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Narayanasamy N, Bingham E, Fadero T, Ozan Bozdag G, Ratcliff WC, Yunker P, Thutupalli S. Metabolically-driven flows enable exponential growth in macroscopic multicellular yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.19.599734. [PMID: 38948761 PMCID: PMC11213004 DOI: 10.1101/2024.06.19.599734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The ecological and evolutionary success of multicellular lineages is due in no small part to their increased size relative to unicellular ancestors. However, large size also poses biophysical challenges, especially regarding the transport of nutrients to all cells; these constraints are typically overcome through multicellular innovations (e.g., a circulatory system). Here we show that an emergent biophysical mechanism - spontaneous fluid flows arising from metabolically-generated density gradients - can alleviate constraints on nutrient transport, enabling exponential growth in nascent multicellular clusters of yeast lacking any multicellular adaptations for nutrient transport or fluid flow. Surprisingly, beyond a threshold size, the metabolic activity of experimentally-evolved snowflake yeast clusters drives large-scale fluid flows that transport nutrients throughout the cluster at speeds comparable to those generated by the cilia of extant multicellular organisms. These flows support exponential growth at macroscopic sizes that theory predicts should be diffusion limited. This work demonstrates how simple physical mechanisms can act as a 'biophysical scaffold' to support the evolution of multicellularity by opening up phenotypic possibilities prior to genetically-encoded innovations. More broadly, our findings highlight how co-option of conserved physical processes is a crucial but underappreciated facet of evolutionary innovation across scales.
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Affiliation(s)
- Nishant Narayanasamy
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences (TIFR), Bangalore, India
| | - Emma Bingham
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - G Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Peter Yunker
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shashi Thutupalli
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences (TIFR), Bangalore, India
- International Centre for Theoretical Sciences (TIFR), Bangalore, India
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2
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Nanda P, Barrere J, LaBar T, Murray AW. A dynamic network model predicts the phenotypes of multicellular clusters from cellular properties. Curr Biol 2024; 34:2672-2683.e4. [PMID: 38823384 DOI: 10.1016/j.cub.2024.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 03/20/2024] [Accepted: 05/08/2024] [Indexed: 06/03/2024]
Abstract
Cell division without cell separation produces multicellular clusters in budding yeast. Two fundamental characteristics of these clusters are their size (the number of cells per cluster) and cellular composition: the fractions of cells with different phenotypes. Using cells as nodes and links between mother and daughter cells as edges, we model cluster growth and breakage by varying three parameters: the cell division rate, the rate at which intercellular connections break, and the kissing number (the maximum number of connections to one cell). We find that the kissing number sets the maximum possible cluster size. Below this limit, the ratio of the cell division rate to the connection breaking rate determines the cluster size. If links have a constant probability of breaking per unit time, the probability that a link survives decreases exponentially with its age. Modeling this behavior recapitulates experimental data. We then use this framework to examine synthetic, differentiating clusters with two cell types, faster-growing germ cells and their somatic derivatives. The fraction of clusters that contain both cell types increases as either of two parameters increase: the kissing number and difference between the growth rate of germ and somatic cells. In a population of clusters, the variation in cellular composition is inversely correlated (r2 = 0.87) with the average fraction of somatic cells in clusters. Our results show how a small number of cellular features can control the phenotypes of multicellular clusters that were potentially the ancestors of more complex forms of multicellular development, organization, and reproduction.
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Affiliation(s)
- Piyush Nanda
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Julien Barrere
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Thomas LaBar
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Andrew W Murray
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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3
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Tong K, Datta S, Cheng V, Haas DJ, Gourisetti S, Yopp HL, Day TC, Lac DT, Conlin PL, Bozdag GO, Ratcliff WC. Whole-genome duplication in the Multicellularity Long Term Evolution Experiment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.588554. [PMID: 38659912 PMCID: PMC11042302 DOI: 10.1101/2024.04.18.588554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Whole-genome duplication (WGD) is widespread across eukaryotes and can promote adaptive evolution1-4. However, given the instability of newly-formed polyploid genomes5-7, understanding how WGDs arise in a population, persist, and underpin adaptations remains a challenge. Using our ongoing Multicellularity Long Term Evolution Experiment (MuLTEE)8, we show that diploid snowflake yeast (Saccharomyces cerevisiae) under selection for larger multicellular size rapidly undergo spontaneous WGD. From its origin within the first 50 days of the experiment, tetraploids persist for the next 950 days (nearly 5,000 generations, the current leading edge of our experiment) in ten replicate populations, despite being genomically unstable. Using synthetic reconstruction, biophysical modeling, and counter-selection experiments, we found that tetraploidy evolved because it confers immediate fitness benefits in this environment, by producing larger, longer cells that yield larger clusters. The same selective benefit also maintained tetraploidy over long evolutionary timescales, inhibiting the reversion to diploidy that is typically seen in laboratory evolution experiments. Once established, tetraploidy facilitated novel genetic routes for adaptation, playing a key role in the evolution of macroscopic multicellular size via the origin of evolutionarily conserved aneuploidy. These results provide unique empirical insights into the evolutionary dynamics and impacts of WGD, showing how it can initially arise due to its immediate adaptive benefits, be maintained by selection, and fuel long-term innovations by creating additional dimensions of heritable genetic variation.
