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Liu S, Takemasa E, Suzuki Y, Mogi M. Exploring an immortal Turritopsis sp. as a less conventional natural system for study of aging. Biochem Biophys Rep 2024; 37:101613. [PMID: 38155942 PMCID: PMC10753042 DOI: 10.1016/j.bbrep.2023.101613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/05/2023] [Accepted: 12/11/2023] [Indexed: 12/30/2023] Open
Abstract
Aim Given its excellent capability of escaping from unavoidable harm and death, Turritopsissp. (T. sp.) has captured the attention and fascination of scientists as a less conventional tool for aging research. The current study introduces a method for establishment of a research model and comprehensive transcriptomic analysis to reveal the structural and functional diversity of T. sp. Methods T. sp. medusae collected from the Pacific Ocean near Japan were reared using a common laboratory setting. Tissues of the gastrovascular cavity part (GP) and nerve ring part (NP) were collected, and total RNA was extracted. Bulk RNA-seq was performed to compare the different transcriptome landscapes between GP and NP. Results The GP fragment could be utilized for studies related to stress response and systemic senescence, while the NP fragment could be used to explore system rejuvenation, self-repair and regeneration. Conclusions As a less conventional system for aging research, by employing the most recently developed tools and techniques in the genomic revolution, comprehensive elucidation of the composition, development, and functions of T. sp. enabled us to explore the underlying mechanisms of the response to environmental stress and rejuvenation.
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Affiliation(s)
- Shuang Liu
- Department of Pharmacology, Ehime University Graduate School of Medicine, Tohon, Ehime, Japan
| | - Erika Takemasa
- Department of Pharmacology, Ehime University Graduate School of Medicine, Tohon, Ehime, Japan
| | - Yasuyuki Suzuki
- Department of Pharmacology, Ehime University Graduate School of Medicine, Tohon, Ehime, Japan
- Department of Anesthesiology, Saiseikai Matsuyama Hospital, Matsuyama, Japan
- Research Division, Saiseikai Research Institute of Health Care and Welfare, Tokyo, Japan
| | - Masaki Mogi
- Department of Pharmacology, Ehime University Graduate School of Medicine, Tohon, Ehime, Japan
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Hasegawa Y, Watanabe T, Otsuka R, Toné S, Kubota S, Hirakawa H. Genome assembly and transcriptomic analyses of the repeatedly rejuvenating jellyfish Turritopsis dohrnii. DNA Res 2022; 30:6909006. [PMID: 36519838 PMCID: PMC9835754 DOI: 10.1093/dnares/dsac047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 11/16/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
Only two hydromedusan species, Turritopsis dohrnii and T. sp., have exhibited experimental multiple-repeat life cycle reversion in the laboratory, which can be artificially induced by various means such as incubation with CsCl, heat shock, and mechanical damage with needles. In the present study, we constructed a genome assembly of T. dohrnii using Pacific Biosciences long-reads and Illumina short-reads, for which the genome DNA was extracted from 1,500 young medusae originated from a single clone. The total length of the draft genome sequence of T. dohrnii was 435.9 Mb (N50 length 747.2 kb). We identified 23,314 high-confidence genes and found the characteristics of RNA expression amongst developmental stages. Our genome assembly and transcriptome data provide a key model system resource that will be useful for understanding cyclical rejuvenation.
