1
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Sarre LA, Kim IV, Ovchinnikov V, Olivetta M, Suga H, Dudin O, Sebé-Pedrós A, de Mendoza A. DNA methylation enables recurrent endogenization of giant viruses in an animal relative. SCIENCE ADVANCES 2024; 10:eado6406. [PMID: 38996012 PMCID: PMC11244446 DOI: 10.1126/sciadv.ado6406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 06/07/2024] [Indexed: 07/14/2024]
Abstract
5-Methylcytosine (5mC) is a widespread silencing mechanism that controls genomic parasites. In eukaryotes, 5mC has gained complex roles in gene regulation beyond parasite control, yet 5mC has also been lost in many lineages. The causes for 5mC retention and its genomic consequences are still poorly understood. Here, we show that the protist closely related to animals Amoebidium appalachense features both transposon and gene body methylation, a pattern reminiscent of invertebrates and plants. Unexpectedly, hypermethylated genomic regions in Amoebidium derive from viral insertions, including hundreds of endogenized giant viruses, contributing 14% of the proteome. Using a combination of inhibitors and genomic assays, we demonstrate that 5mC silences these giant virus insertions. Moreover, alternative Amoebidium isolates show polymorphic giant virus insertions, highlighting a dynamic process of infection, endogenization, and purging. Our results indicate that 5mC is critical for the controlled coexistence of newly acquired viral DNA into eukaryotic genomes, making Amoebidium a unique model to understand the hybrid origins of eukaryotic DNA.
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Affiliation(s)
- Luke A. Sarre
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Iana V. Kim
- CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Vladimir Ovchinnikov
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Marine Olivetta
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Hiroshi Suga
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Shobara, Japan
| | - Omaya Dudin
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Arnau Sebé-Pedrós
- CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- ICREA, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Alex de Mendoza
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
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2
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Gahan JM. In preprints: exciting new insights into the lives of our closest relatives. Development 2024; 151:dev203081. [PMID: 38885079 DOI: 10.1242/dev.203081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Affiliation(s)
- James M Gahan
- University of Galway, Thormøhlens Gate 55, Bergen 5008, Norway
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3
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Shah H, Olivetta M, Bhickta C, Ronchi P, Trupinić M, Tromer EC, Tolić IM, Schwab Y, Dudin O, Dey G. Life-cycle-coupled evolution of mitosis in close relatives of animals. Nature 2024; 630:116-122. [PMID: 38778110 PMCID: PMC11153136 DOI: 10.1038/s41586-024-07430-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 04/16/2024] [Indexed: 05/25/2024]
Abstract
Eukaryotes have evolved towards one of two extremes along a spectrum of strategies for remodelling the nuclear envelope during cell division: disassembling the nuclear envelope in an open mitosis or constructing an intranuclear spindle in a closed mitosis1,2. Both classes of mitotic remodelling involve key differences in the core division machinery but the evolutionary reasons for adopting a specific mechanism are unclear. Here we use an integrated comparative genomics and ultrastructural imaging approach to investigate mitotic strategies in Ichthyosporea, close relatives of animals and fungi. We show that species in this clade have diverged towards either a fungal-like closed mitosis or an animal-like open mitosis, probably to support distinct multinucleated or uninucleated states. Our results indicate that multinucleated life cycles favour the evolution of closed mitosis.
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Affiliation(s)
- Hiral Shah
- Cell Biology and Biophysics, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
| | - Marine Olivetta
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Chandni Bhickta
- Cell Biology and Biophysics, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Paolo Ronchi
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Monika Trupinić
- Division of Molecular Biology, Ruđer Bošković Institute (RBI), Zagreb, Croatia
| | - Eelco C Tromer
- Cell Biochemistry, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Iva M Tolić
- Division of Molecular Biology, Ruđer Bošković Institute (RBI), Zagreb, Croatia
| | - Yannick Schwab
- Cell Biology and Biophysics, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Omaya Dudin
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
| | - Gautam Dey
- Cell Biology and Biophysics, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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4
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Gahan JM, Helfrich LW, Wetzel LA, Bhanu NV, Yuan ZF, Garcia BA, Klose R, Booth DS. Chromatin profiling identifies putative dual roles for H3K27me3 in regulating transposons and cell type-specific genes in choanoflagellates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596151. [PMID: 38854040 PMCID: PMC11160669 DOI: 10.1101/2024.05.28.596151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Gene expression is tightly controlled during animal development to allow the formation of specialized cell types. Our understanding of how animals evolved this exquisite regulatory control remains elusive, but evidence suggests that changes in chromatin-based mechanisms may have contributed. To investigate this possibility, here we examine chromatin-based gene regulatory features in the closest relatives of animals, choanoflagellates. Using Salpingoeca rosetta as a model system, we examined chromatin accessibility and histone modifications at the genome scale and compared these features to gene expression. We first observed that accessible regions of chromatin are primarily associated with gene promoters and found no evidence of distal gene regulatory elements resembling the enhancers that animals deploy to regulate developmental gene expression. Remarkably, a histone modification deposited by polycomb repressive complex 2, histone H3 lysine 27 trimethylation (H3K27me3), appeared to function similarly in S. rosetta to its role in animals, because this modification decorated genes with cell type-specific expression. Additionally, H3K27me3 marked transposons, retaining what appears to be an ancestral role in regulating these elements. We further uncovered a putative new bivalent chromatin state at cell type-specific genes that consists of H3K27me3 and histone H3 lysine 4 mono-methylation (H3K4me1). Together, our discoveries support the scenario that gene-associated histone modification states that underpin development emerged before the evolution of animal multicellularity.
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Affiliation(s)
- James M. Gahan
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Biochemistry, University of Oxford, Oxford, UK
- Present Address: Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Lily W. Helfrich
- Howard Hughes Medical Institute / University of California, Berkeley, Department of Molecular and Cell Biology, Berkeley, CA 94720
- Present Address: Benchling
| | - Laura A. Wetzel
- Howard Hughes Medical Institute / University of California, Berkeley, Department of Molecular and Cell Biology, Berkeley, CA 94720
- Present Address: BioMarin Pharmaceutical Inc
| | - Natarajan V. Bhanu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
| | - Zuo-Fei Yuan
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
| | - Rob Klose
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - David S. Booth
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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5
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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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6
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Trigos AS, Bongiovanni F, Zhang Y, Zethoven M, Tothill R, Pearson R, Papenfuss AT, Goode DL. Disruption of metazoan gene regulatory networks in cancer alters the balance of co-expression between genes of unicellular and multicellular origins. Genome Biol 2024; 25:110. [PMID: 38685127 PMCID: PMC11057133 DOI: 10.1186/s13059-024-03247-1] [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: 08/08/2023] [Accepted: 04/12/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Metazoans inherited genes from unicellular ancestors that perform essential biological processes such as cell division, metabolism, and protein translation. Multicellularity requires careful control and coordination of these unicellular genes to maintain tissue integrity and homeostasis. Gene regulatory networks (GRNs) that arose during metazoan evolution are frequently altered in cancer, resulting in over-expression of unicellular genes. We propose that an imbalance in co-expression of unicellular (UC) and multicellular (MC) genes is a driving force in cancer. RESULTS We combine gene co-expression analysis to infer changes to GRNs in cancer with protein sequence conservation data to distinguish genes with UC and MC origins. Co-expression networks created using RNA sequencing data from 31 tumor types and normal tissue samples are divided into modules enriched for UC genes, MC genes, or mixed UC-MC modules. The greatest differences between tumor and normal tissue co-expression networks occur within mixed UC-MC modules. MC and UC genes not commonly co-expressed in normal tissues form distinct co-expression modules seen only in tumors. The degree of rewiring of genes within mixed UC-MC modules increases with tumor grade and stage. Mixed UC-MC modules are enriched for somatic mutations in cancer genes, particularly amplifications, suggesting an important driver of the rewiring observed in tumors is copy number changes. CONCLUSIONS Our study shows the greatest changes to gene co-expression patterns during tumor progression occur between genes of MC and UC origins, implicating the breakdown and rewiring of metazoan gene regulatory networks in cancer development and progression.
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Affiliation(s)
- Anna S Trigos
- Peter MacCallum Cancer Centre, 305 Grattan St., Melbourne, VIC, 3000, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3168, Australia.
| | - Felicia Bongiovanni
- Peter MacCallum Cancer Centre, 305 Grattan St., Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Yangyi Zhang
- Peter MacCallum Cancer Centre, 305 Grattan St., Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Maia Zethoven
- Peter MacCallum Cancer Centre, 305 Grattan St., Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Richard Tothill
- Centre for Cancer Research, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Richard Pearson
- Peter MacCallum Cancer Centre, 305 Grattan St., Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3168, Australia
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Anthony T Papenfuss
- Peter MacCallum Cancer Centre, 305 Grattan St., Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Bioinformatics Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - David L Goode
- Peter MacCallum Cancer Centre, 305 Grattan St., Melbourne, VIC, 3000, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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7
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Wilson GN, Tonk VS. Clinical-Genomic Analysis of 1261 Patients with Ehlers-Danlos Syndrome Outlines an Articulo-Autonomic Gene Network (Entome). Curr Issues Mol Biol 2024; 46:2620-2643. [PMID: 38534782 DOI: 10.3390/cimb46030166] [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: 01/01/2024] [Revised: 02/08/2024] [Accepted: 03/08/2024] [Indexed: 03/28/2024] Open
Abstract
Systematic evaluation of 80 history and 40 history findings diagnosed 1261 patients with Ehlers-Danlos syndrome (EDS) by direct or online interaction, and 60 key findings were selected for their relation to clinical mechanisms and/or management. Genomic testing results in 566 of these patients supported EDS relevance by their differences from those in 82 developmental disability patients and by their association with general rather than type-specific EDS findings. The 437 nuclear and 79 mitochondrial DNA changes included 71 impacting joint matrix (49 COL5), 39 bone (30 COL1/2/9/11), 22 vessel (12 COL3/8VWF), 43 vessel-heart (17FBN1/11TGFB/BR), 59 muscle (28 COL6/12), 56 neural (16 SCN9A/10A/11A), and 74 autonomic (13 POLG/25porphyria related). These genes were distributed over all chromosomes but the Y, a network analogized to an 'entome' where DNA change disrupts truncal mechanisms (skin constraint, neuromuscular support, joint vessel flexibility) and produces a mirroring cascade of articular and autonomic symptoms. The implied sequences of genes from nodal proteins to hypermobility to branching tissue laxity or dysautonomia symptoms would be ideal for large language/artificial intelligence analyses.
