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Li Y, Hou Y, Sun Q, Zeng H, Meng F, Tian X, He Q, Shao F, Ding J. Cleavage-independent activation of ancient eukaryotic gasdermins and structural mechanisms. Science 2024; 384:adm9190. [PMID: 38662913 DOI: 10.1126/science.adm9190] [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: 11/13/2023] [Accepted: 03/28/2024] [Indexed: 05/18/2024]
Abstract
Gasdermins (GSDMs) are pore-forming proteins that execute pyroptosis for immune defense. GSDMs are two-domain proteins activated by proteolytic removal of the inhibitory domain. In this work, we report two types of cleavage-independent GSDM activation. First, TrichoGSDM, a pore-forming domain-only protein from the basal metazoan Trichoplax adhaerens, is a disulfides-linked autoinhibited dimer activated by reduction of the disulfides. The cryo-electron microscopy (cryo-EM) structure illustrates the assembly mechanism for the 44-mer TrichoGSDM pore. Second, RCD-1-1 and RCD-1-2, encoded by the polymorphic regulator of cell death-1 (rcd-1) gene in filamentous fungus Neurospora crassa, are also pore-forming domain-only GSDMs. RCD-1-1 and RCD-1-2, when encountering each other, form pores and cause pyroptosis, underlying allorecognition in Neurospora. The cryo-EM structure reveals a pore of 11 RCD-1-1/RCD-1-2 heterodimers and a heterodimerization-triggered pore assembly mechanism. This study shows mechanistic diversities in GSDM activation and indicates versatile functions of GSDMs.
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Affiliation(s)
- Yueyue Li
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yanjie Hou
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Sun
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - Huan Zeng
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - Fanyi Meng
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Xiang Tian
- MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Qun He
- MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Feng Shao
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
- Research Unit of Pyroptosis and Immunity, Chinese Academy of Medical Sciences and National Institute of Biological Sciences, Beijing 102206, China
- Changping Laboratory, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
- New Cornerstone Science Laboratory, Shenzhen 518054, China
| | - Jingjin Ding
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 101408, China
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
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Eitel M, Osigus H, Brenzinger B, Wörheide G. Beauty in the beast - Placozoan biodiversity explored through molluscan predator genomics. Ecol Evol 2024; 14:e11220. [PMID: 38606341 PMCID: PMC11007570 DOI: 10.1002/ece3.11220] [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: 08/04/2023] [Revised: 03/17/2024] [Accepted: 03/20/2024] [Indexed: 04/13/2024] Open
Abstract
The marine animal phylum Placozoa is characterized by a poorly explored cryptic biodiversity combined with very limited knowledge of their ecology. While placozoans are typically found as part of the epibenthos of coastal waters, known placozoan predators, namely small, shell-less sea slugs belonging to the family Rhodopidae (Mollusca: Gastropoda: Heterobranchia), inhabit the interstitium of seafloor sediment. In order to gain further insights into this predator-prey relationship and to expand our understanding of placozoan ecological niches, we screened publicly available whole-body metagenomic data from two rhodopid specimens collected from coastal sediments. Our analysis not only revealed the signatures of three previously unknown placozoan lineages in these sea slug samples but also enabled the assembly of three complete and two partial mitochondrial chromosomes belonging to four previously described placozoan genera, substantially extending the picture of placozoan biodiversity. Our findings further refine the molecular phylogeny of the Placozoa, corroborate the recently established taxonomic ranks in this phylum, and provide molecular support that known placozoan clades should be referred to as genera. We finally discuss the main finding of our study - the presence of placozoans in the sea floor sediment interstitium - in the context of their ecological, biological, and natural history implications.
