1
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Klimek A, Mondal D, Block S, Sharma P, Netz RR. Data-driven classification of individual cells by their non-Markovian motion. Biophys J 2024; 123:1173-1183. [PMID: 38515300 PMCID: PMC11140416 DOI: 10.1016/j.bpj.2024.03.023] [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: 01/19/2024] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 03/23/2024] Open
Abstract
We present a method to differentiate organisms solely by their motion based on the generalized Langevin equation (GLE) and use it to distinguish two different swimming modes of strongly confined unicellular microalgae Chlamydomonas reinhardtii. The GLE is a general model for active or passive motion of organisms and particles that can be derived from a time-dependent general many-body Hamiltonian and in particular includes non-Markovian effects (i.e., the trajectory memory of its past). We extract all GLE parameters from individual cell trajectories and perform an unbiased cluster analysis to group them into different classes. For the specific cell population employed in the experiments, the GLE-based assignment into the two different swimming modes works perfectly, as checked by control experiments. The classification and sorting of single cells and organisms is important in different areas; our method, which is based on motion trajectories, offers wide-ranging applications in biology and medicine.
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Affiliation(s)
- Anton Klimek
- Fachbereich Physik, Freie Universität Berlin, Berlin, Germany
| | - Debasmita Mondal
- Department of Physics, Indian Institute of Science, Bangalore, India; James Franck Institute, University of Chicago, Chicago, Illinois
| | - Stephan Block
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Prerna Sharma
- Department of Physics, Indian Institute of Science, Bangalore, India; Department of Bioengineering, Indian Institute of Science, Bangalore, India
| | - Roland R Netz
- Fachbereich Physik, Freie Universität Berlin, Berlin, Germany.
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2
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Wei D, Quaranta G, Aubin-Tam ME, Tam DSW. The younger flagellum sets the beat for Chlamydomonas reinhardtii. eLife 2024; 13:e86102. [PMID: 38752724 PMCID: PMC11098555 DOI: 10.7554/elife.86102] [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: 01/11/2023] [Accepted: 04/03/2024] [Indexed: 05/18/2024] Open
Abstract
Eukaryotes swim with coordinated flagellar (ciliary) beating and steer by fine-tuning the coordination. The model organism for studying flagellate motility, Chlamydomonas reinhardtii, employs synchronous, breaststroke-like flagellar beating to swim, and it modulates the beating amplitudes differentially to steer. This strategy hinges on both inherent flagellar asymmetries (e.g. different response to chemical messengers) and such asymmetries being effectively coordinated in the synchronous beating. In C. reinhardtii, the synchrony of beating is known to be supported by a mechanical connection between flagella; however, how flagellar asymmetries persist in the synchrony remains elusive. For example, it has been speculated for decades that one flagellum leads the beating, as its dynamic properties (i.e. frequency, waveform, etc.) appear to be copied by the other one. In this study, we combine experiments, computations, and modeling efforts to elucidate the roles played by each flagellum in synchronous beating. With a non-invasive technique to selectively load each flagellum, we show that the coordinated beating essentially only responds to load exerted on the cis flagellum; and that such asymmetry in response derives from a unilateral coupling between the two flagella. Our results highlight a distinct role for each flagellum in coordination and have implication for biflagellates' tactic behaviors.
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Affiliation(s)
- Da Wei
- Department of Bionanoscience, Delft University of TechnologyDelftNetherlands
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of SciencesBeijingChina
| | - Greta Quaranta
- Laboratory for Aero and Hydrodynamics, Delft University of TechnologyDelftNetherlands
| | - Marie-Eve Aubin-Tam
- Department of Bionanoscience, Delft University of TechnologyDelftNetherlands
| | - Daniel SW Tam
- Laboratory for Aero and Hydrodynamics, Delft University of TechnologyDelftNetherlands
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3
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Findinier J, Grossman AR. Chlamydomonas: Fast tracking from genomics. JOURNAL OF PHYCOLOGY 2023; 59:644-652. [PMID: 37417760 DOI: 10.1111/jpy.13356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 07/08/2023]
Abstract
Elucidating biological processes has relied on the establishment of model organisms, many of which offer advantageous features such as rapid axenic growth, extensive knowledge of their physiological features and gene content, and the ease with which they can be genetically manipulated. The unicellular green alga Chlamydomonas reinhardtii has been an exemplary model that has enabled many scientific breakthroughs over the decades, especially in the fields of photosynthesis, cilia function and biogenesis, and the acclimation of photosynthetic organisms to their environment. Here, we discuss recent molecular/technological advances that have been applied to C. reinhardtii and how they have further fostered its development as a "flagship" algal system. We also explore the future promise of this alga in leveraging advances in the fields of genomics, proteomics, imaging, and synthetic biology for addressing critical future biological issues.
