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Rosner A, Ballarin L, Barnay-Verdier S, Borisenko I, Drago L, Drobne D, Concetta Eliso M, Harbuzov Z, Grimaldi A, Guy-Haim T, Karahan A, Lynch I, Giulia Lionetto M, Martinez P, Mehennaoui K, Oruc Ozcan E, Pinsino A, Paz G, Rinkevich B, Spagnuolo A, Sugni M, Cambier S. A broad-taxa approach as an important concept in ecotoxicological studies and pollution monitoring. Biol Rev Camb Philos Soc 2024; 99:131-176. [PMID: 37698089 DOI: 10.1111/brv.13015] [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: 08/31/2022] [Revised: 08/23/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023]
Abstract
Aquatic invertebrates play a pivotal role in (eco)toxicological assessments because they offer ethical, cost-effective and repeatable testing options. Additionally, their significance in the food chain and their ability to represent diverse aquatic ecosystems make them valuable subjects for (eco)toxicological studies. To ensure consistency and comparability across studies, international (eco)toxicology guidelines have been used to establish standardised methods and protocols for data collection, analysis and interpretation. However, the current standardised protocols primarily focus on a limited number of aquatic invertebrate species, mainly from Arthropoda, Mollusca and Annelida. These protocols are suitable for basic toxicity screening, effectively assessing the immediate and severe effects of toxic substances on organisms. For more comprehensive and ecologically relevant assessments, particularly those addressing long-term effects and ecosystem-wide impacts, we recommended the use of a broader diversity of species, since the present choice of taxa exacerbates the limited scope of basic ecotoxicological studies. This review provides a comprehensive overview of (eco)toxicological studies, focusing on major aquatic invertebrate taxa and how they are used to assess the impact of chemicals in diverse aquatic environments. The present work supports the use of a broad-taxa approach in basic environmental assessments, as it better represents the natural populations inhabiting various ecosystems. Advances in omics and other biochemical and computational techniques make the broad-taxa approach more feasible, enabling mechanistic studies on non-model organisms. By combining these approaches with in vitro techniques together with the broad-taxa approach, researchers can gain insights into less-explored impacts of pollution, such as changes in population diversity, the development of tolerance and transgenerational inheritance of pollution responses, the impact on organism phenotypic plasticity, biological invasion outcomes, social behaviour changes, metabolome changes, regeneration phenomena, disease susceptibility and tissue pathologies. This review also emphasises the need for harmonised data-reporting standards and minimum annotation checklists to ensure that research results are findable, accessible, interoperable and reusable (FAIR), maximising the use and reusability of data. The ultimate goal is to encourage integrated and holistic problem-focused collaboration between diverse scientific disciplines, international standardisation organisations and decision-making bodies, with a focus on transdisciplinary knowledge co-production for the One-Health approach.
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Affiliation(s)
- Amalia Rosner
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
| | - Loriano Ballarin
- Department of Biology, University of Padova, via Ugo Bassi 58/B, Padova, I-35121, Italy
| | - Stéphanie Barnay-Verdier
- Sorbonne Université; CNRS, INSERM, Université Côte d'Azur, Institute for Research on Cancer and Aging Nice, 28 avenue Valombrose, Nice, F-06107, France
| | - Ilya Borisenko
- Faculty of Biology, Department of Embryology, Saint Petersburg State University, Universitetskaya embankment 7/9, Saint Petersburg, 199034, Russia
| | - Laura Drago
- Department of Biology, University of Padova, via Ugo Bassi 58/B, Padova, I-35121, Italy
| | - Damjana Drobne
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, Ljubljana, 1111, Slovenia
| | - Maria Concetta Eliso
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, 80121, Italy
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Zoya Harbuzov
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
- Leon H. Charney School of Marine Sciences, Department of Marine Biology, University of Haifa, 199 Aba Koushy Ave., Haifa, 3498838, Israel
| | - Annalisa Grimaldi
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant, Varese, 3-21100, Italy
| | - Tamar Guy-Haim
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
| | - Arzu Karahan
- Middle East Technical University, Institute of Marine Sciences, Erdemli-Mersin, PO 28, 33731, Turkey
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Maria Giulia Lionetto
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via prov. le Lecce -Monteroni, Lecce, I-73100, Italy
- NBFC, National Biodiversity Future Center, Piazza Marina, 61, Palermo, I-90133, Italy
| | - Pedro Martinez
- Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain
- Institut Català de Recerca i Estudis Avançats (ICREA), Passeig de Lluís Companys, Barcelona, 08010, Spain
| | - Kahina Mehennaoui
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 41, rue du Brill, Belvaux, L-4422, Luxembourg
| | - Elif Oruc Ozcan
- Faculty of Arts and Science, Department of Biology, Cukurova University, Balcali, Saricam, Adana, 01330, Turkey
| | - Annalisa Pinsino
- National Research Council, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Via Ugo La Malfa 153, Palermo, 90146, Italy
| | - Guy Paz
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
