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Kollmar M, Welz T, Ravi A, Kaufmann T, Alzahofi N, Hatje K, Alghamdi A, Kim J, Briggs DA, Samol-Wolf A, Pylypenko O, Hume AN, Burkhardt P, Faix J, Kerkhoff E. Actomyosin organelle functions of SPIRE actin nucleators precede animal evolution. Commun Biol 2024; 7:832. [PMID: 38977899 PMCID: PMC11231147 DOI: 10.1038/s42003-024-06458-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 06/14/2024] [Indexed: 07/10/2024] Open
Abstract
An important question in cell biology is how cytoskeletal proteins evolved and drove the development of novel structures and functions. Here we address the origin of SPIRE actin nucleators. Mammalian SPIREs work with RAB GTPases, formin (FMN)-subgroup actin assembly proteins and class-5 myosin (MYO5) motors to transport organelles along actin filaments towards the cell membrane. However, the origin and extent of functional conservation of SPIRE among species is unknown. Our sequence searches show that SPIRE exist throughout holozoans (animals and their closest single-celled relatives), but not other eukaryotes. SPIRE from unicellular holozoans (choanoflagellate), interacts with RAB, FMN and MYO5 proteins, nucleates actin filaments and complements mammalian SPIRE function in organelle transport. Meanwhile SPIRE and MYO5 proteins colocalise to organelles in Salpingoeca rosetta choanoflagellates. Based on these observations we propose that SPIRE originated in unicellular ancestors of animals providing an actin-myosin driven exocytic transport mechanism that may have contributed to the evolution of complex multicellular animals.
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Affiliation(s)
- Martin Kollmar
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.
| | - Tobias Welz
- Molecular Cell Biology Laboratory, Department of Neurology, University Hospital Regensburg, Regensburg, Germany
| | - Aishwarya Ravi
- Michael Sars Centre, University of Bergen, Bergen, Norway
| | - Thomas Kaufmann
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Noura Alzahofi
- School of Life Sciences, University of Nottingham, Nottingham, UK
- Biology Department, College of Science, Taibah University, Medina, Kingdom of Saudi Arabia
| | - Klas Hatje
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Asmahan Alghamdi
- School of Life Sciences, University of Nottingham, Nottingham, UK
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh, Kingdom of Saudi Arabia
| | - Jiyu Kim
- Molecular Cell Biology Laboratory, Department of Neurology, University Hospital Regensburg, Regensburg, Germany
- Department of Anatomy, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Deborah A Briggs
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Annette Samol-Wolf
- Molecular Cell Biology Laboratory, Department of Neurology, University Hospital Regensburg, Regensburg, Germany
| | - Olena Pylypenko
- Dynamics of Intra-Cellular Organization, Institute Curie, PSL Research University, CNRS UMR144, Paris, France
| | - Alistair N Hume
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | - Jan Faix
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Eugen Kerkhoff
- Molecular Cell Biology Laboratory, Department of Neurology, University Hospital Regensburg, Regensburg, Germany.
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2
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Gahan JM, Helfrich LW, Wetzel LA, Bhanu NV, Yuan ZF, Garcia BA, Klose R, Booth DS. Chromatin profiling identifies putative dual roles for H3K27me3 in regulating transposons and cell type-specific genes in choanoflagellates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596151. [PMID: 38854040 PMCID: PMC11160669 DOI: 10.1101/2024.05.28.596151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Gene expression is tightly controlled during animal development to allow the formation of specialized cell types. Our understanding of how animals evolved this exquisite regulatory control remains elusive, but evidence suggests that changes in chromatin-based mechanisms may have contributed. To investigate this possibility, here we examine chromatin-based gene regulatory features in the closest relatives of animals, choanoflagellates. Using Salpingoeca rosetta as a model system, we examined chromatin accessibility and histone modifications at the genome scale and compared these features to gene expression. We first observed that accessible regions of chromatin are primarily associated with gene promoters and found no evidence of distal gene regulatory elements resembling the enhancers that animals deploy to regulate developmental gene expression. Remarkably, a histone modification deposited by polycomb repressive complex 2, histone H3 lysine 27 trimethylation (H3K27me3), appeared to function similarly in S. rosetta to its role in animals, because this modification decorated genes with cell type-specific expression. Additionally, H3K27me3 marked transposons, retaining what appears to be an ancestral role in regulating these elements. We further uncovered a putative new bivalent chromatin state at cell type-specific genes that consists of H3K27me3 and histone H3 lysine 4 mono-methylation (H3K4me1). Together, our discoveries support the scenario that gene-associated histone modification states that underpin development emerged before the evolution of animal multicellularity.
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Affiliation(s)
- James M. Gahan
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Biochemistry, University of Oxford, Oxford, UK
- Present Address: Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Lily W. Helfrich
- Howard Hughes Medical Institute / University of California, Berkeley, Department of Molecular and Cell Biology, Berkeley, CA 94720
- Present Address: Benchling
| | - Laura A. Wetzel
- Howard Hughes Medical Institute / University of California, Berkeley, Department of Molecular and Cell Biology, Berkeley, CA 94720
- Present Address: BioMarin Pharmaceutical Inc
| | - Natarajan V. Bhanu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
| | - Zuo-Fei Yuan
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
| | - Rob Klose
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - David S. Booth
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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3
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Phillips JE, Zheng Y, Pan D. Assembling a Hippo: the evolutionary emergence of an animal developmental signaling pathway. Trends Biochem Sci 2024:S0968-0004(24)00102-6. [PMID: 38729842 DOI: 10.1016/j.tibs.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/25/2024] [Accepted: 04/17/2024] [Indexed: 05/12/2024]
Abstract
Decades of work in developmental genetics has given us a deep mechanistic understanding of the fundamental signaling pathways underlying animal development. However, little is known about how these pathways emerged and changed over evolutionary time. Here, we review our current understanding of the evolutionary emergence of the Hippo pathway, a conserved signaling pathway that regulates tissue size in animals. This pathway has deep evolutionary roots, emerging piece by piece in the unicellular ancestors of animals, with a complete core pathway predating the origin of animals. Recent functional studies in close unicellular relatives of animals and early-branching animals suggest an ancestral function Hippo pathway of cytoskeletal regulation, which was subsequently co-opted to regulate proliferation and animal tissue size.
