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Cole AG, Steger J, Hagauer J, Denner A, Ferrer Murguia P, Knabl P, Narayanaswamy S, Wick B, Montenegro JD, Technau U. Updated single cell reference atlas for the starlet anemone Nematostella vectensis. Front Zool 2024; 21:8. [PMID: 38500146 PMCID: PMC10946136 DOI: 10.1186/s12983-024-00529-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/08/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND The recent combination of genomics and single cell transcriptomics has allowed to assess a variety of non-conventional model organisms in much more depth. Single cell transcriptomes can uncover hidden cellular complexity and cell lineage relationships within organisms. The recent developmental cell atlases of the sea anemone Nematostella vectensis, a representative of the basally branching Cnidaria, has provided new insights into the development of all cell types (Steger et al Cell Rep 40(12):111370, 2022; Sebé-Pedrós et al. Cell 173(6):1520-1534.e20). However, the mapping of the single cell reads still suffers from relatively poor gene annotations and a draft genome consisting of many scaffolds. RESULTS Here we present a new wildtype resource of the developmental single cell atlas, by re-mapping of sequence data first published in Steger et al. (2022) and Cole et al. (Nat Commun 14(1):1747, 2023), to the new chromosome-level genome assembly and corresponding gene models in Zimmermann et al. (Nat Commun 14, 8270 (2023). https://doi.org/10.1038/s41467-023-44080-7 ). We expand the pre-existing dataset through the incorporation of additional sequence data derived from the capture and sequencing of cell suspensions from four additional samples: 24 h gastrula, 2d planula, an inter-parietal region of the bodywall from a young unsexed animal, and another adult mesentery from a mature male animal. CONCLUSION Our analyses of the full cell-state inventory provide transcriptomic signatures for 127 distinct cell states, of which 47 correspond to neuroglandular subtypes. We also identify two distinct putatively immune-related transcriptomic profiles that segregate between the inner and outer cell layers. Furthermore, the new gene annotation Nv2 has markedly improved the mapping on the single cell transcriptome data and will therefore be of great value for the community and anyone using the dataset.
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Affiliation(s)
- Alison G Cole
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
- Research Platform Single Cell Regulation of Stem Cells, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Julia Steger
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Julia Hagauer
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Andreas Denner
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Patricio Ferrer Murguia
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Paul Knabl
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Sanjay Narayanaswamy
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Brittney Wick
- UCSC Cellbrowser, University of California, Santa Cruz, USA
| | - Juan D Montenegro
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Ulrich Technau
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
- Research Platform Single Cell Regulation of Stem Cells, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
- Max Perutz Labs, University of Vienna, Dr. Bohrgasse 9, 1090, Vienna, Austria.
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2
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Mörsdorf D, Knabl P, Genikhovich G. Highly conserved and extremely evolvable: BMP signalling in secondary axis patterning of Cnidaria and Bilateria. Dev Genes Evol 2024:10.1007/s00427-024-00714-4. [PMID: 38472535 DOI: 10.1007/s00427-024-00714-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/06/2024] [Indexed: 03/14/2024]
Abstract
Bilateria encompass the vast majority of the animal phyla. As the name states, they are bilaterally symmetric, that is with a morphologically clear main body axis connecting their anterior and posterior ends, a second axis running between their dorsal and ventral surfaces, and with a left side being roughly a mirror image of their right side. Bone morphogenetic protein (BMP) signalling has widely conserved functions in the formation and patterning of the second, dorso-ventral (DV) body axis, albeit to different extents in different bilaterian species. Whilst initial findings in the fruit fly Drosophila and the frog Xenopus highlighted similarities amongst these evolutionarily very distant species, more recent analyses featuring other models revealed considerable diversity in the mechanisms underlying dorsoventral patterning. In fact, as phylogenetic sampling becomes broader, we find that this axis patterning system is so evolvable that even its core components can be deployed differently or lost in different model organisms. In this review, we will try to highlight the diversity of ways by which BMP signalling controls bilaterality in different animals, some of which do not belong to Bilateria. Future research combining functional analyses and modelling is bound to give us some understanding as to where the limits to the extent of the evolvability of BMP-dependent axial patterning may lie.
