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Shah H, Olivetta M, Bhickta C, Ronchi P, Trupinić M, Tromer EC, Tolić IM, Schwab Y, Dudin O, Dey G. Life-cycle-coupled evolution of mitosis in close relatives of animals. Nature 2024; 630:116-122. [PMID: 38778110 PMCID: PMC11153136 DOI: 10.1038/s41586-024-07430-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 04/16/2024] [Indexed: 05/25/2024]
Abstract
Eukaryotes have evolved towards one of two extremes along a spectrum of strategies for remodelling the nuclear envelope during cell division: disassembling the nuclear envelope in an open mitosis or constructing an intranuclear spindle in a closed mitosis1,2. Both classes of mitotic remodelling involve key differences in the core division machinery but the evolutionary reasons for adopting a specific mechanism are unclear. Here we use an integrated comparative genomics and ultrastructural imaging approach to investigate mitotic strategies in Ichthyosporea, close relatives of animals and fungi. We show that species in this clade have diverged towards either a fungal-like closed mitosis or an animal-like open mitosis, probably to support distinct multinucleated or uninucleated states. Our results indicate that multinucleated life cycles favour the evolution of closed mitosis.
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Affiliation(s)
- Hiral Shah
- Cell Biology and Biophysics, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
| | - Marine Olivetta
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Chandni Bhickta
- Cell Biology and Biophysics, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Paolo Ronchi
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Monika Trupinić
- Division of Molecular Biology, Ruđer Bošković Institute (RBI), Zagreb, Croatia
| | - Eelco C Tromer
- Cell Biochemistry, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Iva M Tolić
- Division of Molecular Biology, Ruđer Bošković Institute (RBI), Zagreb, Croatia
| | - Yannick Schwab
- Cell Biology and Biophysics, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Omaya Dudin
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
| | - Gautam Dey
- Cell Biology and Biophysics, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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2
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Larson BT. Perspectives on Principles of Cellular Behavior from the Biophysics of Protists. Integr Comp Biol 2023; 63:1405-1421. [PMID: 37496203 PMCID: PMC10755178 DOI: 10.1093/icb/icad106] [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: 03/22/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 07/28/2023] Open
Abstract
Cells are the fundamental unit of biological organization. Although it may be easy to think of them as little more than the simple building blocks of complex organisms such as animals, single cells are capable of behaviors of remarkable apparent sophistication. This is abundantly clear when considering the diversity of form and function among the microbial eukaryotes, the protists. How might we navigate this diversity in the search for general principles of cellular behavior? Here, we review cases in which the intensive study of protists from the perspective of cellular biophysics has driven insight into broad biological questions of morphogenesis, navigation and motility, and decision making. We argue that applying such approaches to questions of evolutionary cell biology presents rich, emerging opportunities. Integrating and expanding biophysical studies across protist diversity, exploiting the unique characteristics of each organism, will enrich our understanding of general underlying principles.
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Affiliation(s)
- Ben T Larson
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
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3
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Chavhan Y, Dey S, Lind PA. Bacteria evolve macroscopic multicellularity by the genetic assimilation of phenotypically plastic cell clustering. Nat Commun 2023; 14:3555. [PMID: 37322016 PMCID: PMC10272148 DOI: 10.1038/s41467-023-39320-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 06/05/2023] [Indexed: 06/17/2023] Open
Abstract
The evolutionary transition from unicellularity to multicellularity was a key innovation in the history of life. Experimental evolution is an important tool to study the formation of undifferentiated cellular clusters, the likely first step of this transition. Although multicellularity first evolved in bacteria, previous experimental evolution research has primarily used eukaryotes. Moreover, it focuses on mutationally driven (and not environmentally induced) phenotypes. Here we show that both Gram-negative and Gram-positive bacteria exhibit phenotypically plastic (i.e., environmentally induced) cell clustering. Under high salinity, they form elongated clusters of ~ 2 cm. However, under habitual salinity, the clusters disintegrate and grow planktonically. We used experimental evolution with Escherichia coli to show that such clustering can be assimilated genetically: the evolved bacteria inherently grow as macroscopic multicellular clusters, even without environmental induction. Highly parallel mutations in genes linked to cell wall assembly formed the genomic basis of assimilated multicellularity. While the wildtype also showed cell shape plasticity across high versus low salinity, it was either assimilated or reversed after evolution. Interestingly, a single mutation could genetically assimilate multicellularity by modulating plasticity at multiple levels of organization. Taken together, we show that phenotypic plasticity can prime bacteria for evolving undifferentiated macroscopic multicellularity.