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Affiliation(s)
- Golder N Wilson
- Department of Pediatrics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- KinderGenome Genetics Private Practice, 5347 W Mockingbird, Dallas, TX 75209, USA
| | - Vijay S Tonk
- Director of Medical Genetics and the Cytogenomic Laboratory, Department of Pediatrics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
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8
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Girard C. The tri-flow adaptiveness of codes in major evolutionary transitions. Biosystems 2024; 237:105133. [PMID: 38336225 DOI: 10.1016/j.biosystems.2024.105133] [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: 11/17/2023] [Revised: 01/26/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024]
Abstract
Life codes increase in both number and variety with biological complexity. Although our knowledge of codes is constantly expanding, the evolutionary progression of organic, neural, and cultural codes in response to selection pressure remains poorly understood. Greater clarification of the selective mechanisms is achieved by investigating how major evolutionary transitions reduce spatiotemporal and energetic constraints on transmitting heritable code to offspring. Evolution toward less constrained flows is integral to enduring flow architecture everywhere, in both engineered and natural flow systems. Beginning approximately 4 billion years ago, the most basic level for transmitting genetic material to offspring was initiated by protocell division. Evidence from ribosomes suggests that protocells transmitted comma-free or circular codes, preceding the evolution of standard genetic code. This rudimentary information flow within protocells is likely to have first emerged within the geo-energetic and geospatial constraints of hydrothermal vents. A broad-gauged hypothesis is that major evolutionary transitions overcame such constraints with tri-flow adaptations. The interconnected triple flows incorporated energy-converting, spatiotemporal, and code-based informational dynamics. Such tri-flow adaptations stacked sequence splicing code on top of protein-DNA recognition code in eukaryotes, prefiguring the transition to sexual reproduction. Sex overcame the spatiotemporal-energetic constraints of binary fission with further code stacking. Examples are tubulin code and transcription initiation code in vertebrates. In a later evolutionary transition, language reduced metabolic-spatiotemporal constraints on inheritance by stacking phonetic, phonological, and orthographic codes. In organisms that reproduce sexually, each major evolutionary transition is shown to be a tri-flow adaptation that adds new levels of code-based informational exchange. Evolving biological complexity is also shown to increase the nongenetic transmissibility of code.
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Affiliation(s)
- Chris Girard
- Department of Global and Sociocultural Studies, Florida International University, Miami, FL 33199, United States.
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9
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Bozdag GO, Szeinbaum N, Conlin PL, Chen K, Fos SM, Garcia A, Penev PI, Schaible GA, Trubl G. Chapter 5: Major Biological Innovations in the History of Life on Earth. ASTROBIOLOGY 2024; 24:S107-S123. [PMID: 38498818 PMCID: PMC11071111 DOI: 10.1089/ast.2021.0119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/14/2023] [Indexed: 03/20/2024]
Abstract
All organisms living on Earth descended from a single, common ancestral population of cells, known as LUCA-the last universal common ancestor. Since its emergence, the diversity and complexity of life have increased dramatically. This chapter focuses on four key biological innovations throughout Earth's history that had a significant impact on the expansion of phylogenetic diversity, organismal complexity, and ecospace habitation. First is the emergence of the last universal common ancestor, LUCA, which laid the foundation for all life-forms on Earth. Second is the evolution of oxygenic photosynthesis, which resulted in global geochemical and biological transformations. Third is the appearance of a new type of cell-the eukaryotic cell-which led to the origin of a new domain of life and the basis for complex multicellularity. Fourth is the multiple independent origins of multicellularity, resulting in the emergence of a new level of complex individuality. A discussion of these four key events will improve our understanding of the intertwined history of our planet and its inhabitants and better inform the extent to which we can expect life at different degrees of diversity and complexity elsewhere.
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Affiliation(s)
- G. Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nadia Szeinbaum
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Peter L. Conlin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Kimberly Chen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Santiago Mestre Fos
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Amanda Garcia
- Department of Bacteriology, University of Wisconsin–Madison, Wisconsin, USA
| | - Petar I. Penev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - George A. Schaible
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
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10
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Schaible MJ, Szeinbaum N, Bozdag GO, Chou L, Grefenstette N, Colón-Santos S, Rodriguez LE, Styczinski MJ, Thweatt JL, Todd ZR, Vázquez-Salazar A, Adams A, Araújo MN, Altair T, Borges S, Burton D, Campillo-Balderas JA, Cangi EM, Caro T, Catalano E, Chen K, Conlin PL, Cooper ZS, Fisher TM, Fos SM, Garcia A, Glaser DM, Harman CE, Hermis NY, Hooks M, Johnson-Finn K, Lehmer O, Hernández-Morales R, Hughson KHG, Jácome R, Jia TZ, Marlow JJ, McKaig J, Mierzejewski V, Muñoz-Velasco I, Nural C, Oliver GC, Penev PI, Raj CG, Roche TP, Sabuda MC, Schaible GA, Sevgen S, Sinhadc P, Steller LH, Stelmach K, Tarnas J, Tavares F, Trubl G, Vidaurri M, Vincent L, Weber JM, Weng MM, Wilpiszeki RL, Young A. Chapter 1: The Astrobiology Primer 3.0. ASTROBIOLOGY 2024; 24:S4-S39. [PMID: 38498816 DOI: 10.1089/ast.2021.0129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The Astrobiology Primer 3.0 (ABP3.0) is a concise introduction to the field of astrobiology for students and others who are new to the field of astrobiology. It provides an entry into the broader materials in this supplementary issue of Astrobiology and an overview of the investigations and driving hypotheses that make up this interdisciplinary field. The content of this chapter was adapted from the other 10 articles in this supplementary issue and thus represents the contribution of all the authors who worked on these introductory articles. The content of this chapter is not exhaustive and represents the topics that the authors found to be the most important and compelling in a dynamic and changing field.
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Affiliation(s)
- Micah J Schaible
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nadia Szeinbaum
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - G Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Luoth Chou
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Center for Space Sciences and Technology, University of Maryland, Baltimore, Maryland, USA
- Georgetown University, Washington DC, USA
| | - Natalie Grefenstette
- Santa Fe Institute, Santa Fe, New Mexico, USA
- Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - Stephanie Colón-Santos
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Wisconsin, USA
- Department of Botany, University of Wisconsin-Madison, Wisconsin, USA
| | - Laura E Rodriguez
- Lunar and Planetary Institute, Universities Space Research Association, Houston, Texas, USA
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - M J Styczinski
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- University of Washington, Seattle, Washington, USA
| | - Jennifer L Thweatt
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Zoe R Todd
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - Alberto Vázquez-Salazar
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, California, USA
| | - Alyssa Adams
- Center for Space Sciences and Technology, University of Maryland, Baltimore, Maryland, USA
| | - M N Araújo
- Biochemistry Department, University of São Paulo, São Carlos, Brazil
| | - Thiago Altair
- Institute of Chemistry of São Carlos, Universidade de São Paulo, São Carlos, Brazil
- Department of Chemistry, College of the Atlantic, Bar Harbor, Maine, USA
| | | | - Dana Burton
- Department of Anthropology, George Washington University, Washington DC, USA
| | | | - Eryn M Cangi
- Laboratory for Atmospheric and Space Physics, University of Colorado Boulder, Boulder, Colorado, USA
| | - Tristan Caro
- Department of Geological Sciences, University of Colorado Boulder, Boulder, Colorado, USA
| | - Enrico Catalano
- Sant'Anna School of Advanced Studies, The BioRobotics Institute, Pisa, Italy
| | - Kimberly Chen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Peter L Conlin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Z S Cooper
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - Theresa M Fisher
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
| | - Santiago Mestre Fos
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Amanda Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin, USA
| | - D M Glaser
- Arizona State University, Tempe, Arizona, USA
| | - Chester E Harman
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ninos Y Hermis
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Department of Physics and Space Sciences, University of Granada, Granada, Spain
| | - M Hooks
- NASA Johnson Space Center, Houston, Texas, USA
| | - K Johnson-Finn
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, Japan
- Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Owen Lehmer
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - Ricardo Hernández-Morales
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Kynan H G Hughson
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Rodrigo Jácome
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Tony Z Jia
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, Japan
| | - Jeffrey J Marlow
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Jordan McKaig
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Veronica Mierzejewski
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
| | - Israel Muñoz-Velasco
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ceren Nural
- Istanbul Technical University, Istanbul, Turkey
| | - Gina C Oliver
- Department of Geology, San Bernardino Valley College, San Bernardino, California, USA
| | - Petar I Penev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Chinmayee Govinda Raj
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Tyler P Roche
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Mary C Sabuda
- Department of Earth and Environmental Sciences, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
- Biotechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - George A Schaible
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Serhat Sevgen
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Institute of Marine Sciences, Middle East Technical University, Erdemli, Mersin, Turkey
| | - Pritvik Sinhadc
- BEYOND: Center For Fundamental Concepts in Science, Arizona State University, Arizona, USA
- Dubai College, Dubai, United Arab Emirates
| | - Luke H Steller
- Australian Centre for Astrobiology, and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, Australia
| | - Kamil Stelmach
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - J Tarnas
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Frank Tavares
- Space Enabled Research Group, MIT Media Lab, Cambridge, Massachusetts, USA
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Monica Vidaurri
- Center for Space Sciences and Technology, University of Maryland, Baltimore, Maryland, USA
- Department of Physics and Astronomy, Howard University, Washington DC, USA
| | - Lena Vincent
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Wisconsin, USA
| | - Jessica M Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | | | | | - Amber Young
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Northern Arizona University, Flagstaff, Arizona, USA
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11
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Taylor WA, Strother PK. Plant evolution: A tapetum is now effectively present in all land plant lineages. Curr Biol 2024; 34:R146-R148. [PMID: 38412824 DOI: 10.1016/j.cub.2023.12.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
The tapetum, a tissue that elsewhere ensures correct spore development, is missing in some bryophytes. A new study shows that, in the liverwort, Marchantia polymorpha, a gene controlling spore wall deposition is expressed in the capsule lining, so these cells essentially function as a tapetum.
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Affiliation(s)
- Wilson A Taylor
- Department of Biology, University of Wisconsin-Eau Claire, Eau Claire, WI, USA
| | - Paul K Strother
- Department of Earth and Environmental Sciences, Boston College Weston Observatory, Weston, MA, USA.