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Affiliation(s)
- David Mörsdorf
- Dept. Neurosciences and Developmental Biology, University of Vienna, UBB, Djerassiplatz 1, 1030, Vienna, Austria
| | - Paul Knabl
- Dept. Neurosciences and Developmental Biology, University of Vienna, UBB, Djerassiplatz 1, 1030, Vienna, Austria
- Vienna Doctoral School of Ecology and Evolution (VDSEE), University of Vienna, Vienna, Austria
| | - Grigory Genikhovich
- Dept. Neurosciences and Developmental Biology, University of Vienna, UBB, Djerassiplatz 1, 1030, Vienna, Austria.
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3
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Knabl P, Schauer A, Pomreinke AP, Zimmermann B, Rogers KW, Čapek D, Müller P, Genikhovich G. Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. eLife 2024; 13:e80803. [PMID: 38323609 PMCID: PMC10849676 DOI: 10.7554/elife.80803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 01/28/2024] [Indexed: 02/08/2024] Open
Abstract
BMP signaling has a conserved function in patterning the dorsal-ventral body axis in Bilateria and the directive axis in anthozoan cnidarians. So far, cnidarian studies have focused on the role of different BMP signaling network components in regulating pSMAD1/5 gradient formation. Much less is known about the target genes downstream of BMP signaling. To address this, we generated a genome-wide list of direct pSMAD1/5 target genes in the anthozoan Nematostella vectensis, several of which were conserved in Drosophila and Xenopus. Our ChIP-seq analysis revealed that many of the regulatory molecules with documented bilaterally symmetric expression in Nematostella are directly controlled by BMP signaling. We identified several so far uncharacterized BMP-dependent transcription factors and signaling molecules, whose bilaterally symmetric expression may be indicative of their involvement in secondary axis patterning. One of these molecules is zswim4-6, which encodes a novel nuclear protein that can modulate the pSMAD1/5 gradient and potentially promote BMP-dependent gene repression.
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Affiliation(s)
- Paul Knabl
- Department of Neurosciences and Developmental Biology, University of ViennaViennaAustria
- Vienna Doctoral School of Ecology and Evolution (VDSEE), University of ViennaViennaAustria
| | - Alexandra Schauer
- Department of Neurosciences and Developmental Biology, University of ViennaViennaAustria
| | | | - Bob Zimmermann
- Department of Neurosciences and Developmental Biology, University of ViennaViennaAustria
| | | | | | - Patrick Müller
- Friedrich Miescher Laboratory of the Max Planck SocietyTübingenGermany
- University of KonstanzKonstanzGermany
| | - Grigory Genikhovich
- Department of Neurosciences and Developmental Biology, University of ViennaViennaAustria
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4
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Gautam S, Fenner JL, Wang B, Range RC. Evolutionarily conserved Wnt/Sp5 signaling is critical for anterior-posterior axis patterning in sea urchin embryos. iScience 2024; 27:108616. [PMID: 38179064 PMCID: PMC10765061 DOI: 10.1016/j.isci.2023.108616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/30/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Studies across a diverse group of metazoan embryos indicate that Wnt signaling often activates the transcription factor Sp5, forming a signaling 'cassette' that plays critical roles in many developmental processes. This study explores the role of Wnt/Sp5 signaling during the specification and patterning of the primary germ layers during early anterior-posterior axis formation in the deuterostome sea urchin embryo. Our functional analyses show that Sp5 is critical for endomesoderm specification downstream of Wnt/β-catenin in posterior cells as well as anterior neuroectoderm patterning downstream of non-canonical Wnt/JNK signaling in anterior cells. Interestingly, expression and functional data comparisons show that Wnt/Sp5 signaling often plays similar roles in posterior endomesoderm as well as neuroectoderm patterning along the AP axis of several deuterostome embryos, including vertebrates. Thus, our findings provide strong support for the idea that Wnt-Sp5 signaling cassettes were critical for the establishment of early germ layers in the common deuterostome ancestor.
