1
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Schnitzler CE, Chang ES, Waletich J, Quiroga-Artigas G, Wong WY, Nguyen AD, Barreira SN, Doonan LB, Gonzalez P, Koren S, Gahan JM, Sanders SM, Bradshaw B, DuBuc TQ, Febrimarsa, de Jong D, Nawrocki EP, Larson A, Klasfeld S, Gornik SG, Moreland RT, Wolfsberg TG, Phillippy AM, Mullikin JC, Simakov O, Cartwright P, Nicotra M, Frank U, Baxevanis AD. The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals. Genome Res 2024; 34:498-513. [PMID: 38508693 PMCID: PMC11067881 DOI: 10.1101/gr.278382.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
Hydractinia is a colonial marine hydroid that shows remarkable biological properties, including the capacity to regenerate its entire body throughout its lifetime, a process made possible by its adult migratory stem cells, known as i-cells. Here, we provide an in-depth characterization of the genomic structure and gene content of two Hydractinia species, Hydractinia symbiolongicarpus and Hydractinia echinata, placing them in a comparative evolutionary framework with other cnidarian genomes. We also generated and annotated a single-cell transcriptomic atlas for adult male H. symbiolongicarpus and identified cell-type markers for all major cell types, including key i-cell markers. Orthology analyses based on the markers revealed that Hydractinia's i-cells are highly enriched in genes that are widely shared amongst animals, a striking finding given that Hydractinia has a higher proportion of phylum-specific genes than any of the other 41 animals in our orthology analysis. These results indicate that Hydractinia's stem cells and early progenitor cells may use a toolkit shared with all animals, making it a promising model organism for future exploration of stem cell biology and regenerative medicine. The genomic and transcriptomic resources for Hydractinia presented here will enable further studies of their regenerative capacity, colonial morphology, and ability to distinguish self from nonself.
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Affiliation(s)
- Christine E Schnitzler
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida 32080, USA
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA
| | - E Sally Chang
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Justin Waletich
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida 32080, USA
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA
| | - Gonzalo Quiroga-Artigas
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida 32080, USA
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier CEDEX 05, France
| | - Wai Yee Wong
- Department for Neurosciences and Developmental Biology, University of Vienna, 1030 Vienna, Austria
| | - Anh-Dao Nguyen
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Sofia N Barreira
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Liam B Doonan
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway H91 W2TY, Ireland
| | - Paul Gonzalez
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Sergey Koren
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - James M Gahan
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway H91 W2TY, Ireland
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Steven M Sanders
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
- Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Brian Bradshaw
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway H91 W2TY, Ireland
| | - Timothy Q DuBuc
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway H91 W2TY, Ireland
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania 19081, USA
| | - Febrimarsa
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway H91 W2TY, Ireland
- Pharmaceutical Biology Laboratory, Faculty of Pharmacy, Universitas Muhammadiyah Surakarta, Jawa Tengah 57169, Indonesia
| | - Danielle de Jong
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida 32080, USA
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA
| | - Eric P Nawrocki
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Alexandra Larson
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida 32080, USA
| | - Samantha Klasfeld
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Sebastian G Gornik
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway H91 W2TY, Ireland
- Center for Organismal Studies, University of Heidelberg, 69117 Heidelberg, Germany
| | - R Travis Moreland
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Tyra G Wolfsberg
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Adam M Phillippy
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - James C Mullikin
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
- NIH Intramural Sequencing Center, Rockville, Maryland 20852, USA
| | - Oleg Simakov
- Department for Neurosciences and Developmental Biology, University of Vienna, 1030 Vienna, Austria
| | - Paulyn Cartwright
- Department of Evolution and Ecology, University of Kansas, Lawrence, Kansas 66045, USA
| | - Matthew Nicotra
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
- Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Uri Frank
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway H91 W2TY, Ireland
| | - Andreas D Baxevanis
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
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2
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Zeng J, Zhao X, Liang Z, Hidalgo I, Gebert M, Fan P, Wenzl C, Gornik SG, Lohmann JU. Nitric oxide controls shoot meristem activity via regulation of DNA methylation. Nat Commun 2023; 14:8001. [PMID: 38049411 PMCID: PMC10696095 DOI: 10.1038/s41467-023-43705-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 11/16/2023] [Indexed: 12/06/2023] Open
Abstract
Despite the importance of Nitric Oxide (NO) as signaling molecule in both plant and animal development, the regulatory mechanisms downstream of NO remain largely unclear. Here, we show that NO is involved in Arabidopsis shoot stem cell control via modifying expression and activity of ARGONAUTE 4 (AGO4), a core component of the RNA-directed DNA Methylation (RdDM) pathway. Mutations in components of the RdDM pathway cause meristematic defects, and reduce responses of the stem cell system to NO signaling. Importantly, we find that the stem cell inducing WUSCHEL transcription factor directly interacts with AGO4 in a NO dependent manner, explaining how these two signaling systems may converge to modify DNA methylation patterns. Taken together, our results reveal that NO signaling plays an important role in controlling plant stem cell homeostasis via the regulation of de novo DNA methylation.
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Affiliation(s)
- Jian Zeng
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, 69120, Heidelberg, Germany
| | - Xin'Ai Zhao
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, 69120, Heidelberg, Germany
| | - Zhe Liang
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, 69120, Heidelberg, Germany
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Inés Hidalgo
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, 69120, Heidelberg, Germany
| | - Michael Gebert
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, 69120, Heidelberg, Germany
- CureVac, 72076, Tübingen, Germany
| | - Pengfei Fan
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, 69120, Heidelberg, Germany
| | - Christian Wenzl
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, 69120, Heidelberg, Germany
| | - Sebastian G Gornik
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, 69120, Heidelberg, Germany
| | - Jan U Lohmann
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, 69120, Heidelberg, Germany.
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3
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Kishimoto M, Gornik SG, Foulkes NS, Guse A. Negative phototaxis in the photosymbiotic sea anemone Aiptasia as a potential strategy to protect symbionts from photodamage. Sci Rep 2023; 13:17857. [PMID: 37857737 PMCID: PMC10587101 DOI: 10.1038/s41598-023-44583-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023] Open
Abstract
Photosymbiotic cnidarians generally seek bright environments so that their symbionts can be photosynthetically active. However, excess light may result in a breakdown of symbiosis due to the accumulation of photodamage in symbionts causing symbiont loss (bleaching). It is currently unknown if photosymbiotic cnidarians sense light only to regulate spawning time and to facilitate predation, or whether they also use their light-sensing capacities to protect their symbionts from photodamage. In this study, we examined how the sea anemone Aiptasia changes its behaviour when exposed to excess light. We reveal that Aiptasia polyps, when carrying symbionts, contract their bodies when exposed to high light intensities and subsequently migrate away in a direction perpendicular to the light source. Interestingly, this negative phototaxis was only evident under blue light and absent upon UV, green and red light exposure. Non-symbiotic Aiptasia did not exhibit this light response. Our study demonstrates that photosymbiotic Aiptasia polyps display negative phototactic behaviour in response to blue light, and that they also can perceive its direction, despite lacking specialized eye structures. We postulate that Aiptasia uses blue light, which penetrates seawater efficiently, as a general proxy for sunlight exposure to protect its symbionts from photodamage.
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Affiliation(s)
- Mariko Kishimoto
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi, 444-8585, Japan
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
- Department of Translational Genomics, Medical Faculty, University of Cologne, Weyertal 115b, 50931, Cologne, Germany
| | - Sebastian G Gornik
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Nicholas S Foulkes
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany.
- Institute of Biological and Chemical Systems, Karlsruhe Institute of Technology, 76344, Eggenstein-Leopoldshafen, Germany.
| | - Annika Guse
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi, 444-8585, Japan.
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany.
- Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2, 82152, Planegg-Martinsried, Germany.