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12
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Mah JL, Dunn CW. Cell type evolution reconstruction across species through cell phylogenies of single-cell RNA sequencing data. Nat Ecol Evol 2024; 8:325-338. [PMID: 38182680 DOI: 10.1038/s41559-023-02281-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 11/16/2023] [Indexed: 01/07/2024]
Abstract
The origin and evolution of cell types has emerged as a key topic in evolutionary biology. Driven by rapidly accumulating single-cell datasets, recent attempts to infer cell type evolution have largely been limited to pairwise comparisons because we lack approaches to build cell phylogenies using model-based approaches. Here we approach the challenges of applying explicit phylogenetic methods to single-cell data by using principal components as phylogenetic characters. We infer a cell phylogeny from a large, comparative single-cell dataset of eye cells from five distantly related mammals. Robust cell type clades enable us to provide a phylogenetic, rather than phenetic, definition of cell type, allowing us to forgo marker genes and phylogenetically classify cells by topology. We further observe evolutionary relationships between diverse vessel endothelia and identify the myelinating and non-myelinating Schwann cells as sister cell types. Finally, we examine principal component loadings and describe the gene expression dynamics underlying the function and identity of cell type clades that have been conserved across the five species. A cell phylogeny provides a rigorous framework towards investigating the evolutionary history of cells and will be critical to interpret comparative single-cell datasets that aim to ask fundamental evolutionary questions.
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Affiliation(s)
- Jasmine L Mah
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
| | - Casey W Dunn
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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13
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Brown GC. Cell death by phagocytosis. Nat Rev Immunol 2024; 24:91-102. [PMID: 37604896 DOI: 10.1038/s41577-023-00921-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2023] [Indexed: 08/23/2023]
Abstract
Cells can die as a consequence of being phagocytosed by other cells - a form of cell death that has been called phagotrophy, cell cannibalism, programmed cell removal and primary phagocytosis. However, these are all different manifestations of cell death by phagocytosis (termed 'phagoptosis' for short). The engulfed cells die as a result of cytotoxic oxidants, peptides and degradative enzymes within acidic phagolysosomes. Cell death by phagocytosis was discovered by Metchnikov in the 1880s, but was neglected until recently. It is now known to contribute to developmental cell death in nematodes, Drosophila and mammals, and is central to innate and adaptive immunity against pathogens. Cell death by phagocytosis mediates physiological turnover of erythrocytes and other leucocytes, making it the most abundant form of cell death in the mammalian body. Immunity against cancer is also partly mediated by macrophage phagocytosis of cancer cells, but cancer cells can also phagocytose host cells and other cancer cells in order to survive. Recent evidence indicates neurodegeneration and other neuropathologies can be mediated by microglial phagocytosis of stressed neurons. Thus, despite cell death by phagocytosis being poorly recognized, it is one of the oldest, commonest and most important forms of cell death.
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Affiliation(s)
- Guy C Brown
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
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14
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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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15
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Nagahata Y, Kawamoto H. Evolutionary reversion in tumorigenesis. Front Oncol 2023; 13:1282417. [PMID: 38023242 PMCID: PMC10662060 DOI: 10.3389/fonc.2023.1282417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Cells forming malignant tumors are distinguished from those forming normal tissues based on several features: accelerated/dysregulated cell division, disruption of physiologic apoptosis, maturation/differentiation arrest, loss of polarity, and invasive potential. Among them, accelerated cell division and differentiation arrest make tumor cells similar to stem/progenitor cells, and this is why tumorigenesis is often regarded as developmental reversion. Here, in addition to developmental reversion, we propose another insight into tumorigenesis from a phylogeny viewpoint. Based on the finding that tumor cells also share some features with unicellular organisms, we propose that tumorigenesis can be regarded as "evolutionary reversion". Recent advances in sequencing technologies and the ability to identify gene homologous have made it possible to perform comprehensive cross-species transcriptome comparisons and, in our recent study, we found that leukemic cells resulting from a polycomb dysfunction transcriptionally resemble unicellular organisms. Analyzing tumorigenesis from the viewpoint of phylogeny should reveal new aspects of tumorigenesis in the near future, and contribute to overcoming malignant tumors by developing new therapies.
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Affiliation(s)
- Yosuke Nagahata
- Laboratory of Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Hiroshi Kawamoto
- Laboratory of Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
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16
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Ros-Rocher N, Brunet T. What is it like to be a choanoflagellate? Sensation, processing and behavior in the closest unicellular relatives of animals. Anim Cogn 2023; 26:1767-1782. [PMID: 37067637 PMCID: PMC10770216 DOI: 10.1007/s10071-023-01776-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/18/2023]
Abstract
All animals evolved from a single lineage of unicellular precursors more than 600 million years ago. Thus, the biological and genetic foundations for animal sensation, cognition and behavior must necessarily have arisen by modifications of pre-existing features in their unicellular ancestors. Given that the single-celled ancestors of the animal kingdom are extinct, the only way to reconstruct how these features evolved is by comparing the biology and genomic content of extant animals to their closest living relatives. Here, we reconstruct the Umwelt (the subjective, perceptive world) inhabited by choanoflagellates, a group of unicellular (or facultatively multicellular) aquatic microeukaryotes that are the closest living relatives of animals. Although behavioral research on choanoflagellates remains patchy, existing evidence shows that they are capable of chemosensation, photosensation and mechanosensation. These processes often involve specialized sensorimotor cellular appendages (cilia, microvilli, and/or filopodia) that resemble those that underlie perception in most animal sensory cells. Furthermore, comparative genomics predicts an extensive "sensory molecular toolkit" in choanoflagellates, which both provides a potential basis for known behaviors and suggests the existence of a largely undescribed behavioral complexity that presents exciting avenues for future research. Finally, we discuss how facultative multicellularity in choanoflagellates might help us understand how evolution displaced the locus of decision-making from a single cell to a collective, and how a new space of behavioral complexity might have become accessible in the process.
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Affiliation(s)
- Núria Ros-Rocher
- Evolutionary Cell Biology and Evolution of Morphogenesis Unit, Institut Pasteur, Université Paris-Cité, CNRS UMR3691, 25-28 Rue du Docteur Roux, 75015, Paris, France
| | - Thibaut Brunet
- Evolutionary Cell Biology and Evolution of Morphogenesis Unit, Institut Pasteur, Université Paris-Cité, CNRS UMR3691, 25-28 Rue du Docteur Roux, 75015, Paris, France.
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17
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Najle SR, Grau-Bové X, Elek A, Navarrete C, Cianferoni D, Chiva C, Cañas-Armenteros D, Mallabiabarrena A, Kamm K, Sabidó E, Gruber-Vodicka H, Schierwater B, Serrano L, Sebé-Pedrós A. Stepwise emergence of the neuronal gene expression program in early animal evolution. Cell 2023; 186:4676-4693.e29. [PMID: 37729907 PMCID: PMC10580291 DOI: 10.1016/j.cell.2023.08.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/13/2023] [Accepted: 08/22/2023] [Indexed: 09/22/2023]
Abstract
The assembly of the neuronal and other major cell type programs occurred early in animal evolution. We can reconstruct this process by studying non-bilaterians like placozoans. These small disc-shaped animals not only have nine morphologically described cell types and no neurons but also show coordinated behaviors triggered by peptide-secreting cells. We investigated possible neuronal affinities of these peptidergic cells using phylogenetics, chromatin profiling, and comparative single-cell genomics in four placozoans. We found conserved cell type expression programs across placozoans, including populations of transdifferentiating and cycling cells, suggestive of active cell type homeostasis. We also uncovered fourteen peptidergic cell types expressing neuronal-associated components like the pre-synaptic scaffold that derive from progenitor cells with neurogenesis signatures. In contrast, earlier-branching animals like sponges and ctenophores lacked this conserved expression. Our findings indicate that key neuronal developmental and effector gene modules evolved before the advent of cnidarian/bilaterian neurons in the context of paracrine cell signaling.
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Affiliation(s)
- Sebastián R Najle
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Xavier Grau-Bové
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Anamaria Elek
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Cristina Navarrete
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Damiano Cianferoni
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Cristina Chiva
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Didac Cañas-Armenteros
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Arrate Mallabiabarrena
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Kai Kamm
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Harald Gruber-Vodicka
- Max Planck Institute for Marine Microbiology, Bremen, Germany; Zoological Institute, Christian Albrechts University, Kiel, Germany
| | - Bernd Schierwater
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany; American Museum of Natural History, Richard Gilder Graduate School, NY, USA
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; ICREA, Barcelona, Spain
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; ICREA, Barcelona, Spain.
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18
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Brunet T. Cell contractility in early animal evolution. Curr Biol 2023; 33:R966-R985. [PMID: 37751712 DOI: 10.1016/j.cub.2023.07.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
Tissue deformation mediated by collective cell contractility is a signature characteristic of animals. In most animals, fast and reversible contractions of muscle cells mediate behavior, while slow and irreversible contractions of epithelial or mesenchymal cells play a key role in morphogenesis. Animal tissue contractility relies on the activity of the actin/myosin II complex (together referred to as 'actomyosin'), an ancient and versatile molecular machinery that performs a broad range of functions in development and physiology. This review synthesizes emerging insights from morphological and molecular studies into the evolutionary history of animal contractile tissue. The most ancient functions of actomyosin are cell crawling and cytokinesis, which are found in a wide variety of unicellular eukaryotes and in individual metazoan cells. Another contractile functional module, apical constriction, is universal in metazoans and shared with choanoflagellates, their closest known living relatives. The evolution of animal contractile tissue involved two key innovations: firstly, the ability to coordinate and integrate actomyosin assembly across multiple cells, notably to generate supracellular cables, which ensure tissue integrity but also allow coordinated morphogenesis and movements at the organism scale; and secondly, the evolution of dedicated contractile cell types for adult movement, belonging to two broad categories respectively defined by the expression of the fast (striated-type) and slow (smooth/non-muscle-type) myosin II paralogs. Both contractile cell types ancestrally resembled generic contractile epithelial or mesenchymal cells and might have played a versatile role in both behavior and morphogenesis. Modern animal contractile cells span a continuum between unspecialized contractile epithelia (which underlie behavior in modern placozoans), epithelia with supracellular actomyosin cables (found in modern sponges), epitheliomuscular tissues (with a concentration of actomyosin cables in basal processes, for example in sea anemones), and specialized muscle tissue that has lost most or all epithelial properties (as in ctenophores, jellyfish and bilaterians). Recent studies in a broad range of metazoans have begun to reveal the molecular basis of these transitions, powered by the elaboration of the contractile apparatus and the evolution of 'core regulatory complexes' of transcription factors specifying contractile cell identity.
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Affiliation(s)
- Thibaut Brunet
- Institut Pasteur, Université Paris-Cité, CNRS UMR3691, Evolutionary Cell Biology and Evolution of Morphogenesis Unit, 25-28 Rue du Docteur Roux, 75015 Paris, France.