| | - Baruch Rinkevich
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
| | - Antonietta Spagnuolo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, 80121, Italy
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, Via Celoria 26, Milan, 20133, Italy
| | - Sébastien Cambier
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 41, rue du Brill, Belvaux, L-4422, Luxembourg
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Santini S, Schenkelaars Q, Jourda C, Duchesne M, Belahbib H, Rocher C, Selva M, Riesgo A, Vervoort M, Leys SP, Kodjabachian L, Le Bivic A, Borchiellini C, Claverie JM, Renard E. The compact genome of the sponge Oopsacas minuta (Hexactinellida) is lacking key metazoan core genes. BMC Biol 2023; 21:139. [PMID: 37337252 DOI: 10.1186/s12915-023-01619-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 05/09/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND Explaining the emergence of the hallmarks of bilaterians is a central focus of evolutionary developmental biology-evodevo-and evolutionary genomics. For this purpose, we must both expand and also refine our knowledge of non-bilaterian genomes, especially by studying early branching animals, in particular those in the metazoan phylum Porifera. RESULTS We present a comprehensive analysis of the first whole genome of a glass sponge, Oopsacas minuta, a member of the Hexactinellida. Studying this class of sponge is evolutionary relevant because it differs from the three other Porifera classes in terms of development, tissue organization, ecology, and physiology. Although O. minuta does not exhibit drastic body simplifications, its genome is among the smallest of animal genomes sequenced so far, and surprisingly lacks several metazoan core genes (including Wnt and several key transcription factors). Our study also provides the complete genome of a symbiotic Archaea dominating the associated microbial community: a new Thaumarchaeota species. CONCLUSIONS The genome of the glass sponge O. minuta differs from all other available sponge genomes by its compactness and smaller number of encoded proteins. The unexpected loss of numerous genes previously considered ancestral and pivotal for metazoan morphogenetic processes most likely reflects the peculiar syncytial tissue organization in this group. Our work further documents the importance of convergence during animal evolution, with multiple convergent evolution of septate-like junctions, electrical-signaling and multiciliated cells in metazoans.
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Affiliation(s)
- Sébastien Santini
- Aix Marseille Univ, CNRS, IGS, UMR 7256, IMM, IM2B, IOM, Marseille, France
| | - Quentin Schenkelaars
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Cyril Jourda
- Aix Marseille Univ, CNRS, IGS, UMR 7256, IMM, IM2B, IOM, Marseille, France
- CIRAD, UMR PVBMT, La Réunion, France
| | - Marc Duchesne
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Hassiba Belahbib
- Aix Marseille Univ, CNRS, IGS, UMR 7256, IMM, IM2B, IOM, Marseille, France
| | - Caroline Rocher
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France
| | - Marjorie Selva
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France
| | - Ana Riesgo
- Department of Biodiversity and Evolutionary Biology, Madrid, Spain
- Department of Life Sciences, Natural History Museum of London, London, SW7 5BD, UK
| | - Michel Vervoort
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Sally P Leys
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Laurent Kodjabachian
- Aix Marseille Univ, CNRS, IBDM, UMR 7288, Turing Center for Living Systems, Marseille, France
| | - André Le Bivic
- Aix Marseille Univ, CNRS, IBDM, UMR 7288, Marseille, France
| | | | | | - Emmanuelle Renard
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France.
- Aix Marseille Univ, CNRS, IBDM, UMR 7288, Marseille, France.
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Sandoval K, McCormack GP. Actinoporin-like Proteins Are Widely Distributed in the Phylum Porifera. Mar Drugs 2022; 20:md20010074. [PMID: 35049929 PMCID: PMC8778704 DOI: 10.3390/md20010074] [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: 12/15/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 11/16/2022] Open
Abstract
Actinoporins are proteinaceous toxins known for their ability to bind to and create pores in cellular membranes. This quality has generated interest in their potential use as new tools, such as therapeutic immunotoxins. Isolated historically from sea anemones, genes encoding for similar actinoporin-like proteins have since been found in a small number of other animal phyla. Sequencing and de novo assembly of Irish Haliclona transcriptomes indicated that sponges also possess similar genes. An exhaustive analysis of publicly available sequencing data from other sponges showed that this is a potentially widespread feature of the Porifera. While many sponge proteins possess a sequence similarity of 27.70–59.06% to actinoporins, they show consistency in predicted structure. One gene copy from H. indistincta has significant sequence similarity to sea anemone actinoporins and possesses conserved residues associated with the fundamental roles of sphingomyelin recognition, membrane attachment, oligomerization, and pore formation, indicating that it may be an actinoporin. Phylogenetic analyses indicate frequent gene duplication, no distinct clade for sponge-derived proteins, and a stronger signal towards actinoporins than similar proteins from other phyla. Overall, this study provides evidence that a diverse array of Porifera represents a novel source of actinoporin-like proteins which may have biotechnological and pharmaceutical applications.