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4
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Voss PA, Gornik SG, Jacobovitz MR, Rupp S, Dörr M, Maegele I, Guse A. Host nutrient sensing is mediated by mTOR signaling in cnidarian-dinoflagellate symbiosis. Curr Biol 2023; 33:3634-3647.e5. [PMID: 37572664 DOI: 10.1016/j.cub.2023.07.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/31/2023] [Accepted: 07/20/2023] [Indexed: 08/14/2023]
Abstract
To survive in the nutrient-poor waters of the tropics, reef-building corals rely on intracellular, photosynthetic dinoflagellate symbionts. Photosynthates produced by the symbiont are translocated to the host, and this enables corals to form the structural foundation of the most biodiverse of all marine ecosystems. Although the regulation of nutrient exchange between partners is critical for ecosystem stability and health, the mechanisms governing how nutrients are sensed, transferred, and integrated into host cell processes are largely unknown. Ubiquitous among eukaryotes, the mechanistic target of the rapamycin (mTOR) signaling pathway integrates intracellular and extracellular stimuli to influence cell growth and cell-cycle progression and to balance metabolic processes. A functional role of mTOR in the integration of host and symbiont was demonstrated in various nutritional symbioses, and a similar role of mTOR was proposed for coral-algal symbioses. Using the endosymbiosis model Aiptasia, we examined the role of mTOR signaling in both larvae and adult polyps across various stages of symbiosis. We found that symbiosis enhances cell proliferation, and using an Aiptasia-specific antibody, we localized mTOR to symbiosome membranes. We found that mTOR signaling is activated by symbiosis, while inhibition of mTOR signaling disrupts intracellular niche establishment and symbiosis altogether. Additionally, we observed that dysbiosis was a conserved response to mTOR inhibition in the larvae of a reef-building coral species. Our data confim that mTOR signaling plays a pivotal role in integrating symbiont-derived nutrients into host metabolism and symbiosis stability, ultimately allowing symbiotic cnidarians to thrive in challenging environments.
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Affiliation(s)
- Philipp A Voss
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 230, Heidelberg 69120 Germany
| | - Sebastian G Gornik
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 230, Heidelberg 69120 Germany
| | - Marie R Jacobovitz
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 230, Heidelberg 69120 Germany
| | - Sebastian Rupp
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 230, Heidelberg 69120 Germany
| | - Melanie Dörr
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 230, Heidelberg 69120 Germany
| | - Ira Maegele
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 230, Heidelberg 69120 Germany
| | - Annika Guse
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 230, Heidelberg 69120 Germany.
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5
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Schnitzler CE, Chang ES, Waletich J, Quiroga-Artigas G, Wong WY, Nguyen AD, Barreira SN, Doonan L, Gonzalez P, Koren S, Gahan JM, Sanders SM, Bradshaw B, DuBuc TQ, Febrimarsa, de Jong D, Nawrocki EP, Larson A, Klasfeld S, Gornik SG, Moreland RT, Wolfsberg TG, Phillippy AM, Mullikin JC, Simakov O, Cartwright P, Nicotra M, Frank U, Baxevanis AD. The genome of the colonial hydroid Hydractinia reveals their stem cells utilize a toolkit of evolutionarily shared genes with all animals. bioRxiv 2023:2023.08.25.554815. [PMID: 37786714 PMCID: PMC10541594 DOI: 10.1101/2023.08.25.554815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Hydractinia is a colonial marine hydroid that exhibits remarkable biological properties, including the capacity to regenerate its entire body throughout its lifetime, a process made possible by its adult migratory stem cells, known as i-cells. Here, we provide an in-depth characterization of the genomic structure and gene content of two Hydractinia species, H. symbiolongicarpus and H. echinata, placing them in a comparative evolutionary framework with other cnidarian genomes. We also generated and annotated a single-cell transcriptomic atlas for adult male H. symbiolongicarpus and identified cell type markers for all major cell types, including key i-cell markers. Orthology analyses based on the markers revealed that Hydractinia's i-cells are highly enriched in genes that are widely shared amongst animals, a striking finding given that Hydractinia has a higher proportion of phylum-specific genes than any of the other 41 animals in our orthology analysis. These results indicate that Hydractinia's stem cells and early progenitor cells may use a toolkit shared with all animals, making it a promising model organism for future exploration of stem cell biology and regenerative medicine. The genomic and transcriptomic resources for Hydractinia presented here will enable further studies of their regenerative capacity, colonial morphology, and ability to distinguish self from non-self.
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Affiliation(s)
- Christine E Schnitzler
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - E Sally Chang
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Justin Waletich
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Gonzalo Quiroga-Artigas
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier CEDEX 05, France
| | - Wai Yee Wong
- Department of Molecular Evolution and Development, Faculty of Life Science, University of Vienna, A-1090 Vienna, Austria
| | - Anh-Dao Nguyen
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sofia N Barreira
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Liam Doonan
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
| | - Paul Gonzalez
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sergey Koren
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James M Gahan
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Steven M Sanders
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Brian Bradshaw
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
| | - Timothy Q DuBuc
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
- Swarthmore College, Swarthmore, PA 19081, USA
| | - Febrimarsa
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
| | - Danielle de Jong
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Eric P Nawrocki
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexandra Larson
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
| | - Samantha Klasfeld
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sebastian G Gornik
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
- Centre for Organismal Studies, University of Heidelberg, Germany
| | - R Travis Moreland
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tyra G Wolfsberg
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam M Phillippy
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James C Mullikin
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- NIH Intramural Sequencing Center, Rockville, MD 20852, USA
| | - Oleg Simakov
- Department of Molecular Evolution and Development, Faculty of Life Science, University of Vienna, A-1090 Vienna, Austria
| | - Paulyn Cartwright
- Department of Evolution and Ecology, University of Kansas, Lawrence, KS 66045, USA
| | - Matthew Nicotra
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Uri Frank
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
| | - Andreas D Baxevanis
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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6
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Febrimarsa, Gornik SG, Barreira SN, Salinas‐Saavedra M, Schnitzler CE, Baxevanis AD, Frank U. Randomly incorporated genomic N6-methyldeoxyadenosine delays zygotic transcription initiation in a cnidarian. EMBO J 2023; 42:e112934. [PMID: 37708295 PMCID: PMC10390872 DOI: 10.15252/embj.2022112934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 09/16/2023] Open
Abstract
N6-methyldeoxyadenosine (6mA) is a chemical alteration of DNA, observed across all realms of life. Although the functions of 6mA are well understood in bacteria and protists, its roles in animal genomes have been controversial. We show that 6mA randomly accumulates in early embryos of the cnidarian Hydractinia symbiolongicarpus, with a peak at the 16-cell stage followed by clearance to background levels two cell cycles later, at the 64-cell stage-the embryonic stage at which zygotic genome activation occurs in this animal. Knocking down Alkbh1, a putative initiator of animal 6mA clearance, resulted in higher levels of 6mA at the 64-cell stage and a delay in the initiation of zygotic transcription. Our data are consistent with 6mA originating from recycled nucleotides of degraded m6A-marked maternal RNA postfertilization. Therefore, while 6mA does not function as an epigenetic mark in Hydractinia, its random incorporation into the early embryonic genome inhibits transcription. In turn, Alkbh1 functions as a genomic 6mA "cleaner," facilitating timely zygotic genome activation. Given the random nature of genomic 6mA accumulation and its ability to interfere with gene expression, defects in 6mA clearance may represent a hitherto unknown cause of various pathologies.