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Affiliation(s)
- Yoshinori Hasegawa
- To whom correspondence should be addressed. Tel: +81 438 52 3944. Fax: +81 438 52 3921. (Y.H); Tel: +81 438 52 3906. Fax: +81 438 52 3924. (H.H)
| | - Takashi Watanabe
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Reo Otsuka
- Graduate School of Science and Engineering, Tokyo Denki University, Hatoyama, Saitama 350-0394, Japan
| | - Shigenobu Toné
- Graduate School of Science and Engineering, Tokyo Denki University, Hatoyama, Saitama 350-0394, Japan
| | - Shin Kubota
- Turritopsis Immortal Jellyfish Regenerative Biological Research/Experience Laboratory, Arita, Wakayama 643-0002, Japan
| | - Hideki Hirakawa
- To whom correspondence should be addressed. Tel: +81 438 52 3944. Fax: +81 438 52 3921. (Y.H); Tel: +81 438 52 3906. Fax: +81 438 52 3924. (H.H)
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Koch TL, Hauser F, Grimmelikhuijzen CJP. An evolutionary genomics view on neuropeptide genes in Hydrozoa and Endocnidozoa (Myxozoa). BMC Genomics 2021; 22:862. [PMID: 34847889 PMCID: PMC8638164 DOI: 10.1186/s12864-021-08091-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/12/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The animal phylum Cnidaria consists of six classes or subphyla: Hydrozoa, Scyphozoa, Cubozoa, Staurozoa, Anthozoa, and Endocnidozoa. Cnidarians have an early evolutionary origin, diverging before the emergence of the Bilateria. Extant members from this phylum, therefore, are important resources for understanding the evolution of the nervous system. Cnidarian nervous systems are strongly peptidergic. Using genomics, we have recently shown that three neuropeptide families (the X1PRX2amides, GRFamides, and GLWamides) are wide-spread in four (Scyphozoa, Cubozoa, Staurozoa, Anthozoa) out of six cnidarian classes or subphyla, suggesting that these three neuropeptide families emerged in the common cnidarian ancestor. In the current paper, we analyze the remaining cnidarian class, Hydrozoa, and the subphylum Endocnidozoa, to make firm conclusions about the evolution of neuropeptide genes in Cnidaria. RESULTS We analyzed sixteen hydrozoan species with a sequenced genome or transcriptome, using a recently developed software program for discovering neuropeptide genes. These species belonged to various hydrozoan subclasses and orders, among them the laboratory models Hydra, Hydractinia, and Clytia. We found that each species contained three to five neuropeptide families. A common feature for all hydrozoans was that they contained genes coding for (i) X1PRX2amide peptides, (ii) GRFamide peptides, and (iii) GLWamide peptides. These results support our previous conclusions that these three neuropeptide families evolved early in evolution. In addition to these three neuropeptide families, hydrozoans expressed up to two other neuropeptide gene families, which, however, were only occurring in certain animal groups. Endocnidozoa (Myxozoa) are microscopically small endoparasites, which are strongly reduced. For long, it was unknown to which phylum these parasites belonged, but recently they have been associated with cnidarians. We analyzed nine endocnidozoan species and found that two of them (Polypodium hydriforme and Buddenbrockia plumatellae) expressed neuropeptide genes. These genes coded for neuropeptides belonging to the GRFamide and GLWamide families with structures closely resembling them from hydrozoans. CONCLUSIONS We found X1PRX2amide, GRFamide, and GLWamide peptides in all species belonging to the Hydrozoa, confirming that these peptides originated in the common cnidarian ancestor. In addition, we discovered GRFamide and GLWamide peptide genes in some members of the Endocnidozoa, thereby linking these parasites to Hydrozoa.
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Affiliation(s)
- Thomas L. Koch
- Section for Cell and Neurobiology, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Frank Hauser
- Section for Cell and Neurobiology, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Cornelis J. P. Grimmelikhuijzen
- Section for Cell and Neurobiology, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
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The Changes in the p53 Protein across the Animal Kingdom Point to Its Involvement in Longevity. Int J Mol Sci 2021; 22:ijms22168512. [PMID: 34445220 PMCID: PMC8395165 DOI: 10.3390/ijms22168512] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 12/14/2022] Open
Abstract
Recently, the quest for the mythical fountain of youth has produced extensive research programs that aim to extend the healthy lifespan of humans. Despite advances in our understanding of the aging process, the surprisingly extended lifespan and cancer resistance of some animal species remain unexplained. The p53 protein plays a crucial role in tumor suppression, tissue homeostasis, and aging. Long-lived, cancer-free African elephants have 20 copies of the TP53 gene, including 19 retrogenes (38 alleles), which are partially active, whereas humans possess only one copy of TP53 and have an estimated cancer mortality rate of 11–25%. The mechanism through which p53 contributes to the resolution of the Peto’s paradox in Animalia remains vague. Thus, in this work, we took advantage of the available datasets and inspected the p53 amino acid sequence of phylogenetically related organisms that show variations in their lifespans. We discovered new correlations between specific amino acid deviations in p53 and the lifespans across different animal species. We found that species with extended lifespans have certain characteristic amino acid substitutions in the p53 DNA-binding domain that alter its function, as depicted from the Phenotypic Annotation of p53 Mutations, using the PROVEAN tool or SWISS-MODEL workflow. In addition, the loop 2 region of the human p53 DNA-binding domain was identified as the longest region that was associated with longevity. The 3D model revealed variations in the loop 2 structure in long-lived species when compared with human p53. Our findings show a direct association between specific amino acid residues in p53 protein, changes in p53 functionality, and the extended animal lifespan, and further highlight the importance of p53 protein in aging.