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19
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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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20
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Kutluk H, Bastounis EE, Constantinou I. Integration of Extracellular Matrices into Organ-on-Chip Systems. Adv Healthc Mater 2023; 12:e2203256. [PMID: 37018430 DOI: 10.1002/adhm.202203256] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/20/2023] [Indexed: 04/07/2023]
Abstract
The extracellular matrix (ECM) is a complex, dynamic network present within all tissues and organs that not only acts as a mechanical support and anchorage point but can also direct fundamental cell behavior, function, and characteristics. Although the importance of the ECM is well established, the integration of well-controlled ECMs into Organ-on-Chip (OoC) platforms remains challenging and the methods to modulate and assess ECM properties on OoCs remain underdeveloped. In this review, current state-of-the-art design and assessment of in vitro ECM environments is discussed with a focus on their integration into OoCs. Among other things, synthetic and natural hydrogels, as well as polydimethylsiloxane (PDMS) used as substrates, coatings, or cell culture membranes are reviewed in terms of their ability to mimic the native ECM and their accessibility for characterization. The intricate interplay among materials, OoC architecture, and ECM characterization is critically discussed as it significantly complicates the design of ECM-related studies, comparability between works, and reproducibility that can be achieved across research laboratories. Improving the biomimetic nature of OoCs by integrating properly considered ECMs would contribute to their further adoption as replacements for animal models, and precisely tailored ECM properties would promote the use of OoCs in mechanobiology.
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Affiliation(s)
- Hazal Kutluk
- Institute of Microtechnology (IMT), Technical University of Braunschweig, Alte Salzdahlumer Str. 203, 38124, Braunschweig, Germany
- Center of Pharmaceutical Engineering (PVZ), Technical University of Braunschweig, Franz-Liszt-Str. 35a, 38106, Braunschweig, Germany
| | - Effie E Bastounis
- Institute of Microbiology and Infection Medicine (IMIT), Eberhard Karls University of Tübingen, Auf der Morgenstelle 28, E8, 72076, Tübingen, Germany
- Cluster of Excellence "Controlling Microbes to Fight Infections" EXC 2124, Eberhard Karls University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Iordania Constantinou
- Institute of Microtechnology (IMT), Technical University of Braunschweig, Alte Salzdahlumer Str. 203, 38124, Braunschweig, Germany
- Center of Pharmaceutical Engineering (PVZ), Technical University of Braunschweig, Franz-Liszt-Str. 35a, 38106, Braunschweig, Germany
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21
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Husbands AY, Feller A, Aggarwal V, Dresden CE, Holub AS, Ha T, Timmermans MCP. The START domain potentiates HD-ZIPIII transcriptional activity. THE PLANT CELL 2023; 35:2332-2348. [PMID: 36861320 DOI: 10.1093/plcell/koad058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/09/2023] [Accepted: 02/05/2023] [Indexed: 05/30/2023]
Abstract
The CLASS III HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIPIII) transcription factors (TFs) were repeatedly deployed over 725 million years of evolution to regulate central developmental innovations. The START domain of this pivotal class of developmental regulators was recognized over 20 years ago, but its putative ligands and functional contributions remain unknown. Here, we demonstrate that the START domain promotes HD-ZIPIII TF homodimerization and increases transcriptional potency. Effects on transcriptional output can be ported onto heterologous TFs, consistent with principles of evolution via domain capture. We also show the START domain binds several species of phospholipids, and that mutations in conserved residues perturbing ligand binding and/or its downstream conformational readout abolish HD-ZIPIII DNA-binding competence. Our data present a model in which the START domain potentiates transcriptional activity and uses ligand-induced conformational change to render HD-ZIPIII dimers competent to bind DNA. These findings resolve a long-standing mystery in plant development and highlight the flexible and diverse regulatory potential coded within this widely distributed evolutionary module.
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Affiliation(s)
- Aman Y Husbands
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA 19104, USA
| | - Antje Feller
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Vasudha Aggarwal
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Courtney E Dresden
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA 19104, USA
- Molecular, Cellular, and Developmental Biology (MCDB), The Ohio State University, Columbus, OH 43215, USA
| | - Ashton S Holub
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43215, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Marja C P Timmermans
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
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22
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Olivetta M, Dudin O. The nuclear-to-cytoplasmic ratio drives cellularization in the close animal relative Sphaeroforma arctica. Curr Biol 2023; 33:1597-1605.e3. [PMID: 36996815 DOI: 10.1016/j.cub.2023.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/17/2023] [Accepted: 03/07/2023] [Indexed: 03/31/2023]
Abstract
The ratio of nuclear content to cytoplasmic volume (N/C ratio) is a key regulator driving the maternal-to-zygotic transition in most animal embryos. Altering this ratio often impacts zygotic genome activation and deregulates the timing and outcome of embryogenesis.1,2,3 Despite being ubiquitous across animals, little is known about when the N/C ratio evolved to control multicellular development. Such capacity either originated with the emergence of animal multicellularity or was co-opted from the mechanisms present in unicellular organisms.4 An effective strategy to tackle this question is to investigate the close relatives of animals exhibiting life cycles with transient multicellular stages.5 Among these are ichthyosporeans, a lineage of protists undergoing coenocytic development followed by cellularization and cell release.6,7,8 During cellularization, a transient multicellular stage resembling animal epithelia is generated, offering a unique opportunity to examine whether the N/C ratio regulates multicellular development. Here, we use time-lapse microscopy to characterize how the N/C ratio affects the life cycle of the best-studied ichthyosporean model, Sphaeroforma arctica. We uncover that the last stages of cellularization coincide with a significant increase in the N/C ratio. Increasing the N/C ratio by reducing the coenocytic volume accelerates cellularization, whereas decreasing the N/C ratio by lowering the nuclear content halts it. Moreover, centrifugation and pharmacological inhibitor experiments suggest that the N/C ratio is locally sensed at the cortex and relies on phosphatase activity. Altogether, our results show that the N/C ratio drives cellularization in S. arctica, suggesting that its capacity to control multicellular development predates animal emergence.
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Ullo MF, Case LB. How cells sense and integrate information from different sources. WIREs Mech Dis 2023:e1604. [PMID: 36781396 DOI: 10.1002/wsbm.1604] [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: 06/24/2022] [Revised: 01/06/2023] [Accepted: 01/24/2023] [Indexed: 02/15/2023]
Abstract
Cell signaling is a fundamental cellular process that enables cells to sense and respond to information in their surroundings. At the molecular level, signaling is primarily carried out by transmembrane protein receptors that can initiate complex downstream signal transduction cascades to alter cellular behavior. In the human body, different cells can be exposed to a wide variety of environmental conditions, and cells express diverse classes of receptors capable of sensing and integrating different signals. Furthermore, different receptors and signaling pathways can crosstalk with each other to calibrate the cellular response. Crosstalk occurs through multiple mechanisms at different levels of signaling pathways. In this review, we discuss how cells sense and integrate different chemical, mechanical, and spatial signals as well as the mechanisms of crosstalk between pathways. To illustrate these concepts, we use a few well-studied signaling pathways, including receptor tyrosine kinases and integrin receptors. Finally, we discuss the implications of dysregulated cellular sensing on driving diseases such as cancer. This article is categorized under: Cancer > Molecular and Cellular Physiology Metabolic Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Maria F Ullo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Lindsay B Case
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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24
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Acemel RD, Lupiáñez DG. Evolution of 3D chromatin organization at different scales. Curr Opin Genet Dev 2023; 78:102019. [PMID: 36603519 DOI: 10.1016/j.gde.2022.102019] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/30/2022] [Accepted: 12/03/2022] [Indexed: 01/04/2023]
Abstract
Most animal genomes fold in 3D chromatin domains called topologically associated domains (TADs) that facilitate interactions between cis-regulatory elements (CREs) and promoters. Owing to their critical role in the control of developmental gene expression, we explore how TADs have shaped animal evolution. In the light of recent studies that profile TADs in disparate animal lineages, we discuss their phylogenetic distribution and the mechanisms that underlie their formation. We present evidence indicating that TADs are plastic entities composed of genomic strata of different ages: ancient cores are combined with newer regions and brought into extant TADs through genomic rearrangements. We highlight that newly incorporated TAD strata enable the establishment of new CRE-promoter interactions and in turn new expression patterns that can drive phenotypical innovation. We further highlight how subtle changes in chromatin folding may fine-tune the expression levels of developmental genes and hold a potential for evolutionary significance.
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25
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Nielsen C. Hydrodynamics in early animal evolution. Biol Rev Camb Philos Soc 2023; 98:376-385. [PMID: 36216338 DOI: 10.1111/brv.12909] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 01/12/2023]
Abstract
Choanoflagellates and sponges feed by filtering microscopic particles from water currents created by the flagella of microvillar collar complexes situated on the cell bodies of the solitary or colonial choanoflagellates and on the choanocytes in sponges. The filtering mechanism has been known for more than a century, but only recently has the filtering process been studied in detail and also modelled, so that a detailed picture of the water currents has been obtained. In the solitary and most of the colonial choanoflagellates, the water flows freely around the cells, but in some forms, the cells are arranged in an open meshwork through which the water can be pumped. In the sponges, the choanocytes are located in choanocyte chambers (or choanocyte areas) with separate incurrent and excurrent canals/pores located in a larger body, which enables a fixed pattern of water currents through the collar complexes. Previous theories for the origin of sponges show evolutionary stages with choanocyte chambers without any opening or with only one opening, which makes separation of incurrent and excurrent impossible, and such stages must have been unable to feed. Therefore a new theory is proposed, which shows a continuous evolutionary lineage in which all stages are able to feed by means of the collar complexes.
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Affiliation(s)
- Claus Nielsen
- Natural History Museum of Denmark (University of Copenhagen), Zoological Museum, Universitetsparken 15, DK-2990, Copenhagen, Denmark
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26
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Fonseca C, Mendonça Filho JG, Reolid M, Duarte LV, de Oliveira AD, Souza JT, Lézin C. First putative occurrence in the fossil record of choanoflagellates, the sister group of Metazoa. Sci Rep 2023; 13:1242. [PMID: 36690681 PMCID: PMC9870899 DOI: 10.1038/s41598-022-26972-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/22/2022] [Indexed: 01/24/2023] Open
Abstract
Choanoflagellates are microeukaryotes that inhabit freshwater and marine environments and have long been regarded as the closest living relatives of Metazoa. Knowledge on the evolution of choanoflagellates is key for the understanding of the ancestry of animals, and although molecular clock evidence suggests the appearance of choanoflagellates by late Neoproterozoic, no specimens of choanoflagellates are known to occur in the fossil record. Here the first putative occurrence of choanoflagellates in sediments from the Cretaceous (Cenomanian-Turonian) is described by means of several cutting-edge petrographic techniques, and a discussion of its paleoenvironmental significance is performed. Furthermore, their placement in the organic matter classification systems is argued, with a placement in the Zoomorph Subgroup (Palynomorph Group) of the dispersed organic matter classification system being proposed. Regarding the ICCP System 1994, incorporation of choanoflagellates is, at a first glance, straightforward within the liptinite group, but the definition of a new maceral may be necessary to accommodate the genetic origin of these organisms. While modern choanoflagellates may bring light to the cellular foundations of animal origins, this discovery may provide an older term of comparison to their extant specimens and provide guidelines for possible identification of these organic components in other locations and ages throughout the geological record.
