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Kollmar M, Welz T, Ravi A, Kaufmann T, Alzahofi N, Hatje K, Alghamdi A, Kim J, Briggs DA, Samol-Wolf A, Pylypenko O, Hume AN, Burkhardt P, Faix J, Kerkhoff E. Actomyosin organelle functions of SPIRE actin nucleators precede animal evolution. Commun Biol 2024; 7:832. [PMID: 38977899 PMCID: PMC11231147 DOI: 10.1038/s42003-024-06458-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 06/14/2024] [Indexed: 07/10/2024] Open
Abstract
An important question in cell biology is how cytoskeletal proteins evolved and drove the development of novel structures and functions. Here we address the origin of SPIRE actin nucleators. Mammalian SPIREs work with RAB GTPases, formin (FMN)-subgroup actin assembly proteins and class-5 myosin (MYO5) motors to transport organelles along actin filaments towards the cell membrane. However, the origin and extent of functional conservation of SPIRE among species is unknown. Our sequence searches show that SPIRE exist throughout holozoans (animals and their closest single-celled relatives), but not other eukaryotes. SPIRE from unicellular holozoans (choanoflagellate), interacts with RAB, FMN and MYO5 proteins, nucleates actin filaments and complements mammalian SPIRE function in organelle transport. Meanwhile SPIRE and MYO5 proteins colocalise to organelles in Salpingoeca rosetta choanoflagellates. Based on these observations we propose that SPIRE originated in unicellular ancestors of animals providing an actin-myosin driven exocytic transport mechanism that may have contributed to the evolution of complex multicellular animals.
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Affiliation(s)
- Martin Kollmar
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.
| | - Tobias Welz
- Molecular Cell Biology Laboratory, Department of Neurology, University Hospital Regensburg, Regensburg, Germany
| | - Aishwarya Ravi
- Michael Sars Centre, University of Bergen, Bergen, Norway
| | - Thomas Kaufmann
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Noura Alzahofi
- School of Life Sciences, University of Nottingham, Nottingham, UK
- Biology Department, College of Science, Taibah University, Medina, Kingdom of Saudi Arabia
| | - Klas Hatje
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Asmahan Alghamdi
- School of Life Sciences, University of Nottingham, Nottingham, UK
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh, Kingdom of Saudi Arabia
| | - Jiyu Kim
- Molecular Cell Biology Laboratory, Department of Neurology, University Hospital Regensburg, Regensburg, Germany
- Department of Anatomy, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Deborah A Briggs
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Annette Samol-Wolf
- Molecular Cell Biology Laboratory, Department of Neurology, University Hospital Regensburg, Regensburg, Germany
| | - Olena Pylypenko
- Dynamics of Intra-Cellular Organization, Institute Curie, PSL Research University, CNRS UMR144, Paris, France
| | - Alistair N Hume
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | - Jan Faix
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Eugen Kerkhoff
- Molecular Cell Biology Laboratory, Department of Neurology, University Hospital Regensburg, Regensburg, Germany.
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2
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Wang P, Driscoll WW, Travisano M. Genomic sequencing reveals convergent adaptation during experimental evolution in two budding yeast species. Commun Biol 2024; 7:825. [PMID: 38971878 PMCID: PMC11227552 DOI: 10.1038/s42003-024-06485-y] [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: 02/14/2024] [Accepted: 06/21/2024] [Indexed: 07/08/2024] Open
Abstract
Convergent evolution is central in the origins of multicellularity. Identifying the basis for convergent multicellular evolution is challenging because of the diverse evolutionary origins and environments involved. Haploid Kluyveromyces lactis populations evolve multicellularity during selection for increased settling in liquid media. Strong genomic and phenotypic convergence is observed between K. lactis and previously selected S. cerevisiae populations under similar selection, despite their >100-million-year divergence. We find K. lactis multicellularity is conferred by mutations in genes ACE2 or AIM44, with ACE2 being predominant. They are a subset of the six genes involved in the S. cerevisiae multicellularity. Both ACE2 and AIM44 regulate cell division, indicating that the genetic convergence is likely due to conserved cellular replication mechanisms. Complex population dynamics involving multiple ACE2/AIM44 genotypes are found in most K. lactis lineages. The results show common ancestry and natural selection shape convergence while chance and contingency determine the degree of divergence.
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Affiliation(s)
- Pu Wang
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA.
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA.
| | - William W Driscoll
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
- Biology Department, Penn State Harrisburg, Harrisburg, PA, 17057, USA
| | - Michael Travisano
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
- Biotechnology Institute, University of Minnesota, Minneapolis, MN, 55108, USA
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3
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Schaible GA, Jay ZJ, Cliff J, Schulz F, Gauvin C, Goudeau D, Malmstrom RR, Ruff SE, Edgcomb V, Hatzenpichler R. Multicellular magnetotactic bacteria are genetically heterogeneous consortia with metabolically differentiated cells. PLoS Biol 2024; 22:e3002638. [PMID: 38990824 PMCID: PMC11239054 DOI: 10.1371/journal.pbio.3002638] [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: 12/18/2023] [Accepted: 04/24/2024] [Indexed: 07/13/2024] Open
Abstract
Consortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use multiple culture-independent approaches to analyze the genomics and physiology of MMB consortia at single-cell resolution. We separately sequenced the metagenomes of 22 individual MMB consortia, representing 8 new species, and quantified the genetic diversity within each MMB consortium. This revealed that, counter to conventional views, cells within MMB consortia are not clonal. Single consortia metagenomes were then used to reconstruct the species-specific metabolic potential and infer the physiological capabilities of MMB. To validate genomic predictions, we performed stable isotope probing (SIP) experiments and interrogated MMB consortia using fluorescence in situ hybridization (FISH) combined with nanoscale secondary ion mass spectrometry (NanoSIMS). By coupling FISH with bioorthogonal noncanonical amino acid tagging (BONCAT), we explored their in situ activity as well as variation of protein synthesis within cells. We demonstrate that MMB consortia are mixotrophic sulfate reducers and that they exhibit metabolic differentiation between individual cells, suggesting that MMB consortia are more complex than previously thought. These findings expand our understanding of MMB diversity, ecology, genomics, and physiology, as well as offer insights into the mechanisms underpinning the multicellular nature of their unique lifestyle.
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Affiliation(s)
- George A Schaible
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
| | - Zackary J Jay
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
- Thermal Biology Institute, Montana State University, Bozeman, Montana, United States of America
| | - John Cliff
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Frederik Schulz
- Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Colin Gauvin
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
- Thermal Biology Institute, Montana State University, Bozeman, Montana, United States of America
| | - Danielle Goudeau
- Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Rex R Malmstrom
- Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - S Emil Ruff
- Ecosystems Center and Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
| | - Virginia Edgcomb
- Woods Hole Oceanographic Institution, Falmouth, Massachusetts, United States of America
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
- Thermal Biology Institute, Montana State University, Bozeman, Montana, United States of America
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, United States of America
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4
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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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5
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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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6
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Baluška F, Miller WB, Reber AS. Sentient cells as basic units of tissues, organs and organismal physiology. J Physiol 2024; 602:2491-2501. [PMID: 37847422 DOI: 10.1113/jp284419] [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: 06/05/2023] [Accepted: 10/03/2023] [Indexed: 10/18/2023] Open
Abstract
Cells evolved some 4 billion years ago, and since then the integrity of the structural and functional continuity of cellular life has been maintained via highly conserved and ancient processes of cell reproduction and division. The plasma membrane as well as all the cytoplasmic structures are reproduced and inherited uninterruptedly by each of the two daughter cells resulting from every cell division. Although our understanding of the evolutionary emergence of the very first cells is obscured by the extremely long timeline since that revolutionary event, the generally accepted position is that the de novo formation of cells is not possible; all present cells are products of other prior cells. This essential biological principle was first discovered by Robert Remak and then effectively coined as Omnis Cellula e Cellula (every cell of the cell) by Rudolf Virchow: all currently living cells have direct structural and functional connections to the very first cells. Based on our previous theoretical analysis, all cells are endowed with individual sentient cognition that guides their individual agency, behaviour and evolution. There is a vital consequence of this new sentient and cognitive view of cells: when cells assemble as functional tissue ecologies and organs within multicellular organisms, including plants, animals and humans, these cellular aggregates display derivative versions of aggregate tissue- and organ-specific sentience and consciousness. This innovative view of the evolution and physiology of all currently living organisms supports a singular principle: all organismal physiology is based on cellular physiology that extends from unicellular roots.
