1
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Peng F, Nordgren CE, Murray JI. A spatiotemporally resolved atlas of mRNA decay in the C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types. Genome Res 2024; 34:1235-1252. [PMID: 39142810 PMCID: PMC11444186 DOI: 10.1101/gr.278980.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 08/08/2024] [Indexed: 08/16/2024]
Abstract
During embryonic development, cells undergo dynamic changes in gene expression that are required for appropriate cell fate specification. Although both transcription and mRNA degradation contribute to gene expression dynamics, patterns of mRNA decay are less well understood. Here, we directly measure spatiotemporally resolved mRNA decay rates transcriptome-wide throughout C. elegans embryogenesis by transcription inhibition followed by bulk and single-cell RNA sequencing. This allows us to calculate mRNA half-lives within specific cell types and developmental stages, and identify differentially regulated mRNA decay throughout embryonic development. We identify transcript features that are correlated with mRNA stability and find that mRNA decay rates are associated with distinct peaks in gene expression over time. Moreover, we provide evidence that, on average, mRNA is more stable in the germline than in the soma and in later embryonic stages than in earlier stages. This work suggests that differential mRNA decay across cell states and time helps to shape developmental gene expression, and it provides a valuable resource for studies of mRNA turnover regulatory mechanisms.
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Affiliation(s)
- Felicia Peng
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - C Erik Nordgren
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - John Isaac Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
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2
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Heiman MG, Bülow HE. Dendrite morphogenesis in Caenorhabditis elegans. Genetics 2024; 227:iyae056. [PMID: 38785371 PMCID: PMC11151937 DOI: 10.1093/genetics/iyae056] [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: 12/18/2023] [Accepted: 04/02/2024] [Indexed: 05/25/2024] Open
Abstract
Since the days of Ramón y Cajal, the vast diversity of neuronal and particularly dendrite morphology has been used to catalog neurons into different classes. Dendrite morphology varies greatly and reflects the different functions performed by different types of neurons. Significant progress has been made in our understanding of how dendrites form and the molecular factors and forces that shape these often elaborately sculpted structures. Here, we review work in the nematode Caenorhabditis elegans that has shed light on the developmental mechanisms that mediate dendrite morphogenesis with a focus on studies investigating ciliated sensory neurons and the highly elaborated dendritic trees of somatosensory neurons. These studies, which combine time-lapse imaging, genetics, and biochemistry, reveal an intricate network of factors that function both intrinsically in dendrites and extrinsically from surrounding tissues. Therefore, dendrite morphogenesis is the result of multiple tissue interactions, which ultimately determine the shape of dendritic arbors.
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Affiliation(s)
- Maxwell G Heiman
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Hannes E Bülow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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3
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Chen H, Wu Z, Yan Z, Chen C, Zhang Y, Wang Q, Gao Y, Ling K, Hu J, Wei Q. The ARPKD Protein DZIP1L Regulates Ciliary Protein Entry by Modulating the Architecture and Function of Ciliary Transition Fibers. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308820. [PMID: 38634253 PMCID: PMC11200010 DOI: 10.1002/advs.202308820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/13/2024] [Indexed: 04/19/2024]
Abstract
Serving as the cell's sensory antennae, primary cilia are linked to numerous human genetic diseases when they malfunction. DZIP1L, identified as one of the genetic causes of human autosomal recessive polycystic kidney disease (ARPKD), is an evolutionarily conserved ciliary basal body protein. Although it has been reported that DZIP1L is involved in the ciliary entry of PKD proteins, the underlying mechanism remains elusive. Here, an uncharacterized role of DZIP1L is reported in modulating the architecture and function of transition fibers (TFs), striking ciliary base structures essential for selective cilia gating. Using C. elegans as a model, C01G5.7 (hereafter termed DZIP-1) is identified as the sole homolog of DZIP1L, which specifically localizes to TFs. While DZIP-1 or ANKR-26 (the ortholog of ANKRD26) deficiency shows subtle impact on TFs, co-depletion of DZIP-1 and ANKR-26 disrupts TF assembly and cilia gating for soluble and membrane proteins, including the ortholog of ADPKD protein polycystin-2. Notably, the synergistic role for DZIP1L and ANKRD26 in the formation and function of TFs is highly conserved in mammalian cilia. Hence, the findings illuminate an evolutionarily conserved role of DZIP1L in TFs architecture and function, highlighting TFs as a vital part of the ciliary gate implicated in ciliopathies ARPKD.
