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Girich AS. WntA and Wnt4 during the regeneration of internal organs in the holothurian Eupentacta fraudatrix. Genesis 2024; 62:e23562. [PMID: 37846177 DOI: 10.1002/dvg.23562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/18/2023]
Abstract
BACKGROUND Over the past few years, it has been established that wnt genes are involved in the regenerative processes of holothurians. The wnt4 gene was identified as one of the most active genes in Eupentacta fraudatrix regeneration using differential gene expression analysis and qPCR of individual genes. Also, the wntA gene was found in holothurians, which is present only in invertebrates and can perform unique functions. RESULTS In this regard, both these genes and proteins were studied in this work. During regeneration, the Wnt4 protein is found in the cells of the coelomic and ambulacral epithelium, retractor muscles, and radial nerves. Single cells with this protein are also found in the connective tissue of the developing aquapharyngeal bulb and in the hypoderm of the body wall. Cells with WntA are found exclusively in the hypoderm of the body wall. CONCLUSION We assume that both genes are involved in regeneration, but Wnt4 coordinates the formation of the epithelial tissue structure, while WntA maintains the state of the intercellular substance of the body wall.
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Affiliation(s)
- A S Girich
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
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2
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Melotti L, Venerando A, Zivelonghi G, Carolo A, Marzorati S, Martinelli G, Sugni M, Maccatrozzo L, Patruno M. A Second Life for Seafood Waste: Therapeutical Promises of Polyhydroxynapthoquinones Extracted from Sea Urchin by-Products. Antioxidants (Basel) 2023; 12:1730. [PMID: 37760033 PMCID: PMC10526080 DOI: 10.3390/antiox12091730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/02/2023] [Accepted: 09/03/2023] [Indexed: 09/29/2023] Open
Abstract
Coping with a zero-waste, more sustainable economy represents the biggest challenge for food market nowadays. We have previously demonstrated that by applying smart multidisciplinary waste management strategies to purple sea urchin (Paracentrotus lividus) food waste, it is possible to obtain both a high biocompatible collagen to produce novel skin substitutes and potent antioxidant pigments, namely polyhydroxynapthoquinones (PHNQs). Herein, we have analyzed the biological activities of the PHNQs extract, composed of Spinochrome A and B, on human skin fibroblast cells to explore their future applicability in the treatment of non-healing skin wounds with the objective of overcoming the excessive oxidative stress that hinders wound tissue regeneration. Our results clearly demonstrate that the antioxidant activity of PHNQs is not restricted to their ability to scavenge reactive oxygen species; rather, it can be traced back to an upregulating effect on the expression of superoxide dismutase 1, one of the major components of the endogenous antioxidant enzymes defense system. In addition, the PHNQs extract, in combination with Antimycin A, displayed a synergistic pro-apoptotic effect, envisaging its possible employment against chemoresistance in cancer treatments. Overall, this study highlights the validity of a zero-waste approach in the seafood chain to obtain high-value products, which, in turn, may be exploited for different biomedical applications.
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Affiliation(s)
- Luca Melotti
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell’Università 16, 35020 Padova, Italy; (L.M.); (G.Z.); (A.C.); (L.M.); (M.P.)
| | - Andrea Venerando
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy
| | - Giulia Zivelonghi
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell’Università 16, 35020 Padova, Italy; (L.M.); (G.Z.); (A.C.); (L.M.); (M.P.)
| | - Anna Carolo
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell’Università 16, 35020 Padova, Italy; (L.M.); (G.Z.); (A.C.); (L.M.); (M.P.)
| | - Stefania Marzorati
- Department of Environmental Science and Policy, University of Milan, Via Celoria 2, 20133 Milan, Italy; (S.M.); (G.M.); (M.S.)
| | - Giordana Martinelli
- Department of Environmental Science and Policy, University of Milan, Via Celoria 2, 20133 Milan, Italy; (S.M.); (G.M.); (M.S.)
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, Via Celoria 2, 20133 Milan, Italy; (S.M.); (G.M.); (M.S.)
| | - Lisa Maccatrozzo
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell’Università 16, 35020 Padova, Italy; (L.M.); (G.Z.); (A.C.); (L.M.); (M.P.)
| | - Marco Patruno
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell’Università 16, 35020 Padova, Italy; (L.M.); (G.Z.); (A.C.); (L.M.); (M.P.)
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Kor G, Mengal K, Buřič M, Kozák P, Niksirat H. Granules of immune cells are the source of organelles in the regenerated nerves of crayfish antennae. FISH & SHELLFISH IMMUNOLOGY 2023; 137:108787. [PMID: 37141955 DOI: 10.1016/j.fsi.2023.108787] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/24/2023] [Accepted: 04/30/2023] [Indexed: 05/06/2023]
Abstract
Regeneration refers to the regrowing and replacing of injured or lost body parts. Crayfish antennae are nervous organs that are crucial for perceiving environmental signals. Immune cells (hemocytes) are responsible for neurogenesis in crayfish. Here, we used transmission electron microscopy to investigate at ultrastructural levels the potential roles of immune cells in nerve regeneration in crayfish antennae after amputation. The results showed that, while all three types of hemocytes were observed during nerve regeneration, granules of semi-granulocytes and granulocytes are the main sources of new organelles such as mitochondria, the Golgi apparatus and nerve fibres in the regenerated nerves of crayfish antennae. We describe the transformation of immune cell granules into different organelles in the regenerating nerve at ultrastructural levels. Also, we observed that the regeneration process speeds up after crayfish moulting. In conclusion, the granules are compacted packages of versatile materials carried by immune cells and can be converted into different organelles during nerve regeneration in crayfish antennae.
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Affiliation(s)
- Golara Kor
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czech Republic.
| | - Kifayatullah Mengal
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Miloš Buřič
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Pavel Kozák
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Hamid Niksirat
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czech Republic.
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4
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Shaw CG, Pavloudi C, Barela Hudgell MA, Crow RS, Saw JH, Pyron RA, Smith LC. Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium. Pathog Dis 2023; 81:ftad025. [PMID: 37715299 PMCID: PMC10550250 DOI: 10.1093/femspd/ftad025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/09/2023] [Accepted: 09/14/2023] [Indexed: 09/17/2023] Open
Abstract
Bald sea urchin disease (BSUD) is most likely a bacterial infection that occurs in a wide range of sea urchin species and causes the loss of surface appendages. The disease has a variety of additional symptoms, which may be the result of the many bacteria that are associated with BSUD. Previous studies have investigated causative agents of BSUD, however, there are few reports on the surface microbiome associated with the infection. Here, we report changes to the surface microbiome on purple sea urchins in a closed marine aquarium that contracted and then recovered from BSUD in addition to the microbiome of healthy sea urchins in a separate aquarium. 16S rRNA gene sequencing shows that microhabitats of different aquaria are characterized by different microbial compositions, and that diseased, recovered, and healthy sea urchins have distinct microbial compositions, which indicates that there is a correlation between microbial shifts and recovery from disease.
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Affiliation(s)
- Chloe G Shaw
- Department of Biological Sciences, Suite 6000 Science and Engineering Hall, 800 22nd St NW, Washington DC 20052, United States
| | - Christina Pavloudi
- Department of Biological Sciences, Suite 6000 Science and Engineering Hall, 800 22nd St NW, Washington DC 20052, United States
| | - Megan A Barela Hudgell
- Department of Biological Sciences, Suite 6000 Science and Engineering Hall, 800 22nd St NW, Washington DC 20052, United States
| | - Ryley S Crow
- Department of Biological Sciences, Suite 6000 Science and Engineering Hall, 800 22nd St NW, Washington DC 20052, United States
| | - Jimmy H Saw
- Department of Biological Sciences, Suite 6000 Science and Engineering Hall, 800 22nd St NW, Washington DC 20052, United States
| | - R Alexander Pyron
- Department of Biological Sciences, Suite 6000 Science and Engineering Hall, 800 22nd St NW, Washington DC 20052, United States
| | - L Courtney Smith
- Department of Biological Sciences, Suite 6000 Science and Engineering Hall, 800 22nd St NW, Washington DC 20052, United States
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5
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Zhang X, Liu X, Peng J, Song S, Xu G, Yang N, Wu S, Wang L, Wang S, Zhang L, Liu Y, Liang P, Hong L, Xu Z, Song C. Genome-Wide mRNA and Long Non-Coding RNA Analysis of Porcine Trophoblast Cells Infected with Porcine Reproductive and Respiratory Syndrome Virus Associated with Reproductive Failure. Int J Mol Sci 2023; 24:ijms24020919. [PMID: 36674446 PMCID: PMC9866684 DOI: 10.3390/ijms24020919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/30/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
Porcine reproductive and respiratory syndrome (PRRS) is a vertically transmitted reproductive disorder that is typically characterized by miscarriage, premature birth, and stillbirth in pregnant sows after infection. Such characteristics indicate that PRRSV can infect and penetrate the porcine placental barrier to infect fetus piglets. The porcine trophoblast is an important component of the placental barrier, and secretes various hormones, including estrogen and progesterone, to maintain normal pregnancy and embryonic development during pregnancy. It is conceivable that the pathogenic effects of PRRSV infection on porcine trophoblast cells may lead to reproductive failure; however, the underlying detailed mechanism of the interaction between porcine trophoblast (PTR2) cells and PRRSV is unknown. Therefore, we conducted genome-wide mRNA and long non-coding RNA (lncRNA) analysis profiling in PRRSV-infected PTR2. The results showed that 672 mRNAs and 476 lncRNAs were significantly different from the control group after viral infection. Target genes of the co-expression and co-location of differential mRNAs and lncRNAs were enriched by GO (gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, revealing that most of the pathways were involved in cell nutrient metabolism, cell proliferation, and differentiation. Specifically, the estrogen signaling pathway, the PI3K (PhosphoInositide-3 Kinase)-Akt (serine/threonine kinase) signaling pathway, and the insulin secretion related to embryonic development were selected for analysis. Further research found that PRRSV inhibits the expression of G-protein-coupled estrogen receptor 1 (GPER1), thereby reducing estrogen-induced phosphorylation of AKT and the mammalian target of rapamycin (mTOR). The reduction in the phosphorylation of AKT and mTOR blocks the activation of the GPER1- PI3K-AKT-mTOR signaling pathway, consequently restraining insulin secretion, impacting PTR2 cell proliferation, differentiation, and nutrient metabolism. We also found that PRRSV triggered trophoblast cell apoptosis, interrupting the integrity of the placental villus barrier. Furthermore, the interaction network diagram of lncRNA, regulating GPER1 and apoptosis-related genes, was constructed, providing a reference for enriching the functions of these lncRNA in the future. In summary, this article elucidated the differential expression of mRNA and lncRNA in trophoblast cells infected with PRRSV. This infection could inhibit the PI3K-AKT-mTOR pathway and trigger apoptosis, providing insight into the mechanism of the vertical transmission of PRRSV and the manifestation of reproductive failure.
