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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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Puri D, Allison KR. Escherichia coli self-organizes developmental rosettes. Proc Natl Acad Sci U S A 2024; 121:e2315850121. [PMID: 38814871 PMCID: PMC11161754 DOI: 10.1073/pnas.2315850121] [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: 09/12/2023] [Accepted: 05/01/2024] [Indexed: 06/01/2024] Open
Abstract
Rosettes are self-organizing, circular multicellular communities that initiate developmental processes, like organogenesis and embryogenesis, in complex organisms. Their formation results from the active repositioning of adhered sister cells and is thought to distinguish multicellular organisms from unicellular ones. Though common in eukaryotes, this multicellular behavior has not been reported in bacteria. In this study, we found that Escherichia coli forms rosettes by active sister-cell repositioning. After division, sister cells "fold" to actively align at the 2- and 4-cell stages of clonal division, thereby producing rosettes with characteristic quatrefoil configuration. Analysis revealed that folding follows an angular random walk, composed of ~1 µm strokes and directional randomization. We further showed that this motion was produced by the flagellum, the extracellular tail whose rotation generates swimming motility. Rosette formation was found to require de novo flagella synthesis suggesting it must balance the opposing forces of Ag43 adhesion and flagellar propulsion. We went on to show that proper rosette formation was required for subsequent morphogenesis of multicellular chains, rpoS gene expression, and formation of hydrostatic clonal-chain biofilms. Moreover, we found self-folding rosette-like communities in the standard motility assay, indicating that this behavior may be a general response to hydrostatic environments in E. coli. These findings establish self-organization of clonal rosettes by a prokaryote and have implications for evolutionary biology, synthetic biology, and medical microbiology.
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Affiliation(s)
- Devina Puri
- Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA30322
| | - Kyle R. Allison
- Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA30322
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA30322
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4
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Root-Bernstein RS, Bernstein MI. 'Evolutionary poker': an agent-based model of interactome emergence and epistasis tested against Lenski's long-term E. coli experiments. J Physiol 2024; 602:2511-2535. [PMID: 37707489 DOI: 10.1113/jp284421] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/23/2023] [Indexed: 09/15/2023] Open
Abstract
A simple agent-based model is presented that produces results matching the experimental data found by Lenski's group for ≤50,000 generations of Escherichia coli bacteria under continuous selective pressure. Although various mathematical models have been devised previously to model the Lenski data, the present model has advantages in terms of overall simplicity and conceptual accessibility. The model also clearly illustrates a number of features of the evolutionary process that are otherwise not obvious, such as the roles of epistasis and historical contingency in adaptation and why evolution is time irreversible ('Dollo's law'). The reason for this irreversibility is that genomes become increasingly integrated or organized, and this organization becomes a novel selective factor itself, against which future generations must compete. Selection for integrated or synergistic networks, systems or sets of mutations or traits, not for individual mutations, confers the main adaptive advantage. The result is a punctuated form of evolution that follows a logarithmic occurrence probability, in which evolution proceeds very quickly when interactomes begin to form but which slows as interactomes become more robust and the difficulty of integrating new mutations increases. Sufficient parameters exist in the game to suggest not only how equilibrium or stasis is reached but also the conditions in which it will be punctuated, the factors governing the rate at which genomic organization occurs and novel traits appear, and how population size, genome size and gene variability affect these.
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Affiliation(s)
| | - Morton I Bernstein
- Department of Physiology, Michigan State University, East Lansing, MI, USA
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5
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Pineau RM, Libby E, Demory D, 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. Nat Ecol Evol 2024; 8:1010-1020. [PMID: 38486107 PMCID: PMC11090753 DOI: 10.1038/s41559-024-02367-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/15/2024] [Indexed: 03/23/2024]
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 affect eco-evolutionary dynamics. Through long-term experimental evolution, we observed niche partitioning and the adaptive divergence of two specialized lineages from a single multicellular ancestor. Over 715 daily transfers, snowflake yeast were subjected to selection for rapid growth, followed by selection favouring larger group size. Small and large cluster-forming lineages evolved from a monomorphic ancestor, coexisting for over ~4,300 generations, specializing on divergent aspects of a trade-off between growth rate and survival. Through modelling 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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Affiliation(s)
- Rozenn M Pineau
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Eric Libby
- Integrated Science Lab, Umeå university, Umeå, Sweden.