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Affiliation(s)
- Jonathan E Phillips
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Yonggang Zheng
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Duojia Pan
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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4
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Kalinka E, Brody SM, Swafford AJM, Medina EM, Fritz-Laylin LK. Genetic transformation of the frog-killing chytrid fungus Batrachochytrium dendrobatidis. Proc Natl Acad Sci U S A 2024; 121:e2317928121. [PMID: 38236738 PMCID: PMC10823177 DOI: 10.1073/pnas.2317928121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/13/2023] [Indexed: 01/23/2024] Open
Abstract
Batrachochytrium dendrobatidis (Bd), a causative agent of chytridiomycosis, is decimating amphibian populations around the world. Bd belongs to the chytrid lineage, a group of early-diverging fungi that are widely used to study fungal evolution. Like all chytrids, Bd develops from a motile form into a sessile, growth form, a transition that involves drastic changes in its cytoskeletal architecture. Efforts to study Bd cell biology, development, and pathogenicity have been limited by the lack of genetic tools with which to test hypotheses about underlying molecular mechanisms. Here, we report the development of a transient genetic transformation system for Bd. We used electroporation to deliver exogenous DNA into Bd cells and detected transgene expression for up to three generations under both heterologous and native promoters. We also adapted the transformation protocol for selection using an antibiotic resistance marker. Finally, we used this system to express fluorescent protein fusions and, as a proof of concept, expressed a genetically encoded probe for the actin cytoskeleton. Using live-cell imaging, we visualized the distribution and dynamics of polymerized actin at each stage of the Bd life cycle, as well as during key developmental transitions. This transformation system enables direct testing of key hypotheses regarding mechanisms of Bd pathogenesis. This technology also paves the way for answering fundamental questions of chytrid cell, developmental, and evolutionary biology.
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Affiliation(s)
- Erik Kalinka
- Department of Biology, University of Massachusetts, Amherst, MA01003
| | | | | | - Edgar M. Medina
- Department of Biology, University of Massachusetts, Amherst, MA01003
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Ros-Rocher N, Brunet T. What is it like to be a choanoflagellate? Sensation, processing and behavior in the closest unicellular relatives of animals. Anim Cogn 2023; 26:1767-1782. [PMID: 37067637 PMCID: PMC10770216 DOI: 10.1007/s10071-023-01776-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/18/2023]
Abstract
All animals evolved from a single lineage of unicellular precursors more than 600 million years ago. Thus, the biological and genetic foundations for animal sensation, cognition and behavior must necessarily have arisen by modifications of pre-existing features in their unicellular ancestors. Given that the single-celled ancestors of the animal kingdom are extinct, the only way to reconstruct how these features evolved is by comparing the biology and genomic content of extant animals to their closest living relatives. Here, we reconstruct the Umwelt (the subjective, perceptive world) inhabited by choanoflagellates, a group of unicellular (or facultatively multicellular) aquatic microeukaryotes that are the closest living relatives of animals. Although behavioral research on choanoflagellates remains patchy, existing evidence shows that they are capable of chemosensation, photosensation and mechanosensation. These processes often involve specialized sensorimotor cellular appendages (cilia, microvilli, and/or filopodia) that resemble those that underlie perception in most animal sensory cells. Furthermore, comparative genomics predicts an extensive "sensory molecular toolkit" in choanoflagellates, which both provides a potential basis for known behaviors and suggests the existence of a largely undescribed behavioral complexity that presents exciting avenues for future research. Finally, we discuss how facultative multicellularity in choanoflagellates might help us understand how evolution displaced the locus of decision-making from a single cell to a collective, and how a new space of behavioral complexity might have become accessible in the process.
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Affiliation(s)
- Núria Ros-Rocher
- Evolutionary Cell Biology and Evolution of Morphogenesis Unit, Institut Pasteur, Université Paris-Cité, CNRS UMR3691, 25-28 Rue du Docteur Roux, 75015, Paris, France
| | - Thibaut Brunet
- Evolutionary Cell Biology and Evolution of Morphogenesis Unit, Institut Pasteur, Université Paris-Cité, CNRS UMR3691, 25-28 Rue du Docteur Roux, 75015, Paris, France.
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6
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Agarwal P, Cadart C, Fort L, Gahan J, Greenspan L, Juan T, Kameneva P, Miao Y. Pathway to Independence: the future of developmental biology. Development 2023; 150:dev202360. [PMID: 37812057 DOI: 10.1242/dev.202360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
In 2022, Development launched its Pathway to Independence (PI) Programme, aimed at supporting postdocs as they transition to their first independent position. We selected eight talented researchers as the first cohort of PI Fellows. In this article, each of our Fellows provides their perspective on the future of their field. Together, they paint an exciting picture of the current state of and open questions in developmental biology.
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Affiliation(s)
- Priti Agarwal
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Clotilde Cadart
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Loic Fort
- Vanderbilt University School of Medicine, 465 21st Avenue South, U 3200 MRB III, Nashville, TN 37240-7935, USA
| | - James Gahan
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Leah Greenspan
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Thomas Juan
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, D-61231 Bad Nauheim, Germany
| | - Polina Kameneva
- The Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria
| | - Yuchuan Miao
- Department of Genetics, Harvard Medical School and Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
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7
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Ruiz-Trillo I, Kin K, Casacuberta E. The Origin of Metazoan Multicellularity: A Potential Microbial Black Swan Event. Annu Rev Microbiol 2023; 77:499-516. [PMID: 37406343 DOI: 10.1146/annurev-micro-032421-120023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
The emergence of animals from their unicellular ancestors is a major evolutionary event. Thanks to the study of diverse close unicellular relatives of animals, we now have a better grasp of what the unicellular ancestor of animals was like. However, it is unclear how that unicellular ancestor of animals became the first animals. To explain this transition, two popular theories, the choanoblastaea and the synzoospore, have been proposed. We will revise and expose the flaws in these two theories while showing that, due to the limits of our current knowledge, the origin of animals is a biological black swan event. As such, the origin of animals defies retrospective explanations. Therefore, we should be extra careful not to fall for confirmation biases based on few data and, instead, embrace this uncertainty and be open to alternative scenarios. With the aim to broaden the potential explanations on how animals emerged, we here propose two novel and alternative scenarios. In any case, to find the answer to how animals evolved, additional data will be required, as will the hunt for microscopic creatures that are closely related to animals but have not yet been sampled and studied.