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Affiliation(s)
- František Baluška
- Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
| | - William B Miller
- Banner Health Systems - Medicine, Paradise Valley, Phoneix, Arizona, USA
| | - Arthur S Reber
- Department of Psychology, University of British Columbia, Vancouver, British Columbia, Canada
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7
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Oszoli I, Zachar I. Group-selection via aggregative propagule-formation enables cooperative multicellularity in an individual based, spatial model. PLoS Comput Biol 2024; 20:e1012107. [PMID: 38713735 PMCID: PMC11101088 DOI: 10.1371/journal.pcbi.1012107] [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: 10/26/2023] [Revised: 05/17/2024] [Accepted: 04/24/2024] [Indexed: 05/09/2024] Open
Abstract
The emergence of multicellularity is one of the major transitions in evolution that happened multiple times independently. During aggregative multicellularity, genetically potentially unrelated lineages cooperate to form transient multicellular groups. Unlike clonal multicellularity, aggregative multicellular organisms do not rely on kin selection instead other mechanisms maintain cooperation against cheater phenotypes that benefit from cooperators but do not contribute to groups. Spatiality with limited diffusion can facilitate group selection, as interactions among individuals are restricted to local neighbourhoods only. Selection for larger size (e.g. avoiding predation) may facilitate the emergence of aggregation, though it is unknown, whether and how much role such selection played during the evolution of aggregative multicellularity. We have investigated the effect of spatiality and the necessity of predation on the stability of aggregative multicellularity via individual-based modelling on the ecological timescale. We have examined whether aggregation facilitates the survival of cooperators in a temporally heterogeneous environment against cheaters, where only a subset of the population is allowed to periodically colonize a new, resource-rich habitat. Cooperators constitutively produce adhesive molecules to promote aggregation and propagule-formation while cheaters spare this expense to grow faster but cannot aggregate on their own, hence depending on cooperators for long-term survival. We have compared different population-level reproduction modes with and without individual selection (predation) to evaluate the different hypotheses. In a temporally homogeneous environment without propagule-based colonization, cheaters always win. Predation can benefit cooperators, but it is not enough to maintain the necessary cooperator amount in successive dispersals, either randomly or by fragmentation. Aggregation-based propagation however can ensure the adequate ratio of cooperators-to-cheaters in the propagule and is sufficient to do so even without predation. Spatiality combined with temporal heterogeneity helps cooperators via group selection, thus facilitating aggregative multicellularity. External stress selecting for larger size (e.g. predation) may facilitate aggregation, however, according to our results, it is neither necessary nor sufficient for aggregative multicellularity to be maintained when there is effective group-selection.
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Affiliation(s)
- István Oszoli
- Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Loránd University, Budapest, Hungary
| | - István Zachar
- Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Loránd University, Budapest, Hungary
- HUN-REN Institute of Evolution, Centre for Ecological Research, Budapest, Hungary
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8
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Allen B, Khwaja AR, Donahue JL, Kelly TJ, Hyacinthe SR, Proulx J, Lattanzio C, Dementieva YA, Sample C. Nonlinear social evolution and the emergence of collective action. PNAS NEXUS 2024; 3:pgae131. [PMID: 38595801 PMCID: PMC11002786 DOI: 10.1093/pnasnexus/pgae131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 03/21/2024] [Indexed: 04/11/2024]
Abstract
Organisms from microbes to humans engage in a variety of social behaviors, which affect fitness in complex, often nonlinear ways. The question of how these behaviors evolve has consequences ranging from antibiotic resistance to human origins. However, evolution with nonlinear social interactions is challenging to model mathematically, especially in combination with spatial, group, and/or kin assortment. We derive a mathematical condition for natural selection with synergistic interactions among any number of individuals. This result applies to populations with arbitrary (but fixed) spatial or network structure, group subdivision, and/or mating patterns. In this condition, nonlinear fitness effects are ascribed to collectives, and weighted by a new measure of collective relatedness. For weak selection, this condition can be systematically evaluated by computing branch lengths of ancestral trees. We apply this condition to pairwise games between diploid relatives, and to dilemmas of collective help or harm among siblings and on spatial networks. Our work provides a rigorous basis for extending the notion of "actor", in the study of social evolution, from individuals to collectives.
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Affiliation(s)
- Benjamin Allen
- Department of Mathematics, Emmanuel College, Boston, MA 02115, USA
| | | | - James L Donahue
- Department of Mathematics, Emmanuel College, Boston, MA 02115, USA
| | - Theodore J Kelly
- Department of Mathematics, Emmanuel College, Boston, MA 02115, USA
| | | | - Jacob Proulx
- Department of Mathematics, Emmanuel College, Boston, MA 02115, USA
| | | | | | - Christine Sample
- Department of Mathematics, Emmanuel College, Boston, MA 02115, USA
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9
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Szathmáry E. Nonadaptive onset of complex multicellularity. Proc Natl Acad Sci U S A 2024; 121:e2401220121. [PMID: 38437572 PMCID: PMC10945832 DOI: 10.1073/pnas.2401220121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024] Open
Affiliation(s)
- Eörs Szathmáry
- Institute of Evolution, HUN-REN Centre for Ecological Research, Budapest1121, Hungary
- Center for the Conceptual Foundations of Science, Parmenides Foundation, Pöcking82343, Germany
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10
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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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11
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Prentice JA, van de Weerd R, Bridges AA. Cell-lysis sensing drives biofilm formation in Vibrio cholerae. Nat Commun 2024; 15:2018. [PMID: 38443393 PMCID: PMC10914755 DOI: 10.1038/s41467-024-46399-1] [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: 11/06/2023] [Accepted: 02/26/2024] [Indexed: 03/07/2024] Open
Abstract
Matrix-encapsulated communities of bacteria, called biofilms, are ubiquitous in the environment and are notoriously difficult to eliminate in clinical and industrial settings. Biofilm formation likely evolved as a mechanism to protect resident cells from environmental challenges, yet how bacteria undergo threat assessment to inform biofilm development remains unclear. Here we find that population-level cell lysis events induce the formation of biofilms by surviving Vibrio cholerae cells. Survivors detect threats by sensing a cellular component released through cell lysis, which we identify as norspermidine. Lysis sensing occurs via the MbaA receptor with genus-level specificity, and responsive biofilm cells are shielded from phage infection and attacks from other bacteria. Thus, our work uncovers a connection between bacterial lysis and biofilm formation that may be broadly conserved among microorganisms.
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Affiliation(s)
- Jojo A Prentice
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Robert van de Weerd
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Andrew A Bridges
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA.
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12
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Narula K, Sinha A, Choudhary P, Ghosh S, Elagamey E, Sharma A, Sengupta A, Chakraborty N, Chakraborty S. Combining extracellular matrix proteome and phosphoproteome of chickpea and meta-analysis reveal novel proteoforms and evolutionary significance of clade-specific wall-associated events in plant. PLANT DIRECT 2024; 8:e572. [PMID: 38500675 PMCID: PMC10945595 DOI: 10.1002/pld3.572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/27/2023] [Accepted: 02/10/2024] [Indexed: 03/20/2024]
Abstract
Extracellular matrix (ECM) plays central roles in cell architecture, innate defense and cell wall integrity (CWI) signaling. During transition to multicellularity, modular domain structures of ECM proteins and proteoforms have evolved due to continuous adaptation across taxonomic clades under different ecological niche. Although this incredible diversity has to some extent been investigated at protein level, extracellular phosphorylation events and molecular evolution of ECM proteoform families remains unexplored. We developed matrisome proteoform atlas in a grain legume, chickpea and performed meta-analyses of 74 plant matrisomes. MS/MS analysis identified 1,424 proteins and 315 phosphoproteins involved in diverse functions. Cross-species ECM protein network identified proteoforms associated with CWI maintenance system. Phylogenetic characterization of eighteen matrix protein families highlighted the role of taxon-specific paralogs and orthologs. Novel information was acquired on gene expansion and loss, co-divergence, sub functionalization and neofunctionalization during evolution. Modular networks of matrix protein families and hub proteins showed higher diversity across taxonomic clades than among organs. Furthermore, protein families differ in nonsynonymous to synonymous substitution rates. Our study pointed towards the matrix proteoform functionality, sequence divergence variation, interactions between wall remodelers and molecular evolution using a phylogenetic framework. This is the first report on comprehensive matrisome proteoform network illustrating presence of CWI signaling proteins in land plants.
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Affiliation(s)
- Kanika Narula
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Arunima Sinha
- National Institute of Plant Genome ResearchNew DelhiIndia
| | | | - Sudip Ghosh
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Eman Elagamey
- National Institute of Plant Genome ResearchNew DelhiIndia
- Plant Pathology Research InstituteAgricultural Research Center (ARC)GizaEgypt
| | - Archana Sharma
- National Institute of Plant Genome ResearchNew DelhiIndia
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13
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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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14
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Howe J, Cornwallis CK, Griffin AS. Conflict-reducing innovations in development enable increased multicellular complexity. Proc Biol Sci 2024; 291:20232466. [PMID: 38196363 PMCID: PMC10777161 DOI: 10.1098/rspb.2023.2466] [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: 11/03/2023] [Accepted: 12/07/2023] [Indexed: 01/11/2024] Open
Abstract
Obligately multicellular organisms, where cells can only reproduce as part of the group, have evolved multiple times across the tree of life. Obligate multicellularity has only evolved when clonal groups form by cell division, rather than by cells aggregating, as clonality prevents internal conflict. Yet obligately multicellular organisms still vary greatly in 'multicellular complexity' (the number of cells and cell types): some comprise a few cells and cell types, while others have billions of cells and thousands of types. Here, we test whether variation in multicellular complexity is explained by two conflict-suppressing mechanisms, namely a single-cell bottleneck at the start of development, and a strict separation of germline and somatic cells. Examining the life cycles of 129 lineages of plants, animals, fungi and algae, we show using phylogenetic comparative analyses that an early segregation of the germline stem-cell lineage is key to the evolution of more cell types, driven by a strong correlation in the Metazoa. By contrast, the presence of a strict single-cell bottleneck was not related to either the number of cells or the number of cell types, but was associated with early germline segregation. Our results suggest that segregating the germline earlier in development enabled greater evolutionary innovation, although whether this is a consequence of conflict reduction or other non-conflict effects, such as developmental flexibility, is unclear.