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Affiliation(s)
- Febrimarsa
- Centre for Chromosome Biology, School of Biological and Chemical SciencesUniversity of GalwayGalwayRepublic of Ireland
| | - Sebastian G Gornik
- Centre for Chromosome Biology, School of Biological and Chemical SciencesUniversity of GalwayGalwayRepublic of Ireland
- Present address:
Centre for Organismal StudiesHeidelberg UniversityHeidelbergGermany
| | - Sofia N Barreira
- Computational and Statistical Genomics Branch, Division of Intramural ResearchNational Human Genome Research Institute, National Institutes of HealthBethesdaMDUSA
| | - Miguel Salinas‐Saavedra
- Centre for Chromosome Biology, School of Biological and Chemical SciencesUniversity of GalwayGalwayRepublic of Ireland
| | - Christine E Schnitzler
- Whitney Laboratory for Marine BioscienceUniversity of FloridaSt. AugustineFLUSA
- Department of BiologyUniversity of FloridaGainesvilleFLUSA
| | - Andreas D Baxevanis
- Computational and Statistical Genomics Branch, Division of Intramural ResearchNational Human Genome Research Institute, National Institutes of HealthBethesdaMDUSA
| | - Uri Frank
- Centre for Chromosome Biology, School of Biological and Chemical SciencesUniversity of GalwayGalwayRepublic of Ireland
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7
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Török A, Browne MJG, Vilar JC, Patwal I, DuBuc TQ, Febrimarsa, Atcheson E, Frank U, Gornik SG, Flaus A. Hydrozoan sperm-specific SPKK motif-containing histone H2B variants stabilise chromatin with limited compaction. Development 2023; 150:286546. [PMID: 36633190 PMCID: PMC9903204 DOI: 10.1242/dev.201058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 12/02/2022] [Indexed: 01/13/2023]
Abstract
Many animals achieve sperm chromatin compaction and stabilisation by replacing canonical histones with sperm nuclear basic proteins (SNBPs) such as protamines during spermatogenesis. Hydrozoan cnidarians and echinoid sea urchins lack protamines and have evolved a distinctive family of sperm-specific histone H2Bs (spH2Bs) with extended N termini rich in SPK(K/R) motifs. Echinoid sperm packaging is regulated by spH2Bs. Their sperm is negatively buoyant and fertilises on the sea floor. Hydroid cnidarians undertake broadcast spawning but their sperm properties are poorly characterised. We show that Hydractinia echinata and H. symbiolongicarpus sperm chromatin possesses higher stability than somatic chromatin, with reduced accessibility to transposase Tn5 integration and to endonucleases in vitro. In contrast, nuclear dimensions are only moderately reduced in mature Hydractinia sperm. Ectopic expression of spH2B in the background of H2B.1 knockdown results in downregulation of global transcription and cell cycle arrest in embryos, without altering their nuclear density. Taken together, SPKK-containing spH2B variants act to stabilise chromatin and silence transcription in Hydractinia sperm with only limited chromatin compaction. We suggest that spH2Bs could contribute to sperm buoyancy as a reproductive adaptation.
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Affiliation(s)
- Anna Török
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91 TK33, Ireland
| | - Martin J. G. Browne
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91 TK33, Ireland
| | - Jordina C. Vilar
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91 TK33, Ireland
| | - Indu Patwal
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91 TK33, Ireland
| | - Timothy Q. DuBuc
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91 TK33, Ireland
| | - Febrimarsa
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91 TK33, Ireland
| | - Erwan Atcheson
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91 TK33, Ireland
| | - Uri Frank
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91 TK33, Ireland
| | - Sebastian G. Gornik
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91 TK33, Ireland,Authors for correspondence (, )
| | - Andrew Flaus
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91 TK33, Ireland,Authors for correspondence (, )
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8
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Gornik SG, Flores V, Reinhardt F, Erber L, Salas-Leiva DE, Douvropoulou O, Lassadi I, Einarsson E, Mörl M, Git A, Stadler PF, Pain A, Waller RF. Mitochondrial Genomes in Perkinsus Decode Conserved Frameshifts in All Genes. Mol Biol Evol 2022; 39:6701636. [PMID: 36108082 PMCID: PMC9550989 DOI: 10.1093/molbev/msac191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mitochondrial genomes of apicomplexans, dinoflagellates, and chrompodellids that collectively make up the Myzozoa, encode only three proteins (Cytochrome b [COB], Cytochrome c oxidase subunit 1 [COX1], Cytochrome c oxidase subunit 3 [COX3]), contain fragmented ribosomal RNAs, and display extensive recombination, RNA trans-splicing, and RNA-editing. The early-diverging Perkinsozoa is the final major myzozoan lineage whose mitochondrial genomes remained poorly characterized. Previous reports of Perkinsus genes indicated independent acquisition of non-canonical features, namely the occurrence of multiple frameshifts. To determine both ancestral myzozoan and novel perkinsozoan mitochondrial genome features, we sequenced and assembled mitochondrial genomes of four Perkinsus species. These data show a simple ancestral genome with the common reduced coding capacity but disposition for rearrangement. We identified 75 frameshifts across the four species that occur as distinct types and that are highly conserved in gene location. A decoding mechanism apparently employs unused codons at the frameshift sites that advance translation either +1 or +2 frames to the next used codon. The locations of frameshifts are seemingly positioned to regulate protein folding of the nascent protein as it emerges from the ribosome. The cox3 gene is distinct in containing only one frameshift and showing strong selection against residues that are otherwise frequently encoded at the frameshift positions in cox1 and cob. All genes lack cysteine codons implying a reduction to 19 amino acids in these genomes. Furthermore, mitochondrion-encoded rRNA fragment complements are incomplete in Perkinsus spp. but some are found in the nuclear DNA suggesting import into the organelle. Perkinsus demonstrates further remarkable trajectories of organelle genome evolution including pervasive integration of frameshift translation into genome expression.
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Affiliation(s)
| | - Victor Flores
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Franziska Reinhardt
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Lieselotte Erber
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Dayana E Salas-Leiva
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Olga Douvropoulou
- Pathogen Genomics Group, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Imen Lassadi
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Elin Einarsson
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Anna Git
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany,Discrete Biomathematics, Max Planck Institute for Mathematics in the Sciences, 04103 Leipzig, Germany,Theoretical Biochemistry Group, Institute for Theoretical Chemistry, University of Vienna, Währinger Str. 17, Alsergrund, Vienna 1090, Austria,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Arnab Pain
- Pathogen Genomics Group, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia,International Institute for Zoonosis Control, Hokkaido University, 001-0020 North 20, West 10 Kita-ku, Sapporo 001-0020, Japan
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9
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Chrysostomou E, Flici H, Gornik SG, Salinas-Saavedra M, Gahan JM, McMahon ET, Thompson K, Hanley S, Kilcoyne M, Schnitzler CE, Gonzalez P, Baxevanis AD, Frank U. A cellular and molecular analysis of SoxB-driven neurogenesis in a cnidarian. eLife 2022; 11:78793. [PMID: 35608899 PMCID: PMC9173746 DOI: 10.7554/elife.78793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/23/2022] [Indexed: 01/09/2023] Open
Abstract
Neurogenesis is the generation of neurons from stem cells, a process that is regulated by SoxB transcription factors (TFs) in many animals. Although the roles of these TFs are well understood in bilaterians, how their neural function evolved is unclear. Here, we use Hydractinia symbiolongicarpus, a member of the early-branching phylum Cnidaria, to provide insight into this question. Using a combination of mRNA in situ hybridization, transgenesis, gene knockdown, transcriptomics, and in vivo imaging, we provide a comprehensive molecular and cellular analysis of neurogenesis during embryogenesis, homeostasis, and regeneration in this animal. We show that SoxB genes act sequentially at least in some cases. Stem cells expressing Piwi1 and Soxb1, which have broad developmental potential, become neural progenitors that express Soxb2 before differentiating into mature neural cells. Knockdown of SoxB genes resulted in complex defects in embryonic neurogenesis. Hydractinia neural cells differentiate while migrating from the aboral to the oral end of the animal, but it is unclear whether migration per se or exposure to different microenvironments is the main driver of their fate determination. Our data constitute a rich resource for studies aiming at addressing this question, which is at the heart of understanding the origin and development of animal nervous systems.