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Affiliation(s)
- Michael Eitel
- GeoBio‐CenterLudwig‐Maximilians‐Universität MünchenMünchenDeutschland
- Department of Earth and Environmental Sciences, Paleontology and GeobiologyLudwig‐Maximilians‐Universität‐MünchenMünchenDeutschland
| | - Hans‐Jürgen Osigus
- Institut für TierökologieStiftung Tierärztliche Hochschule HannoverHannoverDeutschland
- Present address:
Hochschulbibliothek, Stiftung Tierärztliche Hochschule HannoverHannoverDeutschland
| | - Bastian Brenzinger
- Staatliche Naturwissenschaftliche Sammlungen Bayerns (SNSB) – Zoologische StaatssammlungMünchenDeutschland
| | - Gert Wörheide
- GeoBio‐CenterLudwig‐Maximilians‐Universität MünchenMünchenDeutschland
- Department of Earth and Environmental Sciences, Paleontology and GeobiologyLudwig‐Maximilians‐Universität‐MünchenMünchenDeutschland
- Staatliche Naturwissenschaftliche Sammlungen Bayerns (SNSB) – Bayerische Staatssammlung für Paläontologie und GeologieMünchenDeutschland
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3
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Romanova DY, Varoqueaux F, Eitel M, Yoshida MA, Nikitin MA, Moroz LL. Long-Term Culturing of Placozoans (Trichoplax and Hoilungia). Methods Mol Biol 2024; 2757:509-529. [PMID: 38668981 DOI: 10.1007/978-1-0716-3642-8_21] [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: 05/01/2024]
Abstract
The phylum Placozoa remains one of the least explored among early-branching metazoan lineages. For over 130 years, this phylum had been represented by the single species Trichoplax adhaerens-an animal with the simplest known body plan (three cell layers without any organs) but complex behaviors. Recently, extensive sampling of placozoans across the globe and their subsequent genetic analysis have revealed incredible biodiversity with numerous cryptic species worldwide. However, only a few culture protocols are available to date, and all are for one species only. Here, we describe the breeding of four different species representing two placozoan genera: Trichoplax adhaerens, Trichoplax sp. H2, Hoilungia sp. H4, and Hoilungia hongkongensis originating from diverse biotopes. Our protocols allow to culture all species under comparable conditions. Next, we outlined various food sources and optimized strain-specific parameters enabling long-term culturing. These protocols can facilitate comparative analyses of placozoan biology and behaviors, which together will contribute to deciphering general principles of animal organization.
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Affiliation(s)
- Daria Y Romanova
- Institute of Higher Nervous Activity and Neurophysiology of RAS, Moscow, Russia.
| | - Frédérique Varoqueaux
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.
| | - Michael Eitel
- Department of Earth and Environmental Sciences Palaeontology & Geobiology, LMU München, Munich, Germany
| | - Masa-Aki Yoshida
- Marine Biological Science Section, Education and Research Center for Biological Resources, Faculty of Life and Environmental Science, Shimane University, Okinoshima, Oki, Shimane, Japan
| | - Mikhail A Nikitin
- Institute of Higher Nervous Activity and Neurophysiology of RAS, Moscow, Russia
- Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia
| | - Leonid L Moroz
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, USA.
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA.
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Romanova DY, Moroz LL. Brief History of Placozoa. Methods Mol Biol 2024; 2757:103-122. [PMID: 38668963 DOI: 10.1007/978-1-0716-3642-8_3] [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: 05/04/2024]
Abstract
Placozoans are morphologically the simplest free-living animals. They represent a unique window of opportunities to understand both the origin of the animal organization and the rules of life for the system and synthetic biology of the future. However, despite more than 100 years of their investigations, we know little about their organization, natural habitats, and life strategies. Here, we introduce this unique animal phylum and highlight some directions vital to broadening the frontiers of the biomedical sciences. In particular, understanding the genomic bases of placozoan biodiversity, cell identity, connectivity, reproduction, and cellular bases of behavior are critical hot spots for future studies.
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Affiliation(s)
- Daria Y Romanova
- Institute of Higher Nervous Activity and Neurophysiology of RAS, Moscow, Russian Federation.
| | - Leonid L Moroz
- Department of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL, USA.
- Whitney Laboratory for Marine Biosciences University of Florida, St. Augustine, FL, USA.