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Affiliation(s)
- Kai Tong
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Sayantan Datta
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Vivian Cheng
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Daniella J. Haas
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Mayo Clinic Alix School of Medicine, Rochester, MN, USA
| | - Saranya Gourisetti
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Harley L. Yopp
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Thomas C. Day
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Dung T. Lac
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Peter L. Conlin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - G. Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - William C. Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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4
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Cupo C, Allan C, Ailiani V, Kasza KE. Signatures of structural disorder in developing epithelial tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.12.579900. [PMID: 38405955 PMCID: PMC10888831 DOI: 10.1101/2024.02.12.579900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Epithelial cells generate functional tissues in developing embryos through collective movements and shape changes. In some morphogenetic events, a tissue dramatically reorganizes its internal structure - often generating high degrees of structural disorder - to accomplish changes in tissue shape. However, the origins of structural disorder in epithelia and what roles it might play in morphogenesis are poorly understood. We study this question in the Drosophila germband epithelium, which undergoes dramatic changes in internal structure as cell rearrangements drive elongation of the embryo body axis. Using two order parameters that quantify volumetric and shear disorder, we show that structural disorder increases during body axis elongation and is strongly linked with specific developmental processes. Both disorder metrics begin to increase around the onset of axis elongation, but then plateau at values that are maintained throughout the process. Notably, the disorder plateau values for volumetric disorder are similar to those for random cell packings, suggesting this may reflect a limit on tissue behavior. In mutant embryos with disrupted external stresses from the ventral furrow, both disorder metrics reach wild-type maximum disorder values with a delay, correlating with delays in cell rearrangements. In contrast, in mutants with disrupted internal stresses and cell rearrangements, volumetric disorder is reduced compared to wild type, whereas shear disorder depends on specific external stress patterns. Together, these findings demonstrate that internal and external stresses both contribute to epithelial tissue disorder and suggest that the maximum values of disorder in a developing tissue reflect physical or biological limits on morphogenesis.
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Skene KR. Systems theory, thermodynamics and life: Integrated thinking across ecology, organization and biological evolution. Biosystems 2024; 236:105123. [PMID: 38244715 DOI: 10.1016/j.biosystems.2024.105123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 01/22/2024]
Abstract
In this paper we explore the relevance and integration of system theory and thermodynamics in terms of the Earth system. It is proposed that together, these fields explain the evolution, organization, functionality and directionality of life on Earth. We begin by summarizing historical and current thinking on the definition of life itself. We then investigate the evidence for a single unit of life. Given that any definition of life and its levels of organization are intertwined, we explore how the Earth system is structured and functions from an energetic perspective, by outlining relevant thermodynamic theory relating to molecular, metabolic, cellular, individual, population, species, ecosystem and biome organization. We next investigate the fundamental relationships between systems theory and thermodynamics in terms of the Earth system, examining the key characteristics of self-assembly, self-organization (including autonomy), emergence, non-linearity, feedback and sub-optimality. Finally, we examine the relevance of systems theory and thermodynamics with reference to two specific aspects: the tempo and directionality of evolution and the directional and predictable process of ecological succession. We discuss the importance of the entropic drive in understanding altruism, multicellularity, mutualistic and antagonistic relationships and how maximum entropy production theory may explain patterns thought to evidence the intermediate disturbance hypothesis.
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Affiliation(s)
- Keith R Skene
- Biosphere Research Institute, Angus, United Kingdom.
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6
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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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7
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Skinner DJ, Jeckel H, Martin AC, Drescher K, Dunkel J. Topological packing statistics of living and nonliving matter. SCIENCE ADVANCES 2023; 9:eadg1261. [PMID: 37672580 PMCID: PMC10482333 DOI: 10.1126/sciadv.adg1261] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 07/27/2023] [Indexed: 09/08/2023]
Abstract
Complex disordered matter is of central importance to a wide range of disciplines, from bacterial colonies and embryonic tissues in biology to foams and granular media in materials science to stellar configurations in astrophysics. Because of the vast differences in composition and scale, comparing structural features across such disparate systems remains challenging. Here, by using the statistical properties of Delaunay tessellations, we introduce a mathematical framework for measuring topological distances between general three-dimensional point clouds. The resulting system-agnostic metric reveals subtle structural differences between bacterial biofilms as well as between zebrafish brain regions, and it recovers temporal ordering of embryonic development. We apply the metric to construct a universal topological atlas encompassing bacterial biofilms, snowflake yeast, plant shoots, zebrafish brain matter, organoids, and embryonic tissues as well as foams, colloidal packings, glassy materials, and stellar configurations. Living systems localize within a bounded island-like region of the atlas, reflecting that biological growth mechanisms result in characteristic topological properties.