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Affiliation(s)
- Xinming Zhang
- College of Animal Science & National Engineering Center for Swine Breeding Industry, South China Agriculture University, Guangzhou 510642, China
- Lingnan Modern Agricultural Science and Technology Guangdong Laboratory, Guangzhou 510000, China
| | - Xianhui Liu
- College of Animal Science & National Engineering Center for Swine Breeding Industry, South China Agriculture University, Guangzhou 510642, China
- Lingnan Modern Agricultural Science and Technology Guangdong Laboratory, Guangzhou 510000, China
| | - Jiawei Peng
- College of Animal Science & National Engineering Center for Swine Breeding Industry, South China Agriculture University, Guangzhou 510642, China
- Lingnan Modern Agricultural Science and Technology Guangdong Laboratory, Guangzhou 510000, China
| | - Sunyangzi Song
- College of Biological Science, University of California-Davis, Davis, CA 95616, USA
| | - Ge Xu
- College of Animal Science & National Engineering Center for Swine Breeding Industry, South China Agriculture University, Guangzhou 510642, China
- Lingnan Modern Agricultural Science and Technology Guangdong Laboratory, Guangzhou 510000, China
| | - Ningjia Yang
- College of Animal Science & National Engineering Center for Swine Breeding Industry, South China Agriculture University, Guangzhou 510642, China
- Lingnan Modern Agricultural Science and Technology Guangdong Laboratory, Guangzhou 510000, China
| | - Shoutang Wu
- College of Animal Science & National Engineering Center for Swine Breeding Industry, South China Agriculture University, Guangzhou 510642, China
- Lingnan Modern Agricultural Science and Technology Guangdong Laboratory, Guangzhou 510000, China
| | - Lin Wang
- College of Animal Science & National Engineering Center for Swine Breeding Industry, South China Agriculture University, Guangzhou 510642, China
- Lingnan Modern Agricultural Science and Technology Guangdong Laboratory, Guangzhou 510000, China
| | - Shuangyun Wang
- College of Animal Science & National Engineering Center for Swine Breeding Industry, South China Agriculture University, Guangzhou 510642, China
- Lingnan Modern Agricultural Science and Technology Guangdong Laboratory, Guangzhou 510000, China
| | - Leyi Zhang
- College of Animal Science & National Engineering Center for Swine Breeding Industry, South China Agriculture University, Guangzhou 510642, China
- Lingnan Modern Agricultural Science and Technology Guangdong Laboratory, Guangzhou 510000, China
| | - Yanling Liu
- College of Animal Science & National Engineering Center for Swine Breeding Industry, South China Agriculture University, Guangzhou 510642, China
- Lingnan Modern Agricultural Science and Technology Guangdong Laboratory, Guangzhou 510000, China
| | - Pengshuai Liang
- College of Animal Science & National Engineering Center for Swine Breeding Industry, South China Agriculture University, Guangzhou 510642, China
- Lingnan Modern Agricultural Science and Technology Guangdong Laboratory, Guangzhou 510000, China
| | - Linjun Hong
- College of Animal Science & National Engineering Center for Swine Breeding Industry, South China Agriculture University, Guangzhou 510642, China
- Lingnan Modern Agricultural Science and Technology Guangdong Laboratory, Guangzhou 510000, China
| | - Zheng Xu
- College of Animal Science & National Engineering Center for Swine Breeding Industry, South China Agriculture University, Guangzhou 510642, China
- Lingnan Modern Agricultural Science and Technology Guangdong Laboratory, Guangzhou 510000, China
- Correspondence: (Z.X.); (C.S.)
| | - Changxu Song
- College of Animal Science & National Engineering Center for Swine Breeding Industry, South China Agriculture University, Guangzhou 510642, China
- Lingnan Modern Agricultural Science and Technology Guangdong Laboratory, Guangzhou 510000, China
- Correspondence: (Z.X.); (C.S.)
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Mittal V, Reid RW, Machado DJ, Mashanov V, Janies DA. EchinoDB: an update to the web-based application for genomic and transcriptomic data on echinoderms. BMC Genom Data 2022; 23:75. [PMID: 36274129 PMCID: PMC9590158 DOI: 10.1186/s12863-022-01090-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Here we release a new version of EchinoDB, EchinoDB v2.0 ( https://echinodb.uncc.edu ). EchinoDB is a database of genomic and transcriptomic data on echinoderms. The initial database consisted of groups of 749,397 orthologous and paralogous transcripts arranged in orthoclusters by sequence similarity. RESULTS The updated version of EchinoDB includes two new major datasets: the RNA-Seq data of the brittle star Ophioderma brevispinum and the high-quality genomic assembly data of the green sea urchin Lytechinus variegatus. In addition, we enabled keyword searches for annotated data and installed an updated version of Sequenceserver to allow Basic Local Alignment Search Tool (BLAST) searches. The data are downloadable in FASTA format. The first version of EchinoDB appeared in 2016 and was implemented in GO on a local server. The new version has been updated using R Shiny to include new features and improvements in the application. Furthermore, EchinoDB now runs entirely in the cloud for increased reliability and scaling. CONCLUSION EchinoDB serves a user base drawn from the fields of phylogenetics, developmental biology, genomics, physiology, neurobiology, and regeneration. As use cases, we illustrate the function of EchinoDB in retrieving components of signaling pathways involved in the tissue regeneration process of different echinoderms, including the emerging model species Ophioderma brevispinum. Moreover, we use EchinoDB to shed light on the conservation of the molecular components involved in two echinoderm-specific phenomena: spicule matrix proteins involved in the formation of stereom endoskeleton and the tensilin protein that contributes to the capacity of the connective tissues to quickly change its mechanical properties. The genes involved in the former had been previously studied in echinoids, while gene sequences involved in the latter had been previously described in holothuroids. Specifically, we ask (a) if the biomineralization-related proteins previously reported only in sea urchins are also present in other, non-echinoid, echinoderms and (b) if tensilin, the protein responsible for the control of stiffness of the mutable collagenous tissue, previously described in sea cucumbers, is conserved across the phylum.
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Affiliation(s)
- Varnika Mittal
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC, 28223, USA.
| | - Robert W Reid
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC, 28223, USA
| | - Denis Jacob Machado
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC, 28223, USA
| | - Vladimir Mashanov
- Wake Forest Institute for Regenerative Medicine, 91 Technology Way NE, Winston-Salem, NC, 27101, USA
| | - Daniel A Janies
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC, 28223, USA
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Su F, Yang H, Sun L. A Review of Histocytological Events and Molecular Mechanisms Involved in Intestine Regeneration in Holothurians. BIOLOGY 2022; 11:1095. [PMID: 35892951 PMCID: PMC9332576 DOI: 10.3390/biology11081095] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 11/20/2022]
Abstract
Most species of the class Holothuroidea are able to regenerate most of their internal organs following a typical evisceration process, which is a unique mechanism that allows sea cucumbers to survive in adverse environments. In this review, we compare autotomy among different type of sea cucumber and summarize the histocytological events that occur during the five stages of intestinal regeneration. Multiple cytological activities, such as apoptosis and dedifferentiation, take place during wound healing and anlage formation. Many studies have focused on the molecular regulation mechanisms that underlie regeneration, and herein we describe the techniques that have been used as well as the development-related signaling pathways and key genes that are significantly expressed during intestinal regeneration. Future analyses of the underlying mechanisms responsible for intestinal regeneration should include mapping at the single-cell level. Studies of visceral regeneration in echinoderms provide a unique perspective for understanding whole-body regeneration or appendage regeneration.
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Affiliation(s)
- Fang Su
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (F.S.); (H.Y.)
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China
| | - Hongsheng Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (F.S.); (H.Y.)
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China
- The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430071, China
| | - Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (F.S.); (H.Y.)