- Department of Mathematics and Mathematical Statistics, Umeå university, Umeå, Sweden.
| | - David Demory
- CNRS, Sorbonne Université, USR 3579 Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Dung T Lac
- 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
| | - Pablo Bravo
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Peter J Yunker
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Biology, University of Maryland, College Park, MD, USA
- Department of Physics, University of Maryland, College Park, MD, 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.
- Department of Biology, University of Maryland, College Park, MD, USA.
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6
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Multicellularity drives ecological diversity in a long-term evolution experiment. Nat Ecol Evol 2024; 8:856-857. [PMID: 38519635 DOI: 10.1038/s41559-024-02391-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
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7
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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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8
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Montrose K, Lac DT, Burnetti AJ, Tong K, Bozdag GO, Hukkanen M, Ratcliff WC, Saarikangas J. Proteostatic tuning underpins the evolution of novel multicellular traits. SCIENCE ADVANCES 2024; 10:eadn2706. [PMID: 38457507 PMCID: PMC10923498 DOI: 10.1126/sciadv.adn2706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/06/2024] [Indexed: 03/10/2024]
Abstract
The evolution of multicellularity paved the way for the origin of complex life on Earth, but little is known about the mechanistic basis of early multicellular evolution. Here, we examine the molecular basis of multicellular adaptation in the multicellularity long-term evolution experiment (MuLTEE). We demonstrate that cellular elongation, a key adaptation underpinning increased biophysical toughness and organismal size, is convergently driven by down-regulation of the chaperone Hsp90. Mechanistically, Hsp90-mediated morphogenesis operates by destabilizing the cyclin-dependent kinase Cdc28, resulting in delayed mitosis and prolonged polarized growth. Reinstatement of Hsp90 or Cdc28 expression resulted in shortened cells that formed smaller groups with reduced multicellular fitness. Together, our results show how ancient protein folding systems can be tuned to drive rapid evolution at a new level of biological individuality by revealing novel developmental phenotypes.
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Affiliation(s)
- Kristopher Montrose
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Dung T. Lac
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Anthony J. Burnetti
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kai Tong
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Interdisciplinary Graduate Program in Quantitative Biosciences (QBioS), Georgia Institute of Technology, Atlanta, GA, USA
| | - G. Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mikaela Hukkanen
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - William C. Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Juha Saarikangas
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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9
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Bozdag GO, Szeinbaum N, Conlin PL, Chen K, Fos SM, Garcia A, Penev PI, Schaible GA, Trubl G. Chapter 5: Major Biological Innovations in the History of Life on Earth. ASTROBIOLOGY 2024; 24:S107-S123. [PMID: 38498818 PMCID: PMC11071111 DOI: 10.1089/ast.2021.0119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/14/2023] [Indexed: 03/20/2024]
Abstract
All organisms living on Earth descended from a single, common ancestral population of cells, known as LUCA-the last universal common ancestor. Since its emergence, the diversity and complexity of life have increased dramatically. This chapter focuses on four key biological innovations throughout Earth's history that had a significant impact on the expansion of phylogenetic diversity, organismal complexity, and ecospace habitation. First is the emergence of the last universal common ancestor, LUCA, which laid the foundation for all life-forms on Earth. Second is the evolution of oxygenic photosynthesis, which resulted in global geochemical and biological transformations. Third is the appearance of a new type of cell-the eukaryotic cell-which led to the origin of a new domain of life and the basis for complex multicellularity. Fourth is the multiple independent origins of multicellularity, resulting in the emergence of a new level of complex individuality. A discussion of these four key events will improve our understanding of the intertwined history of our planet and its inhabitants and better inform the extent to which we can expect life at different degrees of diversity and complexity elsewhere.