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Affiliation(s)
- Jack Howe
- Center for Evolutionary Hologenomics, Globe Institute, Copenhagen University, 1350 Copenhagen, Denmark
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15
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Walker LM, Sherpa RN, Ivaturi S, Brock DA, Larsen TJ, Walker JR, Strassmann JE, Queller DC. Parallel evolution of the G protein-coupled receptor GrlG and the loss of fruiting body formation in the social amoeba Dictyostelium discoideum evolved under low relatedness. G3 (BETHESDA, MD.) 2023; 14:jkad235. [PMID: 37832511 PMCID: PMC10755179 DOI: 10.1093/g3journal/jkad235] [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: 07/25/2023] [Revised: 07/25/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023]
Abstract
Aggregative multicellularity relies on cooperation among formerly independent cells to form a multicellular body. Previous work with Dictyostelium discoideum showed that experimental evolution under low relatedness profoundly decreased cooperation, as indicated by the loss of fruiting body formation in many clones and an increase of cheaters that contribute proportionally more to spores than to the dead stalk. Using whole-genome sequencing and variant analysis of these lines, we identified 38 single nucleotide polymorphisms in 29 genes. Each gene had 1 variant except for grlG (encoding a G protein-coupled receptor), which had 10 unique SNPs and 5 structural variants. Variants in the 5' half of grlG-the region encoding the signal peptide and the extracellular binding domain-were significantly associated with the loss of fruiting body formation; the association was not significant in the 3' half of the gene. These results suggest that the loss of grlG was adaptive under low relatedness and that at least the 5' half of the gene is important for cooperation and multicellular development. This is surprising given some previous evidence that grlG encodes a folate receptor involved in predation, which occurs only during the single-celled stage. However, non-fruiting mutants showed little increase in a parallel evolution experiment where the multicellular stage was prevented from happening. This shows that non-fruiting mutants are not generally selected by any predation advantage but rather by something-likely cheating-during the multicellular stage.
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Affiliation(s)
- Laura M Walker
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Rintsen N Sherpa
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sindhuri Ivaturi
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Debra A Brock
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Tyler J Larsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Jason R Walker
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Joan E Strassmann
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - David C Queller
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
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16
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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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17
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Lamża Ł. Diversity of 'simple' multicellular eukaryotes: 45 independent cases and six types of multicellularity. Biol Rev Camb Philos Soc 2023; 98:2188-2209. [PMID: 37475165 DOI: 10.1111/brv.13001] [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: 03/16/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/22/2023]
Abstract
Multicellularity evolved multiple times in the history of life, with most reviewers agreeing that it appeared at least 20 times in eukaryotes. However, a specific list of multicellular eukaryotes with clear criteria for inclusion has not yet been published. Herein, an updated critical review of eukaryotic multicellularity is presented, based on current understanding of eukaryotic phylogeny and new discoveries in microbiology, phycology and mycology. As a result, 45 independent multicellular lineages are identified that fall into six distinct types. Functional criteria, as distinct from a purely topological definition of a cell, are introduced to bring uniformity and clarity to the existing definitions of terms such as colony, multicellularity, thallus or plasmodium. The category of clonal multicellularity is expanded to include: (i) septated multinucleated thalli found in Pseudofungi and early-branching Fungi such as Chytridiomycota and Blastocladiomycota; and (ii) multicellular reproductive structures formed by plasmotomy in intracellular parasites such as Phytomyxea. Furthermore, (iii) endogeneous budding, as found in Paramyxida, is described as a form of multicellularity. The best-known case of clonal multicellularity, i.e. (iv) non-separation of cells after cell division, as known from Metazoa and Ochrophyta, is also discussed. The category of aggregative multicellularity is expanded to include not only (v) pseudoplasmodial forms, such a sorocarp-forming Acrasida, but also (vi) meroplasmodial organisms, such as members of Variosea or Filoreta. A common set of topological, geometric, genetic and life-cycle criteria are presented that form a coherent, philosophically sound framework for discussing multicellularity. A possibility of a seventh type of multicellularity is discussed, that of multi-species superorganisms formed by protists with obligatory bacterial symbionts, such as some members of Oxymonada or Parabasalia. Its inclusion is dependent on the philosophical stance taken towards the concepts of individuality and organism in biology. Taxa that merit special attention are identified, such as colonial Centrohelea, and a new speculative form of multicellularity, possibly present in some reticulopodial amoebae, is briefly described. Because of insufficient phylogenetic and morphological data, not all lineages could be unequivocally identified, and the true total number of all multicellular eukaryotic lineages is therefore higher, likely close to a hundred.
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Affiliation(s)
- Łukasz Lamża
- Copernicus Center for Interdisciplinary Studies, Jagiellonian University, Szczepanska 1, Kraków, 31-011, Poland
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18
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Schaible GA, Jay ZJ, Cliff J, Schulz F, Gauvin C, Goudeau D, Malmstrom RR, Emil Ruff S, Edgcomb V, Hatzenpichler R. Multicellular magnetotactic bacterial consortia are metabolically differentiated and not clonal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.27.568837. [PMID: 38076927 PMCID: PMC10705294 DOI: 10.1101/2023.11.27.568837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Consortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use multiple culture-independent approaches to analyze the genomics and physiology of MMB consortia at single cell resolution. We separately sequenced the metagenomes of 22 individual MMB consortia, representing eight new species, and quantified the genetic diversity within each MMB consortium. This revealed that, counter to conventional views, cells within MMB consortia are not clonal. Single consortia metagenomes were then used to reconstruct the species-specific metabolic potential and infer the physiological capabilities of MMB. To validate genomic predictions, we performed stable isotope probing (SIP) experiments and interrogated MMB consortia using fluorescence in situ hybridization (FISH) combined with nano-scale secondary ion mass spectrometry (NanoSIMS). By coupling FISH with bioorthogonal non-canonical amino acid tagging (BONCAT) we explored their in situ activity as well as variation of protein synthesis within cells. We demonstrate that MMB consortia are mixotrophic sulfate reducers and that they exhibit metabolic differentiation between individual cells, suggesting that MMB consortia are more complex than previously thought. These findings expand our understanding of MMB diversity, ecology, genomics, and physiology, as well as offer insights into the mechanisms underpinning the multicellular nature of their unique lifestyle.
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Affiliation(s)
- George A. Schaible
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717
| | - Zackary J. Jay
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717
- Thermal Biology Institute, Montana State University, Bozeman, MT 59717
| | - John Cliff
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Frederik Schulz
- Department of Energy Joint Genome Institute, Berkeley, CA, 94720
| | - Colin Gauvin
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717
- Thermal Biology Institute, Montana State University, Bozeman, MT 59717
| | - Danielle Goudeau
- Department of Energy Joint Genome Institute, Berkeley, CA, 94720
| | - Rex R. Malmstrom
- Department of Energy Joint Genome Institute, Berkeley, CA, 94720
| | - S. Emil Ruff
- Ecosystems Center and Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, 02543
| | | | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717
- Thermal Biology Institute, Montana State University, Bozeman, MT 59717
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717
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19
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Nanda P, Barrere J, LaBar T, Murray AW. Multicellular growth as a dynamic network of cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.02.565242. [PMID: 37961646 PMCID: PMC10635083 DOI: 10.1101/2023.11.02.565242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
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. However, we do not understand how different cellular features quantitatively influence these two 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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20
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Czarnoleski M, Szlachcic E, Privalova V, Maria Labecka A, Sikorska A, Sobczyk Ł, VandenBrooks J, Angilletta MJ. Oxygen and temperature affect cell sizes differently among tissues and between sexes of Drosophila melanogaster. JOURNAL OF INSECT PHYSIOLOGY 2023; 150:104559. [PMID: 37640139 DOI: 10.1016/j.jinsphys.2023.104559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
Spatio-temporal gradients in thermal and oxygen conditions trigger evolutionary and developmental responses in ectotherms' body size and cell size, which are commonly interpreted as adaptive. However, the evidence for cell-size responses is fragmentary, as cell size is typically assessed in single tissues. In a laboratory experiment, we raised genotypes of Drosophila melanogaster at all combinations of two temperatures (16 °C or 25 °C) and two oxygen levels (10% or 22%) and measured body size and the sizes of cells in different tissues. For each sex, we measured epidermal cells in a wing and a leg and ommatidial cells of an eye. For males, we also measured epithelial cells of a Malpighian tubule and muscle cells of a flight muscle. On average, females emerged at a larger body size than did males, having larger cells in all tissues. Flies of either sex emerged at a smaller body size when raised under warm or hypoxic conditions. Development at 25 °C resulted in smaller cells in most tissues. Development under hypoxia resulted in smaller cells in some tissues, especially among females. Altogether, our results show thermal and oxygen conditions trigger shifts in adult size, coupled with the systemic orchestration of cell sizes throughout the body of a fly. The nature of these patterns supports a model in which an ectotherm adjusts its life-history traits and cellular composition to prevent severe hypoxia at the cellular level. However, our results revealed some inconsistencies linked to sex, cell type, and environmental parameters, which suggest caution in translating information obtained for single type of cells to the organism as a whole.