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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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Lemke M, DeSalle R. The Next Generation of Microbial Ecology and Its Importance in Environmental Sustainability. MICROBIAL ECOLOGY 2023; 85:781-795. [PMID: 36826587 PMCID: PMC10156817 DOI: 10.1007/s00248-023-02185-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/24/2023] [Indexed: 05/04/2023]
Abstract
Collectively, we have been reviewers for microbial ecology, genetics and genomics studies that include environmental DNA (eDNA), microbiome studies, and whole bacterial genome biology for Microbial Ecology and other journals for about three decades. Here, we wish to point out trends and point to areas of study that readers, especially those moving into the next generation of microbial ecology research, might learn and consider. In this communication, we are not saying the work currently being accomplished in microbial ecology and restoration biology is inadequate. What we are saying is that a significant milestone in microbial ecology has been reached, and approaches that may have been overlooked or were unable to be completed before should be reconsidered in moving forward into a new more ecological era where restoration of the ecological trajectory of systems has become critical. It is our hope that this introduction, along with the papers that make up this special issue, will address the sense of immediacy and focus needed to move into the next generation of microbial ecology study.
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Affiliation(s)
- Michael Lemke
- Department of Biology, University of Illinois at Springfield, Springfield, IL, USA.
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.
| | - Rob DeSalle
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
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Tessler M, Galen SC, DeSalle R, Schierwater B. Let’s end taxonomic blank slates with molecular morphology. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1016412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many known evolutionary lineages have yet to be described formally due to a lack of traditional morphological characters. This is true for genetically distinctive groups within the amoeboid Placozoa animals, the protists in ponds, and the bacteria that cover nearly everything. These taxonomic tabula rasae, or blank slates, are problematic; without names, communication is hampered and other scientific progress is slowed. We suggest that the morphology of molecules be used to help alleviate this issue. Molecules, such as proteins, have structure. Proteins are even visualizable with X-ray crystallography, albeit more easily detected by and easier to work with using genomic sequencing. Given their structured nature, we believe they should not be considered as anything less than traditional morphology. Protein-coding gene content (presence/absence) can also be used easily with genomic sequences, and is a convenient binary character set. With molecular morphology, we believe that each taxonomic tabula rasa can be solved.
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Wright BA, Kvansakul M, Schierwater B, Humbert PO. Cell polarity signalling at the birth of multicellularity: What can we learn from the first animals. Front Cell Dev Biol 2022; 10:1024489. [PMID: 36506100 PMCID: PMC9729800 DOI: 10.3389/fcell.2022.1024489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/31/2022] [Indexed: 11/25/2022] Open
Abstract
The innovation of multicellularity has driven the unparalleled evolution of animals (Metazoa). But how is a multicellular organism formed and how is its architecture maintained faithfully? The defining properties and rules required for the establishment of the architecture of multicellular organisms include the development of adhesive cell interactions, orientation of division axis, and the ability to reposition daughter cells over long distances. Central to all these properties is the ability to generate asymmetry (polarity), coordinated by a highly conserved set of proteins known as cell polarity regulators. The cell polarity complexes, Scribble, Par and Crumbs, are considered to be a metazoan innovation with apicobasal polarity and adherens junctions both believed to be present in all animals. A better understanding of the fundamental mechanisms regulating cell polarity and tissue architecture should provide key insights into the development and regeneration of all animals including humans. Here we review what is currently known about cell polarity and its control in the most basal metazoans, and how these first examples of multicellular life can inform us about the core mechanisms of tissue organisation and repair, and ultimately diseases of tissue organisation, such as cancer.
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Affiliation(s)
- Bree A. Wright
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Marc Kvansakul
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia,Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, VIC, Australia
| | - Bernd Schierwater
- Institute of Animal Ecology and Evolution, University of Veterinary Medicine Hannover, Foundation, Bünteweg, Hannover, Germany
| | - Patrick O. Humbert
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia,Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, VIC, Australia,Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, Australia,Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia,*Correspondence: Patrick O. Humbert,
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