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Affiliation(s)
- Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain;
- ICREA, Barcelona, Spain
| | - Koryu Kin
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain;
| | - Elena Casacuberta
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain;
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Coyle MC, Tajima AM, Leon F, Choksi SP, Yang A, Espinoza S, Hughes TR, Reiter JF, Booth DS, King N. An RFX transcription factor regulates ciliogenesis in the closest living relatives of animals. Curr Biol 2023; 33:3747-3758.e9. [PMID: 37552984 PMCID: PMC10530576 DOI: 10.1016/j.cub.2023.07.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 05/30/2023] [Accepted: 07/13/2023] [Indexed: 08/10/2023]
Abstract
Cilia allowed our protistan ancestors to sense and explore their environment, avoid predation, and capture bacterial prey.1,2,3 Regulated ciliogenesis was likely critical for early animal evolution,2,4,5,6 and in modern animals, deploying cilia in the right cells at the right time is crucial for development and physiology. Two transcription factors, RFX and FoxJ1, coordinate ciliogenesis in animals7,8,9 but are absent from the genomes of many other ciliated eukaryotes, raising the question of how the regulation of ciliogenesis in animals evolved.10,11 By comparing the genomes of animals with those of their closest living relatives, the choanoflagellates, we found that the genome of their last common ancestor encoded at least three RFX paralogs and a FoxJ1 homolog. Disruption of the RFX homolog cRFXa in the model choanoflagellate Salpingoeca rosetta resulted in delayed cell proliferation and aberrant ciliogenesis, marked by the collapse and resorption of nascent cilia. In cRFXa mutants, ciliogenesis genes and foxJ1 were significantly downregulated. Moreover, the promoters of S. rosetta ciliary genes are enriched for DNA motifs matching those bound by the cRFXa protein in vitro. These findings suggest that an ancestral cRFXa homolog coordinated ciliogenesis in the progenitors of animals and choanoflagellates and that the selective deployment of the RFX regulatory module may have been necessary to differentiate ciliated from non-ciliated cell types during early animal evolution.
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Affiliation(s)
- Maxwell C Coyle
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Adia M Tajima
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Fredrick Leon
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Semil P Choksi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ally Yang
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, M5S 3E1, Canada
| | - Sarah Espinoza
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Timothy R Hughes
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, M5S 3E1, Canada
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - David S Booth
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Nicole King
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA.
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Excitatory/inhibitory imbalance in autism: the role of glutamate and GABA gene-sets in symptoms and cortical brain structure. Transl Psychiatry 2023; 13:18. [PMID: 36681677 PMCID: PMC9867712 DOI: 10.1038/s41398-023-02317-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 12/22/2022] [Accepted: 01/10/2023] [Indexed: 01/22/2023] Open
Abstract
The excitatory/inhibitory (E/I) imbalance hypothesis posits that imbalance between excitatory (glutamatergic) and inhibitory (GABAergic) mechanisms underlies the behavioral characteristics of autism. However, how E/I imbalance arises and how it may differ across autism symptomatology and brain regions is not well understood. We used innovative analysis methods-combining competitive gene-set analysis and gene-expression profiles in relation to cortical thickness (CT) to investigate relationships between genetic variance, brain structure and autism symptomatology of participants from the AIMS-2-TRIALS LEAP cohort (autism = 359, male/female = 258/101; neurotypical control participants = 279, male/female = 178/101) aged 6-30 years. Using competitive gene-set analyses, we investigated whether aggregated genetic variation in glutamate and GABA gene-sets could be associated with behavioral measures of autism symptoms and brain structural variation. Further, using the same gene-sets, we corelated expression profiles throughout the cortex with differences in CT between autistic and neurotypical control participants, as well as in separate sensory subgroups. The glutamate gene-set was associated with all autism symptom severity scores on the Autism Diagnostic Observation Schedule-2 (ADOS-2) and the Autism Diagnostic Interview-Revised (ADI-R) within the autistic group. In adolescents and adults, brain regions with greater gene-expression of glutamate and GABA genes showed greater differences in CT between autistic and neurotypical control participants although in opposing directions. Additionally, the gene expression profiles were associated with CT profiles in separate sensory subgroups. Our results suggest complex relationships between E/I related genetics and autism symptom profiles as well as brain structure alterations, where there may be differential roles for glutamate and GABA.
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Brunet T, Booth DS. Cell polarity in the protist-to-animal transition. Curr Top Dev Biol 2023; 154:1-36. [PMID: 37100515 DOI: 10.1016/bs.ctdb.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
A signature feature of the animal kingdom is the presence of epithelia: sheets of polarized cells that both insulate the organism from its environment and mediate interactions with it. Epithelial cells display a marked apico-basal polarity, which is highly conserved across the animal kingdom, both in terms of morphology and of molecular regulators. How did this architecture first evolve? Although the last eukaryotic common ancestor almost certainly possessed a simple form of apico-basal polarity (marked by the presence of one or several flagella at a single cellular pole), comparative genomics and evolutionary cell biology reveal that the polarity regulators of animal epithelial cells have a surprisingly complex and stepwise evolutionary history. Here, we retrace their evolutionary assembly. We suggest that the "polarity network" that polarized animal epithelial cells evolved by integration of initially independent cellular modules that evolved at distinct steps of our evolutionary ancestry. The first module dates back to the last common ancestor of animals and amoebozoans and involved Par1, extracellular matrix proteins, and the integrin-mediated adhesion complex. Other regulators, such as Cdc42, Dlg, Par6 and cadherins evolved in ancient unicellular opisthokonts, and might have first been involved in F-actin remodeling and filopodial dynamics. Finally, the bulk of "polarity proteins" as well as specialized adhesion complexes evolved in the metazoan stem-line, in concert with the newly evolved intercellular junctional belts. Thus, the polarized architecture of epithelia can be understood as a palimpsest of components of distinct histories and ancestral functions, which have become tightly integrated in animal tissues.