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Affiliation(s)
- Marcin Czarnoleski
- Life History Evolution Group, Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland.
| | - Ewa Szlachcic
- Life History Evolution Group, Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland.
| | - Valeriya Privalova
- Life History Evolution Group, Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland.
| | - Anna Maria Labecka
- Life History Evolution Group, Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland.
| | - Anna Sikorska
- Life History Evolution Group, Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland.
| | - Łukasz Sobczyk
- Life History Evolution Group, Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland.
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21
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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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22
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Gavrilov-Zimin IA. Ancient reproductive modes and criteria of multicellularity. COMPARATIVE CYTOGENETICS 2023; 17:195-238. [PMID: 37953852 PMCID: PMC10636606 DOI: 10.3897/compcytogen.17.109671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/05/2023] [Indexed: 11/14/2023]
Abstract
It is demonstrated that the initial method of fertilization in animals (Metazoa), embryophyte plants (Embryophyta), most groups of multicellular oogamous algae, oogamous and pseudoogamous multicellular fungi was internal fertilization (in the broad meaning) in/on the body of a maternal organism. Accordingly, during the bisexual process, the initial method of formation of a daughter multicellular organism in animals was viviparity, and in embryophyte plants and most groups of oogamous multicellular algae - the germination of a zygote in/on the body of maternal organism. The reproductive criteria of multicellularity are proposed and discussed. In this regard, the multicellularity is considered to subdivide terminologically into three variants: 1) protonemal, the most simple, characteristic of multicellular prokaryotes, most groups of multicellular algae and gametophytes of some higher plants; 2) siphonoseptal, found among multicellular fungi, some groups of green and yellow-green algae; 3) embryogenic, most complicated, known in all animals (Metazoa), all sporophytes and some gametophytes of higher plants (Embryophyta), charophyte green algae Charophyceae s.s., oogamous species of green and brown algae, some genera of red algae. In addition to the well-known division of reproduction methods into sexual and asexual, it is proposed to divide the reproduction of multicellular organisms into monocytic (the emergence of a new organism from one cell sexually or asexually) and polycytic (fragmentation, longitudinal / transverse division or budding based on many cells of the body of the mother organism), since these two ways have different evolutionary and ontogenetic origins.
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Affiliation(s)
- Ilya A. Gavrilov-Zimin
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, St. Petersburg, 199034, RussiaZoological Institute, Russian Academy of SciencesSt. PetersburgRussia
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23
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Bourke AFG. Conflict and conflict resolution in the major transitions. Proc Biol Sci 2023; 290:20231420. [PMID: 37817595 PMCID: PMC10565403 DOI: 10.1098/rspb.2023.1420] [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: 06/23/2023] [Accepted: 09/14/2023] [Indexed: 10/12/2023] Open
Abstract
Conflict and conflict resolution have been argued to be fundamental to the major transitions in evolution. These were key events in life's history in which previously independently living individuals cooperatively formed a higher-level individual, such as a multicellular organism or eusocial colony. Conflict has its central role because, to proceed stably, the evolution of individuality in each major transition required within-individual conflict to be held in check. This review revisits the role of conflict and conflict resolution in the major transitions, addressing recent work arguing for a minor role. Inclusive fitness logic suggests that differences between the kin structures of clones and sexual families support the absence of conflict at the origin of multicellularity but, by contrast, suggest that key conflicts existed at the origin of eusociality. A principal example is conflict over replacing the founding queen (queen replacement). Following the origin of each transition, conflict remained important, because within-individual conflict potentially disrupts the attainment of maximal individuality (organismality) in the system. The conclusion is that conflict remains central to understanding the major transitions, essentially because conflict arises from differences in inclusive fitness optima while conflict resolution can help the system attain a high degree of coincidence of inclusive fitness interests.
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Affiliation(s)
- Andrew F. G. Bourke
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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24
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Patten MM, Schenkel MA, Ågren JA. Adaptation in the face of internal conflict: the paradox of the organism revisited. Biol Rev Camb Philos Soc 2023; 98:1796-1811. [PMID: 37203364 DOI: 10.1111/brv.12983] [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: 12/08/2022] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/20/2023]
Abstract
The paradox of the organism refers to the observation that organisms appear to function as coherent purposeful entities, despite the potential for within-organismal components like selfish genetic elements and cancer cells to erode them from within. While it is commonly accepted that organisms may pursue fitness maximisation and can be thought to hold particular agendas, there is a growing recognition that genes and cells do so as well. This can lead to evolutionary conflicts between an organism and the parts that reside within it. Here, we revisit the paradox of the organism. We first outline its conception and relationship to debates about adaptation in evolutionary biology. Second, we review the ways selfish elements may exploit organisms, and the extent to which this threatens organismal integrity. To this end, we introduce a novel classification scheme that distinguishes between selfish elements that seek to distort transmission versus those that seek to distort phenotypic traits. Our classification scheme also highlights how some selfish elements elude a multi-level selection decomposition using the Price equation. Third, we discuss how the organism can retain its status as the primary fitness-maximising agent in the face of selfish elements. The success of selfish elements is often constrained by their strategy and further limited by a combination of fitness alignment and enforcement mechanisms controlled by the organism. Finally, we argue for the need for quantitative measures of both internal conflicts and organismality.
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Affiliation(s)
- Manus M Patten
- Department of Biology, Georgetown University, 37th and O St. NW, Washington, DC, 20057, USA
| | - Martijn A Schenkel
- Department of Biology, Georgetown University, 37th and O St. NW, Washington, DC, 20057, USA
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - J Arvid Ågren
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, Uppsala, 752 36, Sweden
- Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, 44195, USA
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25
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Aanen DK, van ’t Padje A, Auxier B. Longevity of Fungal Mycelia and Nuclear Quality Checks: a New Hypothesis for the Role of Clamp Connections in Dikaryons. Microbiol Mol Biol Rev 2023; 87:e0002221. [PMID: 37409939 PMCID: PMC10521366 DOI: 10.1128/mmbr.00022-21] [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] [Indexed: 07/07/2023] Open
Abstract
This paper addresses the stability of mycelial growth in fungi and differences between ascomycetes and basidiomycetes. Starting with general evolutionary theories of multicellularity and the role of sex, we then discuss individuality in fungi. Recent research has demonstrated the deleterious consequences of nucleus-level selection in fungal mycelia, favoring cheaters with a nucleus-level benefit during spore formation but a negative effect on mycelium-level fitness. Cheaters appear to generally be loss-of-fusion (LOF) mutants, with a higher propensity to form aerial hyphae developing into asexual spores. Since LOF mutants rely on heterokaryosis with wild-type nuclei, we argue that regular single-spore bottlenecks can efficiently select against such cheater mutants. We then zoom in on ecological differences between ascomycetes being typically fast-growing but short-lived with frequent asexual-spore bottlenecks and basidiomycetes being generally slow-growing but long-lived and usually without asexual-spore bottlenecks. We argue that these life history differences have coevolved with stricter nuclear quality checks in basidiomycetes. Specifically, we propose a new function for clamp connections, structures formed during the sexual stage in ascomycetes and basidiomycetes but during somatic growth only in basidiomycete dikaryons. During dikaryon cell division, the two haploid nuclei temporarily enter a monokaryotic phase, by alternatingly entering a retrograde-growing clamp cell, which subsequently fuses with the subapical cell to recover the dikaryotic cell. We hypothesize that clamp connections act as screening devices for nuclear quality, with both nuclei continuously testing each other for fusion ability, a test that LOF mutants will fail. By linking differences in longevity of the mycelial phase to ecology and stringency of nuclear quality checks, we propose that mycelia have a constant and low lifetime cheating risk, irrespective of their size and longevity.
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Affiliation(s)
- Duur K. Aanen
- Department of Plant Sciences, Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
| | - Anouk van ’t Padje
- Department of Plant Sciences, Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
| | - Benjamin Auxier
- Department of Plant Sciences, Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
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26
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Ashouri A, Zhang C, Gaiti F. Decoding Cancer Evolution: Integrating Genetic and Non-Genetic Insights. Genes (Basel) 2023; 14:1856. [PMID: 37895205 PMCID: PMC10606072 DOI: 10.3390/genes14101856] [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: 09/01/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
The development of cancer begins with cells transitioning from their multicellular nature to a state akin to unicellular organisms. This shift leads to a breakdown in the crucial regulators inherent to multicellularity, resulting in the emergence of diverse cancer cell subpopulations that have enhanced adaptability. The presence of different cell subpopulations within a tumour, known as intratumoural heterogeneity (ITH), poses challenges for cancer treatment. In this review, we delve into the dynamics of the shift from multicellularity to unicellularity during cancer onset and progression. We highlight the role of genetic and non-genetic factors, as well as tumour microenvironment, in promoting ITH and cancer evolution. Additionally, we shed light on the latest advancements in omics technologies that allow for in-depth analysis of tumours at the single-cell level and their spatial organization within the tissue. Obtaining such detailed information is crucial for deepening our understanding of the diverse evolutionary paths of cancer, allowing for the development of effective therapies targeting the key drivers of cancer evolution.
