6 is necessary for motile ciliary function.
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