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11
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The premetazoan ancestry of the synaptic toolkit and appearance of first neurons. Essays Biochem 2022; 66:781-795. [PMID: 36205407 DOI: 10.1042/ebc20220042] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/31/2022] [Accepted: 09/13/2022] [Indexed: 12/13/2022]
Abstract
Neurons, especially when coupled with muscles, allow animals to interact with and navigate through their environment in ways unique to life on earth. Found in all major animal lineages except sponges and placozoans, nervous systems range widely in organization and complexity, with neurons possibly representing the most diverse cell-type. This diversity has led to much debate over the evolutionary origin of neurons as well as synapses, which allow for the directed transmission of information. The broad phylogenetic distribution of neurons and presence of many of the defining components outside of animals suggests an early origin of this cell type, potentially in the time between the first animal and the last common ancestor of extant animals. Here, we highlight the occurrence and function of key aspects of neurons outside of animals as well as recent findings from non-bilaterian animals in order to make predictions about when and how the first neuron(s) arose during animal evolution and their relationship to those found in extant lineages. With advancing technologies in single cell transcriptomics and proteomics as well as expanding functional techniques in non-bilaterian animals and the close relatives of animals, it is an exciting time to begin unraveling the complex evolutionary history of this fascinating animal cell type.
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12
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Pinskey JM, Lagisetty A, Gui L, Phan N, Reetz E, Tavakoli A, Fu G, Nicastro D. Three-dimensional flagella structures from animals' closest unicellular relatives, the Choanoflagellates. eLife 2022; 11:e78133. [PMID: 36384644 PMCID: PMC9671500 DOI: 10.7554/elife.78133] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 11/01/2022] [Indexed: 11/18/2022] Open
Abstract
In most eukaryotic organisms, cilia and flagella perform a variety of life-sustaining roles related to environmental sensing and motility. Cryo-electron microscopy has provided considerable insight into the morphology and function of flagellar structures, but studies have been limited to less than a dozen of the millions of known eukaryotic species. Ultrastructural information is particularly lacking for unicellular organisms in the Opisthokonta clade, leaving a sizeable gap in our understanding of flagella evolution between unicellular species and multicellular metazoans (animals). Choanoflagellates are important aquatic heterotrophs, uniquely positioned within the opisthokonts as the metazoans' closest living unicellular relatives. We performed cryo-focused ion beam milling and cryo-electron tomography on flagella from the choanoflagellate species Salpingoeca rosetta. We show that the axonemal dyneins, radial spokes, and central pair complex in S. rosetta more closely resemble metazoan structures than those of unicellular organisms from other suprakingdoms. In addition, we describe unique features of S. rosetta flagella, including microtubule holes, microtubule inner proteins, and the flagellar vane: a fine, net-like extension that has been notoriously difficult to visualize using other methods. Furthermore, we report barb-like structures of unknown function on the extracellular surface of the flagellar membrane. Together, our findings provide new insights into choanoflagellate biology and flagella evolution between unicellular and multicellular opisthokonts.
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Affiliation(s)
- Justine M Pinskey
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Adhya Lagisetty
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Long Gui
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Nhan Phan
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Evan Reetz
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Amirrasoul Tavakoli
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Gang Fu
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Daniela Nicastro
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
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13
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Phillips JE, Santos M, Konchwala M, Xing C, Pan D. Genome editing in the unicellular holozoan Capsaspora owczarzaki suggests a premetazoan role for the Hippo pathway in multicellular morphogenesis. eLife 2022; 11:e77598. [PMID: 35659869 PMCID: PMC9170242 DOI: 10.7554/elife.77598] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/23/2022] [Indexed: 12/13/2022] Open
Abstract
Animal development is mediated by a surprisingly small set of canonical signaling pathways such as Wnt, Hedgehog, TGF-beta, Notch, and Hippo pathways. Although once thought to be present only in animals, recent genome sequencing has revealed components of these pathways in the closest unicellular relatives of animals. These findings raise questions about the ancestral functions of these developmental pathways and their potential role in the emergence of animal multicellularity. Here, we provide the first functional characterization of any of these developmental pathways in unicellular organisms by developing techniques for genetic manipulation in Capsaspora owczarzaki, a close unicellular relative of animals that displays aggregative multicellularity. We then use these tools to characterize the Capsaspora ortholog of the Hippo signaling nuclear effector YAP/TAZ/Yorkie (coYki), a key regulator of tissue size in animals. In contrast to what might be expected based on studies in animals, we show that coYki is dispensable for cell proliferation but regulates cytoskeletal dynamics and the three-dimensional (3D) shape of multicellular structures. We further demonstrate that the cytoskeletal abnormalities of individual coYki mutant cells underlie the abnormal 3D shape of coYki mutant aggregates. Taken together, these findings implicate an ancestral role for the Hippo pathway in cytoskeletal dynamics and multicellular morphogenesis predating the origin of animal multicellularity, which was co-opted during evolution to regulate cell proliferation.
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Affiliation(s)
- Jonathan E Phillips
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Maribel Santos
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Mohammed Konchwala
- Eugene McDermott Center for Human Growth & Development, Departments of Bioinformatics and Clinical Sciences, University of Texas Southwestern Medical CenterDallasUnited States
| | - Chao Xing
- Eugene McDermott Center for Human Growth & Development, Departments of Bioinformatics and Clinical Sciences, University of Texas Southwestern Medical CenterDallasUnited States
| | - Duojia Pan
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical CenterDallasUnited States
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14
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Booth DS, King N. The history of Salpingoeca rosetta as a model for reconstructing animal origins. Curr Top Dev Biol 2022; 147:73-91. [PMID: 35337467 DOI: 10.1016/bs.ctdb.2022.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Choanoflagellates, the closest living relatives of animals, have the potential to reveal the genetic and cell biological foundations of complex multicellular development in animals. Here we describe the history of research on the choanoflagellate Salpingoeca rosetta. From its original isolation in 2000 to the establishment of CRISPR-mediated genome editing in 2020, S. rosetta provides an instructive case study in the establishment of a new model organism.
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Affiliation(s)
- David S Booth
- Chan Zuckerberg Biohub and Department of Biochemistry and Biophysics, University of California, San Francisco, CA, United States.
| | - Nicole King
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States.