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Affiliation(s)
- Carolina Fonseca
- Laboratório de Palinofácies e Fácies Orgânica (LAFO), Departamento de Geologia, Instituto de Geociências, Universidade Federal do Rio de Janeiro, Av. Athos da Silveira, 274, prédio do CCMN, sala J1020, Campus Ilha do Fundão, Cidade Universitária, Rio de Janeiro, RJ, CEP 21.949-900, Brazil.
- Universidade de Coimbra, MARE - Centro de Ciências do Mare do Ambiente, ARNET - Aquatic Research Network, Departamento de Ciências da Terra, Rua Sílvio Lima, 3030-790, Coimbra, Portugal.
| | - João Graciano Mendonça Filho
- Laboratório de Palinofácies e Fácies Orgânica (LAFO), Departamento de Geologia, Instituto de Geociências, Universidade Federal do Rio de Janeiro, Av. Athos da Silveira, 274, prédio do CCMN, sala J1020, Campus Ilha do Fundão, Cidade Universitária, Rio de Janeiro, RJ, CEP 21.949-900, Brazil
| | - Matías Reolid
- Departamento de Geología and CEACTEMA, Universidad de Jaén, Campus Las Lagunillas sn, 23071, Jaén, Spain
| | - Luís V Duarte
- Universidade de Coimbra, MARE - Centro de Ciências do Mare do Ambiente, ARNET - Aquatic Research Network, Departamento de Ciências da Terra, Rua Sílvio Lima, 3030-790, Coimbra, Portugal
| | - António Donizeti de Oliveira
- Laboratório de Palinofácies e Fácies Orgânica (LAFO), Departamento de Geologia, Instituto de Geociências, Universidade Federal do Rio de Janeiro, Av. Athos da Silveira, 274, prédio do CCMN, sala J1020, Campus Ilha do Fundão, Cidade Universitária, Rio de Janeiro, RJ, CEP 21.949-900, Brazil
| | - Jaqueline Torres Souza
- Laboratório de Palinofácies e Fácies Orgânica (LAFO), Departamento de Geologia, Instituto de Geociências, Universidade Federal do Rio de Janeiro, Av. Athos da Silveira, 274, prédio do CCMN, sala J1020, Campus Ilha do Fundão, Cidade Universitária, Rio de Janeiro, RJ, CEP 21.949-900, Brazil
| | - Carine Lézin
- Université Toulouse III - Paul Sabatier, OMP, GET (Géosciences Environnement Toulouse), CNRS, IRD, 14 Avenue Édouard Belin, 31400, Toulouse, France
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Gomis-Rüth FX, Stöcker W. Structural and evolutionary insights into astacin metallopeptidases. Front Mol Biosci 2023; 9:1080836. [PMID: 36685277 PMCID: PMC9848320 DOI: 10.3389/fmolb.2022.1080836] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/30/2022] [Indexed: 01/05/2023] Open
Abstract
The astacins are a family of metallopeptidases (MPs) that has been extensively described from animals. They are multidomain extracellular proteins, which have a conserved core architecture encompassing a signal peptide for secretion, a prodomain or prosegment and a zinc-dependent catalytic domain (CD). This constellation is found in the archetypal name-giving digestive enzyme astacin from the European crayfish Astacus astacus. Astacin catalytic domains span ∼200 residues and consist of two subdomains that flank an extended active-site cleft. They share several structural elements including a long zinc-binding consensus sequence (HEXXHXXGXXH) immediately followed by an EXXRXDRD motif, which features a family-specific glutamate. In addition, a downstream SIMHY-motif encompasses a "Met-turn" methionine and a zinc-binding tyrosine. The overall architecture and some structural features of astacin catalytic domains match those of other more distantly related MPs, which together constitute the metzincin clan of metallopeptidases. We further analysed the structures of PRO-, MAM, TRAF, CUB and EGF-like domains, and described their essential molecular determinants. In addition, we investigated the distribution of astacins across kingdoms and their phylogenetic origin. Through extensive sequence searches we found astacin CDs in > 25,000 sequences down the tree of life from humans beyond Metazoa, including Choanoflagellata, Filasterea and Ichtyosporea. We also found < 400 sequences scattered across non-holozoan eukaryotes including some fungi and one virus, as well as in selected taxa of archaea and bacteria that are pathogens or colonizers of animal hosts, but not in plants. Overall, we propose that astacins originate in the root of Holozoa consistent with Darwinian descent and that the latter genes might be the result of horizontal gene transfer from holozoan donors.
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Affiliation(s)
- F. Xavier Gomis-Rüth
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (IBMB), Higher Scientific Research Council (CSIC), Barcelona, Catalonia, Spain,*Correspondence: F. Xavier Gomis-Rüth, ; Walter Stöcker,
| | - Walter Stöcker
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University Mainz (JGU), Mainz, Germany,*Correspondence: F. Xavier Gomis-Rüth, ; Walter Stöcker,
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28
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Liu DX, Hao SL, Yang WX. Crosstalk Between β-CATENIN-Mediated Cell Adhesion and the WNT Signaling Pathway. DNA Cell Biol 2023; 42:1-13. [PMID: 36399409 DOI: 10.1089/dna.2022.0424] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Cell adhesion and stable signaling regulation are fundamental ways of maintaining homeostasis. Among them, the Wnt/β-CATENIN signaling plays a key role in embryonic development and maintenance of body dynamic homeostasis. At the same time, the key signaling molecule β-CATENIN in the Wnt signaling can also function as a cytoskeletal linker protein to regulate tissue barriers, cell migration, and morphogenesis. Dysregulation of the balance between Wnt signaling and adherens junctions can lead to disease. How β-CATENIN maintains the independence of these two functions, or mediates the interaction and balance of these two functions, has been explored and debated for a long time. In this study, we will focus on five aspects of β-CATENIN chaperone molecules, phosphorylation of β-CATENIN and related proteins, epithelial mesenchymal transition, β-CATENIN homolog protein γ-CATENIN and disease, thus deepening the understanding of the Wnt/β-CATENIN signaling and the homeostasis between cell adhesion and further addressing related disease problems.
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Affiliation(s)
- Ding-Xi Liu
- The Sperm Laboratory, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shuang-Li Hao
- The Sperm Laboratory, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Wan-Xi Yang
- The Sperm Laboratory, College of Life Sciences, Zhejiang University, Hangzhou, China
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29
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Nagahata Y, Masuda K, Nishimura Y, Ikawa T, Kawaoka S, Kitawaki T, Nannya Y, Ogawa S, Suga H, Satou Y, Takaori-Kondo A, Kawamoto H. Tracing the evolutionary history of blood cells to the unicellular ancestor of animals. Blood 2022; 140:2611-2625. [PMID: 36112959 PMCID: PMC10653094 DOI: 10.1182/blood.2022016286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/20/2022] Open
Abstract
Blood cells are thought to have emerged as phagocytes in the common ancestor of animals followed by the appearance of novel blood cell lineages such as thrombocytes, erythrocytes, and lymphocytes, during evolution. However, this speculation is not based on genetic evidence and it is still possible to argue that phagocytes in different species have different origins. It also remains to be clarified how the initial blood cells evolved; whether ancient animals have solely developed de novo programs for phagocytes or they have inherited a key program from ancestral unicellular organisms. Here, we traced the evolutionary history of blood cells, and cross-species comparison of gene expression profiles revealed that phagocytes in various animal species and Capsaspora (C.) owczarzaki, a unicellular organism, are transcriptionally similar to each other. We also found that both phagocytes and C. owczarzaki share a common phagocytic program, and that CEBPα is the sole transcription factor highly expressed in both phagocytes and C. owczarzaki. We further showed that the function of CEBPα to drive phagocyte program in nonphagocytic blood cells has been conserved in tunicate, sponge, and C. owczarzaki. We finally showed that, in murine hematopoiesis, repression of CEBPα to maintain nonphagocytic lineages is commonly achieved by polycomb complexes. These findings indicate that the initial blood cells emerged inheriting a unicellular organism program driven by CEBPα and that the program has also been seamlessly inherited in phagocytes of various animal species throughout evolution.
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Affiliation(s)
- Yosuke Nagahata
- Laboratory of Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kyoko Masuda
- Laboratory of Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yuji Nishimura
- Laboratory of Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Tomokatsu Ikawa
- Division of Immunology and Allergy, Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Shinpei Kawaoka
- Inter-Organ Communication Research Team, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Toshio Kitawaki
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroshi Suga
- Department of Life and Environmental Sciences, Prefectural University of Hiroshima, Shobara, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroshi Kawamoto
- Laboratory of Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
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30
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Peterson AF, Ingram K, Huang EJ, Parksong J, McKenney C, Bever GS, Regot S. Systematic analysis of the MAPK signaling network reveals MAP3K-driven control of cell fate. Cell Syst 2022; 13:885-894.e4. [PMID: 36356576 PMCID: PMC9923805 DOI: 10.1016/j.cels.2022.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/15/2022] [Accepted: 10/17/2022] [Indexed: 11/10/2022]
Abstract
The classic network of mitogen-activated protein kinases (MAPKs) is highly interconnected and controls a diverse array of biological processes. In multicellular eukaryotes, the MAPKs ERK, JNK, and p38 control opposing cell behaviors but are often activated simultaneously, raising questions about how input-output specificity is achieved. Here, we use multiplexed MAPK activity biosensors to investigate how cell fate control emerges from the connectivity and dynamics of the MAPK network. Through chemical and genetic perturbation, we systematically explore the outputs and functions of all the MAP3 kinases encoded in the human genome and show that MAP3Ks control cell fate by triggering unique combinations of MAPK activity. We show that these MAPK activity combinations explain the paradoxical dual role of JNK signaling as pro-apoptotic or pro-proliferative kinase. Overall, our integrative analysis indicates that the MAPK network operates as a unit to control cell fate and shifts the focus from MAPKs to MAP3Ks to better understand signaling-mediated control of cell fate.