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Affiliation(s)
- Eleni Chrysostomou
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland GalwayGalwayIreland
| | - Hakima Flici
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland GalwayGalwayIreland
| | - Sebastian G Gornik
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland GalwayGalwayIreland
| | - Miguel Salinas-Saavedra
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland GalwayGalwayIreland
| | - James M Gahan
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland GalwayGalwayIreland
| | - Emma T McMahon
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland GalwayGalwayIreland
| | - Kerry Thompson
- Centre for Microscopy and Imaging, Discipline of Anatomy, National University of Ireland, GalwayGalwayIreland
| | - Shirley Hanley
- National Centre for Biomedical Engineering Science, National University of Ireland, GalwayGalwayIreland
| | - Michelle Kilcoyne
- Carbohydrate Signalling Group, Microbiology, School of Natural Sciences, National University of Ireland GalwayGalwayIreland
| | - Christine E Schnitzler
- Whitney Laboratory for Marine Bioscience, University of FloridaSt. Augustine, FloridaUnited States,Department of Biology, University of FloridaGainesville, FloridaUnited States
| | - Paul Gonzalez
- Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of HealthBethesda, MarylandUnited States
| | - Andreas D Baxevanis
- Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of HealthBethesda, MarylandUnited States
| | - Uri Frank
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland GalwayGalwayIreland
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10
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Einarsson E, Lassadi I, Zielinski J, Guan Q, Wyler T, Pain A, Gornik SG, Waller RF. Development of the Myzozoan Aquatic Parasite Perkinsus marinus as A Versatile Experimental Genetic Model Organism. Protist 2021; 172:125830. [PMID: 34555729 DOI: 10.1016/j.protis.2021.125830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 11/17/2022]
Abstract
The phylum Perkinsozoa is an aquatic parasite lineage that has devastating effects on commercial and natural mollusc populations, and also comprises parasites of algae, fish and amphibians. They are related to dinoflagellates and apicomplexans and thus offer excellent genetic models for both parasitological and evolutionary studies. Genetic transformation was previously achieved for Perkinsus spp. but with few tools for transgene expression and limited selection efficacy. We sought to expand the power of experimental genetic tools for Perkinsus using P. marinus as a model. We constructed a modular plasmid assembly system for expression of multiple genes simultaneously. We developed efficient selection systems for three drugs, puromycin, bleomycin and blasticidin, that are effective in as little as three weeks. We developed eleven new promoters of variable expression strength. Furthermore, we identified that genomic integration of transgenes is predominantly via non-homologous recombination but with transgene fragmentation including deletion of some elements. To counter these dynamic processes, we show that bi-cistronic transcripts using the viral 2A peptides can couple selection to the maintenance of the expression of a transgene of interest. Collectively, these new tools and insights provide great new capacity to genetically modify and study Perkinsus as an aquatic parasite and evolutionary model.
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Affiliation(s)
- Elin Einarsson
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Imen Lassadi
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jana Zielinski
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Qingtian Guan
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Tobias Wyler
- Department of Biochemistry, University of Cambridge, Cambridge, UK; Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
| | - Arnab Pain
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Sebastian G Gornik
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
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11
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Abstract
Anthozoan corals are an ecologically important group of cnidarians, which power the productivity of reef ecosystems. They are sessile, inhabit shallow, tropical oceans and are highly dependent on sun- and moonlight to regulate sexual reproduction, phototaxis, and photosymbiosis. However, their exposure to high levels of sunlight also imposes an increased risk of UV-induced DNA damage. How have these challenging photic environments influenced photoreceptor evolution and function in these animals? To address this question, we initially screened the cnidarian photoreceptor repertoire for Anthozoa-specific signatures by a broad-scale evolutionary analysis. We compared transcriptomic data of more than 36 cnidarian species and revealed a more diverse photoreceptor repertoire in the anthozoan subphylum than in the subphylum Medusozoa. We classified the three principle opsin classes into distinct subtypes and showed that Anthozoa retained all three classes, which diversified into at least six subtypes. In contrast, in Medusozoa, only one class with a single subtype persists. Similarly, in Anthozoa, we documented three photolyase classes and two cryptochrome (CRY) classes, whereas CRYs are entirely absent in Medusozoa. Interestingly, we also identified one anthozoan CRY class, which exhibited unique tandem duplications of the core functional domains. We next explored the functionality of anthozoan photoreceptors in the model species Exaiptasia diaphana (Aiptasia), which recapitulates key photo-behaviors of corals. We show that the diverse opsin genes are differentially expressed in important life stages common to reef-building corals and Aiptasia and that CRY expression is light regulated. We thereby provide important clues linking coral evolution with photoreceptor diversification.
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Affiliation(s)
- Sebastian G Gornik
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | | | - Benoit Morel
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.,Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Nicholas S Foulkes
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany.,Institute of Biological and Chemical Systems, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Annika Guse
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
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12
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Jacobovitz MR, Rupp S, Voss PA, Maegele I, Gornik SG, Guse A. Dinoflagellate symbionts escape vomocytosis by host cell immune suppression. Nat Microbiol 2021; 6:769-782. [PMID: 33927382 PMCID: PMC7611106 DOI: 10.1038/s41564-021-00897-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/25/2021] [Indexed: 02/02/2023]
Abstract
Alveolata comprises diverse taxa of single-celled eukaryotes, many of which are renowned for their ability to live inside animal cells. Notable examples are apicomplexan parasites and dinoflagellate symbionts, the latter of which power coral reef ecosystems. Although functionally distinct, they evolved from a common, free-living ancestor and must evade their host's immune response for persistence. Both the initial cellular events that gave rise to this intracellular lifestyle and the role of host immune modulation in coral-dinoflagellate endosymbiosis are poorly understood. Here, we use a comparative approach in the cnidarian endosymbiosis model Aiptasia, which re-establishes endosymbiosis with free-living dinoflagellates every generation. We find that uptake of microalgae is largely indiscriminate, but non-symbiotic microalgae are expelled by vomocytosis, while symbionts induce host cell innate immune suppression and form a lysosomal-associated membrane protein 1-positive niche. We demonstrate that exogenous immune stimulation results in symbiont expulsion and, conversely, inhibition of canonical Toll-like receptor signalling enhances infection of host animals. Our findings indicate that symbiosis establishment is dictated by local innate immune suppression, to circumvent expulsion and promote niche formation. This work provides insight into the evolution of the cellular immune response and key steps involved in mediating endosymbiotic interactions.
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Affiliation(s)
- Marie R Jacobovitz
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Sebastian Rupp
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Philipp A Voss
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Ira Maegele
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Sebastian G Gornik
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Annika Guse
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany.
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13
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Faktorová D, Nisbet RER, Fernández Robledo JA, Casacuberta E, Sudek L, Allen AE, Ares M, Aresté C, Balestreri C, Barbrook AC, Beardslee P, Bender S, Booth DS, Bouget FY, Bowler C, Breglia SA, Brownlee C, Burger G, Cerutti H, Cesaroni R, Chiurillo MA, Clemente T, Coles DB, Collier JL, Cooney EC, Coyne K, Docampo R, Dupont CL, Edgcomb V, Einarsson E, Elustondo PA, Federici F, Freire-Beneitez V, Freyria NJ, Fukuda K, García PA, Girguis PR, Gomaa F, Gornik SG, Guo J, Hampl V, Hanawa Y, Haro-Contreras ER, Hehenberger E, Highfield A, Hirakawa Y, Hopes A, Howe CJ, Hu I, Ibañez J, Irwin NAT, Ishii Y, Janowicz NE, Jones AC, Kachale A, Fujimura-Kamada K, Kaur B, Kaye JZ, Kazana E, Keeling PJ, King N, Klobutcher LA, Lander N, Lassadi I, Li Z, Lin S, Lozano JC, Luan F, Maruyama S, Matute T, Miceli C, Minagawa J, Moosburner M, Najle SR, Nanjappa D, Nimmo IC, Noble L, Novák Vanclová AMG, Nowacki M, Nuñez I, Pain A, Piersanti A, Pucciarelli S, Pyrih J, Rest JS, Rius M, Robertson D, Ruaud A, Ruiz-Trillo I, Sigg MA, Silver PA, Slamovits CH, Jason Smith G, Sprecher BN, Stern R, Swart EC, Tsaousis AD, Tsypin L, Turkewitz A, Turnšek J, Valach M, Vergé V, von Dassow P, von der Haar T, Waller RF, Wang L, Wen X, Wheeler G, Woods A, Zhang H, Mock T, Worden AZ, Lukeš J. Publisher Correction: Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nat Methods 2020; 17:551. [PMID: 32296171 PMCID: PMC7200595 DOI: 10.1038/s41592-020-0828-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Drahomíra Faktorová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic.