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Affiliation(s)
- Sujan Gautam
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Jennifer L. Fenner
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Boyuan Wang
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Ryan C. Range
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
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5
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Gilbert E, Craggs J, Modepalli V. Gene Regulatory Network that Shaped the Evolution of Larval Apical Organ in Cnidaria. Mol Biol Evol 2024; 41:msad285. [PMID: 38152864 PMCID: PMC10781443 DOI: 10.1093/molbev/msad285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/24/2023] [Accepted: 12/21/2023] [Indexed: 12/29/2023] Open
Abstract
Among non-bilaterian animals, a larval apical sensory organ with integrated neurons is only found in cnidarians. Within cnidarians, an apical organ with a ciliary tuft is mainly found in Actiniaria. Whether this apical tuft has evolved independently in Actiniaria or alternatively originated in the common ancestor of Cnidaria and Bilateria and was lost in specific groups is uncertain. To test this hypothesis, we generated transcriptomes of the apical domain during the planula stage of four species representing three key groups of cnidarians: Aurelia aurita (Scyphozoa), Nematostella vectensis (Actiniaria), and Acropora millepora and Acropora tenuis (Scleractinia). We showed that the canonical genes implicated in patterning the apical domain of N. vectensis are largely absent in A. aurita. In contrast, the apical domain of the scleractinian planula shares gene expression pattern with N. vectensis. By comparing the larval single-cell transcriptomes, we revealed the apical organ cell type of Scleractinia and confirmed its homology to Actiniaria. However, Fgfa2, a vital regulator of the regionalization of the N. vectensis apical organ, is absent in the scleractinian genome. Likewise, we found that FoxJ1 and 245 genes associated with cilia are exclusively expressed in the N. vectensis apical domain, which is in line with the presence of ciliary apical tuft in Actiniaria and its absence in Scleractinia and Scyphozoa. Our findings suggest that the common ancestor of cnidarians lacked a ciliary apical tuft, and it could have evolved independently in the Actiniaria.
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Affiliation(s)
- Eleanor Gilbert
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Jamie Craggs
- Horniman Museum and Gardens, London SE23 3PQ, UK
| | - Vengamanaidu Modepalli
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
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6
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Mańko MK, Munro C, Leclère L. Establishing Bilateral Symmetry in Hydrozoan Planula Larvae, a Review of Siphonophore Early Development. Integr Comp Biol 2023; 63:975-989. [PMID: 37353930 DOI: 10.1093/icb/icad081] [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: 02/28/2023] [Revised: 06/02/2023] [Accepted: 06/11/2023] [Indexed: 06/25/2023] Open
Abstract
Siphonophores are colonial hydrozoans, characterized by complex colony organization and unparalleled zooid functional specialization. Recent genomic studies have offered an evolutionary perspective on how this morphological complexity arose, but a molecular characterization of symmetry breaking in siphonophore embryonic development is still largely missing. Here, bringing together historical data on early development with new immunohistochemical data, we review the diversity of developmental trajectories that lead to the formation of bilaterally symmetric planula larvae in siphonophores. Embryonic development, up to the planula stage, is remarkably similar across siphonophore phylogeny. Then, with the appearance of the lateral endodermal thickening (= ventral endoderm), larval development diverges between taxa, differing in the location and patterning of the primary buds, chronology of budding, establishment of growth zones, and retention of larval zooids. Our work also uncovers a number of open questions in siphonophore development, including homology of different zooids, mechanisms underlying formation and maintenance of spatially restricted growth zone(s), and molecular factors establishing a secondary dorsal-ventral axis in planulae. By discussing siphonophore development and body axes within the broader cnidarian context, we then set the framework for future work on siphonophores, which is finally achievable with the advent of culturing methods.
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Affiliation(s)
- Maciej K Mańko
- Laboratory of Plankton Biology, Department of Marine Biology and Biotechnology, University of Gdańsk, Gdynia, 81-378, Poland
| | - Catriona Munro
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, 75005, France
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Villefranche-sur-Mer, 06230, France
| | - Lucas Leclère
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Villefranche-sur-Mer, 06230, France
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Banyuls-sur-Mer, 66650, France
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7
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Vetrova AA, Kupaeva DM, Kizenko A, Lebedeva TS, Walentek P, Tsikolia N, Kremnyov SV. The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Sci Rep 2023; 13:9382. [PMID: 37296138 PMCID: PMC10256749 DOI: 10.1038/s41598-023-35979-8] [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: 01/20/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Brachyury, a member of T-box gene family, is widely known for its major role in mesoderm specification in bilaterians. It is also present in non-bilaterian metazoans, such as cnidarians, where it acts as a component of an axial patterning system. In this study, we present a phylogenetic analysis of Brachyury genes within phylum Cnidaria, investigate differential expression and address a functional framework of Brachyury paralogs in hydrozoan Dynamena pumila. Our analysis indicates two duplication events of Brachyury within the cnidarian lineage. The first duplication likely appeared in the medusozoan ancestor, resulting in two copies in medusozoans, while the second duplication arose in the hydrozoan ancestor, resulting in three copies in hydrozoans. Brachyury1 and 2 display a conservative expression pattern marking the oral pole of the body axis in D. pumila. On the contrary, Brachyury3 expression was detected in scattered presumably nerve cells of the D. pumila larva. Pharmacological modulations indicated that Brachyury3 is not under regulation of cWnt signaling in contrast to the other two Brachyury genes. Divergence in expression patterns and regulation suggest neofunctionalization of Brachyury3 in hydrozoans.
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Affiliation(s)
- Alexandra A Vetrova
- Laboratory of Morphogenesis Evolution, Koltzov Institute of Developmental Biology RAS, Vavilova 26, Moscow, 119334, Russia
| | - Daria M Kupaeva
- Department of Embryology, Faculty of Biology, Lomonosov Moscow State University, Leninskiye Gory 1/12, Moscow, 119234, Russia
| | - Alena Kizenko
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400, Klosterneuburg, Austria
| | - Tatiana S Lebedeva
- Department for Molecular Evolution and Development, Centre of Organismal Systems Biology, University of Vienna, Althanstraße 14, 1090, Vienna, Austria
| | - Peter Walentek
- Renal Division, Internal Medicine IV, Medical Center, Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany
| | - Nikoloz Tsikolia
- Institute of Anatomy and Embryology, University Medical Center Göttingen, Kreuzbergring 36, 37085, Göttingen, Germany
| | - Stanislav V Kremnyov
- Laboratory of Morphogenesis Evolution, Koltzov Institute of Developmental Biology RAS, Vavilova 26, Moscow, 119334, Russia.
- Department of Embryology, Faculty of Biology, Lomonosov Moscow State University, Leninskiye Gory 1/12, Moscow, 119234, Russia.
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8
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Faltine-Gonzalez D, Havrilak J, Layden MJ. The brain regulatory program predates central nervous system evolution. Sci Rep 2023; 13:8626. [PMID: 37244953 DOI: 10.1038/s41598-023-35721-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/23/2023] [Indexed: 05/29/2023] Open
Abstract
Understanding how brains evolved is critical to determine the origin(s) of centralized nervous systems. Brains are patterned along their anteroposterior axis by stripes of gene expression that appear to be conserved, suggesting brains are homologous. However, the striped expression is also part of the deeply conserved anteroposterior axial program. An emerging hypothesis is that similarities in brain patterning are convergent, arising through the repeated co-option of axial programs. To resolve whether shared brain neuronal programs likely reflect convergence or homology, we investigated the evolution of axial programs in neurogenesis. We show that the bilaterian anteroposterior program patterns the nerve net of the cnidarian Nematostella along the oral-aboral axis arguing that anteroposterior programs regionalized developing nervous systems in the cnidarian-bilaterian common ancestor prior to the emergence of brains. This finding rejects shared patterning as sufficient evidence to support brain homology and provides functional support for the plausibility that axial programs could be co-opted if nervous systems centralized in multiple lineages.
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Affiliation(s)
| | - Jamie Havrilak
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Michael J Layden
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA.
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9
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Schuster HC, Hirth F. Phylogenetic tracing of midbrain-specific regulatory sequences suggests single origin of eubilaterian brains. SCIENCE ADVANCES 2023; 9:eade8259. [PMID: 37224241 PMCID: PMC10208574 DOI: 10.1126/sciadv.ade8259] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 04/18/2023] [Indexed: 05/26/2023]
Abstract
Conserved cis-regulatory elements (CREs) control Engrailed-, Pax2-, and dachshund-related gene expression networks directing the formation and function of corresponding midbrain circuits in arthropods and vertebrates. Polarized outgroup analyses of 31 sequenced metazoan genomes representing all animal clades reveal the emergence of Pax2- and dachshund-related CRE-like sequences in anthozoan Cnidaria. The full complement, including Engrailed-related CRE-like sequences, is only detectable in spiralians, ecdysozoans, and chordates that have a brain; they exhibit comparable genomic locations and extensive nucleotide identities that reveal the presence of a conserved core domain, all of which are absent in non-neural genes and, together, distinguish them from randomly assembled sequences. Their presence concurs with a genetic boundary separating the rostral from caudal nervous systems, demonstrated for the metameric brains of annelids, arthropods, and chordates and the asegmental cycloneuralian and urochordate brain. These findings suggest that gene regulatory networks for midbrain circuit formation evolved within the lineage that led to the common ancestor of protostomes and deuterostomes.
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Affiliation(s)
- Helen C. Schuster
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, and Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
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10
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Tursch A, Holstein TW. From injury to patterning—MAPKs and Wnt signaling in Hydra. Curr Top Dev Biol 2023; 153:381-417. [PMID: 36967201 DOI: 10.1016/bs.ctdb.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Hydra has a regenerative capacity that is not limited to individual organs but encompasses the entire body. Various global and integrative genome, transcriptome and proteome approaches have shown that many of the signaling pathways and transcription factors present in vertebrates are already present in Cnidaria, the sister group of Bilateria, and are also activated in regeneration. It is now possible to investigate one of the central questions of regeneration biology, i.e., how does the patterning system become activated by the injury signals that initiate regeneration. This review will present the current data obtained in Hydra and draw parallels with regeneration in Bilateria. Important findings of this global analysis are that the Wnt signaling pathway has a dual function in the regeneration process. In the early phase Wnt is activated generically and in a second phase of pattern formation it is activated in a position specific manner. Thus, Wnt signaling is part of the generic injury response, in which mitogen-activated protein kinases (MAPKs) are initially activated via calcium and reactive oxygen species (ROS). The MAPKs, p38, c-Jun N-terminal kinases (JNKs) and extracellular signal-regulated kinases (ERK) are essential for Wnt activation in Hydra head and foot regenerates. Furthermore, the antagonism between the ERK signaling pathway and stress-induced MAPKs results in a balanced induction of apoptosis and mitosis. However, the early Wnt genes are activated by MAPK signaling rather than apoptosis. Early Wnt gene activity is differentially integrated with a stable, β-Catenin-based gradient along the primary body axis maintaining axial polarity and activating further Wnts in the regenerating head. Because MAPKs and Wnts are highly evolutionarily conserved, we hypothesize that this mechanism is also present in vertebrates but may be activated to different degrees at the level of early Wnt gene integration.
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11
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Schwaiger M, Andrikou C, Dnyansagar R, Murguia PF, Paganos P, Voronov D, Zimmermann B, Lebedeva T, Schmidt HA, Genikhovich G, Benvenuto G, Arnone MI, Technau U. An ancestral Wnt-Brachyury feedback loop in axial patterning and recruitment of mesoderm-determining target genes. Nat Ecol Evol 2022; 6:1921-1939. [PMID: 36396969 DOI: 10.1038/s41559-022-01905-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/12/2022] [Indexed: 11/18/2022]
Abstract
Transcription factors are crucial drivers of cellular differentiation during animal development and often share ancient evolutionary origins. The T-box transcription factor Brachyury plays a pivotal role as an early mesoderm determinant and neural repressor in vertebrates; yet, the ancestral function and key evolutionary transitions of the role of this transcription factor remain obscure. Here, we present a genome-wide target-gene screen using chromatin immunoprecipitation sequencing in the sea anemone Nematostella vectensis, an early branching non-bilaterian, and the sea urchin Strongylocentrotus purpuratus, a representative of the sister lineage of chordates. Our analysis reveals an ancestral gene regulatory feedback loop connecting Brachyury, FoxA and canonical Wnt signalling involved in axial patterning that predates the cnidarian-bilaterian split about 700 million years ago. Surprisingly, we also found that part of the gene regulatory network controlling the fate of neuromesodermal progenitors in vertebrates was already present in the common ancestor of cnidarians and bilaterians. However, while several endodermal and neuronal Brachyury target genes are ancestrally shared, hardly any of the key mesodermal downstream targets in vertebrates are found in the sea anemone or the sea urchin. Our study suggests that a limited number of target genes involved in mesoderm formation were newly acquired in the vertebrate lineage, leading to a dramatic shift in the function of this ancestral developmental regulator.
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Affiliation(s)
- Michaela Schwaiger
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences,University of Vienna, Vienna, Austria
- Friedrich Miescher Institute for Biomedical Research, Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Carmen Andrikou
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Rohit Dnyansagar
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences,University of Vienna, Vienna, Austria
| | - Patricio Ferrer Murguia
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences,University of Vienna, Vienna, Austria
| | | | - Danila Voronov
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
| | - Bob Zimmermann
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences,University of Vienna, Vienna, Austria
| | - Tatiana Lebedeva
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences,University of Vienna, Vienna, Austria
| | - Heiko A Schmidt
- Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Grigory Genikhovich
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences,University of Vienna, Vienna, Austria
| | | | | | - Ulrich Technau
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences,University of Vienna, Vienna, Austria.
- Max Perutz Labs, University of Vienna, Vienna, Austria.
- Research Platform 'Single Cell Regulation of Stem Cells', University of Vienna, Vienna, Austria.
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12
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Single-cell transcriptomics identifies conserved regulators of neuroglandular lineages. Cell Rep 2022; 40:111370. [PMID: 36130520 DOI: 10.1016/j.celrep.2022.111370] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/01/2022] [Accepted: 08/25/2022] [Indexed: 11/23/2022] Open
Abstract
Communication in bilaterian nervous systems is mediated by electrical and secreted signals; however, the evolutionary origin and relation of neurons to other secretory cell types has not been elucidated. Here, we use developmental single-cell RNA sequencing in the cnidarian Nematostella vectensis, representing an early evolutionary lineage with a simple nervous system. Validated by transgenics, we demonstrate that neurons, stinging cells, and gland cells arise from a common multipotent progenitor population. We identify the conserved transcription factor gene SoxC as a key upstream regulator of all neuroglandular lineages and demonstrate that SoxC knockdown eliminates both neuronal and secretory cell types. While in vertebrates and many other bilaterians neurogenesis is largely restricted to early developmental stages, we show that in the sea anemone, differentiation of neuroglandular cells is maintained throughout all life stages, and follows the same molecular trajectories from embryo to adulthood, ensuring lifelong homeostasis of neuroglandular cell lineages.
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Injury-induced MAPK activation triggers body axis formation in Hydra by default Wnt signaling. Proc Natl Acad Sci U S A 2022; 119:e2204122119. [PMID: 35994642 PMCID: PMC9436372 DOI: 10.1073/pnas.2204122119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydra's almost unlimited regenerative potential is based on Wnt signaling, but so far it is unknown how the injury stimulus is transmitted to discrete patterning fates in head and foot regenerates. We previously identified mitogen-activated protein kinases (MAPKs) among the earliest injury response molecules in Hydra head regeneration. Here, we show that three MAPKs-p38, c-Jun N-terminal kinases (JNKs), and extracellular signal-regulated kinases (ERKs)-are essential to initiate regeneration in Hydra, independent of the wound position. Their activation occurs in response to any injury and requires calcium and reactive oxygen species (ROS) signaling. Phosphorylated MAPKs hereby exhibit cross talk with mutual antagonism between the ERK pathway and stress-induced MAPKs, orchestrating a balance between cell survival and apoptosis. Importantly, Wnt3 and Wnt9/10c, which are induced by MAPK signaling, can partially rescue regeneration in tissues treated with MAPK inhibitors. Also, foot regenerates can be reverted to form head tissue by a pharmacological increase of β-catenin signaling or the application of recombinant Wnts. We propose a model in which a β-catenin-based stable gradient of head-forming capacity along the primary body axis, by differentially integrating an indiscriminate injury response, determines the fate of the regenerating tissue. Hereby, Wnt signaling acquires sustained activation in the head regenerate, while it is transient in the presumptive foot tissue. Given the high level of evolutionary conservation of MAPKs and Wnts, we assume that this mechanism is deeply embedded in our genome.
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Gilbert E, Teeling C, Lebedeva T, Pedersen S, Chrismas N, Genikhovich G, Modepalli V. Molecular and cellular architecture of the larval sensory organ in the cnidarian Nematostella vectensis. Development 2022; 149:276422. [PMID: 36000354 PMCID: PMC9481973 DOI: 10.1242/dev.200833] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022]
Abstract
Cnidarians are the only non-bilaterian group to evolve ciliated larvae with an apical sensory organ, which is possibly homologous to the apical organs of bilaterian primary larvae. Here, we generated transcriptomes of the apical tissue in the sea anemone Nematostella vectensis and showed that it has a unique neuronal signature. By integrating previously published larval single-cell data with our apical transcriptomes, we discovered that the apical domain comprises a minimum of six distinct cell types. We show that the apical organ is compartmentalised into apical tuft cells (spot) and larval-specific neurons (ring). Finally, we identify ISX-like (NVE14554), a PRD class homeobox gene specifically expressed in apical tuft cells, as an FGF signalling-dependent transcription factor responsible for the formation of the apical tuft domain via repression of the neural ring fate in apical cells. With this study, we contribute a comparison of the molecular anatomy of apical organs, which must be carried out across phyla to determine whether this crucial larval structure evolved once or multiple times. Summary:ISX-like homeobox gene is an FGF signalling-dependent transcription factor responsible for the formation of the apical tuft in the sea anemone Nematostella vectensis.
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Affiliation(s)
- Eleanor Gilbert
- Marine Biological Association of the UK, The Laboratory 1 , Citadel Hill, Plymouth PL1 2PB , United Kingdom
- School of Biological and Marine Sciences, University of Plymouth 2 , Plymouth, PL4 8AA , UK
| | - Callum Teeling
- Marine Biological Association of the UK, The Laboratory 1 , Citadel Hill, Plymouth PL1 2PB , United Kingdom
- School of Biological and Marine Sciences, University of Plymouth 2 , Plymouth, PL4 8AA , UK
| | - Tatiana Lebedeva
- University of Vienna 3 Department of Neurosciences and Developmental Biology, Faculty of Life Sciences , , Vienna, 1030 , Austria
- Doctoral School of Ecology and Evolution, University of Vienna 4 , Vienna, 1030 , Austria
| | - Siffreya Pedersen
- Marine Biological Association of the UK, The Laboratory 1 , Citadel Hill, Plymouth PL1 2PB , United Kingdom
| | - Nathan Chrismas
- Marine Biological Association of the UK, The Laboratory 1 , Citadel Hill, Plymouth PL1 2PB , United Kingdom
| | - Grigory Genikhovich
- University of Vienna 3 Department of Neurosciences and Developmental Biology, Faculty of Life Sciences , , Vienna, 1030 , Austria
| | - Vengamanaidu Modepalli
- Marine Biological Association of the UK, The Laboratory 1 , Citadel Hill, Plymouth PL1 2PB , United Kingdom
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15
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Martynov AV, Korshunova TA. Renewed perspectives on the sedentary-pelagic last common bilaterian ancestor. CONTRIBUTIONS TO ZOOLOGY 2022. [DOI: 10.1163/18759866-bja10034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Various evaluations of the last common bilaterian ancestor (lcba) currently suggest that it resembled either a microscopic, non-segmented motile adult; or, on the contrary, a complex segmented adult motile urbilaterian. These fundamental inconsistencies remain largely unexplained. A majority of multidisciplinary data regarding sedentary adult ancestral bilaterian organization is overlooked. The sedentary-pelagic model is supported now by a number of novel developmental, paleontological and molecular phylogenetic data: (1) data in support of sedentary sponges, in the adult stage, as sister to all other Metazoa; (2) a similarity of molecular developmental pathways in both adults and larvae across sedentary sponges, cnidarians, and bilaterians; (3) a cnidarian-bilaterian relationship, including a unique sharing of a bona fide Hox-gene cluster, of which the evolutionary appearance does not connect directly to a bilaterian motile organization; (4) the presence of sedentary and tube-dwelling representatives of the main bilaterian clades in the early Cambrian; (5) an absence of definite taxonomic attribution of Ediacaran taxa reconstructed as motile to any true bilaterian phyla; (6) a similarity of tube morphology (and the clear presence of a protoconch-like apical structure of the Ediacaran sedentary Cloudinidae) among shells of the early Cambrian, and later true bilaterians, such as semi-sedentary hyoliths and motile molluscs; (7) recent data that provide growing evidence for a complex urbilaterian, despite a continuous molecular phylogenetic controversy. The present review compares the main existing models and reconciles the sedentary model of an urbilaterian and the model of a larva-like lcba with a unified sedentary(adult)-pelagic(larva) model of the lcba.