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Affiliation(s)
- Amy F Peterson
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; The Biochemistry, Cellular, and Molecular Biology Graduate Program, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kayla Ingram
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; The Biochemistry, Cellular, and Molecular Biology Graduate Program, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - E J Huang
- Center for Functional Anatomy & Evolution, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jeeun Parksong
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; The Biochemistry, Cellular, and Molecular Biology Graduate Program, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Connor McKenney
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; The Biochemistry, Cellular, and Molecular Biology Graduate Program, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Gabriel S Bever
- Center for Functional Anatomy & Evolution, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Medicine, Division of Cardiology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sergi Regot
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; The Biochemistry, Cellular, and Molecular Biology Graduate Program, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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31
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Rust J. Phenotype-first hypotheses, spandrels and early metazoan evolution. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2022; 44:48. [PMID: 36257998 DOI: 10.1007/s40656-022-00531-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Against the neo-Darwinian assumption that genetic factors are the principal source of variation upon which natural selection operates, a phenotype-first hypothesis strikes us as revolutionary because development would seem to constitute an independent source of variability. Richard Watson and his co-authors have argued that developmental memory constitutes one such variety of phenotypic variability. While this version of the phenotype-first hypothesis is especially well-suited for the late metazoan context, where animals have a sufficient history of selection from which to draw, appeals to developmental memory seem less plausible in the evolutionary context of the early metazoans. I provide an interpretation of Stuart Newman's account of deep metazoan phylogenesis that suggests that spandrels are, in addition to developmental memory, an important reservoir of phenotypic variability. I conclude by arguing that Gerd Müller's "side-effect hypothesis" is an illuminating generalization of the proposed non-Watsonian version of the phenotype-first hypothesis.
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Affiliation(s)
- Joshua Rust
- Stetson University, Unit 8250, 104-C Elizabeth Hall, 421 North Woodland Boulevard, DeLand, Florida, 32723, USA.
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32
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Newman SA. Inherency and agency in the origin and evolution of biological functions. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Although discussed by 20th century philosophers in terms drawn from the sciences of non-living systems, in recent decades biological function has been considered in relationship to organismal capability and purpose. Bringing two phenomena generally neglected in evolutionary theory (i.e. inherency and agency) to bear on questions of function leads to a rejection of the adaptationist ‘selected effects’ notion of biological function. I review work showing that organisms such as the placozoans can thrive with almost no functional embellishments beyond those of their constituent cells and physical properties of their simple tissues. I also discuss work showing that individual tissue cells and their artificial aggregates exhibit agential behaviours that are unprecedented in the histories of their respective lineages. I review findings on the unique metazoan mechanism of developmental gene expression that has recruited, during evolution, inherent ancestral cellular functionalities into specialized cell types and organs of the different animal groups. I conclude that most essential functions in animal species are inherent to the cells from which they evolved, not selected effects, and that many of the others are optional ‘add-ons’, a status inimical to fitness-based models of evolution positing that traits emerge from stringent cycles of selection to meet external challenges.
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Affiliation(s)
- Stuart A Newman
- Department of Cell Biology & Anatomy, New York Medical College , Valhalla, NY 10595 , USA
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33
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Deppisch P, Helfrich-Förster C, Senthilan PR. The Gain and Loss of Cryptochrome/Photolyase Family Members during Evolution. Genes (Basel) 2022; 13:genes13091613. [PMID: 36140781 PMCID: PMC9498864 DOI: 10.3390/genes13091613] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/20/2022] Open
Abstract
The cryptochrome/photolyase (CRY/PL) family represents an ancient group of proteins fulfilling two fundamental functions. While photolyases repair UV-induced DNA damages, cryptochromes mainly influence the circadian clock. In this study, we took advantage of the large number of already sequenced and annotated genes available in databases and systematically searched for the protein sequences of CRY/PL family members in all taxonomic groups primarily focusing on metazoans and limiting the number of species per taxonomic order to five. Using BLASTP searches and subsequent phylogenetic tree and motif analyses, we identified five distinct photolyases (CPDI, CPDII, CPDIII, 6-4 photolyase, and the plant photolyase PPL) and six cryptochrome subfamilies (DASH-CRY, mammalian-type MCRY, Drosophila-type DCRY, cnidarian-specific ACRY, plant-specific PCRY, and the putative magnetoreceptor CRY4. Manually assigning the CRY/PL subfamilies to the species studied, we have noted that over evolutionary history, an initial increase of various CRY/PL subfamilies was followed by a decrease and specialization. Thus, in more primitive organisms (e.g., bacteria, archaea, simple eukaryotes, and in basal metazoans), we find relatively few CRY/PL members. As species become more evolved (e.g., cnidarians, mollusks, echinoderms, etc.), the CRY/PL repertoire also increases, whereas it appears to decrease again in more recent organisms (humans, fruit flies, etc.). Moreover, our study indicates that all cryptochromes, although largely active in the circadian clock, arose independently from different photolyases, explaining their different modes of action.
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35
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Jacques F, Baratchart E, Pienta KJ, Hammarlund EU. Origin and evolution of animal multicellularity in the light of phylogenomics and cancer genetics. Med Oncol 2022; 39:160. [PMID: 35972622 PMCID: PMC9381480 DOI: 10.1007/s12032-022-01740-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 04/23/2022] [Indexed: 11/07/2022]
Abstract
The rise of animals represents a major but enigmatic event in the evolutionary history of life. In recent years, numerous studies have aimed at understanding the genetic basis of this transition. However, genome comparisons of diverse animal and protist lineages suggest that the appearance of gene families that were previously considered animal specific indeed preceded animals. Animals' unicellular relatives, such as choanoflagellates, ichthyosporeans, and filastereans, demonstrate complex life cycles including transient multicellularity as well as genetic toolkits for temporal cell differentiation, cell-to-cell communication, apoptosis, and cell adhesion. This has warranted further exploration of the genetic basis underlying transitions in cellular organization. An alternative model for the study of transitions in cellular organization is tumors, which exploit physiological programs that characterize both unicellularity and multicellularity. Tumor cells, for example, switch adhesion on and off, up- or downregulate specific cell differentiation states, downregulate apoptosis, and allow cell migration within tissues. Here, we use insights from both the fields of phylogenomics and tumor biology to review the evolutionary history of the regulatory systems of multicellularity and discuss their overlap. We claim that while evolutionary biology has contributed to an increased understanding of cancer, broad investigations into tissue-normal and transformed-can also contribute the framework for exploring animal evolution.
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Affiliation(s)
- Florian Jacques
- Tissue Development and Evolution (TiDE), Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Laboratory Medicine, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Etienne Baratchart
- Tissue Development and Evolution (TiDE), Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Laboratory Medicine, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Kenneth J Pienta
- The Cancer Ecology Center, Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, USA
| | - Emma U Hammarlund
- Tissue Development and Evolution (TiDE), Department of Laboratory Medicine, Lund University, Lund, Sweden.
- Department of Laboratory Medicine, Lund Stem Cell Center, Lund University, Lund, Sweden.
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36
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Rischer M, Guo H, Beemelmanns C. Signalling molecules inducing metamorphosis in marine organisms. Nat Prod Rep 2022; 39:1833-1855. [PMID: 35822257 DOI: 10.1039/d1np00073j] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: findings from early 1980s until early 2022Microbial-derived cues of marine biofilms induce settlement and metamorphosis of marine organisms, a process responsible for the emergence of diverse flora and fauna in marine habitats. Although this phenomenon is known for more than 80 years, the research field has only recently gained much momentum. Here, we summarize the currently existing biochemical and microbial knowledge about microbial signalling molecules, con-specific signals, and synthetic compounds that induce or prevent recruitment, settlement, and metamorphosis in invertebrate larvae. We discuss the possible modes of action and conclude with perspectives for future research directions in the field of marine chemical ecology.
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Affiliation(s)
- Maja Rischer
- Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraße 11a, Jena, 07745, Germany.
| | - Huijuan Guo
- Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraße 11a, Jena, 07745, Germany.
| | - Christine Beemelmanns
- Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraße 11a, Jena, 07745, Germany. .,Biochemistry of Microbial Metabolism, Institute of Biochemistry, Leipzig University, Johannisallee 21-23, Leipzig 04103, Germany
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37
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Phillips JE, Santos M, Konchwala M, Xing C, Pan D. Genome editing in the unicellular holozoan Capsaspora owczarzaki suggests a premetazoan role for the Hippo pathway in multicellular morphogenesis. eLife 2022; 11:e77598. [PMID: 35659869 PMCID: PMC9170242 DOI: 10.7554/elife.77598] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/23/2022] [Indexed: 12/13/2022] Open
Abstract
Animal development is mediated by a surprisingly small set of canonical signaling pathways such as Wnt, Hedgehog, TGF-beta, Notch, and Hippo pathways. Although once thought to be present only in animals, recent genome sequencing has revealed components of these pathways in the closest unicellular relatives of animals. These findings raise questions about the ancestral functions of these developmental pathways and their potential role in the emergence of animal multicellularity. Here, we provide the first functional characterization of any of these developmental pathways in unicellular organisms by developing techniques for genetic manipulation in Capsaspora owczarzaki, a close unicellular relative of animals that displays aggregative multicellularity. We then use these tools to characterize the Capsaspora ortholog of the Hippo signaling nuclear effector YAP/TAZ/Yorkie (coYki), a key regulator of tissue size in animals. In contrast to what might be expected based on studies in animals, we show that coYki is dispensable for cell proliferation but regulates cytoskeletal dynamics and the three-dimensional (3D) shape of multicellular structures. We further demonstrate that the cytoskeletal abnormalities of individual coYki mutant cells underlie the abnormal 3D shape of coYki mutant aggregates. Taken together, these findings implicate an ancestral role for the Hippo pathway in cytoskeletal dynamics and multicellular morphogenesis predating the origin of animal multicellularity, which was co-opted during evolution to regulate cell proliferation.