| | - R Ellen R Nisbet
- Department of Biochemistry, University of Cambridge, Cambridge, UK.,School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | | | - Elena Casacuberta
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Lisa Sudek
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Andrew E Allen
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, CA, USA.,Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
| | - Manuel Ares
- Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Cristina Aresté
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Cecilia Balestreri
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | | | - Patrick Beardslee
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Sara Bender
- Gordon and Betty Moore Foundation, Palo Alto, CA, USA
| | - David S Booth
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - François-Yves Bouget
- Sorbonne Université, CNRS UMR7621, Observatoire Océanologique, Banyuls sur Mer, France
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Susana A Breglia
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Colin Brownlee
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - Gertraud Burger
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - Heriberto Cerutti
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Rachele Cesaroni
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Miguel A Chiurillo
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Thomas Clemente
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Duncan B Coles
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Jackie L Collier
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Elizabeth C Cooney
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kathryn Coyne
- University of Delaware College of Earth, Ocean and Environment, Lewes, DE, USA
| | - Roberto Docampo
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Christopher L Dupont
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
| | | | - Elin Einarsson
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Pía A Elustondo
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada.,AGADA Biosciences Inc., Halifax, Nova Scotia, Canada
| | - Fernan Federici
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile
| | - Veronica Freire-Beneitez
- School of Biosciences, University of Kent, Canterbury, Kent, UK.,Laboratory of Molecular and Evolutionary Parasitology, University of Kent, Kent, UK
| | | | - Kodai Fukuda
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Paulo A García
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Boston, MA, USA
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Fatma Gomaa
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Sebastian G Gornik
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Jian Guo
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Yutaka Hanawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Esteban R Haro-Contreras
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Elisabeth Hehenberger
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrea Highfield
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - Yoshihisa Hirakawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Amanda Hopes
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | | | - Ian Hu
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jorge Ibañez
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile
| | - Nicholas A T Irwin
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yuu Ishii
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Natalia Ewa Janowicz
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Adam C Jones
- Gordon and Betty Moore Foundation, Palo Alto, CA, USA
| | - Ambar Kachale
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic
| | - Konomi Fujimura-Kamada
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Binnypreet Kaur
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic
| | | | - Eleanna Kazana
- School of Biosciences, University of Kent, Canterbury, Kent, UK.,Laboratory of Molecular and Evolutionary Parasitology, University of Kent, Kent, UK
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicole King
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Noelia Lander
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Imen Lassadi
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Zhuhong Li
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Jean-Claude Lozano
- Sorbonne Université, CNRS UMR7621, Observatoire Océanologique, Banyuls sur Mer, France
| | - Fulei Luan
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | | | - Tamara Matute
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile
| | - Cristina Miceli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Jun Minagawa
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Aichi, Japan.,Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki, Aichi, Japan
| | - Mark Moosburner
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, CA, USA.,Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
| | - Sebastián R Najle
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain.,Instituto de Biología Molecular y Celular, CONICET, and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Deepak Nanjappa
- University of Delaware College of Earth, Ocean and Environment, Lewes, DE, USA
| | - Isabel C Nimmo
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Luke Noble
- Center for Genomics and Systems Biology, New York University, New York, NY, USA.,Institute de Biologie de l'ENS, Département de biologie, École Normale Supérieure, CNRS, INSERM, Paris, France
| | - Anna M G Novák Vanclová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Isaac Nuñez
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile
| | - Arnab Pain
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Center for Zoonosis Control, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Angela Piersanti
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Jan Pyrih
- School of Biosciences, University of Kent, Canterbury, Kent, UK.,Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Joshua S Rest
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
| | - Mariana Rius
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | | | - Albane Ruaud
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile.,Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain.,Departament de Genètica Microbiologia i Estadıśtica, Universitat de Barcelona, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - Monika A Sigg
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Claudio H Slamovits
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - G Jason Smith
- Department of Environmental Biotechnology, Moss Landing Marine Laboratories, Moss Landing, CA, USA
| | | | - Rowena Stern
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - Estienne C Swart
- Institute of Cell Biology, University of Bern, Bern, Switzerland.,Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Anastasios D Tsaousis
- School of Biosciences, University of Kent, Canterbury, Kent, UK.,Laboratory of Molecular and Evolutionary Parasitology, University of Kent, Kent, UK
| | - Lev Tsypin
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA.,Department of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Aaron Turkewitz
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
| | - Jernej Turnšek
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, CA, USA.,Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Matus Valach
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - Valérie Vergé
- Sorbonne Université, CNRS UMR7621, Observatoire Océanologique, Banyuls sur Mer, France
| | - Peter von Dassow
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile.,Instituto Milenio de Oceanografia de Chile, Concepción, Chile
| | | | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Lu Wang
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Xiaoxue Wen
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Glen Wheeler
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - April Woods
- Department of Environmental Biotechnology, Moss Landing Marine Laboratories, Moss Landing, CA, USA
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich, UK.
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA. .,Ocean EcoSystems Biology Unit, Marine Ecology Division, Helmholtz Centre for Ocean Research, Kiel, Germany.
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic.
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14
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DuBuc TQ, Schnitzler CE, Chrysostomou E, McMahon ET, Febrimarsa, Gahan JM, Buggie T, Gornik SG, Hanley S, Barreira SN, Gonzalez P, Baxevanis AD, Frank U. Transcription factor AP2 controls cnidarian germ cell induction. Science 2020; 367:757-762. [PMID: 32054756 PMCID: PMC7025884 DOI: 10.1126/science.aay6782] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 12/06/2019] [Indexed: 12/18/2022]
Abstract
Clonal animals do not sequester a germ line during embryogenesis. Instead, they have adult stem cells that contribute to somatic tissues or gametes. How germ fate is induced in these animals, and whether this process is related to bilaterian embryonic germline induction, is unknown. We show that transcription factor AP2 (Tfap2), a regulator of mammalian germ lines, acts to commit adult stem cells, known as i-cells, to the germ cell fate in the clonal cnidarian Hydractinia symbiolongicarpus Tfap2 mutants lacked germ cells and gonads. Transplanted wild-type cells rescued gonad development but not germ cell induction in Tfap2 mutants. Forced expression of Tfap2 in i-cells converted them to germ cells. Therefore, Tfap2 is a regulator of germ cell commitment across germ line-sequestering and germ line-nonsequestering animals.
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Affiliation(s)
- Timothy Q DuBuc
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Christine E Schnitzler
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Eleni Chrysostomou
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Emma T McMahon
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Febrimarsa
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - James M Gahan
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Tara Buggie
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Sebastian G Gornik
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Shirley Hanley
- National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland
| | - Sofia N Barreira
- Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Gonzalez
- Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andreas D Baxevanis
- Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Uri Frank
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
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15
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Gornik SG, Hu I, Lassadi I, Waller RF. The Biochemistry and Evolution of the Dinoflagellate Nucleus. Microorganisms 2019; 7:microorganisms7080245. [PMID: 31398798 PMCID: PMC6723414 DOI: 10.3390/microorganisms7080245] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 12/14/2022] Open
Abstract
Dinoflagellates are known to possess a highly aberrant nucleus-the so-called dinokaryon-that exhibits a multitude of exceptional biological features. These include: (1) Permanently condensed chromosomes; (2) DNA in a cholesteric liquid crystalline state, (3) extremely large DNA content (up to 200 pg); and, perhaps most strikingly, (4) a deficit of histones-the canonical building blocks of all eukaryotic chromatin. Dinoflagellates belong to the Alveolata clade (dinoflagellates, apicomplexans, and ciliates) and, therefore, the biological oddities observed in dinoflagellate nuclei are derived character states. Understanding the sequence of changes that led to the dinokaryon has been difficult in the past with poor resolution of dinoflagellate phylogeny. Moreover, lack of knowledge of their molecular composition has constrained our understanding of the molecular properties of these derived nuclei. However, recent advances in the resolution of the phylogeny of dinoflagellates, particularly of the early branching taxa; the realization that divergent histone genes are present; and the discovery of dinoflagellate-specific nuclear proteins that were acquired early in dinoflagellate evolution have all thrown new light nature and evolution of the dinokaryon.