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15
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Xu J, Ericson CF, Lien YW, Rutaganira FUN, Eisenstein F, Feldmüller M, King N, Pilhofer M. Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis. Nat Microbiol 2022; 7:397-410. [PMID: 35165385 PMCID: PMC8894135 DOI: 10.1038/s41564-022-01059-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/05/2022] [Indexed: 12/11/2022]
Abstract
Contractile injection systems (CISs) are phage tail-like nanomachines, mediating bacterial cell–cell interactions as either type VI secretion systems (T6SSs) or extracellular CISs (eCISs). Bioinformatic studies uncovered a phylogenetic group of hundreds of putative CIS gene clusters that are highly diverse and widespread; however, only four systems have been characterized. Here we studied a putative CIS gene cluster in the marine bacterium Algoriphagus machipongonensis. Using an integrative approach, we show that the system is compatible with an eCIS mode of action. Our cryo-electron microscopy structure revealed several features that differ from those seen in other CISs: a ‘cap adaptor’ located at the distal end, a ‘plug’ exposed to the tube lumen, and a ‘cage’ formed by massive extensions of the baseplate. These elements are conserved in other CISs, and our genetic tools identified that they are required for assembly, cargo loading and function. Furthermore, our atomic model highlights specific evolutionary hotspots and will serve as a framework for understanding and re−engineering CISs. The characterization of an extracellular contractile injection system (eCIS) from the marine bacterium Algoriphagus machipongonensis (AlgoCIS) reveals structural features linked to the assembly and function of this nanomachine.
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16
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Woznica A, Kumar A, Sturge CR, Xing C, King N, Pfeiffer JK. STING mediates immune responses in the closest living relatives of animals. eLife 2021; 10:70436. [PMID: 34730512 PMCID: PMC8592570 DOI: 10.7554/elife.70436] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 11/02/2021] [Indexed: 01/18/2023] Open
Abstract
Animals have evolved unique repertoires of innate immune genes and pathways that provide their first line of defense against pathogens. To reconstruct the ancestry of animal innate immunity, we have developed the choanoflagellate Monosiga brevicollis, one of the closest living relatives of animals, as a model for studying mechanisms underlying pathogen recognition and immune response. We found that M. brevicollis is killed by exposure to Pseudomonas aeruginosa bacteria. Moreover, M. brevicollis expresses STING, which, in animals, activates innate immune pathways in response to cyclic dinucleotides during pathogen sensing. M. brevicollis STING increases the susceptibility of M. brevicollis to P. aeruginosa-induced cell death and is required for responding to the cyclic dinucleotide 2'3' cGAMP. Furthermore, similar to animals, autophagic signaling in M. brevicollis is induced by 2'3' cGAMP in a STING-dependent manner. This study provides evidence for a pre-animal role for STING in antibacterial immunity and establishes M. brevicollis as a model system for the study of immune responses.
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Affiliation(s)
- Arielle Woznica
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Ashwani Kumar
- McDermott Center Bioinformatics Lab, University of Texas Southwestern Medical Center, Dallas, United States
| | - Carolyn R Sturge
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Chao Xing
- McDermott Center Bioinformatics Lab, University of Texas Southwestern Medical Center, Dallas, United States
| | - Nicole King
- Howard Hughes Medical Institute, and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Julie K Pfeiffer
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, United States
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17
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Kożyczkowska A, Najle SR, Ocaña-Pallarès E, Aresté C, Shabardina V, Ara PS, Ruiz-Trillo I, Casacuberta E. Stable transfection in protist Corallochytriumlimacisporum identifies novel cellular features among unicellular animals relatives. Curr Biol 2021; 31:4104-4110.e5. [PMID: 34293333 DOI: 10.1016/j.cub.2021.06.061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 05/07/2021] [Accepted: 06/22/2021] [Indexed: 01/31/2023]
Abstract
The evolutionary path from protists to multicellular animals remains a mystery. Recent work on the genomes of several unicellular relatives of animals has shaped our understanding of the genetic changes that may have occurred in this transition.1-3 However, the specific cellular modifications that took place to accommodate these changes remain unclear. To address this, we need to compare metazoan cells with those of their extant relatives, which are choanoflagellates, filastereans, ichthyosporeans, and corallochytreans/pluriformeans. Interestingly, these lineages display a range of developmental patterns potentially homologous to animal ones. Genetic tools have already been established in three of those lineages.4-7 However, there are no genetic tools available for Corallochytrea. We here report the development of stable transfection in the corallochytrean Corallochytrium limacisporum. Using these tools, we discern previously unknown biological features of C. limacisporum. In particular, we identify two different paths for cell division-binary fission and coenocytic growth-that reveal a non-linear life cycle. Additionally, we found that C. limacisporum is binucleate for most of its life cycle, and that, contrary to what happens in most eukaryotes, nuclear division is decoupled from cellular division. Moreover, its actin cytoskeleton shares characteristics with both fungal and animal cells. The establishment of these tools in C. limacisporum fills an important gap in the unicellular relatives of animals, opening up new avenues of research to elucidate the specific cellular changes that occurred in the evolution of animals.
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Affiliation(s)
- Aleksandra Kożyczkowska
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Sebastián R Najle
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Eduard Ocaña-Pallarès
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Cristina Aresté
- Department of Cell Death and Proliferation, IIBB-CSIC, IDIBAPS, 08036 Barcelona, Spain
| | - Victoria Shabardina
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Patricia S Ara
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain; Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Av. Diagonal, 645, 08028 Barcelona, Catalonia, Spain; ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Catalonia, Spain.
| | - Elena Casacuberta
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain.
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18
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Arthur AL, Crawford A, Houdusse A, Titus MA. VASP-mediated actin dynamics activate and recruit a filopodia myosin. eLife 2021; 10:68082. [PMID: 34042588 PMCID: PMC8352590 DOI: 10.7554/elife.68082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/20/2021] [Indexed: 11/17/2022] Open
Abstract
Filopodia are thin, actin-based structures that cells use to interact with their environments. Filopodia initiation requires a suite of conserved proteins but the mechanism remains poorly understood. The actin polymerase VASP and a MyTH-FERM (MF) myosin, DdMyo7 in amoeba, are essential for filopodia initiation. DdMyo7 is localized to dynamic regions of the actin-rich cortex. Analysis of VASP mutants and treatment of cells with anti-actin drugs shows that myosin recruitment and activation in Dictyostelium requires localized VASP-dependent actin polymerization. Targeting of DdMyo7 to the cortex alone is not sufficient for filopodia initiation; VASP activity is also required. The actin regulator locally produces a cortical actin network that activates myosin and together they shape the actin network to promote extension of parallel bundles of actin during filopodia formation. This work reveals how filopodia initiation requires close collaboration between an actin-binding protein, the state of the actin cytoskeleton and MF myosin activity.