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Affiliation(s)
- Jonathan E Phillips
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Maribel Santos
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Mohammed Konchwala
- Eugene McDermott Center for Human Growth & Development, Departments of Bioinformatics and Clinical Sciences, University of Texas Southwestern Medical CenterDallasUnited States
| | - Chao Xing
- Eugene McDermott Center for Human Growth & Development, Departments of Bioinformatics and Clinical Sciences, University of Texas Southwestern Medical CenterDallasUnited States
| | - Duojia Pan
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical CenterDallasUnited States
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38
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Bonforti A, Solé R. Unicellular-multicellular evolutionary branching driven by resource limitations. J R Soc Interface 2022; 19:20220018. [PMID: 35642429 DOI: 10.1098/rsif.2022.0018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Multicellular life forms have evolved many times on our planet, suggesting that this is a common evolutionary innovation. Multiple advantages have been proposed for the emergence of multicellularity (MC). In this paper, we address the problem of how the first precondition for MC, namely 'stay together', might have occurred under spatially limited resources exploited by a population of unicellular agents. Using a minimal model of evolved cell-cell adhesion among growing and dividing cells that exploit a localized resource with a given size, we show that a transition occurs at a critical resource size separating a phase of evolved multicellular aggregates from a phase where unicellularity (UC) is favoured. The two phases are separated by an intermediate domain where both UC and MC can be selected by evolution. This model provides a minimal approach to the early stages that were required to transition from individuality to cohesive groups of cells associated with a physical cooperative effect: when resources are present only in a localized portion of the habitat, MC is a desirable property as it helps cells to keep close to the available local nutrients.
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Affiliation(s)
- Adriano Bonforti
- ICREA-Complex Systems Lab, UPF-PRBB, Dr. Aiguader 80, 08003 Barcelona, Spain.,Institut de Biologia Evolutiva, CSIC-UPF, Passeig Maritim de la Barceloneta 37, 08003 Barcelona, Spain
| | - Ricard Solé
- ICREA-Complex Systems Lab, UPF-PRBB, Dr. Aiguader 80, 08003 Barcelona, Spain.,Institut de Biologia Evolutiva, CSIC-UPF, Passeig Maritim de la Barceloneta 37, 08003 Barcelona, Spain.,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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39
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Minelli A, Valero-Gracia A. Spatially and Temporally Distributed Complexity-A Refreshed Framework for the Study of GRN Evolution. Cells 2022; 11:cells11111790. [PMID: 35681485 PMCID: PMC9179533 DOI: 10.3390/cells11111790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/24/2022] [Accepted: 05/28/2022] [Indexed: 11/16/2022] Open
Abstract
Irrespective of the heuristic value of interpretations of developmental processes in terms of gene regulatory networks (GRNs), larger-angle views often suffer from: (i) an inadequate understanding of the relationship between genotype and phenotype; (ii) a predominantly zoocentric vision; and (iii) overconfidence in a putatively hierarchical organization of animal body plans. Here, we constructively criticize these assumptions. First, developmental biology is pervaded by adultocentrism, but development is not necessarily egg to adult. Second, during development, many unicells undergo transcriptomic profile transitions that are comparable to those recorded in pluricellular organisms; thus, their study should not be neglected from the GRN perspective. Third, the putatively hierarchical nature of the animal body is mirrored in the GRN logic, but in relating genotype to phenotype, independent assessments of the dynamics of the regulatory machinery and the animal’s architecture are required, better served by a combinatorial than by a hierarchical approach. The trade-offs between spatial and temporal aspects of regulation, as well as their evolutionary consequences, are also discussed. Multicellularity may derive from a unicell’s sequential phenotypes turned into different but coexisting, spatially arranged cell types. In turn, polyphenism may have been a crucial mechanism involved in the origin of complex life cycles.
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Affiliation(s)
- Alessandro Minelli
- Department of Biology, University of Padova, Via U. Bassi 58B, 35132 Padova, Italy
- Correspondence:
| | - Alberto Valero-Gracia
- Natural History Museum, University of Oslo, Blindern, P.O. Box 1172, 0318 Oslo, Norway;
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40
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Tice AK, Brown MW. Multicellularity: Amoebae follow the leader to food. Curr Biol 2022; 32:R418-R420. [DOI: 10.1016/j.cub.2022.03.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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41
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Van Etten J, Keddis R, Lisa J, Rauschenbach I. The Diverse World of Protists-an Ideal Community with which to Introduce Microscopy in the Microbiology Teaching Laboratory. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2022; 23:e00142-21. [PMID: 35340451 PMCID: PMC8943629 DOI: 10.1128/jmbe.00142-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
Protists and other eukaryotes are present in diverse terrestrial and aquatic environments. They can easily be collected from local ponds and streams. Although they are typically larger in size than prokaryotes, making them easy to study with even basic microscopes, microbiology laboratory courses often do not discuss them in detail and may only dedicate a short time to observing preserved samples. This laboratory exercise allows students to develop microscope skills, experience real world application of collecting and processing field samples, and delve deeper into the diverse world of protists and other microbial eukaryotes. Students may also engage by sharing their findings on the website iNaturalist to contribute to the scientific knowledge collected around the world. This laboratory module was initially designed for in-person learning but has been successfully adapted to remote learning and can also be applied to a complete online learning environment.
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Affiliation(s)
- Julia Van Etten
- Graduate Program in Ecology and Evolution, Rutgers University, New Brunswick, New Jersey, USA
| | - Ramaydalis Keddis
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
| | - Jessica Lisa
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
- Department of Biology, Georgian Court University, Lakewood, New Jersey, USA
| | - Ines Rauschenbach
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
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42
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Incomplete abscission and cytoplasmic bridges in the evolution of eukaryotic multicellularity. Curr Biol 2022; 32:R385-R397. [DOI: 10.1016/j.cub.2022.03.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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43
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Yin Z, Sun W, Liu P, Chen J, Bottjer DJ, Li J, Zhu M. Diverse and complex developmental mechanisms of early Ediacaran embryo-like fossils from the Weng'an Biota, southwest China. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210032. [PMID: 35125006 PMCID: PMC8819369 DOI: 10.1098/rstb.2021.0032] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The origin and early evolution of animal development remain among the many deep, unresolved problems in evolutionary biology. As a compelling case for the existence of pre-Cambrian animals, the Ediacaran embryo-like fossils (EELFs) from the Weng'an Biota (approx. 609 Myr old, Doushantuo Formation, South China) have great potential to cast light on the origin and early evolution of animal development. However, their biological implications can be fully realized only when their phylogenetic positions are correctly established, and unfortunately, this is the key problem under debate. As a significant feature of developmental biology, the cell division pattern (CDP) characterized by the dynamic spatial arrangement of cells and associated developmental mechanisms is critical to reassess these hypotheses and evaluate the diversity of the EELFs; however, their phylogenetic implications have not been fully realized. Additionally, the scarcity of fossil specimens representing late developmental stages with cell differentiation accounts for much of this debate too. Here, we reconstructed a large number of EELFs using submicron resolution X-ray tomographic microscopy and focused on the CDPs and associated developmental mechanisms as well as features of cell differentiation. Four types of CDPs and specimens with cell differentiation were identified. Contrary to the prevailing view, our results together with recent studies suggest that the diversity and complexity of developmental mechanisms documented by the EELFs are much higher than is often claimed. The diverse CDPs and associated development features including palintomic cleavage, maternal nutrition, asymmetric cell divisions, symmetry breaking, establishment of polarity or axis, spatial cell migration and differentiation constrain some, if not all, EELFs as total-group metazoans. This article is part of the theme issue ‘The impact of Chinese palaeontology on evolutionary research’.
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Affiliation(s)
- Zongjun Yin
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China.,Centre for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China.,Nanjing College, University of Chinese Academy of Sciences, Nanjing 211135, People's Republic of China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Weichen Sun
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China.,University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - Pengju Liu
- Institute of Geology, Chinese Academy of Geological Sciences, Beijing 100037, People's Republic of China
| | - Junyuan Chen
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
| | - David J Bottjer
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Jinhua Li
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing 100029, People's Republic of China
| | - Maoyan Zhu
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China.,Centre for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China.,Nanjing College, University of Chinese Academy of Sciences, Nanjing 211135, People's Republic of China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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44
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Abstract
Post-translational modification with O-linked β-N-acetylglucosamine (O-GlcNAc), a process referred to as O-GlcNAcylation, occurs on a vast variety of proteins. Mounting evidence in the past several decades has clearly demonstrated that O-GlcNAcylation is a unique and ubiquitous modification. Reminiscent of a code, protein O-GlcNAcylation functions as a crucial regulator of nearly all cellular processes studied. The primary aim of this review is to summarize the developments in our understanding of myriad protein substrates modified by O-GlcNAcylation from a systems perspective. Specifically, we provide a comprehensive survey of O-GlcNAcylation in multiple species studied, including eukaryotes (e.g., protists, fungi, plants, Caenorhabditis elegans, Drosophila melanogaster, murine, and human), prokaryotes, and some viruses. We evaluate features (e.g., structural properties and sequence motifs) of O-GlcNAc modification on proteins across species. Given that O-GlcNAcylation functions in a species-, tissue-/cell-, protein-, and site-specific manner, we discuss the functional roles of O-GlcNAcylation on human proteins. We focus particularly on several classes of relatively well-characterized human proteins (including transcription factors, protein kinases, protein phosphatases, and E3 ubiquitin-ligases), with representative O-GlcNAc site-specific functions presented. We hope the systems view of the great endeavor in the past 35 years will help demystify the O-GlcNAc code and lead to more fascinating studies in the years to come.
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Affiliation(s)
- Junfeng Ma
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, United States
| | - Chunyan Hou
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, United States
| | - Ci Wu
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, United States
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45
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Gao Y, Pichugin Y, Gokhale CS, Traulsen A. Evolution of reproductive strategies in incipient multicellularity. J R Soc Interface 2022; 19:20210716. [PMID: 35232276 PMCID: PMC8889184 DOI: 10.1098/rsif.2021.0716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Multicellular organisms potentially show a large degree of diversity in reproductive strategies, producing offspring with varying sizes and compositions compared to their unicellular ancestors. In reality, only a few of these reproductive strategies are prevalent. To understand why this could be the case, we develop a stage-structured population model to probe the evolutionary growth advantages of reproductive strategies in incipient multicellular organisms. The performance of reproductive strategies is evaluated by the growth rates of the corresponding populations. We identify the optimal reproductive strategy, leading to the largest growth rate for a population. Considering the effects of organism size and cellular interaction, we found that distinct reproductive strategies could perform uniquely or equally well under different conditions. If a single reproductive strategy is optimal, it is binary splitting, dividing into two parts. Our results show that organism size and cellular interaction can play crucial roles in shaping reproductive strategies in nascent multicellularity. Our model sheds light on understanding the mechanism driving the evolution of reproductive strategies in incipient multicellularity. Beyond multicellularity, our results imply that a crucial factor in the evolution of unicellular species’ reproductive strategies is organism size.