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Affiliation(s)
- Yashraj Chavhan
- Department of Molecular Biology, Umeå University, Umeå, Sweden.
| | - Sutirth Dey
- Indian Institute of Science Education and Research (IISER) Pune, Pune, India
| | - Peter A Lind
- Department of Molecular Biology, Umeå University, Umeå, Sweden.
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden.
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4
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Barrere J, Nanda P, Murray AW. Alternating selection for dispersal and multicellularity favors regulated life cycles. Curr Biol 2023; 33:1809-1817.e3. [PMID: 37019107 PMCID: PMC10175205 DOI: 10.1016/j.cub.2023.03.031] [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: 10/14/2022] [Revised: 01/23/2023] [Accepted: 03/10/2023] [Indexed: 04/07/2023]
Abstract
The evolution of complex multicellularity opened paths to increased morphological diversity and organizational novelty. This transition involved three processes: cells remained attached to one another to form groups, cells within these groups differentiated to perform different tasks, and the groups evolved new reproductive strategies.1,2,3,4,5 Recent experiments identified selective pressures and mutations that can drive the emergence of simple multicellularity and cell differentiation,6,7,8,9,10,11 but the evolution of life cycles, particularly how simple multicellular forms reproduce, has been understudied. The selective pressure and mechanisms that produced a regular alternation between single cells and multicellular collectives are still unclear.12 To probe the factors regulating simple multicellular life cycles, we examined a collection of wild isolates of the budding yeast S. cerevisiae.12,13 We found that all these strains can exist as multicellular clusters, a phenotype that is controlled by the mating-type locus and strongly influenced by the nutritional environment. Inspired by this variation, we engineered inducible dispersal in a multicellular laboratory strain and demonstrated that a regulated life cycle has an advantage over constitutively single-celled or constitutively multicellular life cycles when the environment alternates between favoring intercellular cooperation (a low sucrose concentration) and dispersal (a patchy environment generated by emulsion). Our results suggest that the separation of mother and daughter cells is under selection in wild isolates and is regulated by their genetic composition and the environments they encounter and that alternating patterns of resource availability may have played a role in the evolution of life cycles.
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Affiliation(s)
- Julien Barrere
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Piyush Nanda
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Andrew W Murray
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
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5
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Olivetta M, Dudin O. The nuclear-to-cytoplasmic ratio drives cellularization in the close animal relative Sphaeroforma arctica. Curr Biol 2023; 33:1597-1605.e3. [PMID: 36996815 DOI: 10.1016/j.cub.2023.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/17/2023] [Accepted: 03/07/2023] [Indexed: 03/31/2023]
Abstract
The ratio of nuclear content to cytoplasmic volume (N/C ratio) is a key regulator driving the maternal-to-zygotic transition in most animal embryos. Altering this ratio often impacts zygotic genome activation and deregulates the timing and outcome of embryogenesis.1,2,3 Despite being ubiquitous across animals, little is known about when the N/C ratio evolved to control multicellular development. Such capacity either originated with the emergence of animal multicellularity or was co-opted from the mechanisms present in unicellular organisms.4 An effective strategy to tackle this question is to investigate the close relatives of animals exhibiting life cycles with transient multicellular stages.5 Among these are ichthyosporeans, a lineage of protists undergoing coenocytic development followed by cellularization and cell release.6,7,8 During cellularization, a transient multicellular stage resembling animal epithelia is generated, offering a unique opportunity to examine whether the N/C ratio regulates multicellular development. Here, we use time-lapse microscopy to characterize how the N/C ratio affects the life cycle of the best-studied ichthyosporean model, Sphaeroforma arctica. We uncover that the last stages of cellularization coincide with a significant increase in the N/C ratio. Increasing the N/C ratio by reducing the coenocytic volume accelerates cellularization, whereas decreasing the N/C ratio by lowering the nuclear content halts it. Moreover, centrifugation and pharmacological inhibitor experiments suggest that the N/C ratio is locally sensed at the cortex and relies on phosphatase activity. Altogether, our results show that the N/C ratio drives cellularization in S. arctica, suggesting that its capacity to control multicellular development predates animal emergence.