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Affiliation(s)
- Ashley L Arthur
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Amy Crawford
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Anne Houdusse
- Structural Motility, Institut Curie, Paris Université Sciences et Lettres, Sorbonne Université, Paris, France
| | - Margaret A Titus
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
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19
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Muhr J, Hagey DW. The cell cycle and differentiation as integrated processes: Cyclins and CDKs reciprocally regulate Sox and Notch to balance stem cell maintenance. Bioessays 2021; 43:e2000285. [PMID: 34008221 DOI: 10.1002/bies.202000285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 04/15/2021] [Accepted: 04/21/2021] [Indexed: 12/18/2022]
Abstract
Development and maintenance of diverse organ systems require context-specific regulation of stem cell behaviour. We hypothesize that this is achieved via reciprocal regulation between the cell cycle machinery and differentiation factors. This idea is supported by the parallel evolutionary emergence of differentiation pathways, cell cycle components and complex multicellularity. In addition, the activities of different cell cycle phases have been found to bias cells towards stem cell maintenance or differentiation. Finally, several direct mechanistic links between these two processes have been established. Here, we focus on interactions between cyclin-CDK complexes and differentiation regulators of the Notch pathway and Sox family of transcription factors within the context of pluripotent and neural stem cells. Thus, this hypothesis formalizes the links between these two processes as an integrated network. Since such factors are common to all stem cells, better understanding their interconnections will help to explain their behaviour in health and disease.
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Affiliation(s)
- Jonas Muhr
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Daniel W Hagey
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
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20
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Ros-Rocher N, Pérez-Posada A, Leger MM, Ruiz-Trillo I. The origin of animals: an ancestral reconstruction of the unicellular-to-multicellular transition. Open Biol 2021; 11:200359. [PMID: 33622103 PMCID: PMC8061703 DOI: 10.1098/rsob.200359] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
How animals evolved from a single-celled ancestor, transitioning from a unicellular lifestyle to a coordinated multicellular entity, remains a fascinating question. Key events in this transition involved the emergence of processes related to cell adhesion, cell–cell communication and gene regulation. To understand how these capacities evolved, we need to reconstruct the features of both the last common multicellular ancestor of animals and the last unicellular ancestor of animals. In this review, we summarize recent advances in the characterization of these ancestors, inferred by comparative genomic analyses between the earliest branching animals and those radiating later, and between animals and their closest unicellular relatives. We also provide an updated hypothesis regarding the transition to animal multicellularity, which was likely gradual and involved the use of gene regulatory mechanisms in the emergence of early developmental and morphogenetic plans. Finally, we discuss some new avenues of research that will complement these studies in the coming years.
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Affiliation(s)
- Núria Ros-Rocher
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Alberto Pérez-Posada
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain.,Centro Andaluz de Biología del Desarrollo (CSIC-Universidad Pablo de Olavide), Carretera de Utrera Km 1, 41013 Sevilla, Andalusia, Spain
| | - Michelle M Leger
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain.,Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Catalonia, Spain.,ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Catalonia, Spain
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21
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Brunet T, Albert M, Roman W, Coyle MC, Spitzer DC, King N. A flagellate-to-amoeboid switch in the closest living relatives of animals. eLife 2021; 10:e61037. [PMID: 33448265 PMCID: PMC7895527 DOI: 10.7554/elife.61037] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 01/14/2021] [Indexed: 12/19/2022] Open
Abstract
Amoeboid cell types are fundamental to animal biology and broadly distributed across animal diversity, but their evolutionary origin is unclear. The closest living relatives of animals, the choanoflagellates, display a polarized cell architecture (with an apical flagellum encircled by microvilli) that resembles that of epithelial cells and suggests homology, but this architecture differs strikingly from the deformable phenotype of animal amoeboid cells, which instead evoke more distantly related eukaryotes, such as diverse amoebae. Here, we show that choanoflagellates subjected to confinement become amoeboid by retracting their flagella and activating myosin-based motility. This switch allows escape from confinement and is conserved across choanoflagellate diversity. The conservation of the amoeboid cell phenotype across animals and choanoflagellates, together with the conserved role of myosin, is consistent with homology of amoeboid motility in both lineages. We hypothesize that the differentiation between animal epithelial and crawling cells might have evolved from a stress-induced switch between flagellate and amoeboid forms in their single-celled ancestors.
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Affiliation(s)
- Thibaut Brunet
- Howard Hughes Medical Institute, Chevy Chase, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Marvin Albert
- Department of Molecular Life Sciences, University of Zürich, Zurich, Switzerland
| | - William Roman
- Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), CIBERNED, Barcelona, Spain
| | - Maxwell C Coyle
- Howard Hughes Medical Institute, Chevy Chase, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Danielle C Spitzer
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Nicole King
- Howard Hughes Medical Institute, Chevy Chase, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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22
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Ruiz-Trillo I, de Mendoza A. Towards understanding the origin of animal development. Development 2020; 147:147/23/dev192575. [PMID: 33272929 DOI: 10.1242/dev.192575] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Almost all animals undergo embryonic development, going from a single-celled zygote to a complex multicellular adult. We know that the patterning and morphogenetic processes involved in development are deeply conserved within the animal kingdom. However, the origins of these developmental processes are just beginning to be unveiled. Here, we focus on how the protist lineages sister to animals are reshaping our view of animal development. Most intriguingly, many of these protistan lineages display transient multicellular structures, which are governed by similar morphogenetic and gene regulatory processes as animal development. We discuss here two potential alternative scenarios to explain the origin of animal embryonic development: either it originated concomitantly at the onset of animals or it evolved from morphogenetic processes already present in their unicellular ancestors. We propose that an integrative study of several unicellular taxa closely related to animals will allow a more refined picture of how the last common ancestor of animals underwent embryonic development.