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Affiliation(s)
- Dominic J Skinner
- Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Hannah Jeckel
- Department of Physics, Philipps-Universität Marburg, Renthof 6, 35032 Marburg, Germany
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Adam C Martin
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Knut Drescher
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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8
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von der Heyde B, von der Heyde EL, Hallmann A. Cell Type-Specific Promoters of Volvox carteri for Molecular Cell Biology Studies. Genes (Basel) 2023; 14:1389. [PMID: 37510294 PMCID: PMC10379329 DOI: 10.3390/genes14071389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
The multicellular green alga Volvox carteri has emerged as a valuable model organism for investigating various aspects of multicellularity and cellular differentiation, photoreception and phototaxis, cell division, biogenesis of the extracellular matrix and morphogenetic movements. While a range of molecular tools and bioinformatics resources have been made available for exploring these topics, the establishment of cell type-specific promoters in V. carteri has not been achieved so far. Therefore, here, we conducted a thorough screening of transcriptome data from RNA sequencing analyses of V. carteri in order to identify potential cell type-specific promoters. Eventually, we chose two putative strong and cell type-specific promoters, with one exhibiting specific expression in reproductive cells (gonidia), the PCY1 promoter, and the other in somatic cells, the PFP promoter. After cloning both promoter regions, they were introduced upstream of a luciferase reporter gene. By using particle bombardment, the DNA constructs were stably integrated into the genome of V. carteri. The results of the expression analyses, which were conducted at both the transcript and protein levels, demonstrated that the two promoters drive cell type-specific expression in their respective target cell types. Transformants with considerably diverse expression levels of the chimeric genes were identifiable. In conclusion, the screening and analysis of transcriptome data from RNA sequencing allowed for the identification of potential cell type-specific promoters in V. carteri. Reporter gene constructs demonstrated the actual usability of two promoters. The investigated PCY1 and PFP promoters were proven to be potent molecular tools for genetic engineering in V. carteri.
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Affiliation(s)
- Benjamin von der Heyde
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Eva Laura von der Heyde
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Armin Hallmann
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
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9
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Pineau RM, Demory D, Libby E, Lac DT, Day TC, Bravo P, Yunker PJ, Weitz JS, Bozdag GO, Ratcliff WC. Emergence and maintenance of stable coexistence during a long-term multicellular evolution experiment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.19.524803. [PMID: 36711513 PMCID: PMC9882323 DOI: 10.1101/2023.01.19.524803] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The evolution of multicellular life spurred evolutionary radiations, fundamentally changing many of Earth’s ecosystems. Yet little is known about how early steps in the evolution of multicellularity transform eco-evolutionary dynamics, e.g., via niche expansion processes that may facilitate coexistence. Using long-term experimental evolution in the snowflake yeast model system, we show that the evolution of multicellularity drove niche partitioning and the adaptive divergence of two distinct, specialized lineages from a single multicellular ancestor. Over 715 daily transfers, snowflake yeast were subject to selection for rapid growth in rich media, followed by selection favoring larger group size. Both small and large cluster-forming lineages evolved from a monomorphic ancestor, coexisting for over ~4,300 generations. These small and large sized snowflake yeast lineages specialized on divergent aspects of a trade-off between growth rate and survival, mirroring predictions from ecological theory. Through modeling and experimentation, we demonstrate that coexistence is maintained by a trade-off between organismal size and competitiveness for dissolved oxygen. Taken together, this work shows how the evolution of a new level of biological individuality can rapidly drive adaptive diversification and the expansion of a nascent multicellular niche, one of the most historically-impactful emergent properties of this evolutionary transition.