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Affiliation(s)
- Huicheng Chen
- CAS Key Laboratory of Insect Developmental and Evolutionary BiologyCAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai200032China
- University of Chinese Academy of SciencesBeijing100039China
- Center for Energy Metabolism and ReproductionInstitute of Biomedicine and BiotechnologyShenzhen Institutes of Advanced TechnologyChinese Academy of Sciences (CAS)Shenzhen518055China
| | - Zhimao Wu
- Center for Energy Metabolism and ReproductionInstitute of Biomedicine and BiotechnologyShenzhen Institutes of Advanced TechnologyChinese Academy of Sciences (CAS)Shenzhen518055China
| | - Ziwei Yan
- CAS Key Laboratory of Insect Developmental and Evolutionary BiologyCAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai200032China
- University of Chinese Academy of SciencesBeijing100039China
| | - Chuan Chen
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMN55905USA
| | - Yingying Zhang
- Center for Energy Metabolism and ReproductionInstitute of Biomedicine and BiotechnologyShenzhen Institutes of Advanced TechnologyChinese Academy of Sciences (CAS)Shenzhen518055China
| | - Qiaoling Wang
- Institute of Medicine and Pharmaceutical SciencesZhengzhou UniversityZhengzhou430000China
| | - Yuqing Gao
- Center for Energy Metabolism and ReproductionInstitute of Biomedicine and BiotechnologyShenzhen Institutes of Advanced TechnologyChinese Academy of Sciences (CAS)Shenzhen518055China
| | - Kun Ling
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMN55905USA
| | - Jinghua Hu
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMN55905USA
| | - Qing Wei
- Center for Energy Metabolism and ReproductionInstitute of Biomedicine and BiotechnologyShenzhen Institutes of Advanced TechnologyChinese Academy of Sciences (CAS)Shenzhen518055China
- School of Synthetic BiologyShanxi Key Laboratory of Nucleic Acid BiopesticidesShanxi UniversityTaiyuan030006China
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4
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Jurisch-Yaksi N, Wachten D, Gopalakrishnan J. The neuronal cilium - a highly diverse and dynamic organelle involved in sensory detection and neuromodulation. Trends Neurosci 2024; 47:383-394. [PMID: 38580512 DOI: 10.1016/j.tins.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/04/2024] [Accepted: 03/14/2024] [Indexed: 04/07/2024]
Abstract
Cilia are fascinating organelles that act as cellular antennae, sensing the cellular environment. Cilia gained significant attention in the late 1990s after their dysfunction was linked to genetic diseases known as ciliopathies. Since then, several breakthrough discoveries have uncovered the mechanisms underlying cilia biogenesis and function. Like most cells in the animal kingdom, neurons also harbor cilia, which are enriched in neuromodulatory receptors. Yet, how neuronal cilia modulate neuronal physiology and animal behavior remains poorly understood. By comparing ciliary biology between the sensory and central nervous systems (CNS), we provide new perspectives on the functions of cilia in brain physiology.
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Affiliation(s)
- Nathalie Jurisch-Yaksi
- Department of Clinical and Molecular Medicine (IKOM), Faculty of Medicine and Health Science, Norwegian University of Science and Technology, Erling Skalgssons gate 1, 7491 Trondheim, Norway.
| | - Dagmar Wachten
- Department of Biophysical Imaging, Institute of Innate Immunity, Medical Faculty, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Jay Gopalakrishnan
- Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany; Institute for Human Genetics, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, 07740 Jena, Germany
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5
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Peng F, Nordgren CE, Murray JI. A spatiotemporally resolved atlas of mRNA decay in the C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575757. [PMID: 38293118 PMCID: PMC10827189 DOI: 10.1101/2024.01.15.575757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
During embryonic development, cells undergo dynamic changes in gene expression that are required for appropriate cell fate specification. Although both transcription and mRNA degradation contribute to gene expression dynamics, patterns of mRNA decay are less well-understood. Here we directly measured spatiotemporally resolved mRNA decay rates transcriptome-wide throughout C. elegans embryogenesis by transcription inhibition followed by bulk and single-cell RNA-sequencing. This allowed us to calculate mRNA half-lives within specific cell types and developmental stages and identify differentially regulated mRNA decay throughout embryonic development. We identified transcript features that are correlated with mRNA stability and found that mRNA decay rates are associated with distinct peaks in gene expression over time. Moreover, we provide evidence that, on average, mRNA is more stable in the germline compared to in the soma and in later embryonic stages compared to in earlier stages. This work suggests that differential mRNA decay across cell states and time helps to shape developmental gene expression, and it provides a valuable resource for studies of mRNA turnover regulatory mechanisms.