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Affiliation(s)
- Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta, 37-49, 08003 Barcelona, Spain .,Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain.,ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Alex de Mendoza
- Queen Mary University of London, School of Biological and Chemical Sciences, London E1 4DQ, UK
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23
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Evolution of the centrosome, from the periphery to the center. Curr Opin Struct Biol 2020; 66:96-103. [PMID: 33242728 DOI: 10.1016/j.sbi.2020.10.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/13/2020] [Accepted: 10/18/2020] [Indexed: 11/24/2022]
Abstract
Centrosomes are central organelles that organize microtubules (MTs) in animals, fungi and several other eukaryotic lineages. Despite an important diversity of structure, the centrosomes of different lineages share the same functions and part of their molecular components. To uncover how divergent centrosomes are related to each other, we need to trace the evolutionary history of MT organization. Careful assessment of cytoskeletal architecture in extant eukaryotic species can help us infer the ancestral state and identify the subsequent changes that took place during evolution. This led to the finding that the last common ancestor of all eukaryotes was very likely a biflagellate cell with a surprisingly complex cytoskeletal organization. Centrosomes are likely derived from the basal bodies of such flagellate, but when and how many times this happened remains unclear. Here, we discuss different hypotheses for how centrosomes evolved in a eukaryotic lineage called Amorphea, to which animals, fungi and amoebozoans belong.
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24
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Booth DS, King N. Genome editing enables reverse genetics of multicellular development in the choanoflagellate Salpingoeca rosetta. eLife 2020; 9:56193. [PMID: 32496191 PMCID: PMC7314544 DOI: 10.7554/elife.56193] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/03/2020] [Indexed: 12/20/2022] Open
Abstract
In a previous study, we established a forward genetic screen to identify genes required for multicellular development in the choanoflagellate, Salpingoeca rosetta (Levin et al., 2014). Yet, the paucity of reverse genetic tools for choanoflagellates has hampered direct tests of gene function and impeded the establishment of choanoflagellates as a model for reconstructing the origin of their closest living relatives, the animals. Here we establish CRISPR/Cas9-mediated genome editing in S. rosetta by engineering a selectable marker to enrich for edited cells. We then use genome editing to disrupt the coding sequence of a S. rosetta C-type lectin gene, rosetteless, and thereby demonstrate its necessity for multicellular rosette development. This work advances S. rosetta as a model system in which to investigate how genes identified from genetic screens and genomic surveys function in choanoflagellates and evolved as critical regulators of animal biology.
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Affiliation(s)
- David S Booth
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Nicole King
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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25
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Medina EM, Robinson KA, Bellingham-Johnstun K, Ianiri G, Laplante C, Fritz-Laylin LK, Buchler NE. Genetic transformation of Spizellomyces punctatus, a resource for studying chytrid biology and evolutionary cell biology. eLife 2020; 9:52741. [PMID: 32392127 PMCID: PMC7213984 DOI: 10.7554/elife.52741] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 04/23/2020] [Indexed: 02/07/2023] Open
Abstract
Chytrids are early-diverging fungi that share features with animals that have been lost in most other fungi. They hold promise as a system to study fungal and animal evolution, but we lack genetic tools for hypothesis testing. Here, we generated transgenic lines of the chytrid Spizellomyces punctatus, and used fluorescence microscopy to explore chytrid cell biology and development during its life cycle. We show that the chytrid undergoes multiple rounds of synchronous nuclear division, followed by cellularization, to create and release many daughter ‘zoospores’. The zoospores, akin to animal cells, crawl using actin-mediated cell migration. After forming a cell wall, polymerized actin reorganizes into fungal-like cortical patches and cables that extend into hyphal-like structures. Actin perinuclear shells form each cell cycle and polygonal territories emerge during cellularization. This work makes Spizellomyces a genetically tractable model for comparative cell biology and understanding the evolution of fungi and early eukaryotes.
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Affiliation(s)
- Edgar M Medina
- University of Program in Genetics and Genomics, Duke University, Durham, United States.,Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Kristyn A Robinson
- Department of Biology, University of Massachusetts, Amherst, United States
| | | | - Giuseppe Ianiri
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Caroline Laplante
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, United States
| | | | - Nicolas E Buchler
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, United States
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26
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Brunet T, Larson BT, Linden TA, Vermeij MJA, McDonald K, King N. Light-regulated collective contractility in a multicellular choanoflagellate. Science 2020; 366:326-334. [PMID: 31624206 DOI: 10.1126/science.aay2346] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 09/16/2019] [Indexed: 12/11/2022]
Abstract
Collective cell contractions that generate global tissue deformations are a signature feature of animal movement and morphogenesis. However, the origin of collective contractility in animals remains unclear. While surveying the Caribbean island of Curaçao for choanoflagellates, the closest living relatives of animals, we isolated a previously undescribed species (here named Choanoeca flexa sp. nov.) that forms multicellular cup-shaped colonies. The colonies rapidly invert their curvature in response to changing light levels, which they detect through a rhodopsin-cyclic guanosine monophosphate pathway. Inversion requires actomyosin-mediated apical contractility and allows alternation between feeding and swimming behavior. C. flexa thus rapidly converts sensory inputs directly into multicellular contractions. These findings may inform reconstructions of hypothesized animal ancestors that existed before the evolution of specialized sensory and contractile cells.
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Affiliation(s)
- Thibaut Brunet
- Howard Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Ben T Larson
- Howard Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.,Biophysics Graduate Group, University of California, Berkeley, CA, USA
| | - Tess A Linden
- Howard Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Mark J A Vermeij
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, CARMABI, Piscaderabaai z/n Willemstad, Curaçao
| | - Kent McDonald
- Electron Microscopy Laboratory, University of California, Berkeley, CA, USA
| | - Nicole King
- Howard Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
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27
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Sprecher BN, Zhang H, Lin S. Nuclear Gene Transformation in the Dinoflagellate Oxyrrhis marina. Microorganisms 2020; 8:E126. [PMID: 31963386 PMCID: PMC7022241 DOI: 10.3390/microorganisms8010126] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/10/2020] [Accepted: 01/14/2020] [Indexed: 11/16/2022] Open
Abstract
The lack of a robust gene transformation tool that allows proper expression of foreign genes and functional testing for the vast number of nuclear genes in dinoflagellates has greatly hampered our understanding of the fundamental biology in this ecologically important and evolutionarily unique lineage of microeukaryotes. Here, we report the development of a dinoflagellate expression vector containing various DNA elements from phylogenetically separate dinoflagellate lineages, an electroporation protocol, and successful expression of introduced genes in an early branching dinoflagellate, Oxyrrhis marina. This protocol, involving the use of Lonza's Nucleofector and a codon-optimized antibiotic resistance gene, has been successfully used to produce consistent results in several independent experiments for O. marina. It is anticipated that this protocol will be adaptable for other dinoflagellates and will allow characterization of many novel dinoflagellate genes.