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Vernale A, Prünster MM, Marchianò F, Debost H, Brouilly N, Rocher C, Massey-Harroche D, Renard E, Le Bivic A, Habermann BH, Borchiellini C. Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis. BMC Ecol Evol 2021; 21:160. [PMID: 34418961 PMCID: PMC8380372 DOI: 10.1186/s12862-021-01866-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/18/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The ancestral presence of epithelia in Metazoa is no longer debated. Porifera seem to be one of the best candidates to be the sister group to all other Metazoa. This makes them a key taxon to explore cell-adhesion evolution on animals. For this reason, several transcriptomic, genomic, histological, physiological and biochemical studies focused on sponge epithelia. Nevertheless, the complete and precise protein composition of cell-cell junctions and mechanisms that regulate epithelial morphogenetic processes still remain at the center of attention. RESULTS To get insights into the early evolution of epithelial morphogenesis, we focused on morphogenic characteristics of the homoscleromorph sponge Oscarella lobularis. Homoscleromorpha are a sponge class with a typical basement membrane and adhaerens-like junctions unknown in other sponge classes. We took advantage of the dynamic context provided by cell dissociation-reaggregation experiments to explore morphogenetic processes in epithelial cells in a non-bilaterian lineage by combining fluorescent and electron microscopy observations and RNA sequencing approaches at key time-points of the dissociation and reaggregation processes. CONCLUSIONS Our results show that part of the molecular toolkit involved in the loss and restoration of epithelial features such as cell-cell and cell-matrix adhesion is conserved between Homoscleromorpha and Bilateria, suggesting their common role in the last common ancestor of animals. In addition, sponge-specific genes are differently expressed during the dissociation and reaggregation processes, calling for future functional characterization of these genes.
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Affiliation(s)
- Amélie Vernale
- Aix Marseille Univ, CNRS, IRD, IMBE UMR 7263, Avignon Université, Institut Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale, Station Marine d'Endoume, Marseille, France
- Aix Marseille Univ, CNRS, UMR 7288, Developmental Biology Institute of Marseille Luminy (IBDM), Marseille, France
| | - Maria Mandela Prünster
- Aix Marseille Univ, CNRS, UMR 7288, Developmental Biology Institute of Marseille Luminy (IBDM), Marseille, France
- Aix Marseille Univ, CNRS, UMR 7288, Developmental Biology Institute of Marseille Luminy (IBDM), Turing Center for Living Systems (CENTURI), Marseille, France
| | - Fabio Marchianò
- Aix Marseille Univ, CNRS, UMR 7288, Developmental Biology Institute of Marseille Luminy (IBDM), Turing Center for Living Systems (CENTURI), Marseille, France
| | - Henry Debost
- Aix Marseille Univ, CNRS, UMR 7288, Developmental Biology Institute of Marseille Luminy (IBDM), Marseille, France
| | - Nicolas Brouilly
- Aix Marseille Univ, CNRS, UMR 7288, Developmental Biology Institute of Marseille Luminy (IBDM), Marseille, France
| | - Caroline Rocher
- Aix Marseille Univ, CNRS, IRD, IMBE UMR 7263, Avignon Université, Institut Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale, Station Marine d'Endoume, Marseille, France
| | - Dominique Massey-Harroche
- Aix Marseille Univ, CNRS, UMR 7288, Developmental Biology Institute of Marseille Luminy (IBDM), Marseille, France
| | - Emmanuelle Renard
- Aix Marseille Univ, CNRS, IRD, IMBE UMR 7263, Avignon Université, Institut Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale, Station Marine d'Endoume, Marseille, France
- Aix Marseille Univ, CNRS, UMR 7288, Developmental Biology Institute of Marseille Luminy (IBDM), Marseille, France
| | - André Le Bivic
- Aix Marseille Univ, CNRS, UMR 7288, Developmental Biology Institute of Marseille Luminy (IBDM), Marseille, France
| | - Bianca H Habermann
- Aix Marseille Univ, CNRS, UMR 7288, Developmental Biology Institute of Marseille Luminy (IBDM), Marseille, France.