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Affiliation(s)
- Sebastian G Gornik
- Centre for Organismal Studies (COS), Universität Heidelberg, 69120 Heidelberg, Germany.
| | - Ian Hu
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Imen Lassadi
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
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16
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Abstract
In this chapter, a short evolutionary history and comparative analysis of sperm nuclear basic proteins (SNBPs) in marine invertebrates are presented based on some of the most recent publications in the field and building upon previously published reviews on the topic. Putative functions of SNBPs in sperm chromatin beyond DNA packaging will also be discussed with a primary focus on outstanding research questions.In somatic cells of all metazoans, DNA is packaged into tightly folded and dynamically accessible chromatin by canonical histones H2A, H2B, H3 and H4. Sperm chromatin of many animals, on the other hand, is organised by small yet structurally highly heterogeneous proteins called SNBPs, which can package sperm DNA on their own or in combination with each other. In extreme cases, sperm chromatin is condensed into a volume 6-10 times smaller than that of a somatic nucleus. SNBPs are classified into three major groups: H1 histone-type proteins (H-type SNBPs), protamines (P-type SNBPs) and protamine-like proteins (PL-type SNBPs). P-type SNBPs are mostly found in vertebrates, while PL-type SNBPs are ubiquitous in many invertebrate phyla. PL-type and P-type SNBPs evolved from histone H-type SNBP precursors through vertical evolution. Porifera, Ctenophora and Crustacea, Echinoidea (phylum Echinodermata) and Hydrozoa (phylum Hydrozoa) lack SNBPs. Echinoidea and Hydrozoa, however, evolved novel nucleosomal histone variants with specific roles during spermatogenesis. Seemingly, chromatin condensation plays a critical role in the silencing and tight packing of the genome within the sperm nucleus of most animals. However, the question of what necessitates the compaction of some sperm DNA beyond classical nucleosomal packaging while other sperm function using 'normal' histones remains unanswered to date.
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Affiliation(s)
- Anna Török
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
| | - Sebastian G Gornik
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany.
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17
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Gahan JM, Schnitzler CE, DuBuc TQ, Doonan LB, Kanska J, Gornik SG, Barreira S, Thompson K, Schiffer P, Baxevanis AD, Frank U. Functional studies on the role of Notch signaling in Hydractinia development. Dev Biol 2017; 428:224-231. [PMID: 28601529 DOI: 10.1016/j.ydbio.2017.06.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/06/2017] [Accepted: 06/06/2017] [Indexed: 11/19/2022]
Abstract
The function of Notch signaling was previously studied in two cnidarians, Hydra and Nematostella, representing the lineages Hydrozoa and Anthozoa, respectively. Using pharmacological inhibition in Hydra and a combination of pharmacological and genetic approaches in Nematostella, it was shown in both animals that Notch is required for tentacle morphogenesis and for late stages of stinging cell maturation. Surprisingly, a role for Notch in neural development, which is well documented in bilaterians, was evident in embryonic Nematostella but not in adult Hydra. Adult neurogenesis in the latter seemed to be unaffected by DAPT, a drug that inhibits Notch signaling. To address this apparent discrepancy, we studied the role of Notch in Hydractinia echinata, an additional hydrozoan, in all life stages. Using CRISPR-Cas9 mediated mutagenesis, transgenesis, and pharmacological interference we show that Notch is dispensable for Hydractinia normal neurogenesis in all life stages but is required for the maturation of stinging cells and for tentacle morphogenesis. Our results are consistent with a conserved role for Notch in morphogenesis and nematogenesis across Cnidaria, and a lineage-specific loss of Notch dependence in neurogenesis in hydrozoans.
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Affiliation(s)
- James M Gahan
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Christine E Schnitzler
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 320803, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA; Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Timothy Q DuBuc
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Liam B Doonan
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Justyna Kanska
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Sebastian G Gornik
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Sofia Barreira
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kerry Thompson
- Centre for Microscopy and Imaging, Discipline of Anatomy, School of Medicine, National University of Ireland, Galway, Galway, Ireland
| | - Philipp Schiffer
- Department for Genetics Environment and Evolution, University College London, London, UK
| | - Andreas D Baxevanis
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Uri Frank
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
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18
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Török A, Schiffer PH, Schnitzler CE, Ford K, Mullikin JC, Baxevanis AD, Bacic A, Frank U, Gornik SG. The cnidarian Hydractinia echinata employs canonical and highly adapted histones to pack its DNA. Epigenetics Chromatin 2016; 9:36. [PMID: 27602058 PMCID: PMC5011920 DOI: 10.1186/s13072-016-0085-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/24/2016] [Indexed: 11/25/2022] Open
Abstract
Background Cnidarians are a group of early branching animals including corals, jellyfish and hydroids that are renowned for their high regenerative ability, growth plasticity and longevity. Because cnidarian genomes are conventional in terms of protein-coding genes, their remarkable features are likely a consequence of epigenetic regulation. To facilitate epigenetics research in cnidarians, we analysed the histone complement of the cnidarian model organism Hydractinia echinata using phylogenomics, proteomics, transcriptomics and mRNA in situ hybridisations. Results We find that the Hydractinia genome encodes 19 histones and analyse their spatial expression patterns, genomic loci and replication-dependency. Alongside core and other replication-independent histone variants, we find several histone replication-dependent variants, including a rare replication-dependent H3.3, a female germ cell-specific H2A.X and an unusual set of five H2B variants, four of which are male germ cell-specific. We further confirm the absence of protamines in Hydractinia. Conclusions Since no protamines are found in hydroids, we suggest that the novel H2B variants are pivotal for sperm DNA packaging in this class of Cnidaria. This study adds to the limited number of full histone gene complements available in animals and sets a comprehensive framework for future studies on the role of histones and their post-translational modifications in cnidarian epigenetics. Finally, it provides insight into the evolution of spermatogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0085-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Török
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Philipp H Schiffer
- Genetics Environment and Evolution, University College London, London, UK
| | - Christine E Schnitzler
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA ; Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080 USA
| | - Kris Ford
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080 USA ; Australian Research Council Centre of Excellence in Plant Cell Walls, School of Biosciences, The University of Melbourne, Parkville, VIC 3010 Australia
| | - James C Mullikin
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA ; NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Rockville, MD 20852 USA
| | - Andreas D Baxevanis
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Antony Bacic
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Biosciences, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Uri Frank
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Sebastian G Gornik
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Ireland
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19
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Waller RF, Gornik SG, Koreny L, Pain A. Metabolic pathway redundancy within the apicomplexan-dinoflagellate radiation argues against an ancient chromalveolate plastid. Commun Integr Biol 2015; 9:e1116653. [PMID: 27066182 PMCID: PMC4802802 DOI: 10.1080/19420889.2015.1116653] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 10/30/2015] [Accepted: 10/30/2015] [Indexed: 11/06/2022] Open
Abstract
The chromalveolate hypothesis presents an attractively simple explanation for the presence of red algal-derived secondary plastids in 5 major eukaryotic lineages: “chromista” phyla, cryptophytes, haptophytes and ochrophytes; and alveolate phyla, dinoflagellates and apicomplexans. It posits that a single secondary endosymbiotic event occurred in a common ancestor of these diverse groups, and that this ancient plastid has since been maintained by vertical inheritance only. Substantial testing of this hypothesis by molecular phylogenies has, however, consistently failed to provide support for the predicted monophyly of the host organisms that harbour these plastids—the “chromalveolates.” This lack of support does not disprove the chromalveolate hypothesis per se, but rather drives the proposed endosymbiosis deeper into the eukaryotic tree, and requires multiple plastid losses to have occurred within intervening aplastidic lineages. An alternative perspective on plastid evolution is offered by considering the metabolic partnership between the endosymbiont and its host cell. A recent analysis of metabolic pathways in a deep-branching dinoflagellate indicates a high level of pathway redundancy in the common ancestor of apicomplexans and dinoflagellates, and differential losses of these pathways soon after radiation of the major extant lineages. This suggests that vertical inheritance of an ancient plastid in alveolates is highly unlikely as it would necessitate maintenance of redundant pathways over very long evolutionary timescales.