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Affiliation(s)
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, 1080 Shennecossett Rd, Groton, CT 06340, USA;
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, 1080 Shennecossett Rd, Groton, CT 06340, USA;
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Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nat Methods 2020; 17:481-494. [PMID: 32251396 PMCID: PMC7200600 DOI: 10.1038/s41592-020-0796-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 03/02/2020] [Indexed: 12/13/2022]
Abstract
Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of protists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways.
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Naumann B, Burkhardt P. Spatial Cell Disparity in the Colonial Choanoflagellate Salpingoeca rosetta. Front Cell Dev Biol 2019; 7:231. [PMID: 31681764 PMCID: PMC6803389 DOI: 10.3389/fcell.2019.00231] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/26/2019] [Indexed: 11/13/2022] Open
Abstract
Choanoflagellates are the closest unicellular relatives of animals (Metazoa). These tiny protists display complex life histories that include sessile as well as different pelagic stages. Some choanoflagellates have the ability to form colonies as well. Up until recently, these colonies have been described to consist of mostly identical cells showing no spatial cell differentiation, which supported the traditional view that spatial cell differentiation, leading to the co-existence of specific cell types in animals, evolved after the split of the last common ancestor of the Choanoflagellata and Metazoa. The recent discovery of single cells in colonies of the choanoflagellate Salpingoeca rosetta that exhibit unique cell morphologies challenges this traditional view. We have now reanalyzed TEM serial sections, aiming to determine the degree of similarity of S. rosetta cells within a rosette colony. We investigated cell morphologies and nuclear, mitochondrial, and food vacuole volumes of 40 individual cells from four different S. rosetta rosette colonies and compared our findings to sponge choanocytes. Our analysis shows that cells in a choanoflagellate colony differ from each other in respect to cell morphology and content ratios of nuclei, mitochondria, and food vacuoles. Furthermore, cell disparity within S. rosetta colonies is slightly higher compared to cell disparity within sponge choanocytes. Moreover, we discovered the presence of plasma membrane contacts between colonial cells in addition to already described intercellular bridges and filo-/pseudopodial contacts. Our findings indicate that the last common ancestor of Choanoflagellata and Metazoa might have possessed plasma membrane contacts and spatial cell disparity during colonial life history stages.
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Affiliation(s)
- Benjamin Naumann
- Institute of Zoology and Evolutionary Research, Friedrich Schiller University Jena, Jena, Germany
| | - Pawel Burkhardt
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
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30
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Sachkova M, Burkhardt P. Exciting times to study the identity and evolution of cell types. Development 2019; 146:146/18/dev178996. [DOI: 10.1242/dev.178996] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
ABSTRACT
The EMBO/EMBL Symposium on ‘The Identity and Evolution of Cell Types’ took place in Heidelberg, Germany, on 15-19 May 2019. The symposium, which brought together a diverse group of speakers addressing a wide range of questions in multiple model systems, provided a platform to discuss how the concept of a cell type should be considered in the era of single cell omics techniques and how cell type evolution can be studied.
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Affiliation(s)
- Maria Sachkova
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
| | - Pawel Burkhardt
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
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31
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Collier JL, Rest JS. Swimming, gliding, and rolling toward the mainstream: cell biology of marine protists. Mol Biol Cell 2019; 30:1245-1248. [PMID: 31084566 PMCID: PMC6724603 DOI: 10.1091/mbc.e18-11-0724] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/14/2019] [Accepted: 03/20/2019] [Indexed: 12/22/2022] Open
Abstract
Marine protists are a polyphyletic group of organisms playing major roles in the ecology and biogeochemistry of the oceans, including performing much of Earth's photosynthesis and driving the carbon, nitrogen, and silicon cycles. In addition, marine protists occupy key positions in the tree of life, including as the closest relatives of metazoans. Despite all the reasons to better understand them, knowledge of the cell biology of most marine protist lineages is sparse. This is beginning to change thanks to vibrant growth in the development of new model organisms. Here, we survey some recent advances in studying the cell biology of marine protists toward understanding the functional basis of their unique features, gaining new perspectives on universal eukaryotic biology, and for understanding homologous biology within metazoans and the evolution of metazoan traits.
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Affiliation(s)
- Jackie L. Collier
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000
| | - Joshua S. Rest
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245
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32
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Abstract
Recent advances in both phylogenetic comparisons and the development of experimentally tractable organisms, in the growing field of evolutionary cell biology, pave the way for gaining a molecular understanding of the development of multicellularity in the animal lineage.
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Affiliation(s)
- Margaret A Titus
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Holly V Goodson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
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33
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Wetzel LA, Levin TC, Hulett RE, Chan D, King GA, Aldayafleh R, Booth DS, Sigg MA, King N. Predicted glycosyltransferases promote development and prevent spurious cell clumping in the choanoflagellate S. rosetta. eLife 2018; 7:e41482. [PMID: 30556809 PMCID: PMC6322860 DOI: 10.7554/elife.41482] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/14/2018] [Indexed: 12/19/2022] Open
Abstract
In a previous study we established forward genetics in the choanoflagellate Salpingoeca rosetta and found that a C-type lectin gene is required for rosette development (Levin et al., 2014). Here we report on critical improvements to genetic screens in S. rosetta while also investigating the genetic basis for rosette defect mutants in which single cells fail to develop into orderly rosettes and instead aggregate promiscuously into amorphous clumps of cells. Two of the mutants, Jumble and Couscous, mapped to lesions in genes encoding two different predicted glycosyltransferases and displayed aberrant glycosylation patterns in the basal extracellular matrix (ECM). In animals, glycosyltransferases sculpt the polysaccharide-rich ECM, regulate integrin and cadherin activity, and, when disrupted, contribute to tumorigenesis. The finding that predicted glycosyltransferases promote proper rosette development and prevent cell aggregation in S. rosetta suggests a pre-metazoan role for glycosyltransferases in regulating development and preventing abnormal tumor-like multicellularity.
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Affiliation(s)
- Laura A Wetzel
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Tera C Levin
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Ryan E Hulett
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Daniel Chan
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Grant A King
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Reef Aldayafleh
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - David S Booth
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Monika Abedin Sigg
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Nicole King
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
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