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Affiliation(s)
- G. Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nadia Szeinbaum
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Peter L. Conlin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Kimberly Chen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Santiago Mestre Fos
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Amanda Garcia
- Department of Bacteriology, University of Wisconsin–Madison, Wisconsin, USA
| | - Petar I. Penev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - George A. Schaible
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
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10
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Montrose K, Lac DT, Burnetti AJ, Tong K, Ozan Bozdag G, Hukkanen M, Ratcliff WC, Saarikangas J. Proteostatic tuning underpins the evolution of novel multicellular traits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.31.543183. [PMID: 37333256 PMCID: PMC10274739 DOI: 10.1101/2023.05.31.543183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The evolution of multicellularity paved the way for the origin of complex life on Earth, but little is known about the mechanistic basis of early multicellular evolution. Here, we examine the molecular basis of multicellular adaptation in the Multicellularity Long Term Evolution Experiment (MuLTEE). We demonstrate that cellular elongation, a key adaptation underpinning increased biophysical toughness and organismal size, is convergently driven by downregulation of the chaperone Hsp90. Mechanistically, Hsp90-mediated morphogenesis operates by destabilizing the cyclin-dependent kinase Cdc28, resulting in delayed mitosis and prolonged polarized growth. Reinstatement of Hsp90 or Cdc28 expression resulted in shortened cells that formed smaller groups with reduced multicellular fitness. Together, our results show how ancient protein folding systems can be tuned to drive rapid evolution at a new level of biological individuality by revealing novel developmental phenotypes.
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Affiliation(s)
- Kristopher Montrose
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki
- Faculty of Biological and Environmental Sciences, University of Helsinki
| | - Dung T. Lac
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Anthony J. Burnetti
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kai Tong
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki
- Faculty of Biological and Environmental Sciences, University of Helsinki
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Interdisciplinary Graduate Program in Quantitative Biosciences (QBioS)
| | - G. Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mikaela Hukkanen
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki
- Faculty of Biological and Environmental Sciences, University of Helsinki
| | - William C. Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Juha Saarikangas
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki
- Faculty of Biological and Environmental Sciences, University of Helsinki
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11
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Stock M, Gorochowski TE. Open-endedness in synthetic biology: A route to continual innovation for biological design. SCIENCE ADVANCES 2024; 10:eadi3621. [PMID: 38241375 DOI: 10.1126/sciadv.adi3621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024]
Abstract
Design in synthetic biology is typically goal oriented, aiming to repurpose or optimize existing biological functions, augmenting biology with new-to-nature capabilities, or creating life-like systems from scratch. While the field has seen many advances, bottlenecks in the complexity of the systems built are emerging and designs that function in the lab often fail when used in real-world contexts. Here, we propose an open-ended approach to biological design, with the novelty of designed biology being at least as important as how well it fulfils its goal. Rather than solely focusing on optimization toward a single best design, designing with novelty in mind may allow us to move beyond the diminishing returns we see in performance for most engineered biology. Research from the artificial life community has demonstrated that embracing novelty can automatically generate innovative and unexpected solutions to challenging problems beyond local optima. Synthetic biology offers the ideal playground to explore more creative approaches to biological design.
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Affiliation(s)
- Michiel Stock
- KERMIT & Biobix, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Thomas E Gorochowski
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
- BrisEngBio, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
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12
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Sakurada K, Ishikawa T. Synthesis of causal and surrogate models by non-equilibrium thermodynamics in biological systems. Sci Rep 2024; 14:1001. [PMID: 38200211 PMCID: PMC10781949 DOI: 10.1038/s41598-024-51426-8] [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: 10/17/2023] [Accepted: 01/04/2024] [Indexed: 01/12/2024] Open
Abstract
We developed a model to represent the time evolution phenomena of life through physics constraints. To do this, we took into account that living organisms are open systems that exchange messages through intracellular communication, intercellular communication and sensory systems, and introduced the concept of a message force field. As a result, we showed that the maximum entropy generation principle is valid in time evolution. Then, in order to explain life phenomena based on this principle, we modelled the living system as a nonlinear oscillator coupled by a message and derived the governing equations. The governing equations consist of two laws: one states that the systems are synchronized when the variation of the natural frequencies between them is small or the coupling strength through the message is sufficiently large, and the other states that the synchronization is broken by the proliferation of biological systems. Next, to simulate the phenomena using data obtained from observations of the temporal evolution of life, we developed an inference model that combines physics constraints and a discrete surrogate model using category theory, and simulated the phenomenon of early embryogenesis using this inference model. The results show that symmetry creation and breaking based on message force fields can be widely used to model life phenomena.