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Affiliation(s)
- Arghavan Ashouri
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Chufan Zhang
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Federico Gaiti
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
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27
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Ruiz-Trillo I, Kin K, Casacuberta E. The Origin of Metazoan Multicellularity: A Potential Microbial Black Swan Event. Annu Rev Microbiol 2023; 77:499-516. [PMID: 37406343 DOI: 10.1146/annurev-micro-032421-120023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
The emergence of animals from their unicellular ancestors is a major evolutionary event. Thanks to the study of diverse close unicellular relatives of animals, we now have a better grasp of what the unicellular ancestor of animals was like. However, it is unclear how that unicellular ancestor of animals became the first animals. To explain this transition, two popular theories, the choanoblastaea and the synzoospore, have been proposed. We will revise and expose the flaws in these two theories while showing that, due to the limits of our current knowledge, the origin of animals is a biological black swan event. As such, the origin of animals defies retrospective explanations. Therefore, we should be extra careful not to fall for confirmation biases based on few data and, instead, embrace this uncertainty and be open to alternative scenarios. With the aim to broaden the potential explanations on how animals emerged, we here propose two novel and alternative scenarios. In any case, to find the answer to how animals evolved, additional data will be required, as will the hunt for microscopic creatures that are closely related to animals but have not yet been sampled and studied.
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Affiliation(s)
- Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain;
- ICREA, Barcelona, Spain
| | - Koryu Kin
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain;
| | - Elena Casacuberta
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain;
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28
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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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29
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Marotta P, Ruggiero A, Bilcke G. Editorial: Unicellular organisms as an evolutionary snapshot toward multicellularity. Front Cell Dev Biol 2023; 11:1254636. [PMID: 37664459 PMCID: PMC10470824 DOI: 10.3389/fcell.2023.1254636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/10/2023] [Indexed: 09/05/2023] Open
Affiliation(s)
| | - Antonella Ruggiero
- Stazione Zoologica Anton Dohrn, Naples, Italy
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Gust Bilcke
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
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30
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Mela AP, Glass NL. Permissiveness and competition within and between Neurospora crassa syncytia. Genetics 2023; 224:iyad112. [PMID: 37313736 PMCID: PMC10411585 DOI: 10.1093/genetics/iyad112] [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: 03/14/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 06/15/2023] Open
Abstract
A multinucleate syncytium is a common growth form in filamentous fungi. Comprehensive functions of the syncytial state remain unknown, but it likely allows for a wide range of adaptations to enable filamentous fungi to coordinate growth, reproduction, responses to the environment, and to distribute nuclear and cytoplasmic elements across a colony. Indeed, the underlying mechanistic details of how syncytia regulate cellular and molecular processes spatiotemporally across a colony are largely unexplored. Here, we implemented a strategy to analyze the relative fitness of different nuclear populations in syncytia of Neurospora crassa, including nuclei with loss-of-function mutations in essential genes, based on production of multinucleate asexual spores using flow cytometry of pairings between strains with differentially fluorescently tagged nuclear histones. The distribution of homokaryotic and heterokaryotic asexual spores in pairings was assessed between different auxotrophic and morphological mutants, as well as with strains that were defective in somatic cell fusion or were heterokaryon incompatible. Mutant nuclei were compartmentalized into both homokaryotic and heterokaryotic asexual spores, a type of bet hedging for maintenance and evolution of mutational events, despite disadvantages to the syncytium. However, in pairings between strains that were blocked in somatic cell fusion or were heterokaryon incompatible, we observed a "winner-takes-all" phenotype, where asexual spores originating from paired strains were predominantly one genotype. These data indicate that syncytial fungal cells are permissive and tolerate a wide array of nuclear functionality, but that cells/colonies that are unable to cooperate via syncytia formation actively compete for resources.
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Affiliation(s)
- Alexander P Mela
- The Plant and Microbial Biology Department, University of California Berkeley, Berkeley, CA 94720, USA
| | - N Louise Glass
- The Plant and Microbial Biology Department, University of California Berkeley, Berkeley, CA 94720, USA
- The Environmental Genomics and Systems Biology Division, The Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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31
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Vroomans RMA, Colizzi ES. Evolution of selfish multicellularity: collective organisation of individual spatio-temporal regulatory strategies. BMC Ecol Evol 2023; 23:35. [PMID: 37468829 PMCID: PMC10357660 DOI: 10.1186/s12862-023-02133-x] [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: 09/01/2022] [Accepted: 06/12/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND The unicellular ancestors of modern-day multicellular organisms were remarkably complex. They had an extensive set of regulatory and signalling genes, an intricate life cycle and could change their behaviour in response to environmental changes. At the transition to multicellularity, some of these behaviours were co-opted to organise the development of the nascent multicellular organism. Here, we focus on the transition to multicellularity before the evolution of stable cell differentiation, to reveal how the emergence of clusters affects the evolution of cell behaviour. RESULTS We construct a computational model of a population of cells that can evolve the regulation of their behavioural state - either division or migration - and study both a unicellular and a multicellular context. Cells compete for reproduction and for resources to survive in a seasonally changing environment. We find that the evolution of multicellularity strongly determines the co-evolution of cell behaviour, by altering the competition dynamics between cells. When adhesion cannot evolve, cells compete for survival by rapidly migrating towards resources before dividing. When adhesion evolves, emergent collective migration alleviates the pressure on individual cells to reach resources. This allows individual cells to maximise their own replication. Migrating adhesive clusters display striking patterns of spatio-temporal cell state changes that visually resemble animal development. CONCLUSIONS Our model demonstrates how emergent selection pressures at the onset of multicellularity can drive the evolution of cellular behaviour to give rise to developmental patterns.
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Affiliation(s)
- Renske M A Vroomans
- Informatics Institute, University of Amsterdam, Amsterdam, Netherlands.
- Origins Center, Groningen, Netherlands.
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK.
| | - Enrico Sandro Colizzi
- Origins Center, Groningen, Netherlands
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Mathematical Institute, Leiden University, Leiden, Netherlands
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32
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Capp J, Thomas F, Marusyk A, M. Dujon A, Tissot S, Gatenby R, Roche B, Ujvari B, DeGregori J, Brown JS, Nedelcu AM. The paradox of cooperation among selfish cancer cells. Evol Appl 2023; 16:1239-1256. [PMID: 37492150 PMCID: PMC10363833 DOI: 10.1111/eva.13571] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 05/19/2023] [Accepted: 06/06/2023] [Indexed: 07/27/2023] Open
Abstract
It is traditionally assumed that during cancer development, tumor cells abort their initially cooperative behavior (i.e., cheat) in favor of evolutionary strategies designed solely to enhance their own fitness (i.e., a "selfish" life style) at the expense of that of the multicellular organism. However, the growth and progress of solid tumors can also involve cooperation among these presumed selfish cells (which, by definition, should be noncooperative) and with stromal cells. The ultimate and proximate reasons behind this paradox are not fully understood. Here, in the light of current theories on the evolution of cooperation, we discuss the possible evolutionary mechanisms that could explain the apparent cooperative behaviors among selfish malignant cells. In addition to the most classical explanations for cooperation in cancer and in general (by-product mutualism, kin selection, direct reciprocity, indirect reciprocity, network reciprocity, group selection), we propose the idea that "greenbeard" effects are relevant to explaining some cooperative behaviors in cancer. Also, we discuss the possibility that malignant cooperative cells express or co-opt cooperative traits normally expressed by healthy cells. We provide examples where considerations of these processes could help understand tumorigenesis and metastasis and argue that this framework provides novel insights into cancer biology and potential strategies for cancer prevention and treatment.
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Affiliation(s)
- Jean‐Pascal Capp
- Toulouse Biotechnology InstituteUniversity of Toulouse, INSA, CNRS, INRAEToulouseFrance
| | - Frédéric Thomas
- CREEC, MIVEGECUniversity of Montpellier, CNRS, IRDMontpellierFrance
| | - Andriy Marusyk
- Department of Cancer PhysiologyH Lee Moffitt Cancer Center and Research InstituteTampaFloridaUSA
| | - Antoine M. Dujon
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
| | - Sophie Tissot
- Department of Biochemistry and Molecular GeneticsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Robert Gatenby
- Department of Cancer PhysiologyH Lee Moffitt Cancer Center and Research InstituteTampaFloridaUSA
| | - Benjamin Roche
- Department of Biochemistry and Molecular GeneticsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Beata Ujvari
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
| | - James DeGregori
- Department of Biochemistry and Molecular GeneticsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Joel S. Brown
- Department of Cancer PhysiologyH Lee Moffitt Cancer Center and Research InstituteTampaFloridaUSA
| | - Aurora M. Nedelcu
- Department of BiologyUniversity of New BrunswickFrederictonNew BrunswickCanada
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33
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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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34
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Cornwallis CK, Svensson-Coelho M, Lindh M, Li Q, Stábile F, Hansson LA, Rengefors K. Single-cell adaptations shape evolutionary transitions to multicellularity in green algae. Nat Ecol Evol 2023; 7:889-902. [PMID: 37081145 PMCID: PMC10250200 DOI: 10.1038/s41559-023-02044-6] [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: 11/01/2022] [Accepted: 03/22/2023] [Indexed: 04/22/2023]
Abstract
The evolution of multicellular life has played a pivotal role in shaping biological diversity. However, we know surprisingly little about the natural environmental conditions that favour the formation of multicellular groups. Here we experimentally examine how key environmental factors (predation, nitrogen and water turbulence) combine to influence multicellular group formation in 35 wild unicellular green algae strains (19 Chlorophyta species). All environmental factors induced the formation of multicellular groups (more than four cells), but there was no evidence this was adaptive, as multicellularity (% cells in groups) was not related to population growth rate under any condition. Instead, population growth was related to extracellular matrix (ECM) around single cells and palmelloid formation, a unicellular life-cycle stage where two to four cells are retained within a mother-cell wall after mitosis. ECM production increased with nitrogen levels resulting in more cells being in palmelloids and higher rates of multicellular group formation. Examining the distribution of 332 algae species across 478 lakes monitored over 55 years, showed that ECM and nitrogen availability also predicted patterns of obligate multicellularity in nature. Our results highlight that adaptations of unicellular organisms to cope with environmental challenges may be key to understanding evolutionary routes to multicellular life.