- Aix Marseille Univ, CNRS, UMR 7288, Developmental Biology Institute of Marseille Luminy (IBDM), Turing Center for Living Systems (CENTURI), Marseille, France.
| | - Carole Borchiellini
- Aix Marseille Univ, CNRS, IRD, IMBE UMR 7263, Avignon Université, Institut Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale, Station Marine d'Endoume, Marseille, France.
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Conservative and Atypical Ferritins of Sponges. Int J Mol Sci 2021; 22:ijms22168635. [PMID: 34445356 PMCID: PMC8395497 DOI: 10.3390/ijms22168635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 08/05/2021] [Accepted: 08/07/2021] [Indexed: 12/26/2022] Open
Abstract
Ferritins comprise a conservative family of proteins found in all species and play an essential role in resistance to redox stress, immune response, and cell differentiation. Sponges (Porifera) are the oldest Metazoa that show unique plasticity and regenerative potential. Here, we characterize the ferritins of two cold-water sponges using proteomics, spectral microscopy, and bioinformatic analysis. The recently duplicated conservative HdF1a/b and atypical HdF2 genes were found in the Halisarca dujardini genome. Multiple related transcripts of HpF1 were identified in the Halichondria panicea transcriptome. Expression of HdF1a/b was much higher than that of HdF2 in all annual seasons and regulated differently during the sponge dissociation/reaggregation. The presence of the MRE and HRE motifs in the HdF1 and HdF2 promotor regions and the IRE motif in mRNAs of HdF1 and HpF indicates that sponge ferritins expression depends on the cellular iron and oxygen levels. The gel electrophoresis combined with specific staining and mass spectrometry confirmed the presence of ferric ions and ferritins in multi-subunit complexes. The 3D modeling predicts the iron-binding capacity of HdF1 and HpF1 at the ferroxidase center and the absence of iron-binding in atypical HdF2. Interestingly, atypical ferritins lacking iron-binding capacity were found in genomes of many invertebrate species. Their function deserves further research.
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Ballarin L, Karahan A, Salvetti A, Rossi L, Manni L, Rinkevich B, Rosner A, Voskoboynik A, Rosental B, Canesi L, Anselmi C, Pinsino A, Tohumcu BE, Jemec Kokalj A, Dolar A, Novak S, Sugni M, Corsi I, Drobne D. Stem Cells and Innate Immunity in Aquatic Invertebrates: Bridging Two Seemingly Disparate Disciplines for New Discoveries in Biology. Front Immunol 2021; 12:688106. [PMID: 34276677 PMCID: PMC8278520 DOI: 10.3389/fimmu.2021.688106] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/31/2021] [Indexed: 12/12/2022] Open
Abstract
The scopes related to the interplay between stem cells and the immune system are broad and range from the basic understanding of organism's physiology and ecology to translational studies, further contributing to (eco)toxicology, biotechnology, and medicine as well as regulatory and ethical aspects. Stem cells originate immune cells through hematopoiesis, and the interplay between the two cell types is required in processes like regeneration. In addition, stem and immune cell anomalies directly affect the organism's functions, its ability to cope with environmental changes and, indirectly, its role in ecosystem services. However, stem cells and immune cells continue to be considered parts of two branches of biological research with few interconnections between them. This review aims to bridge these two seemingly disparate disciplines towards much more integrative and transformative approaches with examples deriving mainly from aquatic invertebrates. We discuss the current understanding of cross-disciplinary collaborative and emerging issues, raising novel hypotheses and comments. We also discuss the problems and perspectives of the two disciplines and how to integrate their conceptual frameworks to address basic equations in biology in a new, innovative way.