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Affiliation(s)
- Yuanxiao Gao
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
| | - Yuriy Pichugin
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
| | - Chaitanya S Gokhale
- Research Group for Theoretical Models of Eco-evolutionary Dynamics, Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
| | - Arne Traulsen
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
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46
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Dudin O, Wielgoss S, New AM, Ruiz-Trillo I. Regulation of sedimentation rate shapes the evolution of multicellularity in a close unicellular relative of animals. PLoS Biol 2022; 20:e3001551. [PMID: 35349578 PMCID: PMC8963540 DOI: 10.1371/journal.pbio.3001551] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/21/2022] [Indexed: 01/03/2023] Open
Abstract
Significant increases in sedimentation rate accompany the evolution of multicellularity. These increases should lead to rapid changes in ecological distribution, thereby affecting the costs and benefits of multicellularity and its likelihood to evolve. However, how genetic and cellular traits control this process, their likelihood of emergence over evolutionary timescales, and the variation in these traits as multicellularity evolves are still poorly understood. Here, using isolates of the ichthyosporean genus Sphaeroforma-close unicellular relatives of animals with brief transient multicellular life stages-we demonstrate that sedimentation rate is a highly variable and evolvable trait affected by at least 2 distinct physical mechanisms. First, we find extensive (>300×) variation in sedimentation rates for different Sphaeroforma species, mainly driven by size and density during the unicellular-to-multicellular life cycle transition. Second, using experimental evolution with sedimentation rate as a focal trait, we readily obtained, for the first time, fast settling and multicellular Sphaeroforma arctica isolates. Quantitative microscopy showed that increased sedimentation rates most often arose by incomplete cellular separation after cell division, leading to clonal "clumping" multicellular variants with increased size and density. Strikingly, density increases also arose by an acceleration of the nuclear doubling time relative to cell size. Similar size- and density-affecting phenotypes were observed in 4 additional species from the Sphaeroforma genus, suggesting that variation in these traits might be widespread in the marine habitat. By resequencing evolved isolates to high genomic coverage, we identified mutations in regulators of cytokinesis, plasma membrane remodeling, and chromatin condensation that may contribute to both clump formation and the increase in the nuclear number-to-volume ratio. Taken together, this study illustrates how extensive cellular control of density and size drive sedimentation rate variation, likely shaping the onset and further evolution of multicellularity.
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Affiliation(s)
- Omaya Dudin
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Sébastien Wielgoss
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Aaron M. New
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Spain
- ICREA, Barcelona, Spain
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47
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Merényi Z, Virágh M, Gluck-Thaler E, Slot JC, Kiss B, Varga T, Geösel A, Hegedüs B, Bálint B, Nagy LG. Gene age shapes the transcriptional landscape of sexual morphogenesis in mushroom forming fungi (Agaricomycetes). eLife 2022; 11:71348. [PMID: 35156613 PMCID: PMC8893723 DOI: 10.7554/elife.71348] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 02/11/2022] [Indexed: 11/13/2022] Open
Abstract
Multicellularity has been one of the most important innovations in the history of life. The role of gene regulatory changes in driving transitions to multicellularity is being increasingly recognized; however, factors influencing gene expression patterns are poorly known in many clades. Here, we compared the developmental transcriptomes of complex multicellular fruiting bodies of eight Agaricomycetes and Cryptococcus neoformans, a closely related human pathogen with a simple morphology. In-depth analysis in Pleurotus ostreatus revealed that allele-specific expression, natural antisense transcripts, and developmental gene expression, but not RNA editing or a ‘developmental hourglass,’ act in concert to shape its transcriptome during fruiting body development. We found that transcriptional patterns of genes strongly depend on their evolutionary ages. Young genes showed more developmental and allele-specific expression variation, possibly because of weaker evolutionary constraint, suggestive of nonadaptive expression variance in fruiting bodies. These results prompted us to define a set of conserved genes specifically regulated only during complex morphogenesis by excluding young genes and accounting for deeply conserved ones shared with species showing simple sexual development. Analysis of the resulting gene set revealed evolutionary and functional associations with complex multicellularity, which allowed us to speculate they are involved in complex multicellular morphogenesis of mushroom fruiting bodies.
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Affiliation(s)
- Zsolt Merényi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | - Máté Virágh
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | - Emile Gluck-Thaler
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Jason C Slot
- Department of Plant Pathology, Ohio State University, Columbus, United States
| | - Brigitta Kiss
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | - Torda Varga
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | - András Geösel
- Department of Vegetable and Mushroom Growing, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| | - Botond Hegedüs
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | - Balázs Bálint
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | - László G Nagy
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
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48
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Reuten R, Mayorca-Guiliani AE, Erler JT. Matritecture: Mapping the extracellular matrix architecture during health and disease. Matrix Biol Plus 2022; 14:100102. [PMID: 35243299 PMCID: PMC8861423 DOI: 10.1016/j.mbplus.2022.100102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 01/24/2022] [Accepted: 01/28/2022] [Indexed: 11/20/2022] Open
Abstract
All cells in multicellular organisms are housed in the extracellular matrix (ECM), an acellular edifice built up by more than a thousand proteins and glycans. Cells engage in a reciprocal relationship with the ECM; they build, inhabit, maintain, and remodel the ECM, while, in turn, the ECM regulates their behavior. The homeostatic balance of cell-ECM interactions can be lost, due to ageing, irritants or diseases, which results in aberrant cell behavior. The ECM can suppress or promote disease progression, depending on the information relayed to cells. Instructions come in the form of biochemical (e.g., composition), biophysical (e.g., stiffness), and topographical (e.g., structure) cues. While advances have been made in many areas, we only have a very limited grasp of ECM topography. A detailed atlas deciphering the spatiotemporal arrangement of all ECM proteins is lacking. We feel that such an extracellular matrix architecture (matritecture) atlas should be a priority goal for ECM research. In this commentary, we will discuss the need to resolve the spatiotemporal matritecture to identify potential disease triggers and therapeutic targets and present strategies to address this goal. Such a detailed matritecture atlas will not only identify disease-specific ECM structures but may also guide future strategies to restructure disease-related ECM patterns reverting to a normal pattern.
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49
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Kin K, Chen ZH, Forbes G, Schaap P. Evolution of a novel cell type in Dictyostelia required gene duplication of a cudA-like transcription factor. Curr Biol 2022; 32:428-437.e4. [PMID: 34883046 PMCID: PMC8808424 DOI: 10.1016/j.cub.2021.11.047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/04/2021] [Accepted: 11/17/2021] [Indexed: 10/31/2022]
Abstract
The evolution of novel cell types has been proposed to result from duplication of gene regulatory networks, but proven examples are rare. In addition to stalk cells and spores that make up the fruiting bodies of three major groups of Dictyostelia, those in group 4 additionally evolved basal disc and cup cells that respectively anchor the stalk to the substratum and the spore mass to the stalk. We noted a putative group-4-specific duplication of a cudA-like transcription factor (TF) in a comparative analysis of group-representative genomes. Using increased taxon sampling, we here confirmed that this TF, cdl1, duplicated into cdl1a and cdl1b in the common ancestor to group 4. cdl1a, but not cdl1b, showed signatures of positive selection, indicative of functional innovation. Deletion of cdl1a in Dictyostelium discoideum resulted in fruiting bodies with sagging spore heads that lacked the supporting cup cells and expression of cup-specific genes. Deletion of cdl1b resulted in thinner fruiting body stalks, while a cdl1b-cdl1a- double knockout showed more severe stalk defects, suggesting an ancestral role of cdl1 in stalk formation. This was confirmed in a closely related non-group 4 species, Polysphondylium violaceum, where cdl1 knockout caused defective stalk formation. These data indicate that the group-specific duplication of cdl1 and subsequent diversification of cdl1a played a pivotal role in the evolution of a novel somatic cell type in group 4 Dictyostelia.
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Affiliation(s)
- Koryu Kin
- University of Dundee, School of Life Sciences, Dow Street, Dundee DD1 5EH, UK; Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - Zhi-Hui Chen
- University of Dundee, School of Life Sciences, Dow Street, Dundee DD1 5EH, UK
| | - Gillian Forbes
- University of Dundee, School of Life Sciences, Dow Street, Dundee DD1 5EH, UK
| | - Pauline Schaap
- University of Dundee, School of Life Sciences, Dow Street, Dundee DD1 5EH, UK.
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Mayorova TD, Hammar K, Jung JH, Aronova MA, Zhang G, Winters CA, Reese TS, Smith CL. Placozoan fiber cells: mediators of innate immunity and participants in wound healing. Sci Rep 2021; 11:23343. [PMID: 34857844 PMCID: PMC8639732 DOI: 10.1038/s41598-021-02735-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 11/19/2021] [Indexed: 12/22/2022] Open
Abstract
Placozoa is a phylum of non-bilaterian marine animals. These small, flat organisms adhere to the substrate via their densely ciliated ventral epithelium, which mediates mucociliary locomotion and nutrient uptake. They have only six morphological cell types, including one, fiber cells, for which functional data is lacking. Fiber cells are non-epithelial cells with multiple processes. We used electron and light microscopic approaches to unravel the roles of fiber cells in Trichoplax adhaerens, a representative member of the phylum. Three-dimensional reconstructions of serial sections of Trichoplax showed that each fiber cell is in contact with several other cells. Examination of fiber cells in thin sections and observations of live dissociated fiber cells demonstrated that they phagocytose cell debris and bacteria. In situ hybridization confirmed that fiber cells express genes involved in phagocytic activity. Fiber cells also are involved in wound healing as evidenced from microsurgery experiments. Based on these observations we conclude that fiber cells are multi-purpose macrophage-like cells. Macrophage-like cells have been described in Porifera, Ctenophora, and Cnidaria and are widespread among Bilateria, but our study is the first to show that Placozoa possesses this cell type. The phylogenetic distribution of macrophage-like cells suggests that they appeared early in metazoan evolution.
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Affiliation(s)
- Tatiana D Mayorova
- Laboratory of Neurobiology, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 49 Convent Drive, Bethesda, MD, 20892, USA.
| | - Katherine Hammar
- Central Microscopy Facility, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA
| | - Jae H Jung
- Laboratory of Neurobiology, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 49 Convent Drive, Bethesda, MD, 20892, USA
| | - Maria A Aronova
- Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, USA
| | - Guofeng Zhang
- Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, USA
| | - Christine A Winters
- Laboratory of Neurobiology, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 49 Convent Drive, Bethesda, MD, 20892, USA
| | - Thomas S Reese
- Laboratory of Neurobiology, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 49 Convent Drive, Bethesda, MD, 20892, USA
| | - Carolyn L Smith
- Light Imaging Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
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