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Affiliation(s)
| | | | - Markus Lindh
- Swedish Meteorological and Hydrological Institute, Västra Frölunda, Sweden
| | - Qinyang Li
- Department of Biology, Lund University, Lund, Sweden
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35
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Privalova V, Labecka AM, Szlachcic E, Sikorska A, Czarnoleski M. Systemic changes in cell size throughout the body of Drosophila melanogaster associated with mutations in molecular cell cycle regulators. Sci Rep 2023; 13:7565. [PMID: 37160985 PMCID: PMC10169805 DOI: 10.1038/s41598-023-34674-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/05/2023] [Indexed: 05/11/2023] Open
Abstract
Along with different life strategies, organisms have evolved dramatic cellular composition differences. Understanding the molecular basis and fitness effects of these differences is key to elucidating the fundamental characteristics of life. TOR/insulin pathways are key regulators of cell size, but whether their activity determines cell size in a systemic or tissue-specific manner awaits exploration. To that end, we measured cells in four tissues in genetically modified Drosophila melanogaster (rictorΔ2 and Mnt1) and corresponding controls. While rictorΔ2 flies lacked the Rictor protein in TOR complex 2, downregulating the functions of this element in TOR/insulin pathways, Mnt1 flies lacked the transcriptional regulator protein Mnt, weakening the suppression of downstream signalling from TOR/insulin pathways. rictorΔ2 flies had smaller epidermal (leg and wing) and ommatidial cells and Mnt1 flies had larger cells in these tissues than the controls. Females had consistently larger cells than males in the three tissue types. In contrast, dorsal longitudinal flight muscle cells (measured only in males) were not altered by mutations. We suggest that mutations in cell cycle control pathways drive the evolution of systemic changes in cell size throughout the body, but additional mechanisms shape the cellular composition of some tissues independent of these mutations.
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Affiliation(s)
- Valeriya Privalova
- Life History Evolution Group, Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Anna Maria Labecka
- Life History Evolution Group, Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Ewa Szlachcic
- Life History Evolution Group, Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Anna Sikorska
- Life History Evolution Group, Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Marcin Czarnoleski
- Life History Evolution Group, Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland.
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36
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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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37
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Isaksson H, Brännström Å, Libby E. Minor variations in multicellular life cycles have major effects on adaptation. PLoS Comput Biol 2023; 19:e1010698. [PMID: 37083675 PMCID: PMC10156057 DOI: 10.1371/journal.pcbi.1010698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 05/03/2023] [Accepted: 03/29/2023] [Indexed: 04/22/2023] Open
Abstract
Multicellularity has evolved several independent times over the past hundreds of millions of years and given rise to a wide diversity of complex life. Recent studies have found that large differences in the fundamental structure of early multicellular life cycles can affect fitness and influence multicellular adaptation. Yet, there is an underlying assumption that at some scale or categorization multicellular life cycles are similar in terms of their adaptive potential. Here, we consider this possibility by exploring adaptation in a class of simple multicellular life cycles of filamentous organisms that only differ in one respect, how many daughter filaments are produced. We use mathematical models and evolutionary simulations to show that despite the similarities, qualitatively different mutations fix. In particular, we find that mutations with a tradeoff between cell growth and group survival, i.e. "selfish" or "altruistic" traits, spread differently. Specifically, altruistic mutations more readily spread in life cycles that produce few daughters while in life cycles producing many daughters either type of mutation can spread depending on the environment. Our results show that subtle changes in multicellular life cycles can fundamentally alter adaptation.
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Affiliation(s)
- Hanna Isaksson
- Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, Sweden
- IceLab, Umeå University, Umeå, Sweden
| | - Åke Brännström
- Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, Sweden
- IceLab, Umeå University, Umeå, Sweden
- Advancing Systems Analysis Program, International Institute for Applied Systems Analysis (IIASA), Laxenburg, Austria
- Complexity Science and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami, Japan
| | - Eric Libby
- Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, Sweden
- IceLab, Umeå University, Umeå, Sweden
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38
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Grochau-Wright ZI, Nedelcu AM, Michod RE. The Genetics of Fitness Reorganization during the Transition to Multicellularity: The Volvocine regA-like Family as a Model. Genes (Basel) 2023; 14:genes14040941. [PMID: 37107699 PMCID: PMC10137558 DOI: 10.3390/genes14040941] [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: 02/17/2023] [Revised: 04/06/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
The evolutionary transition from single-celled to multicellular individuality requires organismal fitness to shift from the cell level to a cell group. This reorganization of fitness occurs by re-allocating the two components of fitness, survival and reproduction, between two specialized cell types in the multicellular group: soma and germ, respectively. How does the genetic basis for such fitness reorganization evolve? One possible mechanism is the co-option of life history genes present in the unicellular ancestors of a multicellular lineage. For instance, single-celled organisms must regulate their investment in survival and reproduction in response to environmental changes, particularly decreasing reproduction to ensure survival under stress. Such stress response life history genes can provide the genetic basis for the evolution of cellular differentiation in multicellular lineages. The regA-like gene family in the volvocine green algal lineage provides an excellent model system to study how this co-option can occur. We discuss the origin and evolution of the volvocine regA-like gene family, including regA-the gene that controls somatic cell development in the model organism Volvox carteri. We hypothesize that the co-option of life history trade-off genes is a general mechanism involved in the transition to multicellular individuality, making volvocine algae and the regA-like family a useful template for similar investigations in other lineages.
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Affiliation(s)
| | - Aurora M Nedelcu
- Biology Department, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Richard E Michod
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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Li G, Chen L, Pang K, Tang Q, Wu C, Yuan X, Zhou C, Xiao S. Tonian carbonaceous compressions indicate that Horodyskia is one of the oldest multicellular and coenocytic macro-organisms. Commun Biol 2023; 6:399. [PMID: 37046079 PMCID: PMC10097871 DOI: 10.1038/s42003-023-04740-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Macrofossils with unambiguous biogenic origin and predating the one-billion-year-old multicellular fossils Bangiomorpha and Proterocladus interpreted as crown-group eukaryotes are quite rare. Horodyskia is one of these few macrofossils, and it extends from the early Mesoproterozoic Era to the terminal Ediacaran Period. The biological interpretation of this enigmatic fossil, however, has been a matter of controversy since its discovery in 1982, largely because there was no evidence for the preservation of organic walls. Here we report new carbonaceous compressions of Horodyskia from the Tonian successions (~950-720 Ma) in North China. The macrofossils herein with bona fide organic walls reinforce the biogenicity of Horodyskia. Aided by the new material, we reconstruct Horodyskia as a colonial organism composed of a chain of organic-walled vesicles that likely represent multinucleated (coenocytic) cells of early eukaryotes. Two species of Horodyskia are differentiated on the basis of vesicle sizes, and their co-existence in the Tonian assemblage provides a link between the Mesoproterozoic (H. moniliformis) and the Ediacaran (H. minor) species. Our study thus provides evidence that eukaryotes have acquired macroscopic size through the combination of coenocytism and colonial multicellularity at least ~1.48 Ga, and highlights an exceptionally long range and morphological stasis of this Proterozoic macrofossils.
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Affiliation(s)
- Guangjin Li
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Lei Chen
- College of Earth Science and Engineering, Shandong University of Science and Technology, Qingdao, 266590, China.
| | - Ke Pang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, Nanjing, 210008, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- University of Chinese Academy of Sciences, Nanjing, 211135, China.
| | - Qing Tang
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing, 210023, China
- Department of Earth Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Chengxi Wu
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xunlai Yuan
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuanming Zhou
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- University of Chinese Academy of Sciences, Nanjing, 211135, China
| | - Shuhai Xiao
- Department of Geosciences and Global Change Center, Virginia Tech, Blacksburg, VA, 24061, USA
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Kelly JR, Clarke G, Harkin A, Corr SC, Galvin S, Pradeep V, Cryan JF, O'Keane V, Dinan TG. Seeking the Psilocybiome: Psychedelics meet the microbiota-gut-brain axis. Int J Clin Health Psychol 2023; 23:100349. [PMID: 36605409 PMCID: PMC9791138 DOI: 10.1016/j.ijchp.2022.100349] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/16/2022] [Indexed: 12/15/2022] Open
Abstract
Moving towards a systems psychiatry paradigm embraces the inherent complex interactions across all levels from micro to macro and necessitates an integrated approach to treatment. Cortical 5-HT2A receptors are key primary targets for the effects of serotonergic psychedelics. However, the therapeutic mechanisms underlying psychedelic therapy are complex and traverse molecular, cellular, and network levels, under the influence of biofeedback signals from the periphery and the environment. At the interface between the individual and the environment, the gut microbiome, via the gut-brain axis, plays an important role in the unconscious parallel processing systems regulating host neurophysiology. While psychedelic and microbial signalling systems operate over different timescales, the microbiota-gut-brain (MGB) axis, as a convergence hub between multiple biofeedback systems may play a role in the preparatory phase, the acute administration phase, and the integration phase of psychedelic therapy. In keeping with an interconnected systems-based approach, this review will discuss the gut microbiome and mycobiome and pathways of the MGB axis, and then explore the potential interaction between psychedelic therapy and the MGB axis and how this might influence mechanism of action and treatment response. Finally, we will discuss the possible implications for a precision medicine-based psychedelic therapy paradigm.