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Seo Y, Chae J, Ki JS. The complete mitochondrial genome of the hydrozoan jellyfish Turritopsis lata Lendenfeld, 1885 (Cnidaria; Hydrozoa; Anthoathecata) with molecular phylogenetic analysis. Mitochondrial DNA B Resour 2021; 6:1992-1993. [PMID: 34179492 PMCID: PMC8205065 DOI: 10.1080/23802359.2021.1938725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/27/2021] [Indexed: 11/20/2022] Open
Abstract
In this study, we sequenced and analyzed the complete mitochondrial genome (mtgenome) of the hydrozoan jellyfish Turritopsis lata. The mtgenome was a complete linear form (15,047 bp in length, 30.9% A, 42.1% T, 12.5% C, and 14.5% G), including 13 protein coding genes (PCGs) (cox1, cox2, cox3, atp6, atp8, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, and cytb), 2 tRNAs (tRNAMet and tRNATrp), and 2 rRNAs (12S and 16S rRNA). The genome structure of the T. lata was completely identical to those of other species within the subclass Hydroidolina. In addition, our molecular phylogenetic analysis using 13 PCGs within hydrozoans showed that T. lata was the closest to Turritopsis dohrnii.
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Affiliation(s)
- Yoseph Seo
- Department of Biotechnology, Sangmyung University, Seoul, South Korea
| | - Jinho Chae
- Marine Environmental Research and Information Laboratory, Gunpo, South Korea
| | - Jang-Seu Ki
- Department of Biotechnology, Sangmyung University, Seoul, South Korea
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Matsumoto Y, Piraino S, Miglietta MP. Transcriptome Characterization of Reverse Development in Turritopsis dohrnii (Hydrozoa, Cnidaria). G3 (BETHESDA, MD.) 2019; 9:4127-4138. [PMID: 31619459 PMCID: PMC6893190 DOI: 10.1534/g3.119.400487] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 10/08/2019] [Indexed: 02/08/2023]
Abstract
Medusae of Turritopsis dohrnii undergo reverse development in response to physical damage, adverse environmental conditions, or aging. Senescent, weakened or damaged medusae transform into a cluster of poorly differentiated cells (known as the cyst stage), which metamorphose back into a preceding life cycle stage, the polyp. During the metamorphosis, cell transdifferentiation occurs. The cyst represents the intermediate stage between a reverting medusa and a healthy polyp, during which cell transdifferentiation and tissue reorganization take place. Here we characterize and compare the transcriptomes of the polyp and newborn medusa stages of T. dohrnii with that of the cyst, to identify biological networks potentially involved in the reverse development and transdifferentiation processes. The polyp, medusa and cyst of T. dohrnii were sequenced through Illumina RNA-sequencing and assembled using a de novo approach, resulting in 92,569, 74,639 and 86,373 contigs, respectively. The transcriptomes were annotated and comparative analyses among the stages identified biological networks that were significantly over-and under-expressed in the cyst as compared to the polyp and medusa stages. Biological processes that occur at the cyst stage such as telomerase activity, regulation of transposable elements and DNA repair systems, and suppression of cell signaling pathways, mitotic cell division and cellular differentiation and development may be involved in T. dohrnii's reverse development and transdifferentiation. Our results are the first attempt to understand T. dohrnii's life-cycle reversal at the genetic level, and indicate possible avenues of future research on developmental strategies, cell transdifferentiation, and aging using T. dohrnii as a non-traditional in vivo system.