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China
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Lee Y, Kim B, Jung J, Koh B, Jhang SY, Ban C, Chi WJ, Kim S, Yu J. Chromosome-level genome assembly of Plazaster borealis sheds light on the morphogenesis of multiarmed starfish and its regenerative capacity. Gigascience 2022; 11:6636911. [PMID: 35809048 PMCID: PMC9270726 DOI: 10.1093/gigascience/giac063] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/22/2022] [Accepted: 05/31/2022] [Indexed: 01/04/2023] Open
Abstract
Background Plazaster borealis has a unique morphology, displaying multiple arms with a clear distinction between disk and arms, rather than displaying pentaradial symmetry, a remarkable characteristic of echinoderms. Herein we report the first chromosome-level reference genome of P. borealis and an essential tool to further investigate the basis of the divergent morphology. Findings In total, 57.76 Gb of a long read and 70.83 Gb of short-read data were generated to assemble a de novo 561-Mb reference genome of P. borealis, and Hi-C sequencing data (57.47 Gb) were used for scaffolding into 22 chromosomal scaffolds comprising 92.38% of the genome. The genome completeness estimated by BUSCO was 98.0% using the metazoan set, indicating a high-quality assembly. Through the comparative genome analysis, we identified evolutionary accelerated genes known to be involved in morphogenesis and regeneration, suggesting their potential role in shaping body pattern and capacity of regeneration. Conclusion This first chromosome-level genome assembly of P. borealis provides fundamental insights into echinoderm biology, as well as the genomic mechanism underlying its unique morphology and regeneration.
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Affiliation(s)
- Yujung Lee
- Department of Research, eGnome, Inc., 26 Beobwon-ro 9-gil, Sonpa-gu, Seoul 05836, Republic of Korea
| | - Bongsang Kim
- Department of Research, eGnome, Inc., 26 Beobwon-ro 9-gil, Sonpa-gu, Seoul 05836, Republic of Korea.,Department of Agricultural and Life Sciences and Research Institute of Population Genomics, Seoul National University, Seoul 08826, Republic of Korea
| | - Jaehoon Jung
- Department of Research, eGnome, Inc., 26 Beobwon-ro 9-gil, Sonpa-gu, Seoul 05836, Republic of Korea.,Department of Agricultural and Life Sciences and Research Institute of Population Genomics, Seoul National University, Seoul 08826, Republic of Korea
| | - Bomin Koh
- Department of Research, eGnome, Inc., 26 Beobwon-ro 9-gil, Sonpa-gu, Seoul 05836, Republic of Korea
| | - So Yun Jhang
- Department of Research, eGnome, Inc., 26 Beobwon-ro 9-gil, Sonpa-gu, Seoul 05836, Republic of Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Republic of Korea
| | - Chaeyoung Ban
- Department of Research, eGnome, Inc., 26 Beobwon-ro 9-gil, Sonpa-gu, Seoul 05836, Republic of Korea
| | - Won-Jae Chi
- Department of Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Soonok Kim
- Department of Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Jaewoong Yu
- Department of Research, eGnome, Inc., 26 Beobwon-ro 9-gil, Sonpa-gu, Seoul 05836, Republic of Korea
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Rinkevich B, Ballarin L, Martinez P, Somorjai I, Ben‐Hamo O, Borisenko I, Berezikov E, Ereskovsky A, Gazave E, Khnykin D, Manni L, Petukhova O, Rosner A, Röttinger E, Spagnuolo A, Sugni M, Tiozzo S, Hobmayer B. A pan-metazoan concept for adult stem cells: the wobbling Penrose landscape. Biol Rev Camb Philos Soc 2022; 97:299-325. [PMID: 34617397 PMCID: PMC9292022 DOI: 10.1111/brv.12801] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 12/17/2022]
Abstract
Adult stem cells (ASCs) in vertebrates and model invertebrates (e.g. Drosophila melanogaster) are typically long-lived, lineage-restricted, clonogenic and quiescent cells with somatic descendants and tissue/organ-restricted activities. Such ASCs are mostly rare, morphologically undifferentiated, and undergo asymmetric cell division. Characterized by 'stemness' gene expression, they can regulate tissue/organ homeostasis, repair and regeneration. By contrast, analysis of other animal phyla shows that ASCs emerge at different life stages, present both differentiated and undifferentiated phenotypes, and may possess amoeboid movement. Usually pluri/totipotent, they may express germ-cell markers, but often lack germ-line sequestering, and typically do not reside in discrete niches. ASCs may constitute up to 40% of animal cells, and participate in a range of biological phenomena, from whole-body regeneration, dormancy, and agametic asexual reproduction, to indeterminate growth. They are considered legitimate units of selection. Conceptualizing this divergence, we present an alternative stemness metaphor to the Waddington landscape: the 'wobbling Penrose' landscape. Here, totipotent ASCs adopt ascending/descending courses of an 'Escherian stairwell', in a lifelong totipotency pathway. ASCs may also travel along lower stemness echelons to reach fully differentiated states. However, from any starting state, cells can change their stemness status, underscoring their dynamic cellular potencies. Thus, vertebrate ASCs may reflect just one metazoan ASC archetype.
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Affiliation(s)
- Baruch Rinkevich
- Israel Oceanographic & Limnological ResearchNational Institute of OceanographyPOB 9753, Tel ShikmonaHaifa3109701Israel
| | - Loriano Ballarin
- Department of BiologyUniversity of PadovaVia Ugo Bassi 58/BPadova35121Italy
| | - Pedro Martinez
- Departament de Genètica, Microbiologia i EstadísticaUniversitat de BarcelonaAv. Diagonal 643Barcelona08028Spain
- Institut Català de Recerca i Estudis Avançats (ICREA)Passeig Lluís Companys 23Barcelona08010Spain
| | - Ildiko Somorjai
- School of BiologyUniversity of St AndrewsSt Andrews, FifeKY16 9ST, ScotlandUK
| | - Oshrat Ben‐Hamo
- Israel Oceanographic & Limnological ResearchNational Institute of OceanographyPOB 9753, Tel ShikmonaHaifa3109701Israel
| | - Ilya Borisenko
- Department of Embryology, Faculty of BiologySaint‐Petersburg State UniversityUniversity Embankment, 7/9Saint‐Petersburg199034Russia
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center GroningenAntonius Deusinglaan 1Groningen9713 AVThe Netherlands
| | - Alexander Ereskovsky
- Department of Embryology, Faculty of BiologySaint‐Petersburg State UniversityUniversity Embankment, 7/9Saint‐Petersburg199034Russia
- Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE), Aix Marseille University, CNRS, IRD, Avignon UniversityJardin du Pharo, 58 Boulevard Charles LivonMarseille13007France
- Koltzov Institute of Developmental Biology of Russian Academy of SciencesUlitsa Vavilova, 26Moscow119334Russia
| | - Eve Gazave
- Université de Paris, CNRS, Institut Jacques MonodParisF‐75006France
| | - Denis Khnykin
- Department of PathologyOslo University HospitalBygg 19, Gaustad Sykehus, Sognsvannsveien 21Oslo0188Norway
| | - Lucia Manni
- Department of BiologyUniversity of PadovaVia Ugo Bassi 58/BPadova35121Italy
| | - Olga Petukhova
- Collection of Vertebrate Cell CulturesInstitute of Cytology, Russian Academy of SciencesTikhoretsky Ave. 4St. Petersburg194064Russia
| | - Amalia Rosner
- Israel Oceanographic & Limnological ResearchNational Institute of OceanographyPOB 9753, Tel ShikmonaHaifa3109701Israel
| | - Eric Röttinger
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN)Nice06107France
- Université Côte d'Azur, Federative Research Institute – Marine Resources (IFR MARRES)28 Avenue de ValroseNice06103France
| | - Antonietta Spagnuolo
- Department of Biology and Evolution of Marine OrganismsStazione Zoologica Anton DohrnVilla ComunaleNaples80121Italy
| | - Michela Sugni
- Department of Environmental Science and Policy (ESP)Università degli Studi di MilanoVia Celoria 26Milan20133Italy
| | - Stefano Tiozzo
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche‐sur‐mer (LBDV)06234 Villefranche‐sur‐MerVillefranche sur MerCedexFrance
| | - Bert Hobmayer
- Institute of Zoology and Center for Molecular Biosciences, University of InnsbruckTechnikerstrInnsbruck256020Austria
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10
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Narvaez CA, Moura AJ, Scutella DF, Cucchiara JP, Stark AY, Russell MP. Plasticity in fluctuating hydrodynamic conditions: Tube feet regeneration in sea urchins. J Exp Biol 2022; 225:274209. [PMID: 35044457 DOI: 10.1242/jeb.242848] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 01/05/2022] [Indexed: 11/20/2022]
Abstract
Regenerating structures critical for survival provide excellent model systems for the study of phenotypic plasticity. These body components must regenerate their morphology and functionality quickly while subjected to different environmental stressors. Sea urchins live in high energy environments where hydrodynamic conditions pose significant challenges. Adhesive tube feet provide secure attachment to the substratum but can be amputated by predation and hydrodynamic forces. Tube feet display functional and morphological plasticity in response to environmental conditions, but regeneration to their pre-amputation status has not been achieved under quiescent laboratory settings. In this study, we assessed the effect of turbulent water movement, periodic emersion, and quiescent conditions on the regeneration process of tube feet morphology (length, disc area) and functionality (maximum disc tenacity, stem breaking force). Disc area showed significant plasticity in response to the treatments; when exposed to emersion and turbulent water movement, disc area was larger than tube feet regenerated in quiescent conditions. However, no treatment stimulated regeneration to pre-amputation sizes. Tube feet length was unaffected by treatments and remained shorter than non-amputated tube feet. Stem breaking force for amputated and not amputated treatments increased in all cases when compared to pre-amputation values. Maximum tenacity (force per unit area) was similar among tube feet subjected to simulated field conditions and amputation treatments. Our results suggest the role of active plasticity of tube feet functional morphology in response to field-like conditions and demonstrate the plastic response of invertebrates to laboratory conditions.