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Affiliation(s)
- Felicia Peng
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - C Erik Nordgren
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - John Isaac Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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6
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Morrissette N, Abbaali I, Ramakrishnan C, Hehl AB. The Tubulin Superfamily in Apicomplexan Parasites. Microorganisms 2023; 11:microorganisms11030706. [PMID: 36985278 PMCID: PMC10056924 DOI: 10.3390/microorganisms11030706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
Microtubules and specialized microtubule-containing structures are assembled from tubulins, an ancient superfamily of essential eukaryotic proteins. Here, we use bioinformatic approaches to analyze features of tubulins in organisms from the phylum Apicomplexa. Apicomplexans are protozoan parasites that cause a variety of human and animal infectious diseases. Individual species harbor one to four genes each for α- and β-tubulin isotypes. These may specify highly similar proteins, suggesting functional redundancy, or exhibit key differences, consistent with specialized roles. Some, but not all apicomplexans harbor genes for δ- and ε-tubulins, which are found in organisms that construct appendage-containing basal bodies. Critical roles for apicomplexan δ- and ε-tubulin are likely to be limited to microgametes, consistent with a restricted requirement for flagella in a single developmental stage. Sequence divergence or the loss of δ- and ε-tubulin genes in other apicomplexans appears to be associated with diminished requirements for centrioles, basal bodies, and axonemes. Finally, because spindle microtubules and flagellar structures have been proposed as targets for anti-parasitic therapies and transmission-blocking strategies, we discuss these ideas in the context of tubulin-based structures and tubulin superfamily properties.
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Affiliation(s)
- Naomi Morrissette
- Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697, USA
- Correspondence: ; Tel.: +1-949-824-9243
| | - Izra Abbaali
- Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Chandra Ramakrishnan
- Institute for Parasitology, University of Zurich, Winterthurerstrasse 266a, 8057 Zürich, Switzerland
| | - Adrian B. Hehl
- Institute for Parasitology, University of Zurich, Winterthurerstrasse 266a, 8057 Zürich, Switzerland
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7
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Mul W, Mitra A, Peterman EJG. Mechanisms of Regulation in Intraflagellar Transport. Cells 2022; 11:2737. [PMID: 36078145 PMCID: PMC9454703 DOI: 10.3390/cells11172737] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/30/2022] Open
Abstract
Cilia are eukaryotic organelles essential for movement, signaling or sensing. Primary cilia act as antennae to sense a cell's environment and are involved in a wide range of signaling pathways essential for development. Motile cilia drive cell locomotion or liquid flow around the cell. Proper functioning of both types of cilia requires a highly orchestrated bi-directional transport system, intraflagellar transport (IFT), which is driven by motor proteins, kinesin-2 and IFT dynein. In this review, we explore how IFT is regulated in cilia, focusing from three different perspectives on the issue. First, we reflect on how the motor track, the microtubule-based axoneme, affects IFT. Second, we focus on the motor proteins, considering the role motor action, cooperation and motor-train interaction plays in the regulation of IFT. Third, we discuss the role of kinases in the regulation of the motor proteins. Our goal is to provide mechanistic insights in IFT regulation in cilia and to suggest directions of future research.
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Affiliation(s)
| | | | - Erwin J. G. Peterman
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
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8
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Maurya AK. Structural diversity in a stereotypic organelle - Sensory cilia of Caenorhabditis elegans. J Cell Physiol 2022; 237:2668-2672. [PMID: 35686462 DOI: 10.1002/jcp.30732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/25/2022] [Accepted: 03/21/2022] [Indexed: 11/07/2022]
Abstract
Sensory cilia, an ancient organelle, displays a high degree of conservation in its structure and functioning. Sensory cilia also fulfill a wide range of sensory functions, from sensing environmental signals (light, sound, chemicals, and mechanical forces) to interpreting intercellular developmental signals. One way they appear to fulfill these diverse and specialized roles is by adopting a variety of shapes and sizes. We are only beginning to document and appreciate this complexity. Here in this review, using the varied and specialized cilia found on Caenorhabditis elegans sensory neurons, I highlight some of the most obvious examples of this structural diversity and the underlying mechanisms if known. Such structural diversity appears to arise from the modulation of deeply conserved molecular pathways and also from cell- and species-specific mechanisms. Studying these ciliary specializations will thus provide for a comprehensive understanding of ciliary biology and might uncover understudied aspects of ciliary disease biology.