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Affiliation(s)
| | - Arzu Karahan
- Middle East Technical University, Institute of Marine Sciences, Erdemli, Mersin, Turkey
| | - Alessandra Salvetti
- Department of Clinical and Experimental Medicine, Unit of Experimental Biology and Genetics, University of Pisa, Pisa, Italy
| | - Leonardo Rossi
- Department of Clinical and Experimental Medicine, Unit of Experimental Biology and Genetics, University of Pisa, Pisa, Italy
| | - Lucia Manni
- Department of Biology, University of Padua, Padua, Italy
| | - Baruch Rinkevich
- Department of Biology, Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Amalia Rosner
- Department of Biology, Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Ayelet Voskoboynik
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, United States
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA, United States
- Department of Biology, Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Benyamin Rosental
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Center for Regenerative Medicine and Stem Cells, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Laura Canesi
- Department of Earth Environment and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | - Chiara Anselmi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, United States
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA, United States
| | - Annalisa Pinsino
- Institute for Biomedical Research and Innovation, National Research Council, Palermo, Italy
| | - Begüm Ece Tohumcu
- Middle East Technical University, Institute of Marine Sciences, Erdemli, Mersin, Turkey
| | - Anita Jemec Kokalj
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Andraž Dolar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Sara Novak
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Ilaria Corsi
- Department of Physical, Earth and Environmental Sciences, University of Siena, Siena, Italy
| | - Damjana Drobne
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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Pozdnyakov I, Agniya S, Sergey K, César R, Thierry P, Irina E, Alexander E. Morphological variability of choanocyte kinetids supports a novel systematic division within Oscarellidae (Porifera, Homoscleromorpha). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Igor Pozdnyakov
- Zoological Institute of Russian Academy of Sciences St. Petersburg Russia
| | - Sokolova Agniya
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences Moscow Russia
| | - Karpov Sergey
- Zoological Institute of Russian Academy of Sciences St. Petersburg Russia
- Department of Invertebrate Zoology Biological Faculty St. Petersburg State University St. Petersburg Russia
| | - Ruiz César
- Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE) Aix Marseille UniversityCNRSIRDAvignon UniversityStation marine d'Endoume Marseille France
| | - Pérez Thierry
- Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE) Aix Marseille UniversityCNRSIRDAvignon UniversityStation marine d'Endoume Marseille France
| | - Ekimova Irina
- Department of Invertebrate Zoology Lomonosov Moscow State University Moscow Russia
| | - Ereskovsky Alexander
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences Moscow Russia
- Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE) Aix Marseille UniversityCNRSIRDAvignon UniversityStation marine d'Endoume Marseille France
- Department of Embryology Biological Faculty St. Petersburg State University St. Petersburg Russia
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8
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Naumann B, Burkhardt P. Spatial Cell Disparity in the Colonial Choanoflagellate Salpingoeca rosetta. Front Cell Dev Biol 2019; 7:231. [PMID: 31681764 PMCID: PMC6803389 DOI: 10.3389/fcell.2019.00231] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/26/2019] [Indexed: 11/13/2022] Open
Abstract
Choanoflagellates are the closest unicellular relatives of animals (Metazoa). These tiny protists display complex life histories that include sessile as well as different pelagic stages. Some choanoflagellates have the ability to form colonies as well. Up until recently, these colonies have been described to consist of mostly identical cells showing no spatial cell differentiation, which supported the traditional view that spatial cell differentiation, leading to the co-existence of specific cell types in animals, evolved after the split of the last common ancestor of the Choanoflagellata and Metazoa. The recent discovery of single cells in colonies of the choanoflagellate Salpingoeca rosetta that exhibit unique cell morphologies challenges this traditional view. We have now reanalyzed TEM serial sections, aiming to determine the degree of similarity of S. rosetta cells within a rosette colony. We investigated cell morphologies and nuclear, mitochondrial, and food vacuole volumes of 40 individual cells from four different S. rosetta rosette colonies and compared our findings to sponge choanocytes. Our analysis shows that cells in a choanoflagellate colony differ from each other in respect to cell morphology and content ratios of nuclei, mitochondria, and food vacuoles. Furthermore, cell disparity within S. rosetta colonies is slightly higher compared to cell disparity within sponge choanocytes. Moreover, we discovered the presence of plasma membrane contacts between colonial cells in addition to already described intercellular bridges and filo-/pseudopodial contacts. Our findings indicate that the last common ancestor of Choanoflagellata and Metazoa might have possessed plasma membrane contacts and spatial cell disparity during colonial life history stages.