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Affiliation(s)
- Carla A Narvaez
- Department of Biology, Villanova University, 800 E. Lancaster Ave., Villanova, Pennsylvania 19085, USA
| | - Andrew J Moura
- Department of Biology, Villanova University, 800 E. Lancaster Ave., Villanova, Pennsylvania 19085, USA
| | - Daniel F Scutella
- Department of Biology, Villanova University, 800 E. Lancaster Ave., Villanova, Pennsylvania 19085, USA
| | - Jack P Cucchiara
- Department of Biology, Villanova University, 800 E. Lancaster Ave., Villanova, Pennsylvania 19085, USA
| | - Alyssa Y Stark
- Department of Biology, Villanova University, 800 E. Lancaster Ave., Villanova, Pennsylvania 19085, USA
| | - Michael P Russell
- Department of Biology, Villanova University, 800 E. Lancaster Ave., Villanova, Pennsylvania 19085, USA
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11
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Zheng M, Zueva O, Hinman V. Regeneration of the larval sea star nervous system by wounding induced respecification to the sox2 lineage. eLife 2022; 11:72983. [PMID: 35029145 PMCID: PMC8809897 DOI: 10.7554/elife.72983] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 01/13/2022] [Indexed: 11/20/2022] Open
Abstract
The ability to restore lost body parts following traumatic injury is a fascinating area of biology that challenges current understanding of the ontogeny of differentiation. The origin of new cells needed to regenerate lost tissue, and whether they are pluripotent or have de- or trans-differentiated, remains one of the most important open questions . Additionally, it is not known whether developmental gene regulatory networks are reused or whether regeneration specific networks are deployed. Echinoderms, including sea stars, have extensive ability for regeneration, however, the technologies for obtaining transgenic echinoderms are limited and tracking cells involved in regeneration, and thus identifying the cellular sources and potencies has proven challenging. In this study, we develop new transgenic tools to follow the fate of populations of cells in the regenerating larva of the sea star Patiria miniata. We show that the larval serotonergic nervous system can regenerate following decapitation. Using a BAC-transgenesis approach we show that expression of the pan ectodermal marker, sox2, is induced in previously sox2 minus cells , even when cell division is inhibited. sox2+ cells give rise to new sox4+ neural precursors that then proceed along an embryonic neurogenesis pathway to reform the anterior nervous systems. sox2+ cells contribute to only neural and ectoderm lineages, indicating that these progenitors maintain their normal, embryonic lineage restriction. This indicates that sea star larval regeneration uses a combination of existing lineage restricted stem cells, as well as respecification of cells into neural lineages, and at least partial reuse of developmental GRNs to regenerate their nervous system.
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Affiliation(s)
- Minyan Zheng
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Olga Zueva
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, United States
| | - Veronica Hinman
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, United States
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12
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Medina-Feliciano JG, García-Arrarás JE. Regeneration in Echinoderms: Molecular Advancements. Front Cell Dev Biol 2021; 9:768641. [PMID: 34977019 PMCID: PMC8718600 DOI: 10.3389/fcell.2021.768641] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/01/2021] [Indexed: 12/18/2022] Open
Abstract
Which genes and gene signaling pathways mediate regenerative processes? In recent years, multiple studies, using a variety of animal models, have aimed to answer this question. Some answers have been obtained from transcriptomic and genomic studies where possible gene and gene pathway candidates thought to be involved in tissue and organ regeneration have been identified. Several of these studies have been done in echinoderms, an animal group that forms part of the deuterostomes along with vertebrates. Echinoderms, with their outstanding regenerative abilities, can provide important insights into the molecular basis of regeneration. Here we review the available data to determine the genes and signaling pathways that have been proposed to be involved in regenerative processes. Our analyses provide a curated list of genes and gene signaling pathways and match them with the different cellular processes of the regenerative response. In this way, the molecular basis of echinoderm regenerative potential is revealed, and is available for comparisons with other animal taxa.
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13
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Dolmatov IY, Kalacheva NV, Tkacheva ES, Shulga AP, Zavalnaya EG, Shamshurina EV, Girich AS, Boyko AV, Eliseikina MG. Expression of Piwi, MMP, TIMP, and Sox during Gut Regeneration in Holothurian Eupentacta fraudatrix (Holothuroidea, Dendrochirotida). Genes (Basel) 2021; 12:1292. [PMID: 34440466 PMCID: PMC8391186 DOI: 10.3390/genes12081292] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 02/07/2023] Open
Abstract
Mesodermal cells of holothurian Eupentacta fraudatrix can transdifferentiate into enterocytes during the regeneration of the digestive system. In this study, we investigated the expression of several genes involved in gut regeneration in E. fraudatrix. Moreover, the localization of progenitor cells of coelomocytes, juvenile cells, and their participation in the formation of the luminal epithelium of the digestive tube were studied. It was shown that Piwi-positive cells were not involved in the formation of the luminal epithelium of the digestive tube. Ef-72 kDa type IV collagenase and Ef-MMP16 had an individual expression profile and possibly different functions. The Ef-tensilin3 gene exhibited the highest expression and indicates its potential role in regeneration. Ef-Sox9/10 and Ef-Sox17 in E. fraudatrix may participate in the mechanism of transdifferentiation of coelomic epithelial cells. Their transcripts mark the cells that plunge into the connective tissue of the gut anlage and give rise to enterocytes. Ef-Sox9/10 probably controls the switching of mesodermal cells to the enterocyte phenotype, while Ef-Sox17 may be involved in the regulation of the initial stages of transdifferentiation.
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Affiliation(s)
- Igor Yu. Dolmatov
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Palchevsky 17, 690041 Vladivostok, Russia; (N.V.K.); (E.S.T.); (A.P.S.); (E.G.Z.); (E.V.S.); (A.S.G.); (A.V.B.); (M.G.E.)
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14
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Wolff A, Hinman V. The Use of Larval Sea Stars and Sea Urchins in the Discovery of Shared Mechanisms of Metazoan Whole-Body Regeneration. Genes (Basel) 2021; 12:1063. [PMID: 34356079 PMCID: PMC8303351 DOI: 10.3390/genes12071063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 02/07/2023] Open
Abstract
The ability to regenerate is scattered among the metazoan tree of life. Further still, regenerative capacity varies widely within these specific organisms. Numerous organisms, all with different regenerative capabilities, have been studied at length and key similarities and disparities in how regeneration occurs have been identified. In order to get a better grasp on understanding regeneration as a whole, we must search for new models that are capable of extensive regeneration, as well as those that have been under sampled in the literature. As invertebrate deuterostomes, echinoderms fit both of these requirements. Multiple members regenerate various tissue types at all life stages, including examples of whole-body regeneration. Interrogations in two highly studied echinoderms, the sea urchin and the sea star, have provided knowledge of tissue and whole-body regeneration at various life stages. Work has begun to examine regeneration in echinoderm larvae, a potential new system for understanding regenerative mechanisms in a basal deuterostome. Here, we review the ways these two animals' larvae have been utilized as a model of regeneration.
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Affiliation(s)
- Andrew Wolff
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA;
| | - Veronica Hinman
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
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15
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Rosner A, Armengaud J, Ballarin L, Barnay-Verdier S, Cima F, Coelho AV, Domart-Coulon I, Drobne D, Genevière AM, Jemec Kokalj A, Kotlarska E, Lyons DM, Mass T, Paz G, Pazdro K, Perić L, Ramšak A, Rakers S, Rinkevich B, Spagnuolo A, Sugni M, Cambier S. Stem cells of aquatic invertebrates as an advanced tool for assessing ecotoxicological impacts. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 771:144565. [PMID: 33736145 DOI: 10.1016/j.scitotenv.2020.144565] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/10/2020] [Accepted: 12/13/2020] [Indexed: 06/12/2023]
Abstract
Environmental stressors are assessed through methods that quantify their impacts on a wide range of metrics including species density, growth rates, reproduction, behaviour and physiology, as on host-pathogen interactions and immunocompetence. Environmental stress may induce additional sublethal effects, like mutations and epigenetic signatures affecting offspring via germline mediated transgenerational inheritance, shaping phenotypic plasticity, increasing disease susceptibility, tissue pathologies, changes in social behaviour and biological invasions. The growing diversity of pollutants released into aquatic environments requires the development of a reliable, standardised and 3R (replacement, reduction and refinement of animals in research) compliant in vitro toolbox. The tools have to be in line with REACH regulation 1907/2006/EC, aiming to improve strategies for potential ecotoxicological risks assessment and monitoring of chemicals threatening human health and aquatic environments. Aquatic invertebrates' adult stem cells (ASCs) are numerous and can be pluripotent, as illustrated by high regeneration ability documented in many of these taxa. This is of further importance as in many aquatic invertebrate taxa, ASCs are able to differentiate into germ cells. Here we propose that ASCs from key aquatic invertebrates may be harnessed for applicable and standardised new tests in ecotoxicology. As part of this approach, a battery of modern techniques and endpoints are proposed to be tested for their ability to correctly identify environmental stresses posed by emerging contaminants in aquatic environments. Consequently, we briefly describe the current status of the available toxicity testing and biota-based monitoring strategies in aquatic environmental ecotoxicology and highlight some of the associated open issues such as replicability, consistency and reliability in the outcomes, for understanding and assessing the impacts of various chemicals on organisms and on the entire aquatic environment. Following this, we describe the benefits of aquatic invertebrate ASC-based tools for better addressing ecotoxicological questions, along with the current obstacles and possible overhaul approaches.