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6
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McCartney B, Dudin O. Cellularization across eukaryotes: Conserved mechanisms and novel strategies. Curr Opin Cell Biol 2023; 80:102157. [PMID: 36857882 DOI: 10.1016/j.ceb.2023.102157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 03/02/2023]
Abstract
Many eukaryotes form multinucleated cells during their development. Some cells persist as such during their lifetime, others choose to cleave each nucleus individually using a specialized cytokinetic process known as cellularization. What is cellularization and how is it achieved across the eukaryotic tree of life? Are there common pathways among all species supporting a shared ancestry, or are there key differences, suggesting independent evolutionary paths? In this review, we discuss common strategies and key mechanistic differences in how cellularization is executed across vastly divergent eukaryotic species. We present a number of novel methods and non-model organisms that may provide important insight into the evolutionary origins of cellularization.
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Affiliation(s)
- Brooke McCartney
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Omaya Dudin
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
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7
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Puttrich T, O’Donnell S, Wong SW, Kotche M, Felder AE, Shin JW. Development of a programmable magnetic agitation device to maintain colloidal suspension of cells during microfluidic syringe pump perfusion. PLoS One 2023; 18:e0282563. [PMID: 36888609 PMCID: PMC9994697 DOI: 10.1371/journal.pone.0282563] [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: 09/16/2022] [Accepted: 02/20/2023] [Indexed: 03/09/2023] Open
Abstract
Droplet-based microfluidic devices have been used to achieve homogeneous cell encapsulation, but cells sediment in a solution, leading to heterogeneous products. In this technical note, we describe automated and programmable agitation device to maintain colloidal suspensions of cells. We demonstrate that the agitation device can be interfaced with a syringe pump for microfluidic applications. Agitation profiles of the device were predictable and corresponded to device settings. The device maintains the concentration of cells in an alginate solution over time without implicating cell viability. This device replaces manual agitation, and hence is suitable for applications that require slow perfusion for a longer period of time in a scalable manner.
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Affiliation(s)
- Tommy Puttrich
- The Richard and Loan Hill Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Steven O’Donnell
- The Richard and Loan Hill Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Sing-Wan Wong
- The Richard and Loan Hill Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Miiri Kotche
- The Richard and Loan Hill Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Anthony E. Felder
- The Richard and Loan Hill Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail: (JWS); (AEF)
| | - Jae-Won Shin
- The Richard and Loan Hill Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail: (JWS); (AEF)
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8
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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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9
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Day TC, Márquez-Zacarías P, Bravo P, Pokhrel AR, MacGillivray KA, Ratcliff WC, Yunker PJ. Varied solutions to multicellularity: The biophysical and evolutionary consequences of diverse intercellular bonds. BIOPHYSICS REVIEWS 2022; 3:021305. [PMID: 35673523 PMCID: PMC9164275 DOI: 10.1063/5.0080845] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/29/2022] [Indexed: 11/16/2022]
Abstract
The diversity of multicellular organisms is, in large part, due to the fact that multicellularity has independently evolved many times. Nonetheless, multicellular organisms all share a universal biophysical trait: cells are attached to each other. All mechanisms of cellular attachment belong to one of two broad classes; intercellular bonds are either reformable or they are not. Both classes of multicellular assembly are common in nature, having independently evolved dozens of times. In this review, we detail these varied mechanisms as they exist in multicellular organisms. We also discuss the evolutionary implications of different intercellular attachment mechanisms on nascent multicellular organisms. The type of intercellular bond present during early steps in the transition to multicellularity constrains future evolutionary and biophysical dynamics for the lineage, affecting the origin of multicellular life cycles, cell-cell communication, cellular differentiation, and multicellular morphogenesis. The types of intercellular bonds used by multicellular organisms may thus result in some of the most impactful historical constraints on the evolution of multicellularity.
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Affiliation(s)
- Thomas C. Day
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | | | | | - Aawaz R. Pokhrel
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | | | - William C. Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Peter J. Yunker
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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10
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Burnetti A, Ratcliff WC. Experimental evolution is not just for model organisms. PLoS Biol 2022; 20:e3001587. [PMID: 35353805 PMCID: PMC8967026 DOI: 10.1371/journal.pbio.3001587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
This Primer explores the implications of a new PLOS Biology study in which the authors evolve simple multicellularity in Sphaeroforma arctica, a unicellular relative of animals; this work establishes a new and open-ended avenue for examining the evolution of multicellularity at the base of the metazoa.
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Affiliation(s)
- Anthony Burnetti
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail: (AB); (WCR)
| | - William C. Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail: (AB); (WCR)
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