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Affiliation(s)
- Benjamin Naumann
- Institute of Zoology and Evolutionary Research, Friedrich Schiller University Jena, Jena, Germany
| | - Pawel Burkhardt
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
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9
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The architecture of cell differentiation in choanoflagellates and sponge choanocytes. PLoS Biol 2019; 17:e3000226. [PMID: 30978201 PMCID: PMC6481868 DOI: 10.1371/journal.pbio.3000226] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 04/24/2019] [Accepted: 03/27/2019] [Indexed: 11/19/2022] Open
Abstract
Although collar cells are conserved across animals and their closest relatives, the choanoflagellates, little is known about their ancestry, their subcellular architecture, or how they differentiate. The choanoflagellate Salpingoeca rosetta expresses genes necessary for animal development and can alternate between unicellular and multicellular states, making it a powerful model for investigating the origin of animal multicellularity and mechanisms underlying cell differentiation. To compare the subcellular architecture of solitary collar cells in S. rosetta with that of multicellular ‘rosette’ colonies and collar cells in sponges, we reconstructed entire cells in 3D through transmission electron microscopy on serial ultrathin sections. Structural analysis of our 3D reconstructions revealed important differences between single and colonial choanoflagellate cells, with colonial cells exhibiting a more amoeboid morphology consistent with higher levels of macropinocytotic activity. Comparison of multiple reconstructed rosette colonies highlighted the variable nature of cell sizes, cell–cell contact networks, and colony arrangement. Importantly, we uncovered the presence of elongated cells in some rosette colonies that likely represent a distinct and differentiated cell type, pointing toward spatial cell differentiation. Intercellular bridges within choanoflagellate colonies displayed a variety of morphologies and connected some but not all neighbouring cells. Reconstruction of sponge choanocytes revealed ultrastructural commonalities but also differences in major organelle composition in comparison to choanoflagellates. Together, our comparative reconstructions uncover the architecture of cell differentiation in choanoflagellates and sponge choanocytes and constitute an important step in reconstructing the cell biology of the last common ancestor of animals. 3D electron microscopy of choanoflagellates and sponge choanocytes reveals a remarkable variety of cell architecture and suggests that cell type differentiation may have been present in the stem lineage leading to the animals. Choanoflagellates are microscopic aquatic organisms that can alternate between single-celled and multicellular states, and sequencing of their genomes has revealed that choanoflagellates are the closest single-celled relatives of animals. Moreover, choanoflagellates are a form of ‘collar cell’—a cell type crowned by an array of finger-like microvilli and a single, whip-like flagellum. This cell type is also found throughout the animal kingdom; therefore, studying the structure of the choanoflagellate collar cell can shed light on how this cell type and animal multicellularity might have evolved. We used electron microscopy to reconstruct in 3D the total subcellular composition of single-celled and multicellular choanoflagellates as well as the collar cells from a marine sponge, which represents an early-branching animal lineage. We found differences between single-celled and multicellular choanoflagellates in structures associated with cellular energetics, membrane trafficking, and cell morphology. Likewise, we describe a complex system of cell–cell connections associated with multicellular choanoflagellates. Finally, comparison of choanoflagellates and sponge collar cells revealed subcellular differences associated with feeding and cellular energetics. Taken together, this study is an important step forward in reconstructing the biology of the last common ancestor of the animals.
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Schippers KJ, Nichols SA. Evidence of Signaling and Adhesion Roles for β-Catenin in the Sponge Ephydatia muelleri. Mol Biol Evol 2019. [PMID: 29522209 DOI: 10.1093/molbev/msy033] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
β-Catenin acts as a transcriptional coactivator in the Wnt/β-catenin signaling pathway and a cytoplasmic effector in cadherin-based cell adhesion. These functions are ancient within animals, but the earliest steps in β-catenin evolution remain unresolved due to limited data from key lineages-sponges, ctenophores, and placozoans. Previous studies in sponges have characterized β-catenin expression dynamics and used GSK3B antagonists to ectopically activate the Wnt/β-catenin pathway; both approaches rely upon untested assumptions about the conservation of β-catenin function and regulation in sponges. Here, we test these assumptions using an antibody raised against β-catenin from the sponge Ephydatia muelleri. We find that cadherin-complex genes coprecipitate with endogenous Em β-catenin from cell lysates, but that Wnt pathway components do not. However, through immunostaining we detect both cell boundary and nuclear populations, and we find evidence that Em β-catenin is a conserved substrate of GSK3B. Collectively, these data support conserved roles for Em β-catenin in both cell adhesion and Wnt signaling. Additionally, we find evidence for an Em β-catenin population associated with the distal ends of F-actin stress fibers in apparent cell-substrate adhesion structures that resemble focal adhesions. This finding suggests a fundamental difference in the adhesion properties of sponge tissues relative to other animals, in which the adhesion functions of β-catenin are typically restricted to cell-cell adhesions.