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Affiliation(s)
- Justin Findinier
- The Carnegie Institution for Science, Biosphere Science and Engineering, Stanford, California, USA
| | - Arthur R Grossman
- The Carnegie Institution for Science, Biosphere Science and Engineering, Stanford, California, USA
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4
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Dougherty LL, Avasthi P. Determinants of cytoplasmic microtubule depolymerization during ciliogenesis in Chlamydomonas reinhardtii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.536038. [PMID: 37066348 PMCID: PMC10104144 DOI: 10.1101/2023.04.07.536038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
At the core of cilia are microtubules which are important for establishing length and assisting ciliary assembly and disassembly; however, another role for microtubule regulation on ciliogenesis lies outside of the cilium. The microtubule cytoskeleton is a highly dynamic structure which polymerizes and depolymerizes rapidly to assist in cellular processes. These processes have been studied across various organisms with chemical as well as 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 cytoplasmic microtubule 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, we find that ciliary shedding through mechanical shearing, cilia regenerate earlier despite intact CytoMTs. Our data suggests that cytoplasmic microtubules are not a sink for a limiting pool of cytoplasmic tubulin in Chlamydomonas, depolymerization that occurs following deciliation is a consequence rather than a requirement for ciliogenesis, and intact CytoMTs in the cytoplasm and the 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, New Hampshire
| | - Prachee Avasthi
- Biochemistry and Cell Biology Department, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire
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5
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Polino AJ, Sviben S, Melena I, Piston DW, Hughes JW. Scanning electron microscopy of human islet cilia. Proc Natl Acad Sci U S A 2023; 120:e2302624120. [PMID: 37205712 PMCID: PMC10235940 DOI: 10.1073/pnas.2302624120] [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: 02/14/2023] [Accepted: 04/12/2023] [Indexed: 05/21/2023] Open
Abstract
Human islet primary cilia are vital glucose-regulating organelles whose structure remains uncharacterized. Scanning electron microscopy (SEM) is a useful technique for studying the surface morphology of membrane projections like cilia, but conventional sample preparation does not reveal the submembrane axonemal structure, which holds key implications for ciliary function. To overcome this challenge, we combined SEM with membrane-extraction techniques to examine primary cilia in native human islets. Our data show well-preserved cilia subdomains which demonstrate both expected and unexpected ultrastructural motifs. Morphometric features were quantified when possible, including axonemal length and diameter, microtubule conformations, and chirality. We further describe a ciliary ring, a structure that may be a specialization in human islets. Key findings are correlated with fluorescence microscopy and interpreted in the context of cilia function as a cellular sensor and communications locus in pancreatic islets.
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Affiliation(s)
- Alexander J. Polino
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO63110
| | - Sanja Sviben
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO63110
| | - Isabella Melena
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO63110
| | - David W. Piston
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO63110
| | - Jing W. Hughes
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO63110
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO63110
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6
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Polino AJ, Sviben S, Melena I, Piston DW, Hughes J. Scanning electron microscopy of human islet cilia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528685. [PMID: 36824775 PMCID: PMC9949088 DOI: 10.1101/2023.02.15.528685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Human islet primary cilia are vital glucose-regulating organelles whose structure remains uncharacterized. Scanning electron microscopy (SEM) is a useful technique for studying the surface morphology of membrane projections like primary cilia, but conventional sample preparation does not reveal the sub-membrane axonemal structure which holds key implications for cilia function. To overcome this challenge, we combined SEM with membrane-extraction techniques to examine cilia in native human islets. Our data show well-preserved cilia subdomains which demonstrate both expected and unexpected ultrastructural motifs. Morphometric features were quantified when possible, including axonemal length and diameter, microtubule conformations and chirality. We further describe a novel ciliary ring, a structure that may be a specialization in human islets. Key findings are correlated with fluorescence microscopy and interpreted in the context of cilia function as a cellular sensor and communications locus in pancreatic islets.
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7
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Luxmi R, King SM. Cilia-derived vesicles: An ancient route for intercellular communication. Semin Cell Dev Biol 2022; 129:82-92. [PMID: 35346578 PMCID: PMC9378432 DOI: 10.1016/j.semcdb.2022.03.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/10/2022] [Accepted: 03/10/2022] [Indexed: 12/11/2022]
Abstract
Extracellular vesicles (EVs) provide a mechanism for intercellular communication that transports complex signals in membrane delimited structures between cells, tissues and organisms. Cells secrete EVs of various subtypes defined by the pathway leading to release and by the pathological condition of the cell. Cilia are evolutionarily conserved organelles that can act as sensory structures surveilling the extracellular environment. Here we discuss the secretory functions of cilia and their biological implications. Studies in multiple species - from the nematode Caenorhabditis elegans and the chlorophyte alga Chlamydomonas reinhardtii to mammals - have revealed that cilia shed bioactive EVs (ciliary EVs or ectosomes) by outward budding of the ciliary membrane. The content of ciliary EVs is distinct from that of other vesicles released by cells. Peptides regulate numerous aspects of metazoan physiology and development through evolutionarily conserved mechanisms. Intriguingly, cilia-derived vesicles have recently been found to mediate peptidergic signaling. C. reinhardtii releases the peptide α-amidating enzyme (PAM), bioactive amidated products and components of the peptidergic signaling machinery in ciliary EVs in a developmentally regulated manner. Considering the origin of cilia in early eukaryotes, it is likely that release of peptidergic signals in ciliary EVs represents an alternative and ancient mode of regulated secretion that cells can utilize in the absence of dedicated secretory granules.
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Affiliation(s)
- Raj Luxmi
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030-3305, USA.
| | - Stephen M King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030-3305, USA.