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10
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Leptos KC, Chioccioli M, Furlan S, Pesci AI, Goldstein RE. Phototaxis of Chlamydomonas arises from a tuned adaptive photoresponse shared with multicellular Volvocine green algae. Phys Rev E 2023; 107:014404. [PMID: 36797913 PMCID: PMC7616094 DOI: 10.1103/physreve.107.014404] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 12/16/2022] [Indexed: 06/18/2023]
Abstract
A fundamental issue in biology is the nature of evolutionary transitions from unicellular to multicellular organisms. Volvocine algae are models for this transition, as they span from the unicellular biflagellate Chlamydomonas to multicellular species of Volvox with up to 50,000 Chlamydomonas-like cells on the surface of a spherical extracellular matrix. The mechanism of phototaxis in these species is of particular interest since they lack a nervous system and intercellular connections; steering is a consequence of the response of individual cells to light. Studies of Volvox and Gonium, a 16-cell organism with a plate-like structure, have shown that the flagellar response to changing illumination of the cellular photosensor is adaptive, with a recovery time tuned to the rotation period of the colony around its primary axis. Here, combining high-resolution studies of the flagellar photoresponse of micropipette-held Chlamydomonas with 3D tracking of freely swimming cells, we show that such tuning also underlies its phototaxis. A mathematical model is developed based on the rotations around an axis perpendicular to the flagellar beat plane that occur through the adaptive response to oscillating light levels as the organism spins. Exploiting a separation of timescales between the flagellar photoresponse and phototurning, we develop an equation of motion that accurately describes the observed photoalignment. In showing that the adaptive timescales in Volvocine algae are tuned to the organisms' rotational periods across three orders of magnitude in cell number, our results suggest a unified picture of phototaxis in green algae in which the asymmetry in torques that produce phototurns arise from the individual flagella of Chlamydomonas, the flagellated edges of Gonium, and the flagellated hemispheres of Volvox.
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Affiliation(s)
- Kyriacos C. Leptos
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
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11
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Abstract
The morphogenesis of two-dimensional bacterial colonies has been well studied. However, little is known about the colony morphologies of bacteria growing in three dimensions, despite the prevalence of three-dimensional environments (e.g., soil, inside hosts) as natural bacterial habitats. Using experiments on bacteria in granular hydrogel matrices, we find that dense multicellular colonies growing in three dimensions undergo a common morphological instability and roughen, adopting a characteristic broccoli-like morphology when they exceed a critical size. Analysis of a continuum “active fluid” model of the expanding colony reveals that this behavior originates from an interplay of competition for nutrients with growth-driven colony expansion, both of which vary spatially. These results shed light on the fundamental biophysical principles underlying growth in three dimensions. How do growing bacterial colonies get their shapes? While colony morphogenesis is well studied in two dimensions, many bacteria grow as large colonies in three-dimensional (3D) environments, such as gels and tissues in the body or subsurface soils and sediments. Here, we describe the morphodynamics of large colonies of bacteria growing in three dimensions. Using experiments in transparent 3D granular hydrogel matrices, we show that dense colonies of four different species of bacteria generically become morphologically unstable and roughen as they consume nutrients and grow beyond a critical size—eventually adopting a characteristic branched, broccoli-like morphology independent of variations in the cell type and environmental conditions. This behavior reflects a key difference between two-dimensional (2D) and 3D colonies; while a 2D colony may access the nutrients needed for growth from the third dimension, a 3D colony inevitably becomes nutrient limited in its interior, driving a transition to unstable growth at its surface. We elucidate the onset of the instability using linear stability analysis and numerical simulations of a continuum model that treats the colony as an “active fluid” whose dynamics are driven by nutrient-dependent cellular growth. We find that when all dimensions of the colony substantially exceed the nutrient penetration length, nutrient-limited growth drives a 3D morphological instability that recapitulates essential features of the experimental observations. Our work thus provides a framework to predict and control the organization of growing colonies—as well as other forms of growing active matter, such as tumors and engineered living materials—in 3D environments.
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Jagdish T, Nguyen Ba AN. Microbial experimental evolution in a massively multiplexed and high-throughput era. Curr Opin Genet Dev 2022; 75:101943. [PMID: 35752001 DOI: 10.1016/j.gde.2022.101943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/11/2022] [Accepted: 05/17/2022] [Indexed: 11/25/2022]
Abstract
Experimental evolution with microbial model systems has transformed our understanding of the basic rules underlying ecology and evolution. Experiments leveraging evolution as a central feature put evolutionary theories to the test, and modern sequencing and engineering tools then characterized the molecular basis of adaptation. As theory and experimentations refined our understanding of evolution, a need to increase throughput and experimental complexity has emerged. Here, we summarize recent technologies that have made high-throughput experiments practical and highlight studies that have capitalized on these tools, defining an exciting new era in microbial experimental evolution. Multiple research directions previously limited by experimental scale are now accessible for study and we believe applying evolutionary lessons from in vitro studies onto these applied settings has the potential for major innovations and discoveries across ecology and medicine.
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Affiliation(s)
- Tanush Jagdish
- Department of Molecular and Cellular Biology and The Program for Systems Synthetic and Quantitative Biology, Harvard University, Cambridge, United States.
| | - Alex N Nguyen Ba
- Department of Biology, University of Toronto at Mississauga, Mississauga, Canada; Department of Cell and Systems Biology, University of Toronto, Toronto, Canada.
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13
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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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