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Affiliation(s)
- Kazuhiro Sakurada
- Department of Extended Intelligence for Medicine, The Ishii-Ishibashi Laboratory, Keio University School of Medicine, Tokyo, Japan.
- Open Systems Information Science Team, Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Tokyo, Japan.
| | - Tetsuo Ishikawa
- Department of Extended Intelligence for Medicine, The Ishii-Ishibashi Laboratory, Keio University School of Medicine, Tokyo, Japan
- Medical Data Mathematical Reasoning Team, Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Yokohama, Japan
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13
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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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14
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Bich L. Integrating Multicellular Systems: Physiological Control and Degrees of Biological Individuality. Acta Biotheor 2023; 72:1. [PMID: 38151680 PMCID: PMC10752842 DOI: 10.1007/s10441-023-09476-4] [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: 08/29/2023] [Accepted: 12/17/2023] [Indexed: 12/29/2023]
Abstract
This paper focuses on physiological integration in multicellular systems, a notion often associated with biological individuality, but which has not received enough attention and needs a thorough theoretical treatment. Broadly speaking, physiological integration consists in how different components come together into a cohesive unit in which they are dependent on one another for their existence and activity. This paper argues that physiological integration can be understood by considering how the components of a biological multicellular system are controlled and coordinated in such a way that their activities can contribute to the maintenance of the system. The main implication of this perspective is that different ways of controlling their parts may give rise to multicellular organizations with different degrees of integration. After defining control, this paper analyses how control is realized in two examples of multicellular systems located at different ends of the spectrum of multicellularity: biofilms and animals. It focuses on differences in control ranges, and it argues that a high degree of integration implies control exerted at both medium and long ranges, and that insofar as biofilms lack long-range control (relative to their size) they can be considered as less integrated than other multicellular systems. It then discusses the implication of this account for the debate on physiological individuality and the idea that degrees of physiological integration imply degrees of individuality.
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Affiliation(s)
- Leonardo Bich
- Department of Philosophy, IAS-Research Centre for Life, Mind and Society, University of the Basque Country (UPV/EHU), Avenida de Tolosa 70, Donostia-San Sebastian, 20018, Spain.
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15
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Carlton JG, Baum B. Roles of ESCRT-III polymers in cell division across the tree of life. Curr Opin Cell Biol 2023; 85:102274. [PMID: 37944425 PMCID: PMC7615534 DOI: 10.1016/j.ceb.2023.102274] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 10/12/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023]
Abstract
Every cell becomes two through a carefully orchestrated process of division. Prior to division, contractile machinery must first be assembled at the cell midzone to ensure that the cut, when it is made, bisects the two separated copies of the genetic material. Second, this contractile machinery must be dynamically tethered to the limiting plasma membrane so as to bring the membrane with it as it constricts. Finally, the connecting membrane must be severed to generate two physically separate daughter cells. In several organisms across the tree of life, Endosomal Sorting Complex Required for Transport (ESCRT)-III family proteins aid cell division by forming composite polymers that function together with the Vps4 AAA-ATPase to constrict and cut the membrane tube connecting nascent daughter cells from the inside. In this review, we discuss unique features of ESCRT-III that enable it to play this role in division in many archaea and eukaryotes.