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Affiliation(s)
- Ross F Waller
- Department of Biochemistry, University of Cambridge , Cambridge, UK
| | - Sebastian G Gornik
- School of Natural Sciences, National University of Ireland Galway , Galway, Ireland
| | - Ludek Koreny
- Department of Biochemistry, University of Cambridge , Cambridge, UK
| | - Arnab Pain
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology , Thuwal, Saudi Arabia
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20
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Woo YH, Ansari H, Otto TD, Klinger CM, Kolisko M, Michálek J, Saxena A, Shanmugam D, Tayyrov A, Veluchamy A, Ali S, Bernal A, del Campo J, Cihlář J, Flegontov P, Gornik SG, Hajdušková E, Horák A, Janouškovec J, Katris NJ, Mast FD, Miranda-Saavedra D, Mourier T, Naeem R, Nair M, Panigrahi AK, Rawlings ND, Padron-Regalado E, Ramaprasad A, Samad N, Tomčala A, Wilkes J, Neafsey DE, Doerig C, Bowler C, Keeling PJ, Roos DS, Dacks JB, Templeton TJ, Waller RF, Lukeš J, Oborník M, Pain A. Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. eLife 2015; 4:e06974. [PMID: 26175406 PMCID: PMC4501334 DOI: 10.7554/elife.06974] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 06/16/2015] [Indexed: 12/18/2022] Open
Abstract
The eukaryotic phylum Apicomplexa encompasses thousands of obligate intracellular parasites of humans and animals with immense socio-economic and health impacts. We sequenced nuclear genomes of Chromera velia and Vitrella brassicaformis, free-living non-parasitic photosynthetic algae closely related to apicomplexans. Proteins from key metabolic pathways and from the endomembrane trafficking systems associated with a free-living lifestyle have been progressively and non-randomly lost during adaptation to parasitism. The free-living ancestor contained a broad repertoire of genes many of which were repurposed for parasitic processes, such as extracellular proteins, components of a motility apparatus, and DNA- and RNA-binding protein families. Based on transcriptome analyses across 36 environmental conditions, Chromera orthologs of apicomplexan invasion-related motility genes were co-regulated with genes encoding the flagellar apparatus, supporting the functional contribution of flagella to the evolution of invasion machinery. This study provides insights into how obligate parasites with diverse life strategies arose from a once free-living phototrophic marine alga. DOI:http://dx.doi.org/10.7554/eLife.06974.001 Single-celled parasites cause many severe diseases in humans and animals. The apicomplexans form probably the most successful group of these parasites and include the parasites that cause malaria. Apicomplexans infect a broad range of hosts, including humans, reptiles, birds, and insects, and often have complicated life cycles. For example, the malaria-causing parasites spread by moving from humans to female mosquitoes and then back to humans. Despite significant differences amongst apicomplexans, these single-celled parasites also share a number of features that are not seen in other living species. How and when these features arose remains unclear. It is known from previous work that apicomplexans are closely related to single-celled algae. But unlike apicomplexans, which depend on a host animal to survive, these algae live freely in their environment, often in close association with corals. Woo et al. have now sequenced the genomes of two photosynthetic algae that are thought to be close living relatives of the apicomplexans. These genomes were then compared to each other and to the genomes of other algae and apicomplexans. These comparisons reconfirmed that the two algae that were studied were close relatives of the apicomplexans. Further analyses suggested that thousands of genes were lost as an ancient free-living algae evolved into the apicomplexan ancestor, and further losses occurred as these early parasites evolved into modern species. The lost genes were typically those that are important for free-living organisms, but are either a hindrance to, or not needed in, a parasitic lifestyle. Some of the ancestor's genes, especially those that coded for the building blocks of flagella (structures which free-living algae use to move around), were repurposed in ways that helped the apicomplexans to invade their hosts. Understanding this repurposing process in greater detail will help to identify key molecules in these deadly parasites that could be targeted by drug treatments. It will also offer answers to one of the most fascinating questions in evolutionary biology: how parasites have evolved from free-living organisms. DOI:http://dx.doi.org/10.7554/eLife.06974.002
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Affiliation(s)
- Yong H Woo
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Hifzur Ansari
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Thomas D Otto
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | | | - Martin Kolisko
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, Canada
| | - Jan Michálek
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Alka Saxena
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | - Annageldi Tayyrov
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Alaguraj Veluchamy
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197 INSERM U1024, Paris, France
| | - Shahjahan Ali
- Bioscience Core Laboratory, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Axel Bernal
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Javier del Campo
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, Canada
| | - Jaromír Cihlář
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Pavel Flegontov
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | | | - Eva Hajdušková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jan Janouškovec
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, Canada
| | | | - Fred D Mast
- Seattle Biomedical Research Institute, Seattle, United States
| | - Diego Miranda-Saavedra
- Centro de Biología Molecular Severo Ochoa, CSIC/Universidad Autónoma de Madrid, Madrid, Spain
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Raeece Naeem
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Mridul Nair
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Aswini K Panigrahi
- Bioscience Core Laboratory, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Neil D Rawlings
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Eriko Padron-Regalado
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Abhinay Ramaprasad
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Nadira Samad
- School of Botany, University of Melbourne, Parkville, Australia
| | - Aleš Tomčala
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jon Wilkes
- Wellcome Trust Centre For Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Daniel E Neafsey
- Broad Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, United States
| | - Christian Doerig
- Department of Microbiology, Monash University, Clayton, Australia
| | - Chris Bowler
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197 INSERM U1024, Paris, France
| | - Patrick J Keeling
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, Canada
| | - David S Roos
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Joel B Dacks
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Thomas J Templeton
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - Ross F Waller
- School of Botany, University of Melbourne, Parkville, Australia
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Miroslav Oborník
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Arnab Pain
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Gornik SG, Cranenburgh A, Waller RF. New host range for Hematodinium in southern Australia and novel tools for sensitive detection of parasitic dinoflagellates. PLoS One 2013; 8:e82774. [PMID: 24324829 PMCID: PMC3855790 DOI: 10.1371/journal.pone.0082774] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 10/28/2013] [Indexed: 11/21/2022] Open
Abstract
Hematodinium is a parasitic dinoflagellate and emerging pathogen of crustaceans. It preferably manifests in haemolymph of marine decapod crustaceans, killing a large variety of genera with significant impacts on fisheries worldwide. There is, however, evidence that some crustacean stocks harbor high prevalence, low intensity infections that may not result in widespread host mortality and are therefore hard to detect. The most widely used methods for detection of Hematodinium are conventional blood smears and polymerase chain reaction (PCR) against ribosomal RNAs. Blood smears demand a trained investigator, are labor intensive and not readily scalable for high-throughput sampling. PCRs only detect parasite DNA and can also suffer from false negatives and positives. In order to develop alternative detection tools for Hematodinium cells in decapod crustaceans we employed an immunological approach against a newly identified, abundant dinoflagellate-specific nuclear protein—Dinoflagellate/Viral NucleoProtein (DVNP). Both immunofluorescence assay (IFA) and Western blot methods against DVNP showed high sensitivity of detection. The Western blot detects Hematodinium parasites to levels of 25 parasites per milliliter of crustacean haemolymph, with the potential for sample pooling and screening of large samples. Using both PCR and these new tools, we have identified Hematodinium cells present in three new host crab taxa, at high prevalence but with no sign of pathogenesis. This extends the known range of Hematodinium to southern Australia.