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Affiliation(s)
- Amalia Rosner
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, P.O. Box 8030, Tel Shikmona, Haifa 3108001, Israel.
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200 Bagnols-sur-Cèze, France.
| | - Loriano Ballarin
- Department of Biology, University of Padova, via Ugo Bassi 58/B, 35121 Padova, Italy.
| | - Stéphanie Barnay-Verdier
- Sorbonne Université; CNRS, INSERM, Université Côte d'Azur, Institute for Research on Cancer and Aging Nice, F-06107 Nice, France.
| | - Francesca Cima
- Department of Biology, University of Padova, via Ugo Bassi 58/B, 35121 Padova, Italy.
| | - Ana Varela Coelho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
| | - Isabelle Domart-Coulon
- Muséum National d'Histoire Naturelle, CNRS, Microorganism Communication and Adaptation Molecules MCAM, Paris F-75005, France.
| | - Damjana Drobne
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Večna pot 111,D, 1000 Ljubljana, Slovenia.
| | - Anne-Marie Genevière
- Sorbonne Université, CNRS, Integrative Biology of Marine Organisms, BIOM, F-6650 Banyuls-sur-mer, France.
| | - Anita Jemec Kokalj
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Večna pot 111,D, 1000 Ljubljana, Slovenia.
| | - Ewa Kotlarska
- Institute of Oceanology of the Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland.
| | - Daniel Mark Lyons
- Center for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, HR-52210 Rovinj, Croatia.
| | - Tali Mass
- Marine Biology Department, Leon H. Charney School of Marine Sciences, 199 Aba Khoushy Ave, University of Haifa, 3498838, Israel.
| | - Guy Paz
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, P.O. Box 8030, Tel Shikmona, Haifa 3108001, Israel.
| | - Ksenia Pazdro
- Institute of Oceanology of the Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - Lorena Perić
- Rudjer Boskovic Institute, Laboratory for Aquaculture and Pathology of Aquaculture Organisms, Bijenička cesta 54, HR-10000 Zagreb, Croatia.
| | - Andreja Ramšak
- National Institute of Biology, Marine Biology Station, Fornače 41, 6330 Piran, Slovenia.
| | | | - Baruch Rinkevich
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, P.O. Box 8030, Tel Shikmona, Haifa 3108001, Israel.
| | - Antonietta Spagnuolo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, Via Celoria 2, 20133 Milano, Italy.
| | - Sébastien Cambier
- Luxembourg Institute of Science and Technology, 5, avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
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16
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Wang Z, Bai Y, Nie H, Xu Q, Yin Z, Zhang Y, Yin X, Yan X. Molecular mechanisms of wound healing and regeneration of siphon in the Manila clam Ruditapes philippinarum revealed by transcriptomic analysis. Genomics 2021; 113:1011-1025. [PMID: 33626340 DOI: 10.1016/j.ygeno.2021.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 01/24/2021] [Accepted: 02/18/2021] [Indexed: 10/22/2022]
Abstract
Ruditapes philippinarum is an economically important marine shellfish aquaculture species, and it has the ability to regenerate its siphons. To gain a greater understanding of the molecular mechanisms at work during siphon regeneration and to provide evidence for morphological regeneration, we examined transcriptome responses of siphon tissue of R. philippinarum during regeneration and observed regenerative siphons under the stereomicroscope. The overall process of siphon regeneration was dissected based on the morphological changes of siphon and the identification of up-regulated key differentially expressed genes (DEGs). The protein biosynthesis and metabolism played important roles in wound healing and siphon regeneration of R. philippinarum. Transcriptomic analysis identified the Wnt and TGF-β signaling pathways by focusing on the function and expression pattern of genes in these pathways during siphon regeneration. In addition, we carried out a genome-wide identification and phylogenetic analysis of TGF-β superfamily in R. philippinarum. The expression profiles of the TGF-β superfamily genes were analyzed in eight adult tissues (adductor muscle, mantle, foot, gill, siphon, digestive gland, gonad, and labial palp) and regenerative siphon. This study shed new light on the process of morphological regeneration and regenerative mechanism of siphon of R. philippinarum.
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Affiliation(s)
- Zhengxing Wang
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China
| | - Yitian Bai
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China
| | - Hongtao Nie
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China.
| | - Qiaoyue Xu
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China
| | - Zhihui Yin
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China
| | - Yanming Zhang
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China
| | - Xuwang Yin
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China.
| | - Xiwu Yan
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China.
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17
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Transcriptomic analysis of early stages of intestinal regeneration in Holothuria glaberrima. Sci Rep 2021; 11:346. [PMID: 33431961 PMCID: PMC7801731 DOI: 10.1038/s41598-020-79436-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 12/04/2020] [Indexed: 01/29/2023] Open
Abstract
Echinoderms comprise a group of animals with impressive regenerative capabilities. They can replace complex internal organs following injury or autotomy. In holothurians or sea cucumbers, cellular processes of intestinal regeneration have been extensively studied. The molecular machinery behind this faculty, however, remains to be understood. Here we assembled and annotated a de novo transcriptome using RNA-seq data consisting of regenerating and non-regenerating intestinal tissues from the sea cucumber Holothuria glaberrima. Comparisons of differential expression were made using the mesentery as a reference against 24 h and 3 days regenerating intestine, revealing a large number of differentially expressed transcripts. Gene ontology and pathway enrichment analysis showed evidence of increasing transcriptional activity. Further analysis of transcripts associated with transcription factors revealed diverse expression patterns with mechanisms involving developmental and cancer-related activity that could be related to the regenerative process. Our study demonstrates the broad and diversified gene expression profile during the early stages of the process using the mesentery as the focal point of intestinal regeneration. It also establishes the genes that are the most important candidates in the cellular processes that underlie regenerative responses.
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18
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Coelomocyte replenishment in adult Asterias rubens: the possible ways. Cell Tissue Res 2020; 383:1043-1060. [PMID: 33237478 DOI: 10.1007/s00441-020-03337-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 11/05/2020] [Indexed: 10/22/2022]
Abstract
The origin of cells involved in regeneration in echinoderms remains an open question. Replenishment of circulatory coelomocytes-cells of the coelomic cavity in starfish-is an example of physiological regeneration. The coelomic epithelium is considered to be the main source of coelomocytes, but many details of this process remain unclear. This study examined the role of coelomocytes outside circulation, named marginal coelomocytes and small undifferentiated cells of the coelomic epithelium in coelomocyte replenishment in Asterias rubens. A qualitative and quantitative comparison of circulatory and marginal coelomocytes, as well as changes of circulatory coelomocyte concentrations in response to injury at different physiological statuses, was analysed. The presence of cells morphologically similar to coelomocytes in the context of coelomic epithelium was evaluated by electron microscopy. The irregular distribution of small cells on the surface and within the coelomic epithelium was demonstrated and the origin of small undifferentiated cells and large agranulocytes from the coelomic epithelium was suggested. Two events have been proposed to mediate the replenishment of coelomocytes in the coelom: migration of mature coelomocytes of the marginal cell pool and migration of small undifferentiated cells of the coelomic epithelium. The proteomic analysis of circulatory coelomocytes, coelomic epithelial cells and a subpopulation of coelomic epithelial cells, enriched in small undifferentiated cells, revealed proteins that were common and specific for each cell pool. Among these molecules were regulatory proteins, potential participants of regenerative processes.
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19
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Ferrario C, Sugni M, Somorjai IML, Ballarin L. Beyond Adult Stem Cells: Dedifferentiation as a Unifying Mechanism Underlying Regeneration in Invertebrate Deuterostomes. Front Cell Dev Biol 2020; 8:587320. [PMID: 33195242 PMCID: PMC7606891 DOI: 10.3389/fcell.2020.587320] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 09/25/2020] [Indexed: 12/15/2022] Open
Abstract
The diversity of regenerative phenomena seen in adult metazoans, as well as their underlying mechanistic bases, are still far from being comprehensively understood. Reviewing both ultrastructural and molecular data, the present work aims to showcase the increasing relevance of invertebrate deuterostomes, i.e., echinoderms, hemichordates, cephalochordates and tunicates, as invaluable models to study cellular aspects of adult regeneration. Our comparative approach suggests a fundamental contribution of local dedifferentiation -rather than mobilization of resident undifferentiated stem cells- as an important cellular mechanism contributing to regeneration in these groups. Thus, elucidating the cellular origins, recruitment and fate of cells, as well as the molecular signals underpinning tissue regrowth in regeneration-competent deuterostomes, will provide the foundation for future research in tackling the relatively limited regenerative abilities of vertebrates, with clear applications in regenerative medicine.