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Affiliation(s)
- John R. Kelly
- Department of Psychiatry, Trinity College, Dublin, Ireland
- Tallaght University Hospital, Dublin, Ireland
| | - Gerard Clarke
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Sinead C. Corr
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Microbiology, Trinity College Dublin, Ireland
| | - Stephen Galvin
- Department of Psychiatry, Trinity College, Dublin, Ireland
| | - Vishnu Pradeep
- Department of Psychiatry, Trinity College, Dublin, Ireland
- Tallaght University Hospital, Dublin, Ireland
| | - John F. Cryan
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Veronica O'Keane
- Department of Psychiatry, Trinity College, Dublin, Ireland
- Tallaght University Hospital, Dublin, Ireland
- Trinity College Institute of Neuroscience, Ireland
| | - Timothy G. Dinan
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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Jiménez-Marín B, Rakijas JB, Tyagi A, Pandey A, Hanschen ER, Anderson J, Heffel MG, Platt TG, Olson BJSC. Gene loss during a transition to multicellularity. Sci Rep 2023; 13:5268. [PMID: 37002250 PMCID: PMC10066295 DOI: 10.1038/s41598-023-29742-2] [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: 07/13/2022] [Accepted: 02/09/2023] [Indexed: 04/03/2023] Open
Abstract
Multicellular evolution is a major transition associated with momentous diversification of multiple lineages and increased developmental complexity. The volvocine algae comprise a valuable system for the study of this transition, as they span from unicellular to undifferentiated and differentiated multicellular morphologies despite their genomes being similar, suggesting multicellular evolution requires few genetic changes to undergo dramatic shifts in developmental complexity. Here, the evolutionary dynamics of six volvocine genomes were examined, where a gradual loss of genes was observed in parallel to the co-option of a few key genes. Protein complexes in the six species exhibited novel interactions, suggesting that gene loss could play a role in evolutionary novelty. This finding was supported by gene network modeling, where gene loss outpaces gene gain in generating novel stable network states. These results suggest gene loss, in addition to gene gain and co-option, may be important for the evolution developmental complexity.
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Affiliation(s)
- Berenice Jiménez-Marín
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
- Interdepartmental Genetics Graduate Program, Kansas State University, Manhattan, KS, 66506, USA
| | - Jessica B Rakijas
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Antariksh Tyagi
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Aakash Pandey
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | | | - Jaden Anderson
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Matthew G Heffel
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
- Interdepartmental Genetics Graduate Program, Kansas State University, Manhattan, KS, 66506, USA
| | - Thomas G Platt
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
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Nitschke MC, Black AJ, Bourrat P, Rainey PB. The effect of bottleneck size on evolution in nested Darwinian populations. J Theor Biol 2023; 561:111414. [PMID: 36639021 DOI: 10.1016/j.jtbi.2023.111414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/15/2022] [Accepted: 01/06/2023] [Indexed: 01/12/2023]
Abstract
Previous work has shown how a minimal ecological structure consisting of patchily distributed resources and recurrent dispersal between patches can scaffold Darwinian properties onto collections of cells. When the timescale of dispersal is long compared with the time to consume resources, patch fitness increases but comes at a cost to cell growth rates. This creates conditions that initiate evolutionary transitions in individuality. A key feature of the scaffold is a bottleneck created during dispersal, causing patches to be founded by single cells. The bottleneck decreases competition within patches and, hence, creates a strong hereditary link at the level of patches. Here, we construct a fully stochastic model to investigate the effect of bottleneck size on the evolutionary dynamics of both cells and collectives. We show that larger bottlenecks simply slow the dynamics, but, at some point, which depends on the parameters of the within-patch model, the direction of evolution towards the equilibrium reverses. Introduction of random fluctuations in bottleneck sizes with some positive probability of smaller sizes counteracts this, even when the probability of smaller bottlenecks is minimal.
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Affiliation(s)
- Matthew C Nitschke
- School of Mathematics and Statistics, University of Sydney, NSW 2006, Australia.
| | - Andrew J Black
- School of Mathematical Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Pierrick Bourrat
- Philosophy Department, Macquarie University, NSW 2109, Australia; Department of Philosophy and Charles Perkins Centre, The University of Sydney, NSW 2006, Australia
| | - Paul B Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany; Laboratoire Biophysique et Évolution, CBI, ESPCI Paris, Université PSL, CNRS, 75005 Paris, France
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43
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Davison DR, Michod RE. Steps to individuality in biology and culture. Philos Trans R Soc Lond B Biol Sci 2023; 378:20210407. [PMID: 36688387 PMCID: PMC9869451 DOI: 10.1098/rstb.2021.0407] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Did human culture arise through an evolutionary transition in individuality (ETI)? To address this question, we examine the steps of biological ETIs to see how they could apply to the evolution of human culture. For concreteness, we illustrate the ETI stages using a well-studied example, the evolution of multicellularity in the volvocine algae. We then consider how those stages could apply to a cultural transition involving integrated groups of cultural traditions and the hominins that create and transmit traditions. We focus primarily on the early Pleistocene and examine hominin carnivory and the cultural change from Oldowan to Acheulean technology. We use Pan behaviour as an outgroup comparison. We summarize the important similarities and differences we find between ETI stages in the biological and cultural realms. As we are not cultural anthropologists, we may overlook or be mistaken in the processes we associate with each step. We hope that by clearly describing these steps to individuality and illustrating them with cultural principles and processes, other researchers may build upon our initial exercise. Our analysis supports the hypothesis that human culture has undergone an ETI beginning with a Pan-like ancestor, continuing during the Pleistocene, and culminating in modern human culture. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.
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Affiliation(s)
- Dinah R. Davison
- Department of Ecology and Evolutionary Biology, College of Science, University of Arizona, Tucson, AZ 85721, USA
| | - Richard E. Michod
- Department of Ecology and Evolutionary Biology, College of Science, University of Arizona, Tucson, AZ 85721, USA
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Bernardo N, Crespo I, Cuppari A, Meijer WJJ, Boer DR. A tetramerization domain in prokaryotic and eukaryotic transcription regulators homologous to p53. Acta Crystallogr D Struct Biol 2023; 79:259-267. [PMID: 36876435 PMCID: PMC9986798 DOI: 10.1107/s2059798323001298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/13/2023] [Indexed: 03/05/2023] Open
Abstract
Transcriptional regulation usually requires the action of several proteins that either repress or activate a promotor of an open reading frame. These proteins can counteract each other, thus allowing tight regulation of the transcription of the corresponding genes, where tight repression is often linked to DNA looping or cross-linking. Here, the tetramerization domain of the bacterial gene repressor Rco from Bacillus subtilis plasmid pLS20 (RcopLS20) has been identified and its structure is shown to share high similarity to the tetramerization domain of the well known p53 family of human tumor suppressors, despite lacking clear sequence homology. In RcopLS20, this tetramerization domain is responsible for inducing DNA looping, a process that involves multiple tetramers. In accordance, it is shown that RcopLS20 can form octamers. This domain was named TetDloop and its occurrence was identified in other Bacillus species. The TetDloop fold was also found in the structure of a transcriptional repressor from Salmonella phage SPC32H. It is proposed that the TetDloop fold has evolved through divergent evolution and that the TetDloop originates from a common ancestor predating the occurrence of multicellular life.
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Affiliation(s)
- Nerea Bernardo
- Experiments Division, ALBA Synchrotron Light Source, Carrer de la Llum 2-26, 08290 Cerdanyola del Vallès, Catalunya, Spain
| | - Isidro Crespo
- Experiments Division, ALBA Synchrotron Light Source, Carrer de la Llum 2-26, 08290 Cerdanyola del Vallès, Catalunya, Spain
| | - Anna Cuppari
- Experiments Division, ALBA Synchrotron Light Source, Carrer de la Llum 2-26, 08290 Cerdanyola del Vallès, Catalunya, Spain
| | - Wilfried J J Meijer
- Centro de Biología Molecular `Severo Ochoa' (CSIC-UAM), Universidad Autónoma de Madrid, Calle Nicolás Cabrera 1, Canto Blanco, 28049 Madrid, Spain
| | - D Roeland Boer
- Experiments Division, ALBA Synchrotron Light Source, Carrer de la Llum 2-26, 08290 Cerdanyola del Vallès, Catalunya, Spain
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Tang S, Pichugin Y, Hammerschmidt K. An environmentally induced multicellular life cycle of a unicellular cyanobacterium. Curr Biol 2023; 33:764-769.e5. [PMID: 36854263 DOI: 10.1016/j.cub.2023.01.069] [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: 09/17/2021] [Revised: 10/19/2022] [Accepted: 01/04/2023] [Indexed: 03/02/2023]
Abstract
Understanding the evolutionary transition to multicellularity is a key problem in biology.1,2,3,4 Nevertheless, the ecological conditions driving such transitions are not well understood. The first known transition to multicellularity occurred 2.5 billion years ago in cyanobacteria,5,6,7 and today's cyanobacteria are characterized by enormous morphological diversity. They range from unicellular species; unicellular cyanobacteria with packet-like phenotypes, e.g., tetrads; and simple filamentous species to highly differentiated filamentous species.8,9,10 The cyanobacterium Cyanothece sp. ATCC 51142, an isolate from the intertidal zone of the U.S. Gulf Coast,11 was classified as a unicellular species.12 We report a facultative life cycle of Cyanothece sp. in which multicellular filaments alternate with unicellular stages. In a series of experiments, we identified salinity and population density as environmental factors triggering the phenotypic switch between the two morphologies. Then, we used numerical models to test hypotheses regarding the nature of the environmental cues and the mechanisms underlying filament dissolution. While the results predict that the observed response is likely caused by an excreted compound in the medium, we cannot fully exclude changes in nutrient availability (as in Tuomi et al.13 and Matz and Jürgens14). The best-fit modeling results show a nonlinear effect of the compound, which is characteristic of density-dependent sensing systems.15,16 Furthermore, filament fragmentation is predicted to occur by connection cleavage rather than cell death of each alternating cell, which is supported by fluorescent and scanning electron microscopy results. The switch between unicellular and multicellular morphology constitutes an environmentally dependent life cycle that is likely an important step en route to permanent multicellularity.