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Affiliation(s)
- Jeremy Graham Carlton
- Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, Guy's Hospital, London, SE1 1UL, UK; Organelle Dynamics Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| | - Buzz Baum
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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16
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Theodorou I, Charrier B. The shift to 3D growth during embryogenesis of kelp species, atlas of cell division and differentiation of Saccharina latissima. Development 2023; 150:dev201519. [PMID: 37882832 PMCID: PMC10660787 DOI: 10.1242/dev.201519] [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: 12/08/2022] [Accepted: 09/12/2023] [Indexed: 10/27/2023]
Abstract
In most organisms, 3D growth takes place at the onset of embryogenesis. In some brown algae, 3D growth occurs later in development, when the organism consists of several hundred cells. We studied the cellular events that take place when 3D growth is established in the embryo of the brown alga Saccharina, a kelp species. Semi-thin sections, taken from where growth shifts from 2D to 3D, show that 3D growth first initiates from symmetrical cell division in the monolayered lamina, and then is enhanced through a series of asymmetrical cell divisions in a peripheral monolayer of cells called the meristoderm. Then, daughter cells rapidly differentiate into cortical and medullary cells, characterised by their position, size and shape. In essence, 3D growth in kelps is based on a series of differentiation steps that occur rapidly after the initiation of a bilayered lamina, followed by further growth of the established differentiated tissues. Our study depicts the cellular landscape necessary to study cell-fate programming in the context of a novel mode of 3D growth in an organism phylogenetically distant from plants and animals.
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Affiliation(s)
- Ioannis Theodorou
- Laboratory of Integrative Marine Models, Station Biologique de Roscoff, UMR8227, CNRS, Sorbonne University, Place Georges Teissier, 29680 Roscoff, France
- Plant Sciences Department, Faculty of Biosciences, Norwegian University of Life Sciences, NO-1432 Ås, Norway
| | - Bénédicte Charrier
- Laboratory of Integrative Marine Models, Station Biologique de Roscoff, UMR8227, CNRS, Sorbonne University, Place Georges Teissier, 29680 Roscoff, France
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17
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Pentz JT, MacGillivray K, DuBose JG, Conlin PL, Reinhardt E, Libby E, Ratcliff WC. Evolutionary consequences of nascent multicellular life cycles. eLife 2023; 12:e84336. [PMID: 37889142 PMCID: PMC10611430 DOI: 10.7554/elife.84336] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 10/08/2023] [Indexed: 10/28/2023] Open
Abstract
A key step in the evolutionary transition to multicellularity is the origin of multicellular groups as biological individuals capable of adaptation. Comparative work, supported by theory, suggests clonal development should facilitate this transition, although this hypothesis has never been tested in a single model system. We evolved 20 replicate populations of otherwise isogenic clonally reproducing 'snowflake' yeast (Δace2/∆ace2) and aggregative 'floc' yeast (GAL1p::FLO1 /GAL1p::FLO1) with daily selection for rapid growth in liquid media, which favors faster cell division, followed by selection for rapid sedimentation, which favors larger multicellular groups. While both genotypes adapted to this regime, growing faster and having higher survival during the group-selection phase, there was a stark difference in evolutionary dynamics. Aggregative floc yeast obtained nearly all their increased fitness from faster growth, not improved group survival; indicating that selection acted primarily at the level of cells. In contrast, clonal snowflake yeast mainly benefited from higher group-dependent fitness, indicating a shift in the level of Darwinian individuality from cells to groups. Through genome sequencing and mathematical modeling, we show that the genetic bottlenecks in a clonal life cycle also drive much higher rates of genetic drift-a result with complex implications for this evolutionary transition. Our results highlight the central role that early multicellular life cycles play in the process of multicellular adaptation.
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Affiliation(s)
| | - Kathryn MacGillivray
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of TechnologyAtlantaUnited States
| | - James G DuBose
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| | - Peter L Conlin
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| | - Emma Reinhardt
- Department of Biology, University of North Carolina at Chapel HillChapel HillUnited States
| | | | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
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18
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Shalev O, Ye X, Ratzke C. Replaying the evolution of multicellularity. Trends Ecol Evol 2023; 38:910-912. [PMID: 37586948 DOI: 10.1016/j.tree.2023.07.007] [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: 07/20/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023]
Abstract
The first organisms on Earth were presumably unicellular. At one point, evolution shaped these individual cells into multicellular organisms, which was a significant transition in the history of life on Earth. To investigate how this change happened, Bozdag et al. re-ran evolution in the lab and observed how single-celled yeast forms large multicellular aggregates.