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Affiliation(s)
- Cinzia Ferrario
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Milan, Italy
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Milan, Italy
- GAIA 2050 Center, Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Ildiko M. L. Somorjai
- The Willie Russel Laboratories, Biomedical Sciences Research Complex, North Haugh, University of St Andrews, St Andrews, United Kingdom
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20
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Polinski JM, Kron N, Smith DR, Bodnar AG. Unique age-related transcriptional signature in the nervous system of the long-lived red sea urchin Mesocentrotus franciscanus. Sci Rep 2020; 10:9182. [PMID: 32514014 PMCID: PMC7280269 DOI: 10.1038/s41598-020-66052-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 05/12/2020] [Indexed: 11/23/2022] Open
Abstract
The red sea urchin, Mesocentrotus franciscanus, is one the earth’s longest-lived animals, reported to live more than 100 years with indeterminate growth, life-long reproduction and no increase in mortality rate with age. To gain insight into mechanisms associated with longevity and negligible senescence, age-related transcriptional profiles were examined in tissues of the red sea urchin. Genome-wide transcriptional profiling using RNA-Seq revealed few age-related changes in gene expression in muscle and esophagus tissue. In contrast, radial nerve showed an unexpected level of complexity with the expression of 3,370 genes significantly altered more than two-fold with age, including genes involved in nerve function, signaling, metabolism, transcriptional regulation and chromatin modification. There was an age-related upregulation in expression of genes involved in synaptogenesis, axonogenesis and neuroprotection suggesting preservation of neuronal processes with age. There was also an upregulation in expression of positive regulators and key components of the AMPK pathway, autophagy, proteasome function, and the unfolded protein response. This unique age-related gene expression profile in the red sea urchin nervous system may play a role in mitigating the detrimental effects of aging in this long-lived animal.
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Affiliation(s)
- Jennifer M Polinski
- Gloucester Marine Genomics Institute, 417 Main Street, Gloucester, MA, 01930, USA
| | - Nicholas Kron
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, United States
| | - Douglas R Smith
- Gloucester Marine Genomics Institute, 417 Main Street, Gloucester, MA, 01930, USA
| | - Andrea G Bodnar
- Gloucester Marine Genomics Institute, 417 Main Street, Gloucester, MA, 01930, USA.
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21
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Abstract
Much recent marine research has been directed towards understanding the effects of anthropogenic-induced environmental change on marine biodiversity, particularly for those animals with heavily calcified exoskeletons, such as corals, molluscs and urchins. This is because life in our oceans is becoming more challenging for these animals with changes in temperature, pH and salinity. In the future, it will be more energetically expensive to make marine skeletons and the increasingly corrosive conditions in seawater are expected to result in the dissolution of these external skeletons. However, initial predictions of wide-scale sensitivity are changing as we understand more about the mechanisms underpinning skeletal production (biomineralization). These studies demonstrate the complexity of calcification pathways and the cellular responses of animals to these altered conditions. Factors including parental conditioning, phenotypic plasticity and epigenetics can significantly impact the production of skeletons and thus future population success. This understanding is paralleled by an increase in our knowledge of the genes and proteins involved in biomineralization, particularly in some phyla, such as urchins, molluscs and corals. This Review will provide a broad overview of our current understanding of the factors affecting skeletal production in marine invertebrates. It will focus on the molecular mechanisms underpinning biomineralization and how knowledge of these processes affects experimental design and our ability to predict responses to climate change. Understanding marine biomineralization has many tangible benefits in our changing world, including improvements in conservation and aquaculture and exploitation of natural calcified structure design using biomimicry approaches that are aimed at producing novel biocomposites.
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Affiliation(s)
- Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
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22
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Senescence and Longevity of Sea Urchins. Genes (Basel) 2020; 11:genes11050573. [PMID: 32443861 PMCID: PMC7288282 DOI: 10.3390/genes11050573] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 11/30/2022] Open
Abstract
Sea urchins are a minor class of marine invertebrates that share genetic similarities with humans. For example, the sea urchin species Strongylocentrotus purpuratus is estimated to have 23,300 genes in which the majority of vertebrate gene families are enveloped. Some of the sea urchin species can demonstrate extreme longevity, such as Mesocentrotus franciscanus, living for well over 100 years. Comparing human to sea urchin aging suggests that the latter do not fit within the classic understanding of biological aging, as both long- and short-lived sea urchin species demonstrate negligible senescence. Sea urchins are highly regenerative organisms. Adults can regenerate external appendages and can maintain their regenerative abilities throughout life. They grow indeterminately and reproduce throughout their entire adult life. Both long- and short-lived species do not exhibit age-associated telomere shortening and display telomerase activity in somatic tissues regardless of age. Aging S. purpuratus urchins show changes in expression patterns of protein coding genes that are involved in several fundamental cellular functions such as the ubiquitin-proteasome system, signaling pathways, translational regulation, and electron transport chain. Sea urchin longevity and senescence research is a new and promising field that holds promise for the understanding of aging in vertebrates and can increase our understanding of human longevity and of healthy aging.
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23
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Mashanov V, Akiona J, Khoury M, Ferrier J, Reid R, Machado DJ, Zueva O, Janies D. Active Notch signaling is required for arm regeneration in a brittle star. PLoS One 2020; 15:e0232981. [PMID: 32396580 PMCID: PMC7217437 DOI: 10.1371/journal.pone.0232981] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 04/24/2020] [Indexed: 12/15/2022] Open
Abstract
Cell signaling pathways play key roles in coordinating cellular events in development. The Notch signaling pathway is highly conserved across all multicellular animals and is known to coordinate a multitude of diverse cellular events, including proliferation, differentiation, fate specification, and cell death. Specific functions of the pathway are, however, highly context-dependent and are not well characterized in post-traumatic regeneration. Here, we use a small-molecule inhibitor of the pathway (DAPT) to demonstrate that Notch signaling is required for proper arm regeneration in the brittle star Ophioderma brevispina, a highly regenerative member of the phylum Echinodermata. We also employ a transcriptome-wide gene expression analysis (RNA-seq) to characterize the downstream genes controlled by the Notch pathway in the brittle star regeneration. We demonstrate that arm regeneration involves an extensive cross-talk between the Notch pathway and other cell signaling pathways. In the regrowing arm, Notch regulates the composition of the extracellular matrix, cell migration, proliferation, and apoptosis, as well as components of the innate immune response. We also show for the first time that Notch signaling regulates the activity of several transposable elements. Our data also suggests that one of the possible mechanisms through which Notch sustains its activity in the regenerating tissues is via suppression of Neuralized1.
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Affiliation(s)
- Vladimir Mashanov
- Department of Biology, University of North Florida, Jacksonville, FL, United states of America
- Wake Forest Institute for Regenerative Medicine, Winston Salem, NC, United states of America
- * E-mail:
| | - Jennifer Akiona
- Department of Biology, University of North Florida, Jacksonville, FL, United states of America
| | - Maleana Khoury
- Department of Biology, University of North Florida, Jacksonville, FL, United states of America
| | - Jacob Ferrier
- University of North Carolina at Charlotte, Charlotte, NC, United states of America
| | - Robert Reid
- University of North Carolina at Charlotte, Charlotte, NC, United states of America
| | - Denis Jacob Machado
- University of North Carolina at Charlotte, Charlotte, NC, United states of America
| | - Olga Zueva
- Department of Biology, University of North Florida, Jacksonville, FL, United states of America
| | - Daniel Janies
- University of North Carolina at Charlotte, Charlotte, NC, United states of America
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24
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Scholnick DA, Winslow AE. The role of fasting on spine regeneration and bacteremia in the purple sea urchin Strongylocentrotus purpuratus. PLoS One 2020; 15:e0228711. [PMID: 32053660 PMCID: PMC7018041 DOI: 10.1371/journal.pone.0228711] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/21/2020] [Indexed: 11/18/2022] Open
Abstract
Fasting has been shown to increase longevity and alter immune function in a variety of animals, but little is understood about how reduced caloric intake may impact regeneration and infections in animals that must regularly repair and regenerate tissue in marine environments that contain high levels of bacteria. We examined the possibility that fasting could enhance spine regeneration and reduce bacteremia in the purple sea urchin Strongylocentrotus purpuratus. A small number of spines were removed from urchins and rates of spine regrowth and levels of culturable bacteria from the coelomic fluid were measured for 21 days in fed and fasted urchins. Fasted urchins had higher rates of spine regrowth and lower levels of colony-forming units (CFU) per milliliter of coeolomic fluid. The predominant bacteria in the coelomic fluid was isolated and identified by DNA sequence-based methods as Vibrio cyclitrophicus. After 21 days, fasted and fed urchins were injected with V. cyclitrophicus. Two hours after injection, fed urchins had about 25% more culturable bacteria remaining in their coelomic fluid compared to fasted urchins. We found no evidence that fasting altered coelomic fluid cell number or righting response, indicators of physiologic and behavioral stress in urchins. Our results demonstrate that V. cyclitrophicus is present in purple urchin coelomic fluid, that fasting can increase spine regeneration and that fasted urchins have much lower levels of culturable bacteria in their coelomic fluid than fed urchins. Overall, our data suggests that fasting may ultimately reduce bacteremia and infection in injured or damaged urchins.