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Affiliation(s)
- Ashish K Maurya
- Department of Biology, Brandeis University, Waltham, Massachusetts, USA
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9
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Hodge SH, Watts A, Marley R, Baines RA, Hafen E, MacDougall LK. Twitchy, the Drosophila orthologue of the ciliary gating protein FBF1/dyf-19, is required for coordinated locomotion and male fertility. Biol Open 2021; 10:bio058531. [PMID: 34357392 PMCID: PMC8353261 DOI: 10.1242/bio.058531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 06/21/2021] [Indexed: 12/13/2022] Open
Abstract
Primary cilia are compartmentalised from the rest of the cell by a ciliary gate comprising transition fibres and a transition zone. The ciliary gate allows the selective import and export of molecules such as transmembrane receptors and transport proteins. These are required for the assembly of the cilium, its function as a sensory and signalling centre and to maintain its distinctive composition. Certain motile cilia can also form within the cytosol as exemplified by human and Drosophila sperm. The role of transition fibre proteins has not been well described in the cytoplasmic cilia. Drosophila have both compartmentalised primary cilia, in sensory neurons, and sperm flagella that form within the cytosol. Here, we describe phenotypes for twitchy the Drosophila orthologue of a transition fibre protein, mammalian FBF1/C. elegans dyf-19. Loss-of-function mutants in twitchy are adult lethal and display a severely uncoordinated phenotype. Twitchy flies are too uncoordinated to mate but RNAi-mediated loss of twitchy specifically within the male germline results in coordinated but infertile adults. Examination of sperm from twitchy RNAi-knockdown flies shows that the flagellar axoneme forms, elongates and is post-translationally modified by polyglycylation but the production of motile sperm is impaired. These results indicate that twitchy is required for the function of both sensory cilia that are compartmentalised from the rest of the cell and sperm flagella that are formed within the cytosol of the cell. Twitchy is therefore likely to function as part of a molecular gate in sensory neurons but may have a distinct function in sperm cells.
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Affiliation(s)
- Suzanne H. Hodge
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Amy Watts
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Richard Marley
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, UK
| | - Richard A. Baines
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, UK
| | - Ernst Hafen
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, 8093, Zürich, Switzerland
| | - Lindsay K. MacDougall
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
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10
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Sensory cilia as the Achilles heel of nematodes when attacked by carnivorous mushrooms. Proc Natl Acad Sci U S A 2020; 117:6014-6022. [PMID: 32123065 DOI: 10.1073/pnas.1918473117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Fungal predatory behavior on nematodes has evolved independently in all major fungal lineages. The basidiomycete oyster mushroom Pleurotus ostreatus is a carnivorous fungus that preys on nematodes to supplement its nitrogen intake under nutrient-limiting conditions. Its hyphae can paralyze nematodes within a few minutes of contact, but the mechanism had remained unclear. We demonstrate that the predator-prey relationship is highly conserved between multiple Pleurotus species and a diversity of nematodes. To further investigate the cellular and molecular mechanisms underlying rapid nematode paralysis, we conducted genetic screens in Caenorhabditis elegans and isolated mutants that became resistant to P. ostreatus We found that paralysis-resistant mutants all harbored loss-of-function mutations in genes required for ciliogenesis, demonstrating that the fungus induced paralysis via the cilia of nematode sensory neurons. Furthermore, we observed that P. ostreatus caused excess calcium influx and hypercontraction of the head and pharyngeal muscle cells, ultimately resulting in rapid necrosis of the entire nervous system and muscle cells throughout the entire organism. This cilia-dependent predatory mechanism is evolutionarily conserved in Pristionchus pacificus, a nematode species estimated to have diverged from C. elegans 280 to 430 million y ago. Thus, P. ostreatus exploits a nematode-killing mechanism that is distinct from widely used anthelmintic drugs such as ivermectin, levamisole, and aldicarb, representing a potential route for targeting parasitic nematodes in plants, animals, and humans.
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11
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Zhao L, Hou Y, McNeill NA, Witman GB. The unity and diversity of the ciliary central apparatus. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190164. [PMID: 31884923 PMCID: PMC7017334 DOI: 10.1098/rstb.2019.0164] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2019] [Indexed: 12/27/2022] Open
Abstract
Nearly all motile cilia and flagella (terms here used interchangeably) have a '9+2' axoneme containing nine outer doublet microtubules and two central microtubules. The central pair of microtubules plus associated projections, termed the central apparatus (CA), is involved in the control of flagellar motility and is essential for the normal movement of '9+2' cilia. Research using the green alga Chlamydomonas reinhardtii, an important model system for studying cilia, has provided most of our knowledge of the protein composition of the CA, and recent work using this organism has expanded the number of known and candidate CA proteins nearly threefold. Here we take advantage of this enhanced proteome to examine the genomes of a wide range of eukaryotic organisms, representing all of the major phylogenetic groups, to identify predicted orthologues of the C. reinhardtii CA proteins and explore how widely the proteins are conserved and whether there are patterns to this conservation. We also discuss in detail two contrasting groups of CA proteins-the ASH-domain proteins, which are broadly conserved, and the PAS proteins, which are restricted primarily to the volvocalean algae. This article is part of the Theo Murphy meeting issue 'Unity and diversity of cilia in locomotion and transport'.
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Affiliation(s)
| | | | | | - George B. Witman
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
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