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Affiliation(s)
| | - Scott A Nichols
- Department of Biological Sciences, University of Denver, Denver, CO
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Muricy G, Domingos C, Lage A, Lanna E, Hardoim CCP, Laport MS, Zilberberg C. Integrative taxonomy widens our knowledge of the diversity, distribution and biology of the genus Plakina (Homosclerophorida: Plakinidae). INVERTEBR SYST 2019. [DOI: 10.1071/is18027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Despite the evolutionary significance of Homoscleromorpha, their diversity and biology are largely unknown. Here we integrate data of morphology, cytology, microbiology, ecology, reproduction, and mitochondrial cox-1 and cob gene sequences to resolve a complex of sympatric species of Plakina in South-eastern Brazil. All datasets congruently supported the delimitation of three species, two of which are new to science. Plakina coerulea has its distribution extended from one locality to over 2360 km wide. Plakina cabofriense, sp. nov. also occurs in North-eastern Brazil. Plakina cyanorosea, sp. nov. occurs only in a single, small tide pool and may be critically endangered. Plakina cyanorosea, sp. nov. produces conspicuous, abundant larvae useful for laboratory investigations. A thin, bright orange organic coat covers some spicules of P. cabofriense, sp. nov. and P. cyanorosea, sp. nov. The three Plakina species harbour diverse microbial symbiont communities, including previously unknown morphologies. Molecular phylogenies and barcoding gaps based on cox-1 and cob sequences supported that each species is monophyletic and distinct from other congeners. The genus Plakina is paraphyletic and strongly needs redefinition. The integrative approach provides new data that widens our knowledge of Homoscleromorpha diversity, distribution and biology.
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Muthye V, Lavrov DV. Characterization of mitochondrial proteomes of nonbilaterian animals. IUBMB Life 2018; 70:1289-1301. [PMID: 30419142 DOI: 10.1002/iub.1961] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/08/2018] [Accepted: 09/29/2018] [Indexed: 12/18/2022]
Abstract
Mitochondria require ~1,500 proteins for their maintenance and proper functionality, which constitute the mitochondrial proteome (mt-proteome). Although a few of these proteins, mostly subunits of the electron transport chain complexes, are encoded in mitochondrial DNA (mtDNA), the vast majority are encoded in the nuclear genome and imported to the organelle. Previous studies have shown a continuous and complex evolution of mt-proteome among eukaryotes. However, there was less attention paid to mt-proteome evolution within Metazoa, presumably because animal mtDNA and, by extension, animal mitochondria are often considered to be uniform. In this analysis, two bioinformatic approaches (Orthologue-detection and Mitochondrial Targeting Sequence prediction) were used to identify mt-proteins in 23 species from four nonbilaterian phyla: Cnidaria, Ctenophora, Placozoa, and Porifera, as well as two choanoflagellates, the closest animal relatives. Our results revealed a large variation in mt-proteome in nonbilaterian animals in size and composition. Myxozoans, highly reduced cnidarian parasites, possessed the smallest inferred mitochondrial proteomes, while calcareous sponges possessed the largest. About 513 mitochondrial orthologous groups were present in all nonbilaterian phyla and human. Interestingly, 42 human mitochondrial proteins were not identified in any nonbilaterian species studied and represent putative innovations along the bilaterian branch. Several of these proteins were involved in apoptosis and innate immunity, two processes known to evolve within Metazoa. Conversely, several proteins identified as mitochondrial in nonbilaterian phyla and animal outgroups were absent in human, representing cases of possible loss. Finally, a few human cytosolic proteins, such as histones and cytosolic ribosomal proteins, were predicted to be targeted to mitochondria in nonbilaterian animals. Overall, our analysis provides the first step in characterization of mt-proteomes in nonbilaterian animals and understanding evolution of animal mt-proteome. © 2018 IUBMB Life, 70(12):1289-1301, 2018.
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Affiliation(s)
- Viraj Muthye
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Dennis V Lavrov
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
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Dnyansagar R, Zimmermann B, Moran Y, Praher D, Sundberg P, Møller LF, Technau U. Dispersal and speciation: The cross Atlantic relationship of two parasitic cnidarians. Mol Phylogenet Evol 2018; 126:346-355. [PMID: 29702219 DOI: 10.1016/j.ympev.2018.04.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 03/12/2018] [Accepted: 04/23/2018] [Indexed: 01/11/2023]
Affiliation(s)
- Rohit Dnyansagar
- Department of Molecular Evolution and Development, University of Vienna, Austria
| | - Bob Zimmermann
- Department of Molecular Evolution and Development, University of Vienna, Austria
| | - Yehu Moran
- Department of Molecular Evolution and Development, University of Vienna, Austria; Department of Ecology, Evolution and Behavior, Hebrew University of Jerusalem, Israel
| | - Daniela Praher
- Department of Molecular Evolution and Development, University of Vienna, Austria
| | - Per Sundberg
- Department of Marine Sciences, University of Gothenburg, Sweden
| | - Lene Friis Møller
- Danish Shellfish Centre, DTU Aqua, Technical University of Denmark, Denmark
| | - Ulrich Technau
- Department of Molecular Evolution and Development, University of Vienna, Austria.