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Affiliation(s)
- David A. Scholnick
- Department of Biology, Pacific University, Forest Grove, Oregon, United States of America
- * E-mail:
| | - Alexandra E. Winslow
- Department of Biology, Pacific University, Forest Grove, Oregon, United States of America
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25
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Cary GA, Wolff A, Zueva O, Pattinato J, Hinman VF. Analysis of sea star larval regeneration reveals conserved processes of whole-body regeneration across the metazoa. BMC Biol 2019; 17:16. [PMID: 30795750 PMCID: PMC6385403 DOI: 10.1186/s12915-019-0633-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 02/04/2019] [Indexed: 12/16/2022] Open
Abstract
Background Metazoan lineages exhibit a wide range of regenerative capabilities that vary among developmental stage and tissue type. The most robust regenerative abilities are apparent in the phyla Cnidaria, Platyhelminthes, and Echinodermata, whose members are capable of whole-body regeneration (WBR). This phenomenon has been well characterized in planarian and hydra models, but the molecular mechanisms of WBR are less established within echinoderms, or any other deuterostome system. Thus, it is not clear to what degree aspects of this regenerative ability are shared among metazoa. Results We characterize regeneration in the larval stage of the Bat Star (Patiria miniata). Following bisection along the anterior-posterior axis, larvae progress through phases of wound healing and re-proportioning of larval tissues. The overall number of proliferating cells is reduced following bisection, and we find evidence for a re-deployment of genes with known roles in embryonic axial patterning. Following axial respecification, we observe a significant localization of proliferating cells to the wound region. Analyses of transcriptome data highlight the molecular signatures of functions that are common to regeneration, including specific signaling pathways and cell cycle controls. Notably, we find evidence for temporal similarities among orthologous genes involved in regeneration from published Platyhelminth and Cnidarian regeneration datasets. Conclusions These analyses show that sea star larval regeneration includes phases of wound response, axis respecification, and wound-proximal proliferation. Commonalities of the overall process of regeneration, as well as gene usage between this deuterostome and other species with divergent evolutionary origins reveal a deep similarity of whole-body regeneration among the metazoa. Electronic supplementary material The online version of this article (10.1186/s12915-019-0633-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gregory A Cary
- Department of Biological Sciences, Carnegie Mellon University, Mellon Institute, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA
| | - Andrew Wolff
- Department of Biological Sciences, Carnegie Mellon University, Mellon Institute, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA
| | - Olga Zueva
- Department of Biological Sciences, Carnegie Mellon University, Mellon Institute, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA
| | - Joseph Pattinato
- Department of Biological Sciences, Carnegie Mellon University, Mellon Institute, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA
| | - Veronica F Hinman
- Department of Biological Sciences, Carnegie Mellon University, Mellon Institute, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA.
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26
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Cao PL, Kumagai N, Inoue T, Agata K, Makino T. JmjC Domain-Encoding Genes Are Conserved in Highly Regenerative Metazoans and Are Associated with Planarian Whole-Body Regeneration. Genome Biol Evol 2019; 11:552-564. [PMID: 30698705 PMCID: PMC6390904 DOI: 10.1093/gbe/evz021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2019] [Indexed: 12/26/2022] Open
Abstract
The capacity for regeneration varies greatly among metazoans, yet little is known about the evolutionary processes leading to such different regeneration abilities. In particular, highly regenerative species such as planarians and cnidarians can regenerate the whole body from an amputated fragment; however, a common molecular basis, if any, among these species remains unclear. Here, we show that genes encoding Jumonji C (JmjC) domain-containing proteins are associated with high regeneration ability. We classified 132 fully sequenced metazoans into two groups with high or low regeneration abilities and identified 118 genes conserved in the high regenerative group that were lost in species in the low regeneration group during evolution. Ninety-six percent of them were JmjC domain-encoding genes. We denoted the candidate genes as high regenerative species-specific JmjC domain-encoding genes (HRJDs). We observed losses of HRJDs in Helobdella robusta, which lost its high regeneration ability during evolution based on phylogenetic analysis. By RNA sequencing analyses, we observed that HRJD orthologs were differentially expressed during regeneration in two Cnidarians, as well as Platyhelminthes and Urochordata, which are highly regenerative species. Furthermore, >50% of the head and tail parts of amputated planarians (Dugesia japonica) died during regeneration after RNA interference of HRJD orthologs. These results indicate that HRJD are strongly associated with a high regeneration ability in metazoans. HRJD paralogs regulate gene expression by histone demethylation; thus, HRJD may be related to epigenetic regulation controlling stem cell renewal and stem cell differentiation during regeneration. We propose that HRJD play a central role in epigenetic regulation during regeneration.
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Affiliation(s)
- Ping-Lin Cao
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
| | - Nobuyoshi Kumagai
- Department of Life Science, Faculty of Science, Graduate Course in Life Science, Graduate School of Science, Gakushuin University, Toshima-ku, Tokyo, Japan
| | - Takeshi Inoue
- Department of Life Science, Faculty of Science, Graduate Course in Life Science, Graduate School of Science, Gakushuin University, Toshima-ku, Tokyo, Japan
| | - Kiyokazu Agata
- Department of Life Science, Faculty of Science, Graduate Course in Life Science, Graduate School of Science, Gakushuin University, Toshima-ku, Tokyo, Japan
| | - Takashi Makino
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
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27
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Abstract
Echinoderms are important research models for a wide range of biological questions. In particular, echinoderm embryos are exemplary models for dissecting the molecular and cellular processes that drive development and testing how these processes can be modified through evolution to produce the extensive morphological diversity observed in the phylum. Modern attempts to characterize these processes depend on some level of genomic analysis; from querying annotated gene sets to functional genomics experiments to identify candidate cis-regulatory sequences. Given how essential these data have become, it is important that researchers using available datasets or performing their own genome-scale experiments understand the nature and limitations of echinoderm genomic analyses. In this chapter we highlight the current state of echinoderm genomic data and provide methodological considerations for common approaches, including analysis of transcriptome and functional genomics datasets.
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28
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Lai AG, Aboobaker AA. EvoRegen in animals: Time to uncover deep conservation or convergence of adult stem cell evolution and regenerative processes. Dev Biol 2018; 433:118-131. [PMID: 29198565 DOI: 10.1016/j.ydbio.2017.10.010] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 01/08/2023]
Abstract
How do animals regenerate specialised tissues or their entire body after a traumatic injury, how has this ability evolved and what are the genetic and cellular components underpinning this remarkable feat? While some progress has been made in understanding mechanisms, relatively little is known about the evolution of regenerative ability. Which elements of regeneration are due to lineage specific evolutionary novelties or have deeply conserved roots within the Metazoa remains an open question. The renaissance in regeneration research, fuelled by the development of modern functional and comparative genomics, now enable us to gain a detailed understanding of both the mechanisms and evolutionary forces underpinning regeneration in diverse animal phyla. Here we review existing and emerging model systems, with the focus on invertebrates, for studying regeneration. We summarize findings across these taxa that tell us something about the evolution of adult stem cell types that fuel regeneration and the growing evidence that many highly regenerative animals harbor adult stem cells with a gene expression profile that overlaps with germline stem cells. We propose a framework in which regenerative ability broadly evolves through changes in the extent to which stem cells generated through embryogenesis are maintained into the adult life history.
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Affiliation(s)
- Alvina G Lai
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
| | - A Aziz Aboobaker
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom.
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29
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Kalacheva NV, Eliseikina MG, Frolova LT, Dolmatov IY. Regeneration of the digestive system in the crinoid Himerometra robustipinna occurs by transdifferentiation of neurosecretory-like cells. PLoS One 2017; 12:e0182001. [PMID: 28753616 PMCID: PMC5533335 DOI: 10.1371/journal.pone.0182001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 07/11/2017] [Indexed: 11/18/2022] Open
Abstract
The structure and regeneration of the digestive system in the crinoid Himerometra robustipinna (Carpenter, 1881) were studied. The gut comprises a spiral tube forming radial lateral processes, which gives it a five-lobed shape. The digestive tube consists of three segments: esophagus, intestine, and rectum. The epithelia of these segments have different cell compositions. Regeneration of the gut after autotomy of the visceral mass progresses very rapidly. Within 6 h after autotomy, an aggregation consisting of amoebocytes, coelomic epithelial cells and juxtaligamental cells (neurosecretory neurons) forms on the inner surface of the skeletal calyx. At 12 h post-autotomy, transdifferentiation of the juxtaligamental cells starts. At 24 h post-autotomy these cells undergo a mesenchymal-epithelial-like transition, resulting in the formation of the luminal epithelium of the gut. Specialization of the intestinal epithelial cells begins on day 2 post-autotomy. At this stage animals acquire the mouth and anal opening. On day 4 post-autotomy the height of both the enterocytes and the visceral mass gradually increases. Proliferation does not play any noticeable role in gut regeneration. The immersion of animals in a 10-7 M solution of colchicine neither stopped formation of the lost structures nor caused accumulation of mitoses in tissues. Weakly EdU-labeled nuclei were observed in the gut only on day 2 post-autotomy and were not detected at later regeneration stages. Single mitotically dividing cells were recorded during the same period. It is concluded that juxtaligamental cells play a major role in gut regeneration in H. robustipinna. The main mechanisms of morphogenesis are cell migration and transdifferentiation.