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8
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Windler M, Stuart R, Deutzmann JS, Mayali X, Navid A, D'haeseleer P, Marcu OE, Lipton M, Nicora C, Spormann AM. Bacterial exometabolites influence Chlamydomonas cell cycle and double algal productivity. FEMS Microbiol Ecol 2022; 98:6670776. [PMID: 35977399 DOI: 10.1093/femsec/fiac091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/10/2022] [Accepted: 08/12/2022] [Indexed: 11/14/2022] Open
Abstract
Algal-bacterial interactions provide clues to algal physiology, but mutualistic interactions are complicated by dynamic exchange. We characterized the response of Chlamydomonas reinhardtii to the presence of a putative alga-benefitting commensal bacterium (Arthrobacter strain 'P2b'). Co-cultivation promoted chlorophyll content, biomass, average cell size, and number of dividing cells, relative to axenic cultures. Addition of bacterial spent medium (whole, size-fractionated and heat-treated) had similar effects, indicating P2b does not require algal interaction to promote growth. Nutrients and pH were excluded as putative effectors, collectively indicating a commensal interaction mediated by Arthrobacter-released small exometabolite(s). Proteogenomic comparison revealed similar response to co-cultivation and spent media, including differential cell cycle regulation, extensive downregulation of flagellar genes and histones, carbonic anhydrase and RubisCO downregulation, upregulation of some chlorophyll, amino acid and carbohydrate biosynthesis genes, and changes to redox and Fe homeostasis. Further, Arthrobacter protein expression indicated some highly expressed putative secondary metabolites. Together, these results revealed that low molecular weight bacterial metabolites can elicit major physiological changes in algal cell cycle regulation, perhaps through a more productive G1 phase, that lead to substantial increases in photosynthetically-produced biomass. This work illustrates that model commensal interactions can be used to shed light on algal response to stimulating bacteria.
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Affiliation(s)
- Miriam Windler
- Department of Civil & Environmental Engineering, Stanford University, United States
| | - Rhona Stuart
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, United States
| | - Joerg S Deutzmann
- Department of Civil & Environmental Engineering, Stanford University, United States
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, United States
| | - Ali Navid
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, United States
| | - Patrik D'haeseleer
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, United States
| | - Oana E Marcu
- SETI Institute, NASA Ames Research Center, United States
| | - Mary Lipton
- Pacific Northwest National Laboratories, United States
| | - Carrie Nicora
- Pacific Northwest National Laboratories, United States
| | - Alfred M Spormann
- Department of Civil & Environmental Engineering, Stanford University, United States.,Department of Chemical Engineering, Stanford University, United States
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9
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von der Heyde EL, Hallmann A. Molecular and cellular dynamics of early embryonic cell divisions in Volvox carteri. THE PLANT CELL 2022; 34:1326-1353. [PMID: 35018470 PMCID: PMC9026201 DOI: 10.1093/plcell/koac004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Cell division is fundamental to all organisms and the green alga used here exhibits both key animal and plant functions. Specifically, we analyzed the molecular and cellular dynamics of early embryonic divisions of the multicellular green alga Volvox carteri (Chlamydomonadales). Relevant proteins related to mitosis and cytokinesis were identified in silico, the corresponding genes were cloned, fused to yfp, and stably expressed in Volvox, and the tagged proteins were studied by live-cell imaging. We reveal rearrangements of the microtubule cytoskeleton during centrosome separation, spindle formation, establishment of the phycoplast, and generation of previously unknown structures. The centrosomes participate in initiation of spindle formation and determination of spindle orientation. Although the nuclear envelope does not break down during early mitosis, intermixing of cytoplasm and nucleoplasm results in loss of nuclear identity. Finally, we present a model for mitosis in Volvox. Our study reveals enormous dynamics, clarifies spatio-temporal relationships of subcellular structures, and provides insight into the evolution of cell division.
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Affiliation(s)
- Eva Laura von der Heyde
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Armin Hallmann
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
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10
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Guichard P, Laporte MH, Hamel V. The centriolar tubulin code. Semin Cell Dev Biol 2021; 137:16-25. [PMID: 34896019 DOI: 10.1016/j.semcdb.2021.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 11/25/2022]
Abstract
Centrioles are microtubule-based cell organelles present in most eukaryotes. They participate in the control of cell division as part of the centrosome, the major microtubule-organizing center of the cell, and are also essential for the formation of primary and motile cilia. During centriole assembly as well as across its lifetime, centriolar tubulin display marks defined by post-translational modifications (PTMs), such as glutamylation or acetylation. To date, the functions of these PTMs at centrioles are not well understood, although pioneering experiments suggest a role in the stability of this organelle. Here, we review the current knowledge regarding PTMs at centrioles with a particular focus on a possible link between these modifications and centriole's architecture, and propose possible hypothesis regarding centriolar tubulin PTMs's function.
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Affiliation(s)
- Paul Guichard
- University of Geneva, Department of Cell Biology, Geneva, Switzerland.
| | - Marine H Laporte
- University of Geneva, Department of Cell Biology, Geneva, Switzerland
| | - Virginie Hamel
- University of Geneva, Department of Cell Biology, Geneva, Switzerland.
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11
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The Cilioprotist Cytoskeleton , a Model for Understanding How Cell Architecture and Pattern Are Specified: Recent Discoveries from Ciliates and Comparable Model Systems. Methods Mol Biol 2021; 2364:251-295. [PMID: 34542858 DOI: 10.1007/978-1-0716-1661-1_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
The cytoskeletons of eukaryotic, cilioprotist microorganisms are complex, highly patterned, and diverse, reflecting the varied and elaborate swimming, feeding, reproductive, and sensory behaviors of the multitude of cilioprotist species that inhabit the aquatic environment. In the past 10-20 years, many new discoveries and technologies have helped to advance our understanding of how cytoskeletal organelles are assembled in many different eukaryotic model systems, in relation to the construction and modification of overall cellular architecture and function. Microtubule organizing centers, particularly basal bodies and centrioles, have continued to reveal their central roles in architectural engineering of the eukaryotic cell, including in the cilioprotists. This review calls attention to (1) published resources that illuminate what is known of the cilioprotist cytoskeleton; (2) recent studies on cilioprotists and other model organisms that raise specific questions regarding whether basal body- and centriole-associated nucleic acids, both DNA and RNA, should continue to be considered when seeking to employ cilioprotists as model systems for cytoskeletal research; and (3) new, mainly imaging, technologies that have already proven useful for, but also promise to enhance, future cytoskeletal research on cilioprotists.
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12
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Yamamoto R, Hwang J, Ishikawa T, Kon T, Sale WS. Composition and function of ciliary inner-dynein-arm subunits studied in Chlamydomonas reinhardtii. Cytoskeleton (Hoboken) 2021; 78:77-96. [PMID: 33876572 DOI: 10.1002/cm.21662] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/30/2021] [Accepted: 04/15/2021] [Indexed: 11/09/2022]
Abstract
Motile cilia (also interchangeably called "flagella") are conserved organelles extending from the surface of many animal cells and play essential functions in eukaryotes, including cell motility and environmental sensing. Large motor complexes, the ciliary dyneins, are present on ciliary outer-doublet microtubules and drive movement of cilia. Ciliary dyneins are classified into two general types: the outer dynein arms (ODAs) and the inner dynein arms (IDAs). While ODAs are important for generation of force and regulation of ciliary beat frequency, IDAs are essential for control of the size and shape of the bend, features collectively referred to as waveform. Also, recent studies have revealed unexpected links between IDA components and human diseases. In spite of their importance, studies on IDAs have been difficult since they are very complex and composed for several types of IDA motors, each unique in composition and location in the axoneme. Thanks in part to genetic, biochemical, and structural analysis of Chlamydomonas reinhardtii, we are beginning to understand the organization and function of the ciliary IDAs. In this review, we summarize the composition of Chlamydomonas IDAs particularly focusing on each subunit, and discuss the assembly, conservation, and functional role(s) of these IDA subunits. Furthermore, we raise several additional questions/challenges regarding IDAs, and discuss future perspectives of IDA studies.
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Affiliation(s)
- Ryosuke Yamamoto
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Juyeon Hwang
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Takashi Ishikawa
- Department of Biology and Chemistry, Paul Scherrer Institute, Villigen PSI, Switzerland.,Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Takahide Kon
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Winfield S Sale
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia, USA
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13
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Jana SC. Centrosome structure and biogenesis: Variations on a theme? Semin Cell Dev Biol 2021; 110:123-138. [PMID: 33455859 DOI: 10.1016/j.semcdb.2020.10.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 10/19/2020] [Accepted: 10/29/2020] [Indexed: 12/30/2022]
Abstract
Centrosomes are composed of two orthogonally arranged centrioles surrounded by an electron-dense matrix called the pericentriolar material (PCM). Centrioles are cylinders with diameters of ~250 nm, are several hundred nanometres in length and consist of 9-fold symmetrically arranged microtubules (MT). In dividing animal cells, centrosomes act as the principal MT-organising centres and they also organise actin, which tunes cytoplasmic MT nucleation. In some specialised cells, the centrosome acquires additional critical structures and converts into the base of a cilium with diverse functions including signalling and motility. These structures are found in most eukaryotes and are essential for development and homoeostasis at both cellular and organism levels. The ultrastructure of centrosomes and their derived organelles have been known for more than half a century. However, recent advances in a number of techniques have revealed the high-resolution structures (at Å-to-nm scale resolution) of centrioles and have begun to uncover the molecular principles underlying their properties, including: protein components; structural elements; and biogenesis in various model organisms. This review covers advances in our understanding of the features and processes that are critical for the biogenesis of the evolutionarily conserved structures of the centrosomes. Furthermore, it discusses how variations of these aspects can generate diversity in centrosome structure and function among different species and even between cell types within a multicellular organism.
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Affiliation(s)
- Swadhin Chandra Jana
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal; National Centre for Biological Sciences-TIFR, Bellary Road, 560065 Bangalore, India.
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14
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Wang Z, Beneke T, Gluenz E, Wheeler RJ. The single flagellum of Leishmania has a fixed polarisation of its asymmetric beat. J Cell Sci 2020; 133:133/20/jcs246637. [PMID: 33093230 PMCID: PMC7595685 DOI: 10.1242/jcs.246637] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 09/17/2020] [Indexed: 12/20/2022] Open
Abstract
Eukaryotic flagella undertake different beat types as necessary for different functions; for example, the Leishmania parasite flagellum undergoes a symmetric tip-to-base beat for forward swimming and an asymmetric base-to-tip beat to rotate the cell. In multi-ciliated tissues or organisms, the asymmetric beats are coordinated, leading to movement of the cell, organism or surrounding fluid. This coordination involves a polarisation of power stroke direction. Here, we asked whether the asymmetric beat of the single Leishmania flagellum also has a fixed polarisation. We developed high frame rate dual-colour fluorescence microscopy to visualise flagellar-associated structures in live swimming cells. This showed that the asymmetric Leishmania beat is polarised, with power strokes only occurring in one direction relative to the asymmetric flagellar machinery. Polarisation of bending was retained in deletion mutants whose flagella cannot beat but have a static bend. Furthermore, deletion mutants for proteins required for asymmetric extra-axonemal and rootlet-like flagellum-associated structures also retained normal polarisation. Leishmania beat polarisation therefore likely arises from either the nine-fold rotational symmetry of the axoneme structure or is due to differences between the outer doublet decorations. Highlighted Article: By using high speed, high-resolution fluorescence microscopy of swimming Leishmania cells, we showed that the asymmetric flagellar beat always wafts in the same direction and investigate which structures are involved.
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Affiliation(s)
- Ziyin Wang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Tom Beneke
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Eva Gluenz
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Richard John Wheeler
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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15
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Gateau H, Blanckaert V, Veidl B, Burlet-Schiltz O, Pichereaux C, Gargaros A, Marchand J, Schoefs B. Application of pulsed electric fields for the biocompatible extraction of proteins from the microalga Haematococcus pluvialis. Bioelectrochemistry 2020; 137:107588. [PMID: 33147566 DOI: 10.1016/j.bioelechem.2020.107588] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 12/19/2022]
Abstract
This study aims to employ a pulsed electric field (PEF) treatment for the biocompatible (non-destructive) extraction of proteins from living cells of the green microalga Haematococcus pluvialis. Using a field strength of 1 kV cm-1, we achieved the extraction of 10.2 µg protein per mL of culture, which corresponded to 46% of the total amount of proteins that could be extracted by complete destructive extraction (i.e. the grinding of biomass with glass beads). We found that the extraction yield was not improved by stronger field strengths and was not dependent on the pulse frequency. A biocompatibility index (BI) was defined as the relative abundance of cells that remained alive after the PEF treatment. This index relied on measurements of several physiological parameters after a PEF treatment. It was found that at 1 kV cm-1 that cultures recovered after 72 h. Therefore, these PEF conditions constituted a good compromise between protein extraction efficiency and culture survival. To characterize the PEF treatment further at a molecular level, mass spectrometry-based proteomics analyses of PEF-prepared extracts was used. This led to the identification of 52 electro-extracted proteins. Of these, only 16 proteins were identified when proteins were extracted with PEF at 0.5 cm-1. They belong to core metabolism, stress response and cell movement. Unassigned proteins were also extracted. Their physiological implications and possible utilization in food as alimentary complements are discussed.
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Affiliation(s)
- Hélène Gateau
- Metabolism, Bioengineering of Molecules from Microalgae and Applications (MIMMA), Mer Molécules Santé, IUML - FR 3473 CNRS, Le Mans University, Le Mans, France
| | - Vincent Blanckaert
- Metabolism, Bioengineering of Molecules from Microalgae and Applications (MIMMA), Mer Molécules Santé, IUML - FR 3473 CNRS, IUT de Laval, Le Mans University, Le Mans, France
| | - Brigitte Veidl
- Metabolism, Bioengineering of Molecules from Microalgae and Applications (MIMMA), Mer Molécules Santé, IUML - FR 3473 CNRS, Le Mans University, Le Mans, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse UPS, CNRS, Toulouse, France
| | - Carole Pichereaux
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse UPS, CNRS, Toulouse, France; Fédération de Recherche (FR3450), Agrobiosciences, Interactions et Biodiversité (FRAIB), CNRS, Toulouse, France
| | | | - Justine Marchand
- Metabolism, Bioengineering of Molecules from Microalgae and Applications (MIMMA), Mer Molécules Santé, IUML - FR 3473 CNRS, Le Mans University, Le Mans, France
| | - Benoît Schoefs
- Metabolism, Bioengineering of Molecules from Microalgae and Applications (MIMMA), Mer Molécules Santé, IUML - FR 3473 CNRS, Le Mans University, Le Mans, France.
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16
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Ochi T, Quarantotti V, Lin H, Jullien J, Rosa E Silva I, Boselli F, Barnabas DD, Johnson CM, McLaughlin SH, Freund SMV, Blackford AN, Kimata Y, Goldstein RE, Jackson SP, Blundell TL, Dutcher SK, Gergely F, van Breugel M. CCDC61/VFL3 Is a Paralog of SAS6 and Promotes Ciliary Functions. Structure 2020; 28:674-689.e11. [PMID: 32375023 PMCID: PMC7267773 DOI: 10.1016/j.str.2020.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 02/24/2020] [Accepted: 04/11/2020] [Indexed: 01/08/2023]
Abstract
Centrioles are cylindrical assemblies whose peripheral microtubule array displays a 9-fold rotational symmetry that is established by the scaffolding protein SAS6. Centriole symmetry can be broken by centriole-associated structures, such as the striated fibers in Chlamydomonas that are important for ciliary function. The conserved protein CCDC61/VFL3 is involved in this process, but its exact role is unclear. Here, we show that CCDC61 is a paralog of SAS6. Crystal structures of CCDC61 demonstrate that it contains two homodimerization interfaces that are similar to those found in SAS6, but result in the formation of linear filaments rather than rings. Furthermore, we show that CCDC61 binds microtubules and that residues involved in CCDC61 microtubule binding are important for ciliary function in Chlamydomonas. Together, our findings suggest that CCDC61 and SAS6 functionally diverged from a common ancestor while retaining the ability to scaffold the assembly of basal body-associated structures or centrioles, respectively.
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Affiliation(s)
- Takashi Ochi
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Valentina Quarantotti
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Huawen Lin
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, St Louis, MO 63110, USA
| | - Jerome Jullien
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; CRTI, INSERM, UNIV Nantes, Nantes, France
| | - Ivan Rosa E Silva
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Francesco Boselli
- DAMTP, Centre for Mathematical Sciences, Wilberforce Road, Cambridge CB3 0WA, UK
| | - Deepak D Barnabas
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Christopher M Johnson
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Stephen H McLaughlin
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Stefan M V Freund
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Andrew N Blackford
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Yuu Kimata
- Department of Genetics, University of Cambridge, Cambridge CB4 1AR, UK; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Raymond E Goldstein
- DAMTP, Centre for Mathematical Sciences, Wilberforce Road, Cambridge CB3 0WA, UK
| | - Stephen P Jackson
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Susan K Dutcher
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, St Louis, MO 63110, USA
| | - Fanni Gergely
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Mark van Breugel
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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17
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von der Heyde EL, Hallmann A. Babo1, formerly Vop1 and Cop1/2, is no eyespot photoreceptor but a basal body protein illuminating cell division in Volvox carteri. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:276-298. [PMID: 31778231 DOI: 10.1111/tpj.14623] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/29/2019] [Accepted: 11/19/2019] [Indexed: 06/10/2023]
Abstract
In photosynthetic organisms many processes are light dependent and sensing of light requires light-sensitive proteins. The supposed eyespot photoreceptor protein Babo1 (formerly Vop1) has previously been classified as an opsin due to the capacity for binding retinal. Here, we analyze Babo1 and provide evidence that it is no opsin. Due to the localization at the basal bodies, the former Vop1 and Cop1/2 proteins were renamed V.c. Babo1 and C.r. Babo1. We reveal a large family of more than 60 Babo1-related proteins from a wide range of species. The detailed subcellular localization of fluorescence-tagged Babo1 shows that it accumulates at the basal apparatus. More precisely, it is located predominantly at the basal bodies and to a lesser extent at the four strands of rootlet microtubules. We trace Babo1 during basal body separation and cell division. Dynamic structural rearrangements of Babo1 particularly occur right before the first cell division. In four-celled embryos Babo1 was exclusively found at the oldest basal bodies of the embryo and on the corresponding d-roots. The unequal distribution of Babo1 in four-celled embryos could be an integral part of a geometrical system in early embryogenesis, which establishes the anterior-posterior polarity and influences the spatial arrangement of all embryonic structures and characteristics. Due to its retinal-binding capacity, Babo1 could also be responsible for the unequal distribution of retinoids, knowing that such concentration gradients of retinoids can be essential for the correct patterning during embryogenesis of more complex organisms. Thus, our findings push the Babo1 research in another direction.
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Affiliation(s)
- Eva L von der Heyde
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr 25, 33615, Bielefeld, Germany
| | - Armin Hallmann
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr 25, 33615, Bielefeld, Germany
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18
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Long H, Huang K. Transport of Ciliary Membrane Proteins. Front Cell Dev Biol 2020; 7:381. [PMID: 31998723 PMCID: PMC6970386 DOI: 10.3389/fcell.2019.00381] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 12/17/2019] [Indexed: 12/24/2022] Open
Abstract
Cilia and flagella are highly conserved organelles in eukaryotic cells that drive cell movement and act as cell antennae that receive and transmit signals. In addition to receiving and transducing external signals that activate signal cascades, cilia also secrete ciliary ectosomes that send signals to recipient cells, and thereby mediate cell–cell communication. Abnormal ciliary function leads to various ciliopathies, and the precise transport and localization of ciliary membrane proteins are essential for cilium function. This review summarizes current knowledge about the transport processes of ciliary membrane proteins after their synthesis at the endoplasmic reticulum: modification and sorting in the Golgi apparatus, transport through vesicles to the ciliary base, entrance into cilia through the diffusion barrier, and turnover by ectosome secretion. The molecular mechanisms and regulation involved in each step are also discussed. Transport of ciliary membrane proteins is a complex, precise cellular process coordinated among multiple organelles. By systematically analyzing the existing research, we identify topics that should be further investigated to promote progress in this field of research.
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Affiliation(s)
- Huan Long
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Kaiyao Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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19
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Abstract
Even single-celled eukaryotes are capable of highly complex behaviors. A new study reveals how one unicellular predator actively manipulates and remodels its unique cytoskeletal morphology to achieve rapid shape changes and a remarkable hunting strategy.
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Affiliation(s)
- Kirsty Y Wan
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, UK.
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20
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Keeling PJ. Combining morphology, behaviour and genomics to understand the evolution and ecology of microbial eukaryotes. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190085. [PMID: 31587641 DOI: 10.1098/rstb.2019.0085] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Microbial eukaryotes (protists) are structurally, developmentally and behaviourally more complex than their prokaryotic cousins. This complexity makes it more difficult to translate genomic and metagenomic data into accurate functional inferences about systems ranging all the way from molecular and cellular levels to global ecological networks. This problem can be traced back to the advent of the cytoskeleton and endomembrane systems at the origin of eukaryotes, which endowed them with a range of complex structures and behaviours that still largely dominate how they evolve and interact within microbial communities. But unlike the diverse metabolic properties that evolved within prokaryotes, the structural and behavioural characteristics that strongly define how protists function in the environment cannot readily be inferred from genomic data, since there is generally no simple correlation between a gene and a discrete activity or function. A deeper understanding of protists at both cellular and ecological levels, therefore, requires not only high-throughput genomics but also linking such data to direct observations of natural history and cell biology. This is challenging since these observations typically require cultivation, which is lacking for most protists. Potential remedies with current technology include developing a more phylogenetically diverse range of model systems to better represent the diversity, as well as combining high-throughput, single-cell genomics with microscopic documentation of the subject cells to link sequence with structure and behaviour. This article is part of a discussion meeting issue 'Single cell ecology'.
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Affiliation(s)
- Patrick J Keeling
- Botany Department, University of British Columbia, Vancouver, British Columbia, Canada V6T1Z4
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21
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Nanjundappa R, Kong D, Shim K, Stearns T, Brody SL, Loncarek J, Mahjoub MR. Regulation of cilia abundance in multiciliated cells. eLife 2019; 8:e44039. [PMID: 31025935 PMCID: PMC6504233 DOI: 10.7554/elife.44039] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/25/2019] [Indexed: 12/14/2022] Open
Abstract
Multiciliated cells (MCC) contain hundreds of motile cilia used to propel fluid over their surface. To template these cilia, each MCC produces between 100-600 centrioles by a process termed centriole amplification. Yet, how MCC regulate the precise number of centrioles and cilia remains unknown. Airway progenitor cells contain two parental centrioles (PC) and form structures called deuterosomes that nucleate centrioles during amplification. Using an ex vivo airway culture model, we show that ablation of PC does not perturb deuterosome formation and centriole amplification. In contrast, loss of PC caused an increase in deuterosome and centriole abundance, highlighting the presence of a compensatory mechanism. Quantification of centriole abundance in vitro and in vivo identified a linear relationship between surface area and centriole number. By manipulating cell size, we discovered that centriole number scales with surface area. Our results demonstrate that a cell-intrinsic surface area-dependent mechanism controls centriole and cilia abundance in multiciliated cells.
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Affiliation(s)
- Rashmi Nanjundappa
- Nephrology Division, Department of MedicineWashington UniversitySt LouisUnited States
| | - Dong Kong
- Center for Cancer Research, National Cancer InstituteFrederickUnited States
| | - Kyuhwan Shim
- Nephrology Division, Department of MedicineWashington UniversitySt LouisUnited States
| | - Tim Stearns
- Department of BiologyStanford UniversityStanfordUnited States
| | - Steven L Brody
- Pulmonary Division, Department of MedicineWashington UniversitySt LouisUnited States
| | - Jadranka Loncarek
- Center for Cancer Research, National Cancer InstituteFrederickUnited States
| | - Moe R Mahjoub
- Nephrology Division, Department of MedicineWashington UniversitySt LouisUnited States
- Department of Cell Biology and PhysiologyWashington UniversitySt LouisUnited States
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22
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Sasso S, Stibor H, Mittag M, Grossman AR. From molecular manipulation of domesticated Chlamydomonas reinhardtii to survival in nature. eLife 2018; 7:39233. [PMID: 30382941 PMCID: PMC6211829 DOI: 10.7554/elife.39233] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/12/2018] [Indexed: 01/19/2023] Open
Abstract
In the mid-20th century, the unicellular and genetically tractable green alga Chlamydomonas reinhardtii was first developed as a model organism to elucidate fundamental cellular processes such as photosynthesis, light perception and the structure, function and biogenesis of cilia. Various studies of C. reinhardtii have profoundly advanced plant and cell biology, and have also impacted algal biotechnology and our understanding of human disease. However, the 'real' life of C. reinhardtii in the natural environment has largely been neglected. To extend our understanding of the biology of C. reinhardtii, it will be rewarding to explore its behavior in its natural habitats, learning more about its abundance and life cycle, its genetic and physiological diversity, and its biotic and abiotic interactions.
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Affiliation(s)
- Severin Sasso
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Jena, Germany
| | - Herwig Stibor
- Department Biology II, Ludwig Maximilian University, Munich, Germany
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Jena, Germany
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23
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Gupta A, Kitagawa D. Ultrastructural diversity between centrioles of eukaryotes. J Biochem 2018; 164:1-8. [PMID: 29462371 DOI: 10.1093/jb/mvy031] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/07/2018] [Indexed: 01/05/2023] Open
Abstract
Several decades of centriole research have revealed the beautiful symmetry present in these microtubule-based organelles, which are required to form centrosomes, cilia and flagella in many eukaryotes. Centriole architecture is largely conserved across most organisms; however, individual centriolar features such as the central cartwheel or microtubule walls exhibit considerable variability when examined with finer resolution. In this paper, we review the ultrastructural characteristics of centrioles in commonly studied organisms, highlighting the subtle and not-so-subtle differences between specific structural components of these centrioles. In addition, we survey some non-canonical centriole structures that have been discovered in various species, from the coaxial bicentrioles of protists and lower land plants to the giant irregular centrioles of the fungus gnat Sciara. Finally, we speculate on the functional significance of these differences between centrioles, and the contribution of individual structural elements such as the cartwheel or microtubules towards the stability of centrioles.
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Affiliation(s)
- Akshari Gupta
- Division of Centrosome Biology, Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.,Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan.,Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
| | - Daiju Kitagawa
- Division of Centrosome Biology, Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.,Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan
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24
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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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25
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Atkins KC, Cross FR. Interregulation of CDKA/CDK1 and the Plant-Specific Cyclin-Dependent Kinase CDKB in Control of the Chlamydomonas Cell Cycle. THE PLANT CELL 2018; 30:429-446. [PMID: 29367304 PMCID: PMC5868683 DOI: 10.1105/tpc.17.00759] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 11/17/2017] [Accepted: 01/24/2018] [Indexed: 05/09/2023]
Abstract
The cyclin-dependent kinase CDK1 is essential for mitosis in fungi and animals. Plant genomes contain the CDK1 ortholog CDKA and a plant kingdom-specific relative, CDKB. The green alga Chlamydomonas reinhardtii has a long G1 growth period followed by rapid cycles of DNA replication and cell division. We show that null alleles of CDKA extend the growth period prior to the first division cycle and modestly extend the subsequent division cycles, but do not prevent cell division, indicating at most a minor role for the CDK1 ortholog in mitosis in Chlamydomonas. A null allele of cyclin A has a similar though less extreme phenotype. In contrast, both CDKB and cyclin B are essential for mitosis. CDK kinase activity measurements imply that the predominant in vivo complexes are probably cyclin A-CDKA and cyclin B-CDKB. We propose a negative feedback loop: CDKA activates cyclin B-CDKB. Cyclin B-CDKB in turn promotes mitotic entry and inactivates cyclin A-CDKA. Cyclin A-CDKA and cyclin B-CDKB may redundantly promote DNA replication. We show that the anaphase-promoting complex is required for inactivation of both CDKA and CDKB and is essential for anaphase. These results are consistent with findings in Arabidopsis thaliana and may delineate the core of plant kingdom cell cycle control that, compared with the well-studied yeast and animal systems, exhibits deep conservation in some respects and striking divergence in others.
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26
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Liu Y, Visetsouk M, Mynlieff M, Qin H, Lechtreck KF, Yang P. H +- and Na +- elicited rapid changes of the microtubule cytoskeleton in the biflagellated green alga Chlamydomonas. eLife 2017; 6:26002. [PMID: 28875932 PMCID: PMC5779235 DOI: 10.7554/elife.26002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 09/05/2017] [Indexed: 12/27/2022] Open
Abstract
Although microtubules are known for dynamic instability, the dynamicity is considered to be tightly controlled to support a variety of cellular processes. Yet diverse evidence suggests that this is not applicable to Chlamydomonas, a biflagellate fresh water green alga, but intense autofluorescence from photosynthesis pigments has hindered the investigation. By expressing a bright fluorescent reporter protein at the endogenous level, we demonstrate in real time discreet sweeping changes in algal microtubules elicited by rises of intracellular H+ and Na+. These results from this model organism with characteristics of animal and plant cells provide novel explanations regarding how pH may drive cellular processes; how plants may respond to, and perhaps sense stresses; and how organisms with a similar sensitive cytoskeleton may be susceptible to environmental changes.
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Affiliation(s)
- Yi Liu
- Department of Biological Sciences, Marquette University, Milwaukee, United States
| | - Mike Visetsouk
- Department of Biological Sciences, Marquette University, Milwaukee, United States
| | - Michelle Mynlieff
- Department of Biological Sciences, Marquette University, Milwaukee, United States
| | - Hongmin Qin
- Department of Biology, Texas A&M University, College Station, United States
| | - Karl F Lechtreck
- Department of Cellular Biology, University of Georgia, Athen, United States
| | - Pinfen Yang
- Department of Biological Sciences, Marquette University, Milwaukee, United States
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27
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Aubusson-Fleury A, Balavoine G, Lemullois M, Bouhouche K, Beisson J, Koll F. Centrin diversity and basal body patterning across evolution: new insights from Paramecium. Biol Open 2017; 6:765-776. [PMID: 28432105 PMCID: PMC5483020 DOI: 10.1242/bio.024273] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
First discovered in unicellular eukaryotes, centrins play crucial roles in basal body duplication and anchoring mechanisms. While the evolutionary status of the founding members of the family, Centrin2/Vfl2 and Centrin3/cdc31 has long been investigated, the evolutionary origin of other members of the family has received less attention. Using a phylogeny of ciliate centrins, we identify two other centrin families, the ciliary centrins and the centrins present in the contractile filaments (ICL centrins). In this paper, we carry on the functional analysis of still not well-known centrins, the ICL1e subfamily identified in Paramecium, and show their requirement for correct basal body anchoring through interactions with Centrin2 and Centrin3. Using Paramecium as well as a eukaryote-wide sampling of centrins from completely sequenced genomes, we revisited the evolutionary story of centrins. Their phylogeny shows that the centrins associated with the ciliate contractile filaments are widespread in eukaryotic lineages and could be as ancient as Centrin2 and Centrin3. Summary: Functional and phylogenetic analyses reveal the existence of five centrin families and show that basal body patterning in Paramecium requires a third centrin present in many eukaryote lineages.
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Affiliation(s)
- Anne Aubusson-Fleury
- Institute for Integrative Biology of the Cell (I2BC), Cell Biology Department, CEA, CNRS, Université Paris Sud, Université Paris-Saclay, 1 Avenue de la Terrasse, Gif sur Yvette 91198, France
| | - Guillaume Balavoine
- Institut Jacques Monod, Evolution and development of Metazoa, UMR 7592, CNRS/Université Paris Diderot, 15 rue Hélène Brion, Paris 75013, France
| | - Michel Lemullois
- Institute for Integrative Biology of the Cell (I2BC), Cell Biology Department, CEA, CNRS, Université Paris Sud, Université Paris-Saclay, 1 Avenue de la Terrasse, Gif sur Yvette 91198, France
| | - Khaled Bouhouche
- INRA, UMR 1061 Unité de Génétique Moléculaire Animale, Université de Limoges, IFR 145, Faculté des Sciences et Techniques, Limoges 87060, France
| | - Janine Beisson
- Institute for Integrative Biology of the Cell (I2BC), Cell Biology Department, CEA, CNRS, Université Paris Sud, Université Paris-Saclay, 1 Avenue de la Terrasse, Gif sur Yvette 91198, France
| | - France Koll
- Institute for Integrative Biology of the Cell (I2BC), Cell Biology Department, CEA, CNRS, Université Paris Sud, Université Paris-Saclay, 1 Avenue de la Terrasse, Gif sur Yvette 91198, France
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