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Affiliation(s)
- Or Shalev
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence EXC 2124 'Controlling Microbes to Fight Infections' (CMFI), University of Tübingen, Calwerstrasse 7/1, 72076 Tübingen, Germany
| | - Xiaozhou Ye
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence EXC 2124 'Controlling Microbes to Fight Infections' (CMFI), University of Tübingen, Calwerstrasse 7/1, 72076 Tübingen, Germany
| | - Christoph Ratzke
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence EXC 2124 'Controlling Microbes to Fight Infections' (CMFI), University of Tübingen, Calwerstrasse 7/1, 72076 Tübingen, Germany.
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19
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Zamani-Dahaj SA, Burnetti A, Day TC, Yunker PJ, Ratcliff WC, Herron MD. Spontaneous Emergence of Multicellular Heritability. Genes (Basel) 2023; 14:1635. [PMID: 37628687 PMCID: PMC10454505 DOI: 10.3390/genes14081635] [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: 06/19/2023] [Revised: 07/27/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
The major transitions in evolution include events and processes that result in the emergence of new levels of biological individuality. For collectives to undergo Darwinian evolution, their traits must be heritable, but the emergence of higher-level heritability is poorly understood and has long been considered a stumbling block for nascent evolutionary transitions. Using analytical models, synthetic biology, and biologically-informed simulations, we explored the emergence of trait heritability during the evolution of multicellularity. Prior work on the evolution of multicellularity has asserted that substantial collective-level trait heritability either emerges only late in the transition or requires some evolutionary change subsequent to the formation of clonal multicellular groups. In a prior analytical model, we showed that collective-level heritability not only exists but is usually more heritable than the underlying cell-level trait upon which it is based, as soon as multicellular groups form. Here, we show that key assumptions and predictions of that model are borne out in a real engineered biological system, with important implications for the emergence of collective-level heritability.
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Affiliation(s)
- Seyed Alireza Zamani-Dahaj
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA;
- Georgia Institute of Technology, School of Physics, Atlanta, GA 30332, USA; (T.C.D.); (P.J.Y.)
| | - Anthony Burnetti
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA 30332, USA; (A.B.); (M.D.H.)
| | - Thomas C. Day
- Georgia Institute of Technology, School of Physics, Atlanta, GA 30332, USA; (T.C.D.); (P.J.Y.)
| | - Peter J. Yunker
- Georgia Institute of Technology, School of Physics, Atlanta, GA 30332, USA; (T.C.D.); (P.J.Y.)
| | - William C. Ratcliff
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA 30332, USA; (A.B.); (M.D.H.)
| | - Matthew D. Herron
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA 30332, USA; (A.B.); (M.D.H.)
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Schulz AK, Schneider N, Zhang M, Singal K. A Year at the Forefront of Hydrostat Motion. Biol Open 2023; 12:bio059834. [PMID: 37566395 PMCID: PMC10434360 DOI: 10.1242/bio.059834] [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: 08/12/2023] Open
Abstract
Currently, in the field of interdisciplinary work in biology, there has been a significant push by the soft robotic community to understand the motion and maneuverability of hydrostats. This Review seeks to expand the muscular hydrostat hypothesis toward new structures, including plants, and introduce innovative techniques to the hydrostat community on new modeling, simulating, mimicking, and observing hydrostat motion methods. These methods range from ideas of kirigami, origami, and knitting for mimic creation to utilizing reinforcement learning for control of bio-inspired soft robotic systems. It is now being understood through modeling that different mechanisms can inhibit traditional hydrostat motion, such as skin, nostrils, or sheathed layered muscle walls. The impact of this Review will highlight these mechanisms, including asymmetries, and discuss the critical next steps toward understanding their motion and how species with hydrostat structures control such complex motions, highlighting work from January 2022 to December 2022.
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Affiliation(s)
- Andrew K. Schulz
- School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Nikole Schneider
- Department of Biology, University of South Dakota, Vermillion, SD 57069, USA
| | - Margaret Zhang
- School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Krishma Singal
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
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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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