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Affiliation(s)
- Nadezhda V. Kalacheva
- A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
- Far Eastern Federal University, Vladivostok, Russia
| | - Marina G. Eliseikina
- A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
- Far Eastern Federal University, Vladivostok, Russia
| | - Lidia T. Frolova
- A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
| | - Igor Yu. Dolmatov
- A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
- Far Eastern Federal University, Vladivostok, Russia
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30
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Emerson CE, Reinardy HC, Bates NR, Bodnar AG. Ocean acidification impacts spine integrity but not regenerative capacity of spines and tube feet in adult sea urchins. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170140. [PMID: 28573022 PMCID: PMC5451823 DOI: 10.1098/rsos.170140] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/19/2017] [Indexed: 05/15/2023]
Abstract
Increasing atmospheric carbon dioxide (CO2) has resulted in a change in seawater chemistry and lowering of pH, referred to as ocean acidification. Understanding how different organisms and processes respond to ocean acidification is vital to predict how marine ecosystems will be altered under future scenarios of continued environmental change. Regenerative processes involving biomineralization in marine calcifiers such as sea urchins are predicted to be especially vulnerable. In this study, the effect of ocean acidification on regeneration of external appendages (spines and tube feet) was investigated in the sea urchin Lytechinus variegatus exposed to ambient (546 µatm), intermediate (1027 µatm) and high (1841 µatm) partial pressure of CO2 (pCO2) for eight weeks. The rate of regeneration was maintained in spines and tube feet throughout two periods of amputation and regrowth under conditions of elevated pCO2. Increased expression of several biomineralization-related genes indicated molecular compensatory mechanisms; however, the structural integrity of both regenerating and homeostatic spines was compromised in high pCO2 conditions. Indicators of physiological fitness (righting response, growth rate, coelomocyte concentration and composition) were not affected by increasing pCO2, but compromised spine integrity is likely to have negative consequences for defence capabilities and therefore survival of these ecologically and economically important organisms.
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Affiliation(s)
- Chloe E. Emerson
- Bermuda Institute of Ocean Sciences, 17 Biological Station, St George's GE 01, Bermuda
| | - Helena C. Reinardy
- Bermuda Institute of Ocean Sciences, 17 Biological Station, St George's GE 01, Bermuda
| | - Nicholas R. Bates
- Bermuda Institute of Ocean Sciences, 17 Biological Station, St George's GE 01, Bermuda
- Department of Ocean and Earth Science, National Oceanography Centre, University of Southampton, Southampton, UK
| | - Andrea G. Bodnar
- Bermuda Institute of Ocean Sciences, 17 Biological Station, St George's GE 01, Bermuda
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31
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Brown LR, Caldwell GS. Tissue and spine regeneration in the temperate sea urchin Psammechinus miliaris. INVERTEBR REPROD DEV 2017. [DOI: 10.1080/07924259.2017.1287779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Leah R. Brown
- School of Marine Science and Technology, Newcastle University, Newcastle upon Tyne, UK
| | - Gary S. Caldwell
- School of Marine Science and Technology, Newcastle University, Newcastle upon Tyne, UK
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32
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Reinardy HC, Chapman J, Bodnar AG. Induction of innate immune gene expression following methyl methanesulfonate-induced DNA damage in sea urchins. Biol Lett 2016; 12:20151057. [PMID: 26911343 DOI: 10.1098/rsbl.2015.1057] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Sea urchins are noted for the absence of neoplastic disease and represent a novel model to investigate cellular and systemic cancer protection mechanisms. Following intracoelomic injection of the DNA alkylating agent methyl methanesulfonate, DNA damage was detected in sea urchin cells and tissues (coelomocytes, muscle, oesophagus, ampullae and gonad) by the alkaline unwinding, fast micromethod. Gene expression analyses of the coelomocytes indicated upregulation of innate immune markers, including genes involved in NF-κB signalling. Results suggest that activation of the innate immune system following DNA damage may contribute to the naturally occurring resistance to neoplastic disease observed in sea urchins.
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Affiliation(s)
- H C Reinardy
- Molecular Discovery Laboratory, Bermuda Institute of Ocean Sciences, 17 Biological Station, St George's GE01, Bermuda
| | - J Chapman
- Molecular Discovery Laboratory, Bermuda Institute of Ocean Sciences, 17 Biological Station, St George's GE01, Bermuda
| | - A G Bodnar
- Molecular Discovery Laboratory, Bermuda Institute of Ocean Sciences, 17 Biological Station, St George's GE01, Bermuda
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33
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Kamenev YO, Dolmatov IY. Anterior regeneration after fission in the holothurianCladolabes schmeltzii(Dendrochirotida: Holothuroidea). Microsc Res Tech 2016; 80:183-194. [DOI: 10.1002/jemt.22786] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 07/21/2016] [Accepted: 09/15/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Yaroslav O. Kamenev
- A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology, Far Eastern Branch; Russian Academy of Sciences; Vladivostok Russia
| | - Igor Y. Dolmatov
- A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology, Far Eastern Branch; Russian Academy of Sciences; Vladivostok Russia
- Far Eastern Federal University; Vladivostok Russia
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34
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Bodnar AG, Coffman JA. Maintenance of somatic tissue regeneration with age in short- and long-lived species of sea urchins. Aging Cell 2016; 15:778-87. [PMID: 27095483 PMCID: PMC4933669 DOI: 10.1111/acel.12487] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/28/2016] [Indexed: 01/08/2023] Open
Abstract
Aging in many animals is characterized by a failure to maintain tissue homeostasis and the loss of regenerative capacity. In this study, the ability to maintain tissue homeostasis and regenerative potential was investigated in sea urchins, a novel model to study longevity and negligible senescence. Sea urchins grow indeterminately, regenerate damaged appendages and reproduce throughout their lifespan and yet different species are reported to have very different life expectancies (ranging from 4 to more than 100 years). Quantitative analyses of cell proliferation and apoptosis indicated a low level of cell turnover in tissues of young and old sea urchins of species with different lifespans (Lytechinus variegatus, Strongylocentrotus purpuratus and Mesocentrotus franciscanus). The ability to regenerate damaged tissue was maintained with age as assessed by the regrowth of amputated spines and tube feet (motor and sensory appendages). Expression of genes involved in cell proliferation (pcna), telomere maintenance (tert) and multipotency (seawi and vasa) was maintained with age in somatic tissues. Immunolocalization of the Vasa protein to areas of the tube feet, spines, radial nerve, esophagus and a sub-population of circulating coelomocytes suggests the presence of multipotent cells that may play a role in normal tissue homeostasis and the regenerative potential of external appendages. The results indicate that regenerative potential was maintained with age regardless of lifespan, contrary to the expectation that shorter lived species would invest less in maintenance and repair.
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Affiliation(s)
- Andrea G. Bodnar
- Bermuda Institute of Ocean Sciences 17 Biological Station St. George's GE01 Bermuda
| | - James A. Coffman
- MDI Biological Laboratory 159 Old Bar Harbor Road Salisbury Cove ME 04672 USA
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35
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Czarkwiani A, Ferrario C, Dylus DV, Sugni M, Oliveri P. Skeletal regeneration in the brittle star Amphiura filiformis. Front Zool 2016; 13:18. [PMID: 27110269 PMCID: PMC4841056 DOI: 10.1186/s12983-016-0149-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 04/12/2016] [Indexed: 12/17/2022] Open
Abstract
Background Brittle stars regenerate their whole arms post-amputation. Amphiura filiformis can now be used for molecular characterization of arm regeneration due to the availability of transcriptomic data. Previous work showed that specific developmental transcription factors known to take part in echinoderm skeletogenesis are expressed during adult arm regeneration in A. filiformis; however, the process of skeleton formation remained poorly understood. Here, we present the results of an in-depth microscopic analysis of skeletal morphogenesis during regeneration, using calcein staining, EdU labeling and in situ hybridization. Results To better compare different samples, we propose a staging system for the early A. filiformis arm regeneration stages based on morphological landmarks identifiable in living animals and supported by histological analysis. We show that the calcified spicules forming the endoskeleton first appear very early during regeneration in the dermal layer of regenerates. These spicules then mature into complex skeletal elements of the differentiated arm during late regeneration. The mesenchymal cells in the dermal area express the skeletal marker genes Afi-c-lectin, Afi-p58b and Afi-p19; however, EdU labeling shows that these dermal cells do not proliferate. Conclusions A. filiformis arms regenerate through a consistent set of developmental stages using a distalization-intercalation mode, despite variability in regeneration rate. Skeletal elements form in a mesenchymal cell layer that does not proliferate and thus must be supplied from a different source. Our work provides the basis for future cellular and molecular studies of skeleton regeneration in brittle stars. Electronic supplementary material The online version of this article (doi:10.1186/s12983-016-0149-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Czarkwiani
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Cinzia Ferrario
- Department of Biosciences, University of Milan, Milan, Italy
| | - David Viktor Dylus
- Department of Genetics, Evolution and Environment, University College London, London, UK ; Centre for Mathematics, Physics and Engineering in the Life Sciences and Experimental Biology, University College London, London, UK ; Present address: Department of Ecology and Evolution & Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Michela Sugni
- Department of Biosciences, University of Milan, Milan, Italy
| | - Paola Oliveri
- Department of Genetics, Evolution and Environment, University College London, London, UK ; Research Department of Genetics, Evolution and Environment, University College London, Room 426, Darwin Building, Gower Street, London, WC1E 6BT UK
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Abstract
Primordial germ cells are usually made early in the development of an organism. These are the mother of all stem cells that are necessary for propagation of the species, yet use highly diverse mechanisms between organisms. How they are specified, and when and where they form, are central to developmental biology. Using diverse organisms to study this development is illuminating for understanding the mechanics these cells use in this essential function and for identifying the breadth of evolutionary changes that have occurred between species. This essay emphasizes how echinoderms may contribute to the patchwork quilt of our understanding of germ line formation during embryogenesis.
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Affiliation(s)
- Gary M Wessel
- Department of Molecular and Cellular Biology, Brown University, Providence, Rhode Island, USA.
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