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Affiliation(s)
- Si Tang
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Yuriy Pichugin
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany.
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Shekhar S, Guo H, Colin SP, Marshall W, Kanso E, Costello JH. Cooperative hydrodynamics accompany multicellular-like colonial organization in the unicellular ciliate Stentor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.10.523506. [PMID: 36711609 PMCID: PMC9882025 DOI: 10.1101/2023.01.10.523506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Evolution of multicellularity from early unicellular ancestors is arguably one of the most important transitions since the origin of life1,2. Multicellularity is often associated with higher nutrient uptake3, better defense against predation, cell specialization and better division of labor4. While many single-celled organisms exhibit both solitary and colonial existence3,5,6, the organizing principles governing the transition and the benefits endowed are less clear. Using the suspension-feeding unicellular protist Stentor coeruleus, we show that hydrodynamic coupling between proximal neighbors results in faster feeding flows that depend on the separation between individuals. Moreover, we find that the accrued benefits in feeding current enhancement are typically asymmetric- individuals with slower solitary currents gain more from partnering than those with faster currents. We find that colony-formation is ephemeral in Stentor and individuals in colonies are highly dynamic unlike other colony-forming organisms like Volvox carteri 3. Our results demonstrate benefits endowed by the colonial organization in a simple unicellular organism and can potentially provide fundamental insights into the selective forces favoring early evolution of multicellular organization.
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Affiliation(s)
- Shashank Shekhar
- Department of Physics, Emory University, Atlanta, USA
- Whitman Center, Marine Biological Laboratory, Woods Hole, USA
- Department of Cell Biology, Emory University, Atlanta, USA
| | - Hanliang Guo
- Department of Mathematics and Computer Science, Ohio Wesleyan University, Delaware, USA
| | - Sean P. Colin
- Whitman Center, Marine Biological Laboratory, Woods Hole, USA
- Department of Marine Biology and Environmental Science, Roger Williams University, Bristol, USA
| | - Wallace Marshall
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, USA
| | - Eva Kanso
- Department of Aerospace and Mechanical Engineering, University of Southern California, Los Angeles, USA
| | - John H. Costello
- Whitman Center, Marine Biological Laboratory, Woods Hole, USA
- Department of Biology, Providence College, Providence, USA
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47
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Forget M, Adiba S, Brunnet LG, De Monte S. Heterogeneous individual motility biases group composition in a model of aggregating cells. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1052309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Aggregative life cycles are characterized by alternating phases of unicellular growth and multicellular development. Their multiple, independent evolutionary emergence suggests that they may have coopted pervasive properties of single-celled ancestors. Primitive multicellular aggregates, where coordination mechanisms were less efficient than in extant aggregative microbes, must have faced high levels of conflict between different co-aggregating populations. Such conflicts within a multicellular body manifest in the differential reproductive output of cells of different types. Here, we study how heterogeneity in cell motility affects the aggregation process and creates a mismatch between the composition of the population and that of self-organized groups of active adhesive particles. We model cells as self-propelled particles and describe aggregation in a plane starting from a dispersed configuration. Inspired by the life cycle of aggregative model organisms such as Dictyostelium discoideum or Myxococcus xanthus, whose cells interact for a fixed duration before the onset of chimeric multicellular development, we study finite-time configurations for identical particles and in binary mixes. We show that co-aggregation results in three different types of frequency-dependent biases, one of which is associated to evolutionarily stable coexistence of particles with different motility. We propose a heuristic explanation of such observations, based on the competition between delayed aggregation of slower particles and detachment of faster particles. Unexpectedly, despite the complexity and non-linearity of the system, biases can be largely predicted from the behavior of the two corresponding homogenous populations. This model points to differential motility as a possibly important factor in driving the evolutionary emergence of facultatively multicellular life-cycles.
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Schüler SC, Liu Y, Dumontier S, Grandbois M, Le Moal E, Cornelison DDW, Bentzinger CF. Extracellular matrix: Brick and mortar in the skeletal muscle stem cell niche. Front Cell Dev Biol 2022; 10:1056523. [PMID: 36523505 PMCID: PMC9745096 DOI: 10.3389/fcell.2022.1056523] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/03/2022] [Indexed: 11/30/2022] Open
Abstract
The extracellular matrix (ECM) is an interconnected macromolecular scaffold occupying the space between cells. Amongst other functions, the ECM provides structural support to tissues and serves as a microenvironmental niche that conveys regulatory signals to cells. Cell-matrix adhesions, which link the ECM to the cytoskeleton, are dynamic multi-protein complexes containing surface receptors and intracellular effectors that control various downstream pathways. In skeletal muscle, the most abundant tissue of the body, each individual muscle fiber and its associated muscle stem cells (MuSCs) are surrounded by a layer of ECM referred to as the basal lamina. The core scaffold of the basal lamina consists of self-assembling polymeric laminins and a network of collagens that tether proteoglycans, which provide lateral crosslinking, establish collateral associations with cell surface receptors, and serve as a sink and reservoir for growth factors. Skeletal muscle also contains the fibrillar collagenous interstitial ECM that plays an important role in determining tissue elasticity, connects the basal laminae to each other, and contains matrix secreting mesenchymal fibroblast-like cell types and blood vessels. During skeletal muscle regeneration fibroblast-like cell populations expand and contribute to the transitional fibronectin-rich regenerative matrix that instructs angiogenesis and MuSC function. Here, we provide a comprehensive overview of the role of the skeletal muscle ECM in health and disease and outline its role in orchestrating tissue regeneration and MuSC function.
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Affiliation(s)
- Svenja C. Schüler
- Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la Santé, Institut de Pharmacologie de Sherbrooke, Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Yuguo Liu
- Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la Santé, Institut de Pharmacologie de Sherbrooke, Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Simon Dumontier
- Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la Santé, Institut de Pharmacologie de Sherbrooke, Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Michel Grandbois
- Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la Santé, Institut de Pharmacologie de Sherbrooke, Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Emmeran Le Moal
- Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la Santé, Institut de Pharmacologie de Sherbrooke, Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - DDW Cornelison
- Division of Biological Sciences Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - C. Florian Bentzinger
- Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la Santé, Institut de Pharmacologie de Sherbrooke, Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC, Canada
- *Correspondence: C. Florian Bentzinger,
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Wright BA, Kvansakul M, Schierwater B, Humbert PO. Cell polarity signalling at the birth of multicellularity: What can we learn from the first animals. Front Cell Dev Biol 2022; 10:1024489. [PMID: 36506100 PMCID: PMC9729800 DOI: 10.3389/fcell.2022.1024489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/31/2022] [Indexed: 11/25/2022] Open
Abstract
The innovation of multicellularity has driven the unparalleled evolution of animals (Metazoa). But how is a multicellular organism formed and how is its architecture maintained faithfully? The defining properties and rules required for the establishment of the architecture of multicellular organisms include the development of adhesive cell interactions, orientation of division axis, and the ability to reposition daughter cells over long distances. Central to all these properties is the ability to generate asymmetry (polarity), coordinated by a highly conserved set of proteins known as cell polarity regulators. The cell polarity complexes, Scribble, Par and Crumbs, are considered to be a metazoan innovation with apicobasal polarity and adherens junctions both believed to be present in all animals. A better understanding of the fundamental mechanisms regulating cell polarity and tissue architecture should provide key insights into the development and regeneration of all animals including humans. Here we review what is currently known about cell polarity and its control in the most basal metazoans, and how these first examples of multicellular life can inform us about the core mechanisms of tissue organisation and repair, and ultimately diseases of tissue organisation, such as cancer.
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Affiliation(s)
- Bree A. Wright
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Marc Kvansakul
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia,Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, VIC, Australia
| | - Bernd Schierwater
- Institute of Animal Ecology and Evolution, University of Veterinary Medicine Hannover, Foundation, Bünteweg, Hannover, Germany
| | - Patrick O. Humbert
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia,Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, VIC, Australia,Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, Australia,Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia,*Correspondence: Patrick O. Humbert,
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Cancer – A devastating disease, but also an eye-opener and window into the deep mysteries of life and its origins. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 175:131-139. [DOI: 10.1016/j.pbiomolbio.2022.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/01/2022] [Accepted: 09/28/2022] [Indexed: 01/04/2023]
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