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Affiliation(s)
- Yui Matsumoto
- Texas A&M University at Galveston, Galveston, TX and
| | - Stefano Piraino
- Università del Salento, Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, 73100 Lecce, Italy
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R L Morlighem JÉ, Huang C, Liao Q, Braga Gomes P, Daniel Pérez C, de Brandão Prieto-da-Silva ÁR, Ming-Yuen Lee S, Rádis-Baptista G. The Holo-Transcriptome of the Zoantharian Protopalythoa variabilis (Cnidaria: Anthozoa): A Plentiful Source of Enzymes for Potential Application in Green Chemistry, Industrial and Pharmaceutical Biotechnology. Mar Drugs 2018; 16:E207. [PMID: 29899267 PMCID: PMC6025448 DOI: 10.3390/md16060207] [Citation(s) in RCA: 6] [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: 05/01/2018] [Revised: 06/05/2018] [Accepted: 06/08/2018] [Indexed: 02/08/2023] Open
Abstract
Marine invertebrates, such as sponges, tunicates and cnidarians (zoantharians and scleractinian corals), form functional assemblages, known as holobionts, with numerous microbes. This type of species-specific symbiotic association can be a repository of myriad valuable low molecular weight organic compounds, bioactive peptides and enzymes. The zoantharian Protopalythoa variabilis (Cnidaria: Anthozoa) is one such example of a marine holobiont that inhabits the coastal reefs of the tropical Atlantic coast and is an interesting source of secondary metabolites and biologically active polypeptides. In the present study, we analyzed the entire holo-transcriptome of P. variabilis, looking for enzyme precursors expressed in the zoantharian-microbiota assemblage that are potentially useful as industrial biocatalysts and biopharmaceuticals. In addition to hundreds of predicted enzymes that fit into the classes of hydrolases, oxidoreductases and transferases that were found, novel enzyme precursors with multiple activities in single structures and enzymes with incomplete Enzyme Commission numbers were revealed. Our results indicated the predictive expression of thirteen multifunctional enzymes and 694 enzyme sequences with partially characterized activities, distributed in 23 sub-subclasses. These predicted enzyme structures and activities can prospectively be harnessed for applications in diverse areas of industrial and pharmaceutical biotechnology.
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Affiliation(s)
- Jean-Étienne R L Morlighem
- Northeast Biotechnology Network (RENORBIO), Post-Graduation Program in Biotechnology, Federal University of Ceará, Fortaleza 60440-900, Brazil.
- Laboratory of Biochemistry and Biotechnology, Institute for Marine Sciences, Federal University of Ceará, Fortaleza 60165-081, Brazil.
| | - Chen Huang
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau 519020, China.
| | - Qiwen Liao
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau 519020, China.
| | - Paula Braga Gomes
- Department of Biology, Federal Rural University of Pernambuco, Recife 52171-900, Brazil.
| | - Carlos Daniel Pérez
- Academic Center in Vitória, Federal University of Pernambuco, Vitória de Santo Antão 50670-901, Pernambuco, Brazil.
| | | | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau 519020, China.
| | - Gandhi Rádis-Baptista
- Northeast Biotechnology Network (RENORBIO), Post-Graduation Program in Biotechnology, Federal University of Ceará, Fortaleza 60440-900, Brazil.
- Laboratory of Biochemistry and Biotechnology, Institute for Marine Sciences, Federal University of Ceará, Fortaleza 60165-081, Brazil.
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Li JY, Guo DH, Wu PC, He LS. Ontogeny reversal and phylogenetic analysis of Turritopsis sp.5 (Cnidaria, Hydrozoa, Oceaniidae), a possible new species endemic to Xiamen, China. PeerJ 2018; 6:e4225. [PMID: 29333345 PMCID: PMC5764029 DOI: 10.7717/peerj.4225] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 12/13/2017] [Indexed: 11/20/2022] Open
Abstract
Ontogeny reversal, as seen in some cnidarians, is an unprecedented phenomenon in the animal kingdom involving reversal of the ordinary life cycle. Three species of Turritopsis have been shown to be capable of inverted metamorphosis, a process in which the pelagic medusa transforms back into a juvenile benthic polyp stage when faced with adverse conditions. Turritopsis sp.5 is a species of Turritopsis collected from Xiamen, China which presents a similar ability, being able to reverse its life cycle if injured by mechanical stress. Phylogenetic analysis based on both 16S rDNA and cytochrome c oxidase subunit I (COI) genetic barcodes shows that Turritopsis sp.5 is phylogenetