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陈 一, 凌 晓, 于 浩, 丁 俊. [Role of Liquid-Liquid Phase Separation in Cell Fate Transition and Diseases]. Sichuan Da Xue Xue Bao Yi Xue Ban 2023; 54:857-862. [PMID: 37866939 PMCID: PMC10579061 DOI: 10.12182/20230960302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Indexed: 10/24/2023]
Abstract
Liquid-liquid phase separation (LLPS), a novel mechanism of the organization and formation of cellular structures, plays a vital role in regulating cell fate transitions and disease pathogenesis and is gaining widespread attention. LLPS may lead to the assemblage of cellular structures with liquid-like fluidity, such as germ granules, stress granules, and nucleoli, which are classic membraneless organelles. These structures are typically formed through the high-concentration liquid aggregation of biomacromolecules driven by weak multivalent interactions. LLPS is involved in regulating various intracellular life activities and its dysregulation may cause the disruption of cellular functions, thereby contributing to the pathogenesis and development of neurodegenerative diseases, infectious diseases, cancers, etc. Herein, we summarized published findings on the LLPS dynamics of membraneless organelles in physiological and pathological cell fate transition, revealing their crucial roles in cell differentiation, development, and various pathogenic processes. This paper provides a fresh theoretical framework and potential therapeutic targets for LLPS-related studies, opening new avenues for future research.
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Affiliation(s)
- 一龙 陈
- 四川大学医学大数据中心 (成都 610041)Medical Big Data Center, Sichuan University, Chengdu 610041, China
- 四川大学华西医院 生物医学大数据中心 (成都 610041)West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China
- 四川大学“医学+信息”中心 (成都 610041)Med-X Center for Informatics, Sichuan University, Chengdu 610041, China
| | - 晓茹 凌
- 四川大学医学大数据中心 (成都 610041)Medical Big Data Center, Sichuan University, Chengdu 610041, China
| | - 浩澎 于
- 四川大学医学大数据中心 (成都 610041)Medical Big Data Center, Sichuan University, Chengdu 610041, China
- 四川大学华西医院 生物医学大数据中心 (成都 610041)West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China
- 四川大学“医学+信息”中心 (成都 610041)Med-X Center for Informatics, Sichuan University, Chengdu 610041, China
| | - 俊军 丁
- 四川大学医学大数据中心 (成都 610041)Medical Big Data Center, Sichuan University, Chengdu 610041, China
- 四川大学华西医院 生物医学大数据中心 (成都 610041)West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China
- 四川大学“医学+信息”中心 (成都 610041)Med-X Center for Informatics, Sichuan University, Chengdu 610041, China
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Miao Y, Guo X, Zhu K, Zhao W. Biomolecular condensates tunes immune signaling at the Host-Pathogen interface. Curr Opin Plant Biol 2023; 74:102374. [PMID: 37148673 DOI: 10.1016/j.pbi.2023.102374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 05/08/2023]
Abstract
Membraneless organelles participate in diverse spatiotemporal regulation of cellular signal transduction by recruiting necessary signaling factors. During host-pathogen interactions, the plasma membrane (PM) at the interface between the plant and microbes serves as a central platform for forming multicomponent immune signaling hubs. The macromolecular condensation of the immune complex and regulators is important in regulating immune signaling outputs regarding strength, timing, and crosstalk between signaling pathways. This review discusses mechanisms that regulate specific and crosstalk of plant immune signal transduction pathways through macromolecular assembly and condensation.
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Affiliation(s)
- Yansong Miao
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore; Institute for Digital Molecular Analytics and Science, Nanyang Technological University, 636921, Singapore.
| | - Xiangfu Guo
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, 637457, Singapore
| | - Kexin Zhu
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Wenting Zhao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, 637457, Singapore; Institute for Digital Molecular Analytics and Science, Nanyang Technological University, 636921, Singapore
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Burrell A, Marugan-Hernandez V, Graefin Von Der Recke K, Aguiar-Martins K, Gabriel HB, Tomley FM, Vaughan S. Refractile bodies of Eimeria tenella are proteinaceous membrane-less organelles that undergo dynamic changes during infection. Front Cell Infect Microbiol 2023; 13:1082622. [PMID: 37033474 PMCID: PMC10081493 DOI: 10.3389/fcimb.2023.1082622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/27/2023] [Indexed: 03/11/2023] Open
Abstract
IntroductionRefractile bodies (RB) are large membrane-less organelles (MLO) of unknown function found as a prominent mismatched pair within the sporozoite stages of all species of Eimeria, parasitic coccidian protozoa.MethodsHigh resolution imaging methods including time-lapse live confocal microscopy and serial block face-scanning electron microscopy (SBF-SEM) were used to investigate the morphology of RB and other intracellular organelles before and after sporozoite invasion of host cells.ResultsLive cell imaging of MDBK cells infected with E. tenella sporozoites confirmed previous reports that RB reduce from two to one post-infection and showed that reduction in RB number occurs via merger of the anterior RB with the posterior RB, a process that lasts 20-40 seconds and takes place between 2- and 5-hours post-infection. Ultrastructural studies using SBF-SEM on whole individual sporozoites, both pre- and post-host cell invasion, confirmed the live cell imaging observations and showed also that changes to the overall sporozoite cell shape accompanied RB merger. Furthermore, the single RB post-merger was found to be larger in volume than the two RB pre-merger. Actin inhibitors were used to investigate a potential role for actin in RB merger, Cytochalasin D significantly inhibited both RB merger and the accompanying changes in sporozoite cell shape.DiscussionMLOs in eukaryotic organisms are characterised by their lack of a membrane and ability to undergo liquid-liquid phase separation (LLPS) and fusion, usually in an actin-mediated fashion. Based on the changes in sporozoite cell shape observed at the time of RB merger together with a potential role for actin in this process, we propose that RB are classed as an MLO and recognised as one of the largest MLOs so far characterised.
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Affiliation(s)
- Alana Burrell
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, North Mymms, United Kingdom
| | - Virginia Marugan-Hernandez
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, North Mymms, United Kingdom
- *Correspondence: Virginia Marugan-Hernandez, ; Sue Vaughan,
| | - Karolin Graefin Von Der Recke
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, North Mymms, United Kingdom
| | - Kelsilandia Aguiar-Martins
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, North Mymms, United Kingdom
| | - Heloisa Berti Gabriel
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Fiona M. Tomley
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, North Mymms, United Kingdom
| | - Sue Vaughan
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
- *Correspondence: Virginia Marugan-Hernandez, ; Sue Vaughan,
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4
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Abstract
One of the grand challenges in cellular biophysics is understanding the precision with which cells assemble and maintain subcellular structures. Organelle sizes, for example, must be flexible enough to allow cells to grow or shrink them as environments demand yet be maintained within homeostatic limits. Despite identification of molecular factors that regulate organelle sizes we lack insight into the quantitative principles underlying organelle size control. Here we show experimentally that cells can robustly control average fluctuations in organelle size. By demonstrating that organelle sizes obey a universal scaling relationship we predict theoretically, our framework suggests that organelles grow in random bursts from a limiting pool of building blocks. Burstlike growth provides a general biophysical mechanism by which cells can maintain on average reliable yet plastic organelle sizes.
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Affiliation(s)
| | - Asa Kalish
- Department of Physics, Washington University in St. Louis
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5
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Colin L, Martin-Arevalillo R, Bovio S, Bauer A, Vernoux T, Caillaud MC, Landrein B, Jaillais Y. Imaging the living plant cell: From probes to quantification. Plant Cell 2022; 34:247-272. [PMID: 34586412 PMCID: PMC8774089 DOI: 10.1093/plcell/koab237] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/20/2021] [Indexed: 05/20/2023]
Abstract
At the center of cell biology is our ability to image the cell and its various components, either in isolation or within an organism. Given its importance, biological imaging has emerged as a field of its own, which is inherently highly interdisciplinary. Indeed, biologists rely on physicists and engineers to build new microscopes and imaging techniques, chemists to develop better imaging probes, and mathematicians and computer scientists for image analysis and quantification. Live imaging collectively involves all the techniques aimed at imaging live samples. It is a rapidly evolving field, with countless new techniques, probes, and dyes being continuously developed. Some of these new methods or reagents are readily amenable to image plant samples, while others are not and require specific modifications for the plant field. Here, we review some recent advances in live imaging of plant cells. In particular, we discuss the solutions that plant biologists use to live image membrane-bound organelles, cytoskeleton components, hormones, and the mechanical properties of cells or tissues. We not only consider the imaging techniques per se, but also how the construction of new fluorescent probes and analysis pipelines are driving the field of plant cell biology.
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Affiliation(s)
- Leia Colin
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, 69342 Lyon, France
| | - Raquel Martin-Arevalillo
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, 69342 Lyon, France
| | - Simone Bovio
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, 69342 Lyon, France
- LYMIC-PLATIM imaging and microscopy core facility, Univ Lyon, SFR Biosciences, ENS de Lyon, Inserm US8, CNRS UMS3444, UCBL-50 Avenue Tony Garnier, 69007 Lyon, France
| | - Amélie Bauer
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, 69342 Lyon, France
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, 69342 Lyon, France
| | - Marie-Cecile Caillaud
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, 69342 Lyon, France
| | - Benoit Landrein
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, 69342 Lyon, France
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Staufer O, De Lora JA, Bailoni E, Bazrafshan A, Benk AS, Jahnke K, Manzer ZA, Otrin L, Díez Pérez T, Sharon J, Steinkühler J, Adamala KP, Jacobson B, Dogterom M, Göpfrich K, Stefanovic D, Atlas SR, Grunze M, Lakin MR, Shreve AP, Spatz JP, López GP. Building a community to engineer synthetic cells and organelles from the bottom-up. eLife 2021; 10:e73556. [PMID: 34927583 PMCID: PMC8716100 DOI: 10.7554/elife.73556] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/17/2021] [Indexed: 12/19/2022] Open
Abstract
Employing concepts from physics, chemistry and bioengineering, 'learning-by-building' approaches are becoming increasingly popular in the life sciences, especially with researchers who are attempting to engineer cellular life from scratch. The SynCell2020/21 conference brought together researchers from different disciplines to highlight progress in this field, including areas where synthetic cells are having socioeconomic and technological impact. Conference participants also identified the challenges involved in designing, manipulating and creating synthetic cells with hierarchical organization and function. A key conclusion is the need to build an international and interdisciplinary research community through enhanced communication, resource-sharing, and educational initiatives.
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Affiliation(s)
- Oskar Staufer
- Max Planck Institute for Medical ResearchHeidelbergGermany
- Max Planck School Matter to LifeHeidelbergGermany
- Max Planck Bristol Center for Minimal Biology, University of BristolBristolUnited Kingdom
| | | | | | | | - Amelie S Benk
- Max Planck Institute for Medical ResearchHeidelbergGermany
| | - Kevin Jahnke
- Max Planck Institute for Medical ResearchHeidelbergGermany
| | | | - Lado Otrin
- Max Planck Institute for Dynamics of Complex Technical SystemsMagdeburgGermany
| | | | | | | | | | | | | | - Kerstin Göpfrich
- Max Planck Institute for Medical ResearchHeidelbergGermany
- Max Planck School Matter to LifeHeidelbergGermany
| | | | | | - Michael Grunze
- Max Planck Institute for Medical ResearchHeidelbergGermany
- Max Planck School Matter to LifeHeidelbergGermany
| | | | | | - Joachim P Spatz
- Max Planck Institute for Medical ResearchHeidelbergGermany
- Max Planck School Matter to LifeHeidelbergGermany
- Max Planck Bristol Center for Minimal Biology, University of BristolBristolUnited Kingdom
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Abstract
Conventional thermal biology has elucidated the physiological function of temperature homeostasis through spontaneous thermogenesis and responses to variations in environmental temperature in organisms. In addition to research on individual physiological phenomena, the molecular mechanisms of fever and physiological events such as temperature-dependent sex determination have been intensively addressed. Thermosensitive biomacromolecules such as heat shock proteins (HSPs) and transient receptor potential (TRP) channels were systematically identified, and their sophisticated functions were clarified. Complementarily, recent progress in intracellular thermometry has opened new research fields in thermal biology. High-resolution intracellular temperature mapping has uncovered thermogenic organelles, and the thermogenic functions of brown adipocytes were ascertained by the combination of intracellular thermometry and classic molecular biology. In addition, intracellular thermometry has introduced a new concept, "thermal signaling", in which temperature variation within biological cells acts as a signal in a cascade of intriguing biological events.
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Affiliation(s)
- Kohki Okabe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
- JST, PRESTO, Saitama, Japan.
| | - Seiichi Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
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8
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Galotto G, Wisanpitayakorn P, Bibeau JP, Liu YC, Furt F, Pierce EC, Simpson PJ, Tüzel E, Vidali L. Myosin XI drives polarized growth by vesicle focusing and local enrichment of F-actin in Physcomitrium patens. Plant Physiol 2021; 187:2509-2529. [PMID: 34890463 PMCID: PMC8932395 DOI: 10.1093/plphys/kiab435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/13/2021] [Indexed: 05/22/2023]
Abstract
In tip-growing plant cells, growth results from myosin XI and F-actin-mediated deposition of cell wall polysaccharides contained in secretory vesicles. Previous evidence showed that myosin XI anticipates F-actin accumulation at the cell's tip, suggesting a mechanism where vesicle clustering via myosin XI increases F-actin polymerization. To evaluate this model, we used a conditional loss-of-function strategy by generating moss (Physcomitrium patens) plants harboring a myosin XI temperature-sensitive allele. We found that loss of myosin XI function alters tip cell morphology, vacuolar homeostasis, and cell viability but not following F-actin depolymerization. Importantly, our conditional loss-of-function analysis shows that myosin XI focuses and directs vesicles at the tip of the cell, which induces formin-dependent F-actin polymerization, increasing F-actin's local concentration. Our findings support the role of myosin XI in vesicle focusing, possibly via clustering and F-actin organization, necessary for tip growth, and deepen our understanding of additional myosin XI functions.
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Affiliation(s)
- Giulia Galotto
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, USA
| | | | - Jeffrey P Bibeau
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, USA
| | - Yen-Chun Liu
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, USA
| | - Fabienne Furt
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, USA
| | - Ellen C Pierce
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, USA
| | - Parker J Simpson
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, USA
| | - Erkan Tüzel
- Bioengineering Department, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Luis Vidali
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, USA
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, USA
- Author for communication:
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9
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Sołtys K, Ożyhar A. Transcription Regulators and Membraneless Organelles Challenges to Investigate Them. Int J Mol Sci 2021; 22:12758. [PMID: 34884563 PMCID: PMC8657783 DOI: 10.3390/ijms222312758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/19/2021] [Accepted: 11/23/2021] [Indexed: 12/13/2022] Open
Abstract
Eukaryotic cells are composed of different bio-macromolecules that are divided into compartments called organelles providing optimal microenvironments for many cellular processes. A specific type of organelles is membraneless organelles. They are formed via a process called liquid-liquid phase separation that is driven by weak multivalent interactions between particular bio-macromolecules. In this review, we gather crucial information regarding different classes of transcription regulators with the propensity to undergo liquid-liquid phase separation and stress the role of intrinsically disordered regions in this phenomenon. We also discuss recently developed experimental systems for studying formation and properties of membraneless organelles.
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Affiliation(s)
- Katarzyna Sołtys
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland;
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10
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Tesei G, Schulze TK, Crehuet R, Lindorff-Larsen K. Accurate model of liquid-liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties. Proc Natl Acad Sci U S A 2021; 118:2111696118. [PMID: 34716273 DOI: 10.1101/2021.06.23.449550] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/15/2021] [Indexed: 05/25/2023] Open
Abstract
Many intrinsically disordered proteins (IDPs) may undergo liquid-liquid phase separation (LLPS) and participate in the formation of membraneless organelles in the cell, thereby contributing to the regulation and compartmentalization of intracellular biochemical reactions. The phase behavior of IDPs is sequence dependent, and its investigation through molecular simulations requires protein models that combine computational efficiency with an accurate description of intramolecular and intermolecular interactions. We developed a general coarse-grained model of IDPs, with residue-level detail, based on an extensive set of experimental data on single-chain properties. Ensemble-averaged experimental observables are predicted from molecular simulations, and a data-driven parameter-learning procedure is used to identify the residue-specific model parameters that minimize the discrepancy between predictions and experiments. The model accurately reproduces the experimentally observed conformational propensities of a set of IDPs. Through two-body as well as large-scale molecular simulations, we show that the optimization of the intramolecular interactions results in improved predictions of protein self-association and LLPS.
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Affiliation(s)
- Giulio Tesei
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark;
| | - Thea K Schulze
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Ramon Crehuet
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
- CSIC-Institute for Advanced Chemistry of Catalonia (IQAC), E-08034 Barcelona, Spain
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark;
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11
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Tesei G, Schulze TK, Crehuet R, Lindorff-Larsen K. Accurate model of liquid-liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties. Proc Natl Acad Sci U S A 2021; 118:e2111696118. [PMID: 34716273 PMCID: PMC8612223 DOI: 10.1073/pnas.2111696118] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/15/2021] [Indexed: 11/18/2022] Open
Abstract
Many intrinsically disordered proteins (IDPs) may undergo liquid-liquid phase separation (LLPS) and participate in the formation of membraneless organelles in the cell, thereby contributing to the regulation and compartmentalization of intracellular biochemical reactions. The phase behavior of IDPs is sequence dependent, and its investigation through molecular simulations requires protein models that combine computational efficiency with an accurate description of intramolecular and intermolecular interactions. We developed a general coarse-grained model of IDPs, with residue-level detail, based on an extensive set of experimental data on single-chain properties. Ensemble-averaged experimental observables are predicted from molecular simulations, and a data-driven parameter-learning procedure is used to identify the residue-specific model parameters that minimize the discrepancy between predictions and experiments. The model accurately reproduces the experimentally observed conformational propensities of a set of IDPs. Through two-body as well as large-scale molecular simulations, we show that the optimization of the intramolecular interactions results in improved predictions of protein self-association and LLPS.
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Affiliation(s)
- Giulio Tesei
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark;
| | - Thea K Schulze
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Ramon Crehuet
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
- CSIC-Institute for Advanced Chemistry of Catalonia (IQAC), E-08034 Barcelona, Spain
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark;
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12
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Shi Y, Zou X, Wen S, Gao L, Li J, Han J, Han S. An organelle-directed chemical ligation approach enables dual-color detection of mitophagy. Autophagy 2021; 17:3475-3490. [PMID: 33435798 PMCID: PMC8632332 DOI: 10.1080/15548627.2021.1875597] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 01/08/2021] [Indexed: 12/22/2022] Open
Abstract
Dysfunctional organelles and defective turnover of organelles are engaged in multiple human diseases, but are elusive to image with conventional organelle probes. To overcome this, we developed intra-mitochondrial CLICK to assess mitophagy (IMCLAM), using a pair of conventional ΔΨm probes, where each probe alone fails to track dysfunctional mitochondria. The in situ formed optical triad is stably trapped in mitochondria without resorting to ΔΨm. Utilizing an acidity-responsive ΔΨm probe, IMCLAM enabled fluorescence-on detection of mitophagy by sensing pH acidification upon delivery of mitochondria into lysosomes. Moreover, we applied IMCLAM to assay mitophagy induced by pharmacological compounds in living cells and wild-type zebrafish embryos. Thus, IMCLAM offers a simplified tool to study mitochondria and mitophagy and provide a basis for screening mitophagy-inducing compounds. Abbreviations: CCCP, carbonyl cyanide m-chlorophenylhydrazone; IMCLAM, intra-mitochondrial CLICK to assess mitophagy; ROX, X-rhodamine; SPAAC, stain-promoted azide-alkyne Click Chemistry; TPP, triphenylphosphonium.
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Affiliation(s)
- Yilong Shi
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiaoxue Zou
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, the Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory for Physical Chemistry of Solid Surfaces, the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Xiamen University, Xiamen, China
| | - Shixiong Wen
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Lei Gao
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, the Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory for Physical Chemistry of Solid Surfaces, the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Xiamen University, Xiamen, China
| | - Jian Li
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, the Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory for Physical Chemistry of Solid Surfaces, the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Xiamen University, Xiamen, China
| | - Jiahuai Han
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shoufa Han
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, the Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory for Physical Chemistry of Solid Surfaces, the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Xiamen University, Xiamen, China
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Ryan F, Khoshnam SE, Khodagholi F, Ashabi G, Ahmadiani A. How cytosolic compartments play safeguard functions against neuroinflammation and cell death in cerebral ischemia. Metab Brain Dis 2021; 36:1445-1467. [PMID: 34173922 DOI: 10.1007/s11011-021-00770-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 06/06/2021] [Indexed: 11/26/2022]
Abstract
Ischemic stroke is the second leading cause of mortality and disability globally. Neuronal damage following ischemic stroke is rapid and irreversible, and eventually results in neuronal death. In addition to activation of cell death signaling, neuroinflammation is also considered as another pathogenesis that can occur within hours after cerebral ischemia. Under physiological conditions, subcellular organelles play a substantial role in neuronal functionality and viability. However, their functions can be remarkably perturbed under neurological disorders, particularly cerebral ischemia. Therefore, their biochemical and structural response has a determining role in the sequel of neuronal cells and the progression of disease. However, their effects on cell death and neuroinflammation, as major underlying mechanisms of ischemic stroke, are still not understood. This review aims to provide a comprehensive overview of the contribution of each organelle on these pathological processes after ischemic stroke.
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Affiliation(s)
- Fari Ryan
- Centre for Research in Neuroscience, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Seyed Esmaeil Khoshnam
- Persian Gulf Physiology Research Centre, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Fariba Khodagholi
- Neuroscience Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ghorbangol Ashabi
- Department of Physiology, Faculty of Medicine, Tehran University of Medical Sciences, PO Box: 1417613151, Tehran, Iran.
| | - Abolhassan Ahmadiani
- Neuroscience Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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14
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Abstract
Circadian clocks have evolved in most light-sensitive organisms, from unicellular organisms to mammals. Consequently, a myriad of biological functions exhibits circadian rhythmicity, from behavior to physiology, through tissue and cellular functions to subcellular processes. Circadian rhythms in intracellular organelles are an emerging and exciting research arena. We summarize herein the current literature for rhythmicity in major intracellular organelles in mammals. These include changes in the morphology, content, and functions of different intracellular organelles. While these data highlight the presence of rhythmicity in these organelles, a gap remains in our knowledge regarding the underlying molecular mechanisms and their functional significance. Finally, we discuss the importance and challenges faced by spatio-temporal studies on these organelles and speculate on the presence of oscillators in organelles and their potential mode of communication. As circadian biology has been and continues to be studied throughout temporal and spatial axes, circadian organelles appear to be the next frontier.
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Affiliation(s)
| | | | - Gad Asher
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel; (R.A.); (Y.A.)
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15
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Figon F, Hurbain I, Heiligenstein X, Trépout S, Lanoue A, Medjoubi K, Somogyi A, Delevoye C, Raposo G, Casas J. Catabolism of lysosome-related organelles in color-changing spiders supports intracellular turnover of pigments. Proc Natl Acad Sci U S A 2021; 118:e2103020118. [PMID: 34433668 PMCID: PMC8536372 DOI: 10.1073/pnas.2103020118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pigment organelles of vertebrates belong to the lysosome-related organelle (LRO) family, of which melanin-producing melanosomes are the prototypes. While their anabolism has been extensively unraveled through the study of melanosomes in skin melanocytes, their catabolism remains poorly known. Here, we tap into the unique ability of crab spiders to reversibly change body coloration to examine the catabolism of their pigment organelles. By combining ultrastructural and metal analyses on high-pressure frozen integuments, we first assess whether pigment organelles of crab spiders belong to the LRO family and second, how their catabolism is intracellularly processed. Using scanning transmission electron microscopy, electron tomography, and nanoscale Synchrotron-based scanning X-ray fluorescence, we show that pigment organelles possess ultrastructural and chemical hallmarks of LROs, including intraluminal vesicles and metal deposits, similar to melanosomes. Monitoring ultrastructural changes during bleaching suggests that the catabolism of pigment organelles involves the degradation and removal of their intraluminal content, possibly through lysosomal mechanisms. In contrast to skin melanosomes, anabolism and catabolism of pigments proceed within the same cell without requiring either cell death or secretion/phagocytosis. Our work hence provides support for the hypothesis that the endolysosomal system is fully functionalized for within-cell turnover of pigments, leading to functional maintenance under adverse conditions and phenotypic plasticity. First formulated for eye melanosomes in the context of human vision, the hypothesis of intracellular turnover of pigments gets unprecedented strong support from pigment organelles of spiders.
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Affiliation(s)
- Florent Figon
- Institut de Recherche sur la Biologie de l'Insecte, CNRS UMR 7261, Université de Tours, 37200 Tours, France;
| | - Ilse Hurbain
- Institut Curie, CNRS UMR 144, Structure and Membrane Compartments, Paris Sciences & Lettres (PSL) Research University, 75005 Paris, France
- Institut Curie, CNRS UMR 144, Cell and Tissue Imaging Facility (Plateforme d'Imagerie Cellulaire et Tissulaire, Infrastructures en Biologie, Santé et Agronomie [PICT-IBiSA]), PSL Research University, 75005 Paris, France
| | | | - Sylvain Trépout
- Institut Curie, INSERM U1196, CNRS UMR 9187, Université Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Arnaud Lanoue
- Biomolécules et Biotechnologies Végétales, Équipe d'Accueil 2106, Université de Tours, 37200 Tours, France
| | | | | | - Cédric Delevoye
- Institut Curie, CNRS UMR 144, Structure and Membrane Compartments, Paris Sciences & Lettres (PSL) Research University, 75005 Paris, France
- Institut Curie, CNRS UMR 144, Cell and Tissue Imaging Facility (Plateforme d'Imagerie Cellulaire et Tissulaire, Infrastructures en Biologie, Santé et Agronomie [PICT-IBiSA]), PSL Research University, 75005 Paris, France
| | - Graça Raposo
- Institut Curie, CNRS UMR 144, Structure and Membrane Compartments, Paris Sciences & Lettres (PSL) Research University, 75005 Paris, France
- Institut Curie, CNRS UMR 144, Cell and Tissue Imaging Facility (Plateforme d'Imagerie Cellulaire et Tissulaire, Infrastructures en Biologie, Santé et Agronomie [PICT-IBiSA]), PSL Research University, 75005 Paris, France
| | - Jérôme Casas
- Institut de Recherche sur la Biologie de l'Insecte, CNRS UMR 7261, Université de Tours, 37200 Tours, France;
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16
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Edwards DM, Røyrvik EC, Chustecki JM, Giannakis K, Glastad RC, Radzvilavicius AL, Johnston IG. Avoiding organelle mutational meltdown across eukaryotes with or without a germline bottleneck. PLoS Biol 2021; 19:e3001153. [PMID: 33891583 PMCID: PMC8064548 DOI: 10.1371/journal.pbio.3001153] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/23/2021] [Indexed: 11/25/2022] Open
Abstract
Mitochondrial DNA (mtDNA) and plastid DNA (ptDNA) encode vital bioenergetic apparatus, and mutations in these organelle DNA (oDNA) molecules can be devastating. In the germline of several animals, a genetic “bottleneck” increases cell-to-cell variance in mtDNA heteroplasmy, allowing purifying selection to act to maintain low proportions of mutant mtDNA. However, most eukaryotes do not sequester a germline early in development, and even the animal bottleneck remains poorly understood. How then do eukaryotic organelles avoid Muller’s ratchet—the gradual buildup of deleterious oDNA mutations? Here, we construct a comprehensive and predictive genetic model, quantitatively describing how different mechanisms segregate and decrease oDNA damage across eukaryotes. We apply this comprehensive theory to characterise the animal bottleneck with recent single-cell observations in diverse mouse models. Further, we show that gene conversion is a particularly powerful mechanism to increase beneficial cell-to-cell variance without depleting oDNA copy number, explaining the benefit of observed oDNA recombination in diverse organisms which do not sequester animal-like germlines (for example, sponges, corals, fungi, and plants). Genomic, transcriptomic, and structural datasets across eukaryotes support this mechanism for generating beneficial variance without a germline bottleneck. This framework explains puzzling oDNA differences across taxa, suggesting how Muller’s ratchet is avoided in different eukaryotes. A comprehensive model for mitochondrial and plasmid DNA segregation, supported by with genomic, transcriptomic, and single-cell data, shows how the attritional effects of Muller’s ratchet can be avoided in the organelles of diverse eukaryotes.
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Affiliation(s)
| | | | | | | | | | | | - Iain G. Johnston
- Department of Mathematics, University of Bergen, Norway
- Computational Biology Unit, University of Bergen, Norway
- * E-mail:
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17
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Tang Y, Mu A, Zhang Y, Zhou S, Wang W, Lai Y, Zhou X, Liu F, Yang X, Gong H, Wang Q, Rao Z. Cryo-EM structure of Mycobacterium smegmatis DyP-loaded encapsulin. Proc Natl Acad Sci U S A 2021; 118:e2025658118. [PMID: 33853951 PMCID: PMC8072242 DOI: 10.1073/pnas.2025658118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Encapsulins containing dye-decolorizing peroxidase (DyP)-type peroxidases are ubiquitous among prokaryotes, protecting cells against oxidative stress. However, little is known about how they interact and function. Here, we have isolated a native cargo-packaging encapsulin from Mycobacterium smegmatis and determined its complete high-resolution structure by cryogenic electron microscopy (cryo-EM). This encapsulin comprises an icosahedral shell and a dodecameric DyP cargo. The dodecameric DyP consists of two hexamers with a twofold axis of symmetry and stretches across the interior of the encapsulin. Our results reveal that the encapsulin shell plays a role in stabilizing the dodecameric DyP. Furthermore, we have proposed a potential mechanism for removing the hydrogen peroxide based on the structural features. Our study also suggests that the DyP is the primary cargo protein of mycobacterial encapsulins and is a potential target for antituberculosis drug discovery.
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Affiliation(s)
- Yanting Tang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300353 Tianjin, China
| | - An Mu
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Yuying Zhang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300353 Tianjin, China
| | - Shan Zhou
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, 300071 Tianjin, China
| | - Weiwei Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Yuezheng Lai
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300353 Tianjin, China
| | - Xiaoting Zhou
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Fengjiang Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Hongri Gong
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300353 Tianjin, China;
| | - Quan Wang
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China;
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300353 Tianjin, China
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, 300071 Tianjin, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
- Laboratory of Structural Biology, Tsinghua University, 100084 Beijing, China
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18
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Abstract
Our cells are comprised of billions of proteins, lipids, and other small molecules packed into their respective subcellular organelles, with the daunting task of maintaining cellular homeostasis over a lifetime. However, it is becoming increasingly evident that organelles do not act as autonomous discrete units but rather as interconnected hubs that engage in extensive communication through membrane contacts. In the last few years, our understanding of how these contacts coordinate organelle function has redefined our view of the cell. This review aims to present novel findings on the cellular interorganelle communication network and how its dysfunction may contribute to aging and neurodegeneration. The consequences of disturbed interorganellar communication are intimately linked with age-related pathologies. Given that both aging and neurodegenerative diseases are characterized by the concomitant failure of multiple cellular pathways, coordination of organelle communication and function could represent an emerging regulatory mechanism critical for long-term cellular homeostasis. We anticipate that defining the relationships between interorganelle communication, aging, and neurodegeneration will open new avenues for therapeutics.
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Affiliation(s)
- Maja Petkovic
- Department of Physiology, University of California at San Francisco, San Francisco, California 94158, USA
| | - Caitlin E O'Brien
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94158, USA
| | - Yuh Nung Jan
- Department of Physiology, University of California at San Francisco, San Francisco, California 94158, USA
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94158, USA
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA
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19
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Hayashi Y, Ford LK, Fioriti L, McGurk L, Zhang M. Liquid-Liquid Phase Separation in Physiology and Pathophysiology of the Nervous System. J Neurosci 2021; 41:834-844. [PMID: 33472825 PMCID: PMC7880275 DOI: 10.1523/jneurosci.1656-20.2020] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022] Open
Abstract
Molecules within cells are segregated into functional domains to form various organelles. While some of those organelles are delimited by lipid membranes demarcating their constituents, others lack a membrane enclosure. Recently, liquid-liquid phase separation (LLPS) revolutionized our view of how segregation of macromolecules can produce membraneless organelles. While the concept of LLPS has been well studied in the areas of soft matter physics and polymer chemistry, its significance has only recently been recognized in the field of biology. It occurs typically between macromolecules that have multivalent interactions. Interestingly, these features are present in many molecules that exert key functions within neurons. In this review, we cover recent topics of LLPS in different contexts of neuronal physiology and pathology.
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Affiliation(s)
- Yasunori Hayashi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Lenzie K Ford
- Zuckerman Mind, Brain, Behavior Institute, Columbia University, New York, New York 10027
| | - Luana Fioriti
- Department of Neuroscience, Mario Negri Institute for Pharmacological Research, Istituto Di Ricovero e Cura a Carattere Scientifico, Milan 20156, Italy
| | - Leeanne McGurk
- Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Mingjie Zhang
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
- School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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20
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Farhat S, Le P, Kayal E, Noel B, Bigeard E, Corre E, Maumus F, Florent I, Alberti A, Aury JM, Barbeyron T, Cai R, Da Silva C, Istace B, Labadie K, Marie D, Mercier J, Rukwavu T, Szymczak J, Tonon T, Alves-de-Souza C, Rouzé P, Van de Peer Y, Wincker P, Rombauts S, Porcel BM, Guillou L. Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp. BMC Biol 2021; 19:1. [PMID: 33407428 PMCID: PMC7789003 DOI: 10.1186/s12915-020-00927-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 11/12/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Dinoflagellates are aquatic protists particularly widespread in the oceans worldwide. Some are responsible for toxic blooms while others live in symbiotic relationships, either as mutualistic symbionts in corals or as parasites infecting other protists and animals. Dinoflagellates harbor atypically large genomes (~ 3 to 250 Gb), with gene organization and gene expression patterns very different from closely related apicomplexan parasites. Here we sequenced and analyzed the genomes of two early-diverging and co-occurring parasitic dinoflagellate Amoebophrya strains, to shed light on the emergence of such atypical genomic features, dinoflagellate evolution, and host specialization. RESULTS We sequenced, assembled, and annotated high-quality genomes for two Amoebophrya strains (A25 and A120), using a combination of Illumina paired-end short-read and Oxford Nanopore Technology (ONT) MinION long-read sequencing approaches. We found a small number of transposable elements, along with short introns and intergenic regions, and a limited number of gene families, together contribute to the compactness of the Amoebophrya genomes, a feature potentially linked with parasitism. While the majority of Amoebophrya proteins (63.7% of A25 and 59.3% of A120) had no functional assignment, we found many orthologs shared with Dinophyceae. Our analyses revealed a strong tendency for genes encoded by unidirectional clusters and high levels of synteny conservation between the two genomes despite low interspecific protein sequence similarity, suggesting rapid protein evolution. Most strikingly, we identified a large portion of non-canonical introns, including repeated introns, displaying a broad variability of associated splicing motifs never observed among eukaryotes. Those introner elements appear to have the capacity to spread over their respective genomes in a manner similar to transposable elements. Finally, we confirmed the reduction of organelles observed in Amoebophrya spp., i.e., loss of the plastid, potential loss of a mitochondrial genome and functions. CONCLUSION These results expand the range of atypical genome features found in basal dinoflagellates and raise questions regarding speciation and the evolutionary mechanisms at play while parastitism was selected for in this particular unicellular lineage.
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Affiliation(s)
- Sarah Farhat
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, 11794, USA
| | - Phuong Le
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ehsan Kayal
- Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Estelle Bigeard
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Erwan Corre
- Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Isabelle Florent
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR7245), Muséum national d'Histoire naturelle, CNRS, CP 52, 57 rue Cuvier, 75005, Paris, France
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Tristan Barbeyron
- Sorbonne Université, CNRS, UMR 8227, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Ruibo Cai
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Benjamin Istace
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Dominique Marie
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Jonathan Mercier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Tsinda Rukwavu
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jeremy Szymczak
- Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Thierry Tonon
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Catharina Alves-de-Souza
- Algal Resources Collection, MARBIONC, Center for Marine Sciences, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, USA
| | - Pierre Rouzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Betina M Porcel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France.
| | - Laure Guillou
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France.
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21
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Abstract
Complex inter-bacterial interactions largely influence the structure and function of the gut microbial community. Though several host-associated phenomena have often been shown to be involved in the stability, structure, and function of the gut microbial community, the implication of contact-dependent and contact-independent inter-bacterial interactions has been overlooked. Such interactions are tightly governed at multiple layers through several extracellular organelles, including contact-dependent inhibition (CDI), nanotubes, type VI secretion system (T6SS), and membrane vesicles (MVs). Recent advancements in molecular techniques have revealed that such extracellular organelles function beyond exhibiting competitive behavior and are also involved in manifesting cooperative behaviors. Cooperation between bacteria occurs through the sharing of several beneficial molecules including nucleic acids, proteins, metabolites, and nutrients among the members of the community, while competition occurs by means of multiple toxins. Intrinsic coordination between contact-dependent and contact-independent mechanisms collectively provides a fitness advantage and increased colonization resistance to the gut microbiota, where molecular trafficking plays a key role. This review is intended to provide a comprehensive view of the salient features of the different bacterial interactions and to highlight how microbiota deploy multifaceted organelles, for exerting both cooperative and competitive behaviors. We discuss the current knowledge of bacterial molecular trafficking and its impact on shaping the gut microbial community.
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Affiliation(s)
- Seenivasan Boopathi
- School of Life and Pharmaceutical Sciences, Key Laboratory of Tropical Biological Resources of Ministry Education, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Danrui Liu
- School of Life and Pharmaceutical Sciences, Key Laboratory of Tropical Biological Resources of Ministry Education, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Ai-Qun Jia
- School of Life and Pharmaceutical Sciences, Key Laboratory of Tropical Biological Resources of Ministry Education, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
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22
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Abstract
High quality transmission electron micrographs have played a major role in shaping our views on organelles in plant cells. However, these snapshots of dead, fixed and sectioned tissue do not automatically convey an appreciation of the dynamic nature of organelles in living cells. Advances in the imaging of subcellular structures in living cells using multicoloured, targeted fluorescent proteins reveal considerable changes in organelle pleomorphy that might be limited to small regions of the cell. The fresh data and insights also challenge several existing ideas on organelle behaviour and interactivity. Here, using succinct examples from plastids, mitochondria, peroxisomes, and the endoplasmic reticulum I present an evolving view of subcellular dynamics in the plant cell.
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Affiliation(s)
- Jaideep Mathur
- Laboratory of Plant Development and Interactions, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road, Guelph, Ontario, N1G2W1, Canada
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23
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Wang X, Sheng X, Tian X, Zhang Y, Li Y. Organelle movement and apical accumulation of secretory vesicles in pollen tubes of Arabidopsis thaliana depend on class XI myosins. Plant J 2020; 104:1685-1697. [PMID: 33067901 DOI: 10.1111/tpj.15030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 09/12/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
F-actin and myosin XI play important roles in plant organelle movement. A few myosin XI genes in the genome of Arabidopsis are mainly expressed in mature pollen, which suggests that they may play a crucial role in pollen germination and pollen tube tip growth. In this study, a genetic complementation assay was conducted in a myosin xi-c (myo11c1) myosin xi-e (myo11c2) double mutant, and fluorescence labeling combined with microscopic observation was applied. We found that myosin XI-E (Myo11C2)-green fluorescent protein (GFP) restored the slow pollen tube growth and seed deficiency phenotypes of the myo11c1 myo11c2 double mutant and Myo11C2-GFP partially colocalized with mitochondria, peroxisomes and Golgi stacks. Furthermore, decreased mitochondrial movement and subapical accumulation were detected in myo11c1 myo11c2 double mutant pollen tubes. Fluorescence recovery after photobleaching experiments showed that the fluorescence recoveries of GFP-RabA4d and AtPRK1-GFP at the pollen tube tip of the myo11c1 myo11c2 double mutant were lower than those of the wild type were after photobleaching. These results suggest that Myo11C2 may be associated with mitochondria, peroxisomes and Golgi stacks, and play a crucial role in organelle movement and apical accumulation of secretory vesicles in pollen tubes of Arabidopsis thaliana.
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Affiliation(s)
- Xingjuan Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiaojing Sheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiulin Tian
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yu Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yan Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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24
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Abstract
Biological macromolecules have intricate structures that underpin their biological functions. Understanding their structure-function relationships remains a challenge due to their structural complexity and functional variability. Although de Rham-Hodge theory, a landmark of twentieth-century mathematics, has had a tremendous impact on mathematics and physics, it has not been devised for macromolecular modeling and analysis. In this work, we introduce de Rham-Hodge theory as a unified paradigm for analyzing the geometry, topology, flexibility, and Hodge mode analysis of biological macromolecules. Geometric characteristics and topological invariants are obtained either from the Helmholtz-Hodge decomposition of the scalar, vector, and/or tensor fields of a macromolecule or from the spectral analysis of various Laplace-de Rham operators defined on the molecular manifolds. We propose Laplace-de Rham spectral-based models for predicting macromolecular flexibility. We further construct a Laplace-de Rham-Helfrich operator for revealing cryo-EM natural frequencies. Extensive experiments are carried out to demonstrate that the proposed de Rham-Hodge paradigm is one of the most versatile tools for the multiscale modeling and analysis of biological macromolecules and subcellular organelles. Accurate, reliable, and topological structure-preserving algorithms for implementing discrete exterior calculus (DEC) have been developed to facilitate the aforementioned modeling and analysis of biological macromolecules. The proposed de Rham-Hodge paradigm has potential applications to subcellular organelles and the structure construction from medium- or low-resolution cryo-EM maps, and functional predictions from massive biomolecular datasets.
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Affiliation(s)
- Rundong Zhao
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA
| | - Menglun Wang
- Department of Mathematics, Michigan State University, East Lansing, MI, 48824, USA
| | - Jiahui Chen
- Department of Mathematics, Michigan State University, East Lansing, MI, 48824, USA
| | - Yiying Tong
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA.
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
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25
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Chen YS, Lian WS, Kuo CW, Ke HJ, Wang SY, Kuo PC, Jahr H, Wang FS. Epigenetic Regulation of Skeletal Tissue Integrity and Osteoporosis Development. Int J Mol Sci 2020; 21:ijms21144923. [PMID: 32664681 PMCID: PMC7404082 DOI: 10.3390/ijms21144923] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/09/2020] [Accepted: 07/09/2020] [Indexed: 12/22/2022] Open
Abstract
Bone turnover is sophisticatedly balanced by a dynamic coupling of bone formation and resorption at various rates. The orchestration of this continuous remodeling of the skeleton further affects other skeletal tissues through organ crosstalk. Chronic excessive bone resorption compromises bone mass and its porous microstructure as well as proper biomechanics. This accelerates the development of osteoporotic disorders, a leading cause of skeletal degeneration-associated disability and premature death. Bone-forming cells play important roles in maintaining bone deposit and osteoclastic resorption. A poor organelle machinery, such as mitochondrial dysfunction, endoplasmic reticulum stress, and defective autophagy, etc., dysregulates growth factor secretion, mineralization matrix production, or osteoclast-regulatory capacity in osteoblastic cells. A plethora of epigenetic pathways regulate bone formation, skeletal integrity, and the development of osteoporosis. MicroRNAs inhibit protein translation by binding the 3'-untranslated region of mRNAs or promote translation through post-transcriptional pathways. DNA methylation and post-translational modification of histones alter the chromatin structure, hindering histone enrichment in promoter regions. MicroRNA-processing enzymes and DNA as well as histone modification enzymes catalyze these modifying reactions. Gain and loss of these epigenetic modifiers in bone-forming cells affect their epigenetic landscapes, influencing bone homeostasis, microarchitectural integrity, and osteoporotic changes. This article conveys productive insights into biological roles of DNA methylation, microRNA, and histone modification and highlights their interactions during skeletal development and bone loss under physiological and pathological conditions.
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Affiliation(s)
- Yu-Shan Chen
- Core Laboratory for Phenomics and Diagnostics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (Y.-S.C.); (W.-S.L.); (C.-W.K.); (H.-J.K.); (S.-Y.W.); (P.-C.K.)
- Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan
| | - Wei-Shiung Lian
- Core Laboratory for Phenomics and Diagnostics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (Y.-S.C.); (W.-S.L.); (C.-W.K.); (H.-J.K.); (S.-Y.W.); (P.-C.K.)
- Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan
| | - Chung-Wen Kuo
- Core Laboratory for Phenomics and Diagnostics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (Y.-S.C.); (W.-S.L.); (C.-W.K.); (H.-J.K.); (S.-Y.W.); (P.-C.K.)
- Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan
| | - Huei-Jing Ke
- Core Laboratory for Phenomics and Diagnostics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (Y.-S.C.); (W.-S.L.); (C.-W.K.); (H.-J.K.); (S.-Y.W.); (P.-C.K.)
- Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan
| | - Shao-Yu Wang
- Core Laboratory for Phenomics and Diagnostics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (Y.-S.C.); (W.-S.L.); (C.-W.K.); (H.-J.K.); (S.-Y.W.); (P.-C.K.)
- Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan
| | - Pei-Chen Kuo
- Core Laboratory for Phenomics and Diagnostics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (Y.-S.C.); (W.-S.L.); (C.-W.K.); (H.-J.K.); (S.-Y.W.); (P.-C.K.)
- Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan
| | - Holger Jahr
- Department of Anatomy and Cell Biology, University Hospital RWTH Aachen, 52074 Aachen, Germany;
- Department of Orthopedic Surgery, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
| | - Feng-Sheng Wang
- Core Laboratory for Phenomics and Diagnostics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (Y.-S.C.); (W.-S.L.); (C.-W.K.); (H.-J.K.); (S.-Y.W.); (P.-C.K.)
- Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan
- Graduate Institute of Clinical Medical Science, Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan
- Correspondence: ; Tel.: +886-7-7317123 (ext. 6404)
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26
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Marï Chal E. From a Free-Living Cyanobacteria to an Obligate Endosymbiotic Organelle: Early Steps in Lipid Metabolism Integration in Paulinellidae. Plant Cell Physiol 2020; 61:865-868. [PMID: 32267946 DOI: 10.1093/pcp/pcaa043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Eric Marï Chal
- Laboratoire de Physiologie Cellulaire et V�g�tale, CNRS, CEA, Universit� Grenoble Alpes, INRAE, IRIG, CEA Grenoble, 17 rue des Martyrs, 38000 Grenoble, France
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27
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Abstract
PURPOSE OF REVIEW Impairments in mitochondrial function in patients with insulin resistance and type 2 diabetes have been disputed for decades. This review aims to briefly summarize the current knowledge on mitochondrial dysfunction in metabolic tissues and to particularly focus on addressing a new perspective of mitochondrial dysfunction, the altered capacity of mitochondria to communicate with other organelles within insulin-resistant tissues. RECENT FINDINGS Organelle interactions are temporally and spatially formed connections essential for normal cell function. Recent studies have shown that mitochondria interact with various cellular organelles, such as the endoplasmic reticulum, lysosomes and lipid droplets, forming inter-organelle junctions. We will discuss the current knowledge on alterations in these mitochondria-organelle interactions in insulin resistance and diabetes, with a focus on changes in mitochondria-lipid droplet communication as a major player in ectopic lipid accumulation, lipotoxicity and insulin resistance.
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Affiliation(s)
- Stacey N Keenan
- Department of Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Matthew J Watt
- Department of Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Magdalene K Montgomery
- Department of Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia.
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28
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Lasker K, von Diezmann L, Zhou X, Ahrens DG, Mann TH, Moerner WE, Shapiro L. Selective sequestration of signalling proteins in a membraneless organelle reinforces the spatial regulation of asymmetry in Caulobacter crescentus. Nat Microbiol 2020; 5:418-429. [PMID: 31959967 PMCID: PMC7549192 DOI: 10.1038/s41564-019-0647-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/25/2019] [Indexed: 12/16/2022]
Abstract
Selective recruitment and concentration of signalling proteins within membraneless compartments is a ubiquitous mechanism for subcellular organization1-3. The dynamic flow of molecules into and out of these compartments occurs on faster timescales than for membrane-enclosed organelles, presenting a possible mechanism to control spatial patterning within cells. Here, we combine single-molecule tracking and super-resolution microscopy, light-induced subcellular localization, reaction-diffusion modelling and a spatially resolved promoter activation assay to study signal exchange in and out of the 200 nm cytoplasmic pole-organizing protein popZ (PopZ) microdomain at the cell pole of the asymmetrically dividing bacterium Caulobacter crescentus4-8. Two phospho-signalling proteins, the transmembrane histidine kinase CckA and the cytoplasmic phosphotransferase ChpT, provide the only phosphate source for the cell fate-determining transcription factor CtrA9-18. We find that all three proteins exhibit restricted rates of entry into and escape from the microdomain as well as enhanced phospho-signalling within, leading to a submicron gradient of activated CtrA-P19 that is stable and sublinear. Entry into the microdomain is selective for cytosolic proteins and requires a binding pathway to PopZ. Our work demonstrates how nanoscale protein assemblies can modulate signal propagation with fine spatial resolution, and that in Caulobacter, this modulation serves to reinforce asymmetry and differential cell fate of the two daughter cells.
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Affiliation(s)
- Keren Lasker
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lexy von Diezmann
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT, USA
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Xiaofeng Zhou
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel G Ahrens
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas H Mann
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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29
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Abstract
Motile cilia are a striking example of the functional cellular organelle, conserved across all the eukaryotic species. Motile cilia allow the swimming of cells and small organisms and transport of liquids across epithelial tissues. Whilst the molecular structure is now very well understood, the dynamics of cilia is not well established either at the single cilium level nor at the level of collective beating. Indeed, a full understanding of this requires connecting together behaviour across various lengthscales, from the molecular to the organelle, then at the cellular level and up to the tissue scale. Aside from the fundamental interest in this system, understanding beating is important to elucidate aspects of embryonic development and a variety of health conditions from fertility to genetic and infectious diseases of the airways.
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Affiliation(s)
- Pietro Cicuta
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, U.K
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30
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Sandoz PA, Tremblay C, van der Goot FG, Frechin M. Image-based analysis of living mammalian cells using label-free 3D refractive index maps reveals new organelle dynamics and dry mass flux. PLoS Biol 2019; 17:e3000553. [PMID: 31856161 PMCID: PMC6922317 DOI: 10.1371/journal.pbio.3000553] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/15/2019] [Indexed: 12/22/2022] Open
Abstract
Holo-tomographic microscopy (HTM) is a label-free microscopy method reporting the fine changes of a cell's refractive indices (RIs) in three dimensions at high spatial and temporal resolution. By combining HTM with epifluorescence, we demonstrate that mammalian cellular organelles such as lipid droplets (LDs) and mitochondria show specific RI 3D patterns. To go further, we developed a computer-vision strategy using FIJI, CellProfiler3 (CP3), and custom code that allows us to use the fine images obtained by HTM in quantitative approaches. We could observe the shape and dry mass dynamics of LDs, endocytic structures, and entire cells' division that have so far, to the best of our knowledge, been out of reach. We finally took advantage of the capacity of HTM to capture the motion of many organelles at the same time to report a multiorganelle spinning phenomenon and study its dynamic properties using pattern matching and homography analysis. This work demonstrates that HTM gives access to an uncharted field of biological dynamics and describes a unique set of simple computer-vision strategies that can be broadly used to quantify HTM images.
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Affiliation(s)
- Patrick A. Sandoz
- Global Health Institute, Life Sciences Faculty, EPFL, Lausanne, Switzerland
| | - Christopher Tremblay
- Global Health Institute, Life Sciences Faculty, EPFL, Lausanne, Switzerland
- Nanolive SA, EPFL Innovation Park, Ecublens, Switzerland
| | - F. Gisou van der Goot
- Global Health Institute, Life Sciences Faculty, EPFL, Lausanne, Switzerland
- * E-mail: (GvdG); (MF)
| | - Mathieu Frechin
- Nanolive SA, EPFL Innovation Park, Ecublens, Switzerland
- * E-mail: (GvdG); (MF)
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31
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Abstract
Nonsegmented negative-strand RNA viruses, including measles virus (MeV), a member of the Paramyxoviridae family, are assumed to replicate in cytoplasmic inclusion bodies. These cytoplasmic viral factories are not membrane bound, and they serve to concentrate the viral RNA replication machinery. Although inclusion bodies are a prominent feature in MeV-infected cells, their biogenesis and regulation are not well understood. Here, we show that infection with MeV triggers inclusion body formation via liquid-liquid phase separation (LLPS), a process underlying the formation of membraneless organelles. We find that the viral nucleoprotein (N) and phosphoprotein (P) are sufficient to trigger MeV phase separation, with the C-terminal domains of the viral N and P proteins playing a critical role in the phase transition. We provide evidence suggesting that the phosphorylation of P and dynein-mediated transport facilitate the growth of these organelles, implying that they may have key regulatory roles in the biophysical assembly process. In addition, our findings support the notion that these inclusions change from liquid to gel-like structures as a function of time after infection, leaving open the intriguing possibility that the dynamics of these organelles can be tuned during infection to optimally suit the changing needs during the viral replication cycle. Our study provides novel insight into the process of formation of viral inclusion factories, and taken together with earlier studies, suggests that Mononegavirales have broadly evolved to utilize LLPS as a common strategy to assemble cytoplasmic replication factories in infected cells.IMPORTANCE Measles virus remains a pathogen of significant global concern. Despite an effective vaccine, outbreaks continue to occur, and globally ∼100,000 measles-related deaths are seen annually. Understanding the molecular basis of virus-host interactions that impact the efficiency of virus replication is essential for the further development of prophylactic and therapeutic strategies. Measles virus replication occurs in the cytoplasm in association with discrete bodies, though little is known of the nature of the inclusion body structures. We recently established that the cellular protein WD repeat-containing protein 5 (WDR5) enhances MeV growth and is enriched in cytoplasmic viral inclusion bodies that include viral proteins responsible for RNA replication. Here, we show that MeV N and P proteins are sufficient to trigger the formation of WDR5-containing inclusion bodies, that these structures display properties characteristic of phase-separated liquid organelles, and that P phosphorylation together with the host dynein motor affect the efficiency of the liquid-liquid phase separation process.
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Affiliation(s)
- Yuqin Zhou
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
| | - Justin M Su
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
| | - Charles E Samuel
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
| | - Dzwokai Ma
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
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32
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Peterman E, Gibieža P, Schafer J, Skeberdis VA, Kaupinis A, Valius M, Heiligenstein X, Hurbain I, Raposo G, Prekeris R. The post-abscission midbody is an intracellular signaling organelle that regulates cell proliferation. Nat Commun 2019; 10:3181. [PMID: 31320617 PMCID: PMC6639393 DOI: 10.1038/s41467-019-10871-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 06/01/2019] [Indexed: 01/05/2023] Open
Abstract
Once thought to be a remnant of cell division, the midbody (MB) has recently been shown to have roles beyond its primary function of orchestrating abscission. Despite the emerging roles of post-abscission MBs, how MBs accumulate in the cytoplasm and signal to regulate cellular functions remains unknown. Here, we show that extracellular post-abscission MBs can be internalized by interphase cells, where they reside in the cytoplasm as a membrane-bound signaling structure that we have named the MBsome. We demonstrate that MBsomes stimulate cell proliferation and that MBsome formation is a phagocytosis-like process that depends on a phosphatidylserine/integrin complex, driven by actin-rich membrane protrusions. Finally, we show that MBsomes rely on dynamic actin coats to slow lysosomal degradation and propagate their signaling function. In summary, MBsomes may sometimes serve as intracellular organelles that signal via integrin and EGFR-dependent pathways to promote cell proliferation and anchorage-independent growth and survival.
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Affiliation(s)
- Eric Peterman
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Paulius Gibieža
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, 44307, Lithuania
| | - Johnathon Schafer
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | | | - Algirdas Kaupinis
- Proteomics Center, Institute of Biochemistry, Vilnius University Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania
| | - Mindaugas Valius
- Proteomics Center, Institute of Biochemistry, Vilnius University Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania
| | - Xavier Heiligenstein
- Institut Curie, PSL Research University, CNRS, UMR144, Structure and Membrane Compartments, Paris, 75005, France
| | - Ilse Hurbain
- Institut Curie, PSL Research University, CNRS, UMR144, Structure and Membrane Compartments, Paris, 75005, France
- Institut Curie, PSL Research University, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, 75005, France
| | - Graca Raposo
- Institut Curie, PSL Research University, CNRS, UMR144, Structure and Membrane Compartments, Paris, 75005, France
- Institut Curie, PSL Research University, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, 75005, France
| | - Rytis Prekeris
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
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33
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Abstract
Centrosomes and primary cilia are usually considered as distinct organelles, although both are assembled with the same evolutionary conserved, microtubule-based templates, the centrioles. Centrosomes serve as major microtubule- and actin cytoskeleton-organizing centers and are involved in a variety of intracellular processes, whereas primary cilia receive and transduce environmental signals to elicit cellular and organismal responses. Understanding the functional relationship between centrosomes and primary cilia is important because defects in both structures have been implicated in various diseases, including cancer. Here, we discuss evidence that the animal centrosome evolved, with the transition to complex multicellularity, as a hybrid organelle comprised of the two distinct, but intertwined, structural-functional modules: the centriole/primary cilium module and the pericentriolar material/centrosome module. The evolution of the former module may have been caused by the expanding cellular diversification and intercommunication, whereas that of the latter module may have been driven by the increasing complexity of mitosis and the requirement for maintaining cell polarity, individuation, and adhesion. Through its unique ability to serve both as a plasma membrane-associated primary cilium organizer and a juxtanuclear microtubule-organizing center, the animal centrosome has become an ideal integrator of extracellular and intracellular signals with the cytoskeleton and a switch between the non-cell autonomous and the cell-autonomous signaling modes. In light of this hypothesis, we discuss centrosome dynamics during cell proliferation, migration, and differentiation and propose a model of centrosome-driven microtubule assembly in mitotic and interphase cells. In addition, we outline the evolutionary benefits of the animal centrosome and highlight the hierarchy and modularity of the centrosome biogenesis networks.
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Affiliation(s)
- Vladimir Joukov
- N.N. Petrov National Medical Research Center of Oncology, 197758 Saint-Petersburg, Russia.
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Yamashita K, Yagi T, Isono T, Nishiyama Y, Hashimoto M, Yamada K, Suzuki K, Tokunaga E. Absorbance spectra of the hematochrome-like granules and eyespot of Euglena gracilis by scan-free absorbance spectral imaging A(x, y, λ) within the live cells. J Plant Res 2019; 132:431-438. [PMID: 30980216 DOI: 10.1007/s10265-019-01102-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 03/10/2019] [Indexed: 06/09/2023]
Abstract
Euglena gracilis has an organelle resembling hematochrome, with an appearance similar to the eyespot and the absorption band spectrally overlapped with that of the carotenoid. To discriminate the hematochrome-like granules and eyespot, scan-free, non-invasive, absorbance spectral imaging A(x, y, λ) microscopy of single live cells, where A(x, y, λ) means absorbance at a position (x, y) on a two-dimensional image at a specific wavelength λ was applied. This technique was demonstrated to be a powerful tool for basic research on intracellular structural analysis. By this method, characteristic absorption spectra specific to the hematochrome-like granule or eyespot were identified among a variety of spectra observed depending on the location inside the organelles. The hematochrome-like granule was dark orange and deep green in its outline and had a characteristic absorption peak at 620 nm as well as at 676 to 698 nm, suggesting that its origin is a component of chloroplast including chlorophyll a. Furthermore, the representative spectra of these organelles were derived by principal component analysis of the absorbance and its position in absorbance image, indicating that they can be distinguished from each other and other regions. It was also confirmed that even in areas where these organelles and chloroplasts overlap, one can distinguish them from each other. The present research clarified the absorption spectra of the eyespot with 1 × 1 µm spatial resolution and those unpublished of hematochrome-like granules of E. gracilis, and indicated that one can statistically distinguish these organelles by this method.
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Affiliation(s)
- Kyohei Yamashita
- Department of Physics, Faculty of Science, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan
| | - Takafumi Yagi
- Department of Physics, Faculty of Science, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan
| | - Takumi Isono
- Department of Physics, Faculty of Science, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan
| | - Yusuke Nishiyama
- Department of Physics, Faculty of Science, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan
| | - Masafumi Hashimoto
- Department of Physics, Faculty of Science, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan
| | - Koji Yamada
- euglena Co., Ltd., Yokohama-shi, Kanagawa, Japan
| | - Kengo Suzuki
- euglena Co., Ltd., Yokohama-shi, Kanagawa, Japan
| | - Eiji Tokunaga
- Department of Physics, Faculty of Science, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan.
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35
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Abstract
CTP synthase (CTPsyn) is a metabolic enzyme essential for the de novo synthesis of CTP the nucleotide. CTPsyn can be compartmented into filamentous structures named cytoophidia. Cytoophidia are conserved in a wide range of species and are highly abundant in Drosophila ovaries. Here we report that cytoophidia elongate upon nutrient deprivation, CTPsyn overexpression or heat shock in Drosophila ovaries. We also show that the curvature of cytoophidia changes during apoptosis. Moreover, cytoophidia can be transported from nurse cells to the oocyte via ring canals. Our study demonstrates that cytoophidia can respond to stress and are very dynamic in Drosophila ovaries.
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Affiliation(s)
- Zheng Wu
- School of Life Science and Technology, ShanghaiTech University, 230 Haike Road, 201210 Shanghai, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, 230 Haike Road, 201210 Shanghai, China; MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, United Kingdom.
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36
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Steinmark IE, James AL, Chung PH, Morton PE, Parsons M, Dreiss CA, Lorenz CD, Yahioglu G, Suhling K. Targeted fluorescence lifetime probes reveal responsive organelle viscosity and membrane fluidity. PLoS One 2019; 14:e0211165. [PMID: 30763333 PMCID: PMC6375549 DOI: 10.1371/journal.pone.0211165] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/08/2019] [Indexed: 11/19/2022] Open
Abstract
The only way to visually observe cellular viscosity, which can greatly influence biological reactions and has been linked to several human diseases, is through viscosity imaging. Imaging cellular viscosity has allowed the mapping of viscosity in cells, and the next frontier is targeted viscosity imaging of organelles and their microenvironments. Here we present a fluorescent molecular rotor/FLIM framework to image both organellar viscosity and membrane fluidity, using a combination of chemical targeting and organelle extraction. For demonstration, we image matrix viscosity and membrane fluidity of mitochondria, which have been linked to human diseases, including Alzheimer's Disease and Leigh's syndrome. We find that both are highly dynamic and responsive to small environmental and physiological changes, even under non-pathological conditions. This shows that neither viscosity nor fluidity can be assumed to be fixed and underlines the need for single-cell, and now even single-organelle, imaging.
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Affiliation(s)
| | - Arjuna L. James
- Department of Physics, King’s College London, London, United Kingdom
| | - Pei-Hua Chung
- Department of Physics, King’s College London, London, United Kingdom
| | - Penny E. Morton
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
| | - Maddy Parsons
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
| | - Cécile A. Dreiss
- Institute of Pharmaceutical Science, King’s College London, London, United Kingdom
| | | | - Gokhan Yahioglu
- Department of Chemistry, Imperial College London, London, United Kingdom
| | - Klaus Suhling
- Department of Physics, King’s College London, London, United Kingdom
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37
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Affiliation(s)
- Tanja Woyke
- U.S. Department of Energy Joint Genome InstituteWalnut Creek, CA94598USA
| | - Frederik Schulz
- U.S. Department of Energy Joint Genome InstituteWalnut Creek, CA94598USA
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38
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Biskou O, Casanova V, Hooper KM, Kemp S, Wright GP, Satsangi J, Barlow PG, Stevens C. The type III intermediate filament vimentin regulates organelle distribution and modulates autophagy. PLoS One 2019; 14:e0209665. [PMID: 30699149 PMCID: PMC6353089 DOI: 10.1371/journal.pone.0209665] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 12/10/2018] [Indexed: 12/21/2022] Open
Abstract
The cytoskeletal protein vimentin plays a key role in positioning of organelles within the cytosol and has been linked to the regulation of numerous cellular processes including autophagy, however, how vimentin regulates autophagy remains relatively unexplored. Here we report that inhibition of vimentin using the steroidal lactone Withaferin A (WFA) causes vimentin to aggregate, and this is associated with the relocalisation of organelles including autophagosomes and lysosomes from the cytosol to a juxtanuclear location. Vimentin inhibition causes autophagosomes to accumulate, and we demonstrate this results from modulation of mechanistic target of rapamycin (mTORC1) activity, and disruption of autophagosome-lysosome fusion. We suggest that vimentin plays a physiological role in autophagosome and lysosome positioning, thus identifying vimentin as a key factor in the regulation of mTORC1 and autophagy.
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Affiliation(s)
- Olga Biskou
- School of Applied Sciences, Edinburgh Napier University, Sighthill Campus, Sighthill Court, Edinburgh, United Kingdom
| | - Victor Casanova
- School of Applied Sciences, Edinburgh Napier University, Sighthill Campus, Sighthill Court, Edinburgh, United Kingdom
| | - Kirsty M. Hooper
- School of Applied Sciences, Edinburgh Napier University, Sighthill Campus, Sighthill Court, Edinburgh, United Kingdom
| | - Sadie Kemp
- School of Applied Sciences, Edinburgh Napier University, Sighthill Campus, Sighthill Court, Edinburgh, United Kingdom
| | - Graham P. Wright
- School of Applied Sciences, Edinburgh Napier University, Sighthill Campus, Sighthill Court, Edinburgh, United Kingdom
| | - Jack Satsangi
- Centre for Genomic & Experimental Medicine, University of Edinburgh, Western General Hospital Campus, Crewe Road, Edinburgh, United Kingdom
- Translational Gastroenterology Unit, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Peter G. Barlow
- School of Applied Sciences, Edinburgh Napier University, Sighthill Campus, Sighthill Court, Edinburgh, United Kingdom
| | - Craig Stevens
- School of Applied Sciences, Edinburgh Napier University, Sighthill Campus, Sighthill Court, Edinburgh, United Kingdom
- * E-mail:
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39
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Abstract
We study the crucial role of membrane fluctuations in maintaining a narrow gap between a fluid membrane tube and an enclosed solid particle. Solvent flows can occur in this gap, hence giving rise to a finite particle mobility along the tube. While our study has relevance for how cells are able to transport large organelles or other cargo along connecting membrane tubes, known as tunneling nanotubes, our calculations are also framed so that they can be tested by a specific in vitro experiment: A tubular membrane tether can be pulled from a membrane reservoir, such as an aspirated Giant Unilamellar Vesicle (GUV), e.g. using a conjugated bead that binds to the membrane and is held in a laser trap. We compute the subsequent mobility of colloidal particles trapped in the tube, focusing on the case when the particle is large compared to the equilibrium tube radius. We predict that the particle mobility should scale as ∼ σ−2/3, with σ the membrane tension.
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Affiliation(s)
- D. R. Daniels
- College of Engineering, Swansea University, Bay Campus, Swansea, United Kingdom
- * E-mail:
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40
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Sparkes I. Lessons from optical tweezers: quantifying organelle interactions, dynamics and modelling subcellular events. Curr Opin Plant Biol 2018; 46:55-61. [PMID: 30081386 DOI: 10.1016/j.pbi.2018.07.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/06/2018] [Accepted: 07/13/2018] [Indexed: 05/24/2023]
Abstract
Optical tweezers enable users to physically trap organelles and move them laterally within the plant cell. Recent advances have highlighted physical interactions between functionally related organelle pairs, such as ER-Golgi and peroxisome-chloroplast, and have shown how organelle positioning affects plant growth. Quantification of these processes has provided insight into the force components which ultimately drive organelle movement and positioning in plant cells. Application of optical tweezers has therefore revolutionised our understanding of plant organelle dynamics.
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Affiliation(s)
- Imogen Sparkes
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.
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41
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Yokawa K, Kagenishi T, Pavlovič A, Gall S, Weiland M, Mancuso S, Baluška F. Anaesthetics stop diverse plant organ movements, affect endocytic vesicle recycling and ROS homeostasis, and block action potentials in Venus flytraps. Ann Bot 2018; 122:747-756. [PMID: 29236942 PMCID: PMC6215046 DOI: 10.1093/aob/mcx155] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/18/2017] [Indexed: 05/09/2023]
Abstract
Background and Aims Anaesthesia for medical purposes was introduced in the 19th century. However, the physiological mode of anaesthetic drug actions on the nervous system remains unclear. One of the remaining questions is how these different compounds, with no structural similarities and even chemically inert elements such as the noble gas xenon, act as anaesthetic agents inducing loss of consciousness. The main goal here was to determine if anaesthetics affect the same or similar processes in plants as in animals and humans. Methods A single-lens reflex camera was used to follow organ movements in plants before, during and after recovery from exposure to diverse anaesthetics. Confocal microscopy was used to analyse endocytic vesicle trafficking. Electrical signals were recorded using a surface AgCl electrode. Key Results Mimosa leaves, pea tendrils, Venus flytraps and sundew traps all lost both their autonomous and touch-induced movements after exposure to anaesthetics. In Venus flytrap, this was shown to be due to the loss of action potentials under diethyl ether anaesthesia. The same concentration of diethyl ether immobilized pea tendrils. Anaesthetics also impeded seed germination and chlorophyll accumulation in cress seedlings. Endocytic vesicle recycling and reactive oxygen species (ROS) balance, as observed in intact Arabidopsis root apex cells, were also affected by all anaesthetics tested. Conclusions Plants are sensitive to several anaesthetics that have no structural similarities. As in animals and humans, anaesthetics used at appropriate concentrations block action potentials and immobilize organs via effects on action potentials, endocytic vesicle recycling and ROS homeostasis. Plants emerge as ideal model objects to study general questions related to anaesthesia, as well as to serve as a suitable test system for human anaesthesia.
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Affiliation(s)
- K Yokawa
- IZMB, University of Bonn, Bonn, Germany
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan
| | - T Kagenishi
- IZMB, University of Bonn, Bonn, Germany
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan
| | - A Pavlovič
- Department of Biophysics, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, Olomouc, Czech Republic
| | - S Gall
- IZMB, University of Bonn, Bonn, Germany
| | - M Weiland
- IZMB, University of Bonn, Bonn, Germany
- Department of Plant, Soil and Environmental Science & LINV, University of Florence, Sesto Fiorentino, Italy
| | - S Mancuso
- Department of Plant, Soil and Environmental Science & LINV, University of Florence, Sesto Fiorentino, Italy
| | - F Baluška
- IZMB, University of Bonn, Bonn, Germany
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42
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Ahmed K, Ahmad HR. Where have all the cell organelles gone during the cell division?l. J PAK MED ASSOC 2018; 68:1547. [PMID: 30317363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
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43
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Mathieu S, Manneville JB. Intracellular mechanics: connecting rheology and mechanotransduction. Curr Opin Cell Biol 2018; 56:34-44. [PMID: 30253328 DOI: 10.1016/j.ceb.2018.08.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 08/21/2018] [Accepted: 08/27/2018] [Indexed: 12/30/2022]
Abstract
Cell mechanics is crucial for a wide range of cell functions, including proliferation, polarity, migration and differentiation. Cells sense external physical cues and translate them into a cellular response. While force sensing occurs in the vicinity of the plasma membrane, forces can reach deep in the cell interior and to the nucleus. We review here the recent developments in the field of intracellular mechanics. We focus first on intracellular rheology, the study of the mechanical properties of the cell interior, and recapitulate the contribution of active mechanisms, the cytoskeleton and intracellular organelles to cell rheology. We then discuss how forces are transmitted inside the cell during mechanotransduction events, through direct force transmission and biochemical signaling, and how intracellular rheology and mechanotransduction are connected.
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Affiliation(s)
- Samuel Mathieu
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, F-75005, Paris, France; Sorbonne Université, UPMC University Paris 06, CNRS, UMR 144, 26 rue d'Ulm, F-75005, Paris, France
| | - Jean-Baptiste Manneville
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, F-75005, Paris, France; Sorbonne Université, UPMC University Paris 06, CNRS, UMR 144, 26 rue d'Ulm, F-75005, Paris, France.
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44
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Abstract
Chloroplasts (plastids) and mitochondria evolved from endosymbiotic bacteria. These organelles perform vital functions in photosynthetic eukaryotes, such as harvesting and converting energy for use in biological processes. Consistent with their evolutionary origins, plastids and mitochondria proliferate by the binary fission of pre-existing organelles. Here, I review the structures and functions of the supramolecular machineries driving plastid and mitochondrial division, which were discovered and first studied in the primitive red alga Cyanidioschyzon merolae. In the past decade, intact division machineries have been isolated from plastids and mitochondria and examined to investigate their underlying structure and molecular mechanisms. A series of studies has elucidated how these division machineries assemble and transform during the fission of these organelles, and which of the component proteins generate the motive force for their contraction. Plastid- and mitochondrial-division machineries have important similarities in their structures and mechanisms despite sharing no component proteins, implying that these division machineries evolved in parallel. The establishment of these division machineries might have enabled the host eukaryotic ancestor to permanently retain these endosymbiotic organelles by regulating their binary fission and the equal distribution of resources to daughter cells. These findings provide key insights into the establishment of endosymbiotic organelles and have opened new avenues of research into their evolution and mechanisms of proliferation.
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Affiliation(s)
- Yamato Yoshida
- Department of Science, College of Science, Ibaraki University, Ibaraki, 310-8512, Japan.
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45
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Antanavičiūtė I, Gibieža P, Prekeris R, Skeberdis VA. Midbody: From the Regulator of Cytokinesis to Postmitotic Signaling Organelle. ACTA ACUST UNITED AC 2018; 54:medicina54040053. [PMID: 30344284 PMCID: PMC6174351 DOI: 10.3390/medicina54040053] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/26/2018] [Accepted: 07/26/2018] [Indexed: 01/13/2023]
Abstract
Faithful cell division is crucial for successful proliferation, differentiation, and development of cells, tissue homeostasis, and preservation of genomic integrity. Cytokinesis is a terminal stage of cell division, leaving two genetically identical daughter cells connected by an intercellular bridge (ICB) containing the midbody (MB), a large protein-rich organelle, in the middle. Cell division may result in asymmetric or symmetric abscission of the ICB. In the first case, the ICB is severed on the one side of the MB, and the MB is inherited by the opposite daughter cell. In the second case, the MB is cut from both sides, expelled into the extracellular space, and later it can be engulfed by surrounding cells. Cells with lower autophagic activity, such as stem cells and cancer stem cells, are inclined to accumulate MBs. Inherited MBs affect cell polarity, modulate intra- and intercellular communication, enhance pluripotency of stem cells, and increase tumorigenic potential of cancer cells. In this review, we briefly summarize the latest knowledge on MB formation, inheritance, degradation, and function, and in addition, present and discuss our recent findings on the electrical and chemical communication of cells connected through the MB-containing ICB.
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Affiliation(s)
- Ieva Antanavičiūtė
- Institute of Cardiology, Medical Academy, Lithuanian University of Health Sciences, LT-50162 Kaunas, Lithuania.
| | - Paulius Gibieža
- Institute of Cardiology, Medical Academy, Lithuanian University of Health Sciences, LT-50162 Kaunas, Lithuania.
| | - Rytis Prekeris
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Vytenis Arvydas Skeberdis
- Institute of Cardiology, Medical Academy, Lithuanian University of Health Sciences, LT-50162 Kaunas, Lithuania.
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46
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Abstract
Cells have to organize their complex biochemistry to regulate their metabolism and respond to changes in the environment. Traditionally, intracellular organization has been associated with compartments that are surrounded by lipid membranes. However, in recent years, phase transitions have emerged as a novel form of cellular organization. Phase transition is a physical process whereby a substance changes from one physical state to another. Examples are provided by the freezing of water into ice (liquid to solid) or the heating of water to generate water vapor (liquid to gas).
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Affiliation(s)
- Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
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47
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Boeynaems S, Alberti S, Fawzi NL, Mittag T, Polymenidou M, Rousseau F, Schymkowitz J, Shorter J, Wolozin B, Van Den Bosch L, Tompa P, Fuxreiter M. Protein Phase Separation: A New Phase in Cell Biology. Trends Cell Biol 2018. [PMID: 29602697 DOI: 10.1016/j.tcb.2018.1002.1004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Cellular compartments and organelles organize biological matter. Most well-known organelles are separated by a membrane boundary from their surrounding milieu. There are also many so-called membraneless organelles and recent studies suggest that these organelles, which are supramolecular assemblies of proteins and RNA molecules, form via protein phase separation. Recent discoveries have shed light on the molecular properties, formation, regulation, and function of membraneless organelles. A combination of techniques from cell biology, biophysics, physical chemistry, structural biology, and bioinformatics are starting to help establish the molecular principles of an emerging field, thus paving the way for exciting discoveries, including novel therapeutic approaches for the treatment of age-related disorders.
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Affiliation(s)
- Steven Boeynaems
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; KU Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), Leuven, Belgium; VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, Leuven, Belgium.
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Frederic Rousseau
- Switch Laboratory, VIB, Leuven, Belgium; KU Leuven, Department for Cellular and Molecular Medicine, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB, Leuven, Belgium; KU Leuven, Department for Cellular and Molecular Medicine, Leuven, Belgium
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin Wolozin
- Department of Pharmacology, Boston University School of Medicine, Boston, MA, USA; Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Ludo Van Den Bosch
- KU Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), Leuven, Belgium; VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, Leuven, Belgium.
| | - Peter Tompa
- VIB, Center for Structural Biology (CSB), Vrije Universiteit Brussel (VUB), Brussels, Belgium; Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.
| | - Monika Fuxreiter
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary.
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48
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Abstract
Bacterial microcompartments (BMCs) are self-assembling organelles that consist of an enzymatic core that is encapsulated by a selectively permeable protein shell. The potential to form BMCs is widespread and found across the kingdom Bacteria. BMCs have crucial roles in carbon dioxide fixation in autotrophs and the catabolism of organic substrates in heterotrophs. They contribute to the metabolic versatility of bacteria, providing a competitive advantage in specific environmental niches. Although BMCs were first visualized more than 60 years ago, it is mainly in the past decade that progress has been made in understanding their metabolic diversity and the structural basis of their assembly and function. This progress has not only heightened our understanding of their role in microbial metabolism but is also beginning to enable their use in a variety of applications in synthetic biology. In this Review, we focus on recent insights into the structure, assembly, diversity and function of BMCs.
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Affiliation(s)
- Cheryl A. Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Clement Aussignargues
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jan Zarzycki
- Max-Planck-Institute for Terrestrial Microbiology, D-35043, Marburg, Germany
| | - Fei Cai
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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49
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Abstract
The delivery of intracellular material within cells is crucial for maintaining normal function. Myosins transport a wide variety of cargo, ranging from vesicles to ribonuclear protein particles (RNPs), in plants, fungi, and metazoa. The properties of a given myosin transporter are adapted to move on different actin filament tracks, either on the disordered actin networks at the cell cortex or along highly organized actin bundles to distribute their cargo in a localized manner or move it across long distances in the cell. Transport is controlled by selective recruitment of the myosin to its cargo that also plays a role in activation of the motor.
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Affiliation(s)
- Margaret A Titus
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455
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50
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Suzuki R, Nishii I, Okada S, Noguchi T. 3D reconstruction of endoplasmic reticulum in a hydrocarbon-secreting green alga, Botryococcus braunii (Race B). Planta 2018; 247:663-677. [PMID: 29164368 DOI: 10.1007/s00425-017-2811-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/09/2017] [Indexed: 06/07/2023]
Abstract
Based on 3D sections through cells of Botryococcus braunii, the structure of three domains of endoplasmic reticulum, and their spatial and functional relationships to other organelles are clarified. Oil production by photosynthetic microalgae has attracted attention since these oils can be converted into renewable, carbon-neutral fuels. The green alga B. braunii accumulates large amounts of hydrocarbons, 30-50% of cell dry weight, in extracellular spaces rather than its cytoplasm. To advance the knowledge of hydrocarbon biosynthesis and transport pathways in this alga, we utilized transmission EM combined with rapid freezing and image reconstruction. We constructed detailed 3D maps distinguishing three ER domains: rdER with ribosomes on both sides, rsER with ribosomes on one side, and sER without ribosomes. The rsER and sER domains were especially prominent during the oil body formation and oil secretion stages. The ER contacted the chloroplasts, oil bodies, or plasma membrane via the rsER domains, oriented with the ribosome-free surface facing the organelles. We discuss the following transport pathway for hydrocarbons and their precursors in the cytoplasm: chloroplast → endoplasmic reticulum (ER) → oil bodies → ER → plasma membrane → secretion. This study represents the first 3D study of the three-domain classification (rdER, rsER and sER) of the ER network among eukaryotic cells. Finally, we propose the novel features of the ERs in plant cells that are distinct from the latest proposed model for the ERs in mammalian cells.
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Affiliation(s)
- Reiko Suzuki
- Nara Women's University, Kitauoya-nishimachi, Nara, 630-8506, Japan
- JST, CREST, 5 Sanbancho, Chiyoda, Tokyo, 102-0075, Japan
| | - Ichiro Nishii
- Department of Biological Sciences, Faculty of Science, Nara Women's University, Kitauoya-nishimachi, Nara, 630-8506, Japan
- JST, CREST, 5 Sanbancho, Chiyoda, Tokyo, 102-0075, Japan
| | - Shigeru Okada
- Department of Aquatic Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
- JST, CREST, 5 Sanbancho, Chiyoda, Tokyo, 102-0075, Japan
| | - Tetsuko Noguchi
- Nara Women's University, Kitauoya-nishimachi, Nara, 630-8506, Japan.
- JST, CREST, 5 Sanbancho, Chiyoda, Tokyo, 102-0075, Japan.
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