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Renard E, Leys SP, Wörheide G, Borchiellini C. Understanding Animal Evolution: The Added Value of Sponge Transcriptomics and Genomics: The disconnect between gene content and body plan evolution. Bioessays 2018; 40:e1700237. [PMID: 30070368 DOI: 10.1002/bies.201700237] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 06/22/2018] [Indexed: 02/06/2023]
Abstract
Sponges are important but often-neglected organisms. The absence of classical animal traits (nerves, digestive tract, and muscles) makes sponges challenging for non-specialists to work with and has delayed getting high quality genomic data compared to other invertebrates. Yet analyses of sponge genomes and transcriptomes currently available have radically changed our understanding of animal evolution. Sponges are of prime evolutionary importance as one of the best candidates to form the sister group of all other animals, and genomic data are essential to understand the mechanisms that control animal evolution and diversity. Here we review the most significant outcomes of current genomic and transcriptomic analyses of sponges, and discuss limitations and future directions of sponge transcriptomic and genomic studies.
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Affiliation(s)
- Emmanuelle Renard
- Aix Marseille Univ., Univ Avignon, CNRS, IRD, UMR 7263, Mediterranean Institute of Marine and Continental Biodiversity and Ecology (IMBE), Station Marine d'Endoume, Marseille, France.,Aix Marseille Univ., CNRS, UMR 7288, IBDM, Marseille, France
| | - Sally P Leys
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany.,Bavarian State Collection for Paleontology and Geology, Munich, Germany
| | - Carole Borchiellini
- Aix Marseille Univ., Univ Avignon, CNRS, IRD, UMR 7263, Mediterranean Institute of Marine and Continental Biodiversity and Ecology (IMBE), Station Marine d'Endoume, Marseille, France
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Miller PW, Pokutta S, Mitchell JM, Chodaparambil JV, Clarke DN, Nelson WJ, Weis WI, Nichols SA. Analysis of a vinculin homolog in a sponge (phylum Porifera) reveals that vertebrate-like cell adhesions emerged early in animal evolution. J Biol Chem 2018; 293:11674-11686. [PMID: 29880641 PMCID: PMC6066325 DOI: 10.1074/jbc.ra117.001325] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 05/21/2018] [Indexed: 01/27/2023] Open
Abstract
The evolution of cell-adhesion mechanisms in animals facilitated the assembly of organized multicellular tissues. Studies in traditional animal models have revealed two predominant adhesion structures, the adherens junction (AJ) and focal adhesions (FAs), which are involved in the attachment of neighboring cells to each other and to the secreted extracellular matrix (ECM), respectively. The AJ (containing cadherins and catenins) and FAs (comprising integrins, talin, and paxillin) differ in protein composition, but both junctions contain the actin-binding protein vinculin. The near ubiquity of these structures in animals suggests that AJ and FAs evolved early, possibly coincident with multicellularity. However, a challenge to this perspective is that previous studies of sponges-a divergent animal lineage-indicate that their tissues are organized primarily by an alternative, sponge-specific cell-adhesion mechanism called "aggregation factor." In this study, we examined the structure, biochemical properties, and tissue localization of a vinculin ortholog in the sponge Oscarella pearsei (Op). Our results indicate that Op vinculin localizes to both cell-cell and cell-ECM contacts and has biochemical and structural properties similar to those of vertebrate vinculin. We propose that Op vinculin played a role in cell adhesion and tissue organization in the last common ancestor of sponges and other animals. These findings provide compelling evidence that sponge tissues are indeed organized like epithelia in other animals and support the notion that AJ- and FA-like structures extend to the earliest periods of animal evolution.
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Affiliation(s)
| | - Sabine Pokutta
- From the Departments of Molecular and Cellular Physiology and
- Structural Biology, School of Medicine and
| | - Jennyfer M Mitchell
- the Department of Biological Sciences, University of Denver, Denver, Colorado 80208
| | - Jayanth V Chodaparambil
- From the Departments of Molecular and Cellular Physiology and
- Structural Biology, School of Medicine and
| | - D Nathaniel Clarke
- the Department of Biology, Stanford University, Stanford, California 94305 and
| | - W James Nelson
- From the Departments of Molecular and Cellular Physiology and
- the Department of Biology, Stanford University, Stanford, California 94305 and
| | - William I Weis
- From the Departments of Molecular and Cellular Physiology and
- Structural Biology, School of Medicine and
| | - Scott A Nichols
- the Department of Biological Sciences, University of Denver, Denver, Colorado 80208
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