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Affiliation(s)
- Alexander V. Martynov
- Zoological Museum, Moscow State University, Bolshaya Nikitskaya Str. 6, 125009 Moscow, Russia,
| | - Tatiana A. Korshunova
- Koltzov Institute of Developmental Biology RAS, 26 Vavilova Str., 119334 Moscow, Russia
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16
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Holstein TW. The role of cnidarian developmental biology in unraveling axis formation and Wnt signaling. Dev Biol 2022; 487:74-98. [DOI: 10.1016/j.ydbio.2022.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 12/12/2022]
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17
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Erofeeva TV, Grigorenko AP, Gusev FE, Kosevich IA, Rogaev EI. Studying of Molecular Regulation of Developmental Processes of Lower Metazoans Exemplified by Cnidaria Using High-Throughput Sequencing. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:269-293. [PMID: 35526848 DOI: 10.1134/s0006297922030075] [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: 10/28/2021] [Revised: 12/13/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
A unique set of features and characteristics of species of the Cnidaria phylum is the one reason that makes them a model for a various studies. The plasticity of a life cycle and the processes of cell differentiation and development of an integral multicellular organism associated with it are of a specific scientific interest. A new stage of development of molecular genetic methods, including methods for high-throughput genome, transcriptome, and epigenome sequencing, both at the level of the whole organism and at the level of individual cells, makes it possible to obtain a detailed picture of the development of these animals. This review examines some modern approaches and advances in the reconstruction of the processes of ontogenesis of cnidarians by studying the regulatory signal transduction pathways and their interactions.
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Affiliation(s)
- Taisia V Erofeeva
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Anastasia P Grigorenko
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia.
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Fedor E Gusev
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Igor A Kosevich
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia
- Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Evgeny I Rogaev
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
- Lomonosov Moscow State University, Moscow, 119234, Russia
- Department of Psychiatry, UMass Chan Medical School, Shrewsbury, MA 01545, USA
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Binagui-Casas A, Dias A, Guillot C, Metzis V, Saunders D. Building consensus in neuromesodermal research: Current advances and future biomedical perspectives. Curr Opin Cell Biol 2021; 73:133-140. [PMID: 34717142 DOI: 10.1016/j.ceb.2021.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 08/12/2021] [Accepted: 08/31/2021] [Indexed: 10/20/2022]
Abstract
The development of the vertebrate body axis relies on the activity of different populations of axial progenitors, including neuromesodermal progenitors. Currently, the term 'Neuromesodermal progenitors' is associated with various definitions. Here, we use distinct terminologies to highlight advances in our understanding of this cell type at both the single-cell and population levels. We discuss how these recent insights prompt new opportunities to address a range of biomedical questions spanning cancer metastasis, congenital disorders, cellular metabolism, regenerative medicine, and evolution. Finally, we outline some of the major unanswered questions and propose future directions at the forefront of neuromesodermal research.
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Affiliation(s)
- Anahí Binagui-Casas
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU, UK
| | - André Dias
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal.
| | - Charlène Guillot
- Department of Pathology, Brigham and Women's Hospital & Department of Genetics, Harvard Medical School, 60 Fenwood Road, Boston, MA, USA; Institute of Genetics, Reproduction and Development, Medical school, University of Clermont Auvergne, 28, Place Henri Dunant, 63001 Clermont-Ferrand, France
| | - Vicki Metzis
- Institute of Clinical Sciences, Imperial College London, London, W12 0NN, UK
| | - Dillan Saunders
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
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