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Affiliation(s)
- Sebastian G. Gornik
- School of Botany, University of Melbourne, Melbourne, Victoria, Australia
- * E-mail: (RFW); (SGG)
| | - Andrea Cranenburgh
- School of Botany, University of Melbourne, Melbourne, Victoria, Australia
| | - Ross F. Waller
- School of Botany, University of Melbourne, Melbourne, Victoria, Australia
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (RFW); (SGG)
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Bachvaroff TR, Gornik SG, Concepcion GT, Waller RF, Mendez GS, Lippmeier JC, Delwiche CF. Dinoflagellate phylogeny revisited: using ribosomal proteins to resolve deep branching dinoflagellate clades. Mol Phylogenet Evol 2013; 70:314-22. [PMID: 24135237 DOI: 10.1016/j.ympev.2013.10.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 09/24/2013] [Accepted: 10/07/2013] [Indexed: 10/26/2022]
Abstract
The alveolates are composed of three major lineages, the ciliates, dinoflagellates, and apicomplexans. Together these 'protist' taxa play key roles in primary production and ecology, as well as in illness of humans and other animals. The interface between the dinoflagellate and apicomplexan clades has been an area of recent discovery, blurring the distinction between these two clades. Moreover, phylogenetic analysis has yet to determine the position of basal dinoflagellate clades hence the deepest branches of the dinoflagellate tree currently remain unresolved. Large-scale mRNA sequencing was applied to 11 species of dinoflagellates, including strains of the syndinean genera Hematodinium and Amoebophrya, parasites of crustaceans and dinoflagellates, respectively, to optimize and update the dinoflagellate tree. From the transcriptome-scale data a total of 73 ribosomal protein-coding genes were selected for phylogeny. After individual gene orthology assessment, the genes were concatenated into a >15,000 amino acid alignment with 76 taxa from dinoflagellates, apicomplexans, ciliates, and the outgroup heterokonts. Overall the tree was well resolved and supported, when the data was subsampled with gblocks or constraint trees were tested with the approximately unbiased test. The deepest branches of the dinoflagellate tree can now be resolved with strong support, and provides a clearer view of the evolution of the distinctive traits of dinoflagellates.
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Affiliation(s)
- Tsvetan R Bachvaroff
- Smithsonian Environmental Research Center, 647 Contees Wharf Rd., Edgewater, MD 21037, United States.
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Abstract
Dinoflagellates are known for their development of highly aberrant organelle genetic systems. Both their plastid and mitochondrial genomes are extremely reduced in gene number and rearranged into numerous unconventional genomic elements. Transcription processes are also elaborately modified including extensive RNA editing and trans-splicing. Some dinoflagellates have replaced their original plastid through serial endosymbiotic events. Karlodinium veneficum is such an example that now contains a haptophyte plastid. This tertiary plastid provides a case of a more conventional genetic system introduced into a cellular environment with a known penchant for genetic oddities. Here, we show that K. veneficum plastid transcripts undergo extensive substitutional editing. The substitution types are more diverse than those seen in most other plastids but are similar to those of dinoflagellate organelles. There is no evidence for RNA editing of plastid-encoded transcripts from extant haptophytes, suggesting that K. veneficum plastid editing developed after the uptake of the tertiary endosymbiont.
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Danne JC, Gornik SG, Macrae JI, McConville MJ, Waller RF. Alveolate mitochondrial metabolic evolution: dinoflagellates force reassessment of the role of parasitism as a driver of change in apicomplexans. Mol Biol Evol 2012; 30:123-39. [PMID: 22923466 DOI: 10.1093/molbev/mss205] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mitochondrial metabolism is central to the supply of ATP and numerous essential metabolites in most eukaryotic cells. Across eukaryotic diversity, however, there is evidence of much adaptation of the function of this organelle according to specific metabolic requirements and/or demands imposed by different environmental niches. This includes substantial loss or retailoring of mitochondrial function in many parasitic groups that occupy potentially nutrient-rich environments in their metazoan hosts. Infrakingdom Alveolata comprises a well-supported alliance of three disparate eukaryotic phyla-dinoflagellates, apicomplexans, and ciliates. These major taxa represent diverse lifestyles of free-living phototrophs, parasites, and predators and offer fertile territory for exploring character evolution in mitochondria. The mitochondria of apicomplexan parasites provide much evidence of loss or change of function from analysis of mitochondrial protein genes. Much less, however, is known of mitochondrial function in their closest relatives, the dinoflagellate algae. In this study, we have developed new models of mitochondrial metabolism in dinoflagellates based on gene predictions and stable isotope labeling experiments. These data show that many changes in mitochondrial gene content previously only known from apicomplexans are found in dinoflagellates also. For example, loss of the pyruvate dehydrogenase complex and changes in tricarboxylic acid (TCA) cycle enzyme complement are shared by both groups and, therefore, represent ancestral character states. Significantly, we show that these changes do not result in loss of typical TCA cycle activity fueled by pyruvate. Thus, dinoflagellate data show that many changes in alveolate mitochondrial metabolism are independent of the major lifestyle changes seen in these lineages and provide a revised view of mitochondria character evolution during evolution of parasitism in apicomplexans.
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Affiliation(s)
- Jillian C Danne
- School of Botany, University of Melbourne, Victoria, Australia
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Danne JC, Gornik SG, Waller RF. An Assessment of Vertical Inheritance versus Endosymbiont Transfer of Nucleus-encoded Genes for Mitochondrial Proteins Following Tertiary Endosymbiosis in Karlodinium micrum. Protist 2012; 163:76-90. [DOI: 10.1016/j.protis.2011.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 03/27/2011] [Indexed: 11/30/2022]
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Jackson CJ, Gornik SG, Waller RF. The mitochondrial genome and transcriptome of the basal dinoflagellate Hematodinium sp.: character evolution within the highly derived mitochondrial genomes of dinoflagellates. Genome Biol Evol 2011; 4:59-72. [PMID: 22113794 PMCID: PMC3268668 DOI: 10.1093/gbe/evr122] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The sister phyla dinoflagellates and apicomplexans inherited a drastically reduced mitochondrial genome (mitochondrial DNA, mtDNA) containing only three protein-coding (cob, cox1, and cox3) genes and two ribosomal RNA (rRNA) genes. In apicomplexans, single copies of these genes are encoded on the smallest known mtDNA chromosome (6 kb). In dinoflagellates, however, the genome has undergone further substantial modifications, including massive genome amplification and recombination resulting in multiple copies of each gene and gene fragments linked in numerous combinations. Furthermore, protein-encoding genes have lost standard stop codons, trans-splicing of messenger RNAs (mRNAs) is required to generate complete cox3 transcripts, and extensive RNA editing recodes most genes. From taxa investigated to date, it is unclear when many of these unusual dinoflagellate mtDNA characters evolved. To address this question, we investigated the mitochondrial genome and transcriptome character states of the deep branching dinoflagellate Hematodinium sp. Genomic data show that like later-branching dinoflagellates Hematodinium sp. also contains an inflated, heavily recombined genome of multicopy genes and gene fragments. Although stop codons are also lacking for cox1 and cob, cox3 still encodes a conventional stop codon. Extensive editing of mRNAs also occurs in Hematodinium sp. The mtDNA of basal dinoflagellate Hematodinium sp. indicates that much of the mtDNA modification in dinoflagellates occurred early in this lineage, including genome amplification and recombination, and decreased use of standard stop codons. Trans-splicing, on the other hand, occurred after Hematodinium sp. diverged. Only RNA editing presents a nonlinear pattern of evolution in dinoflagellates as this process occurs in Hematodinium sp. but is absent in some later-branching taxa indicating that this process was either lost in some lineages or developed more than once during the evolution of the highly unusual dinoflagellate mtDNA.
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Affiliation(s)
- C J Jackson
- School of Botany, University of Melbourne, Australia
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Albalat A, Gornik SG, Mullen W, Crozier A, Atkinson RJA, Coombs GH, Neil DM. Quality changes in chilled Norway lobster (Nephrops norvegicus) tail meat and the effects of delayed icing. Int J Food Sci Technol 2011. [DOI: 10.1111/j.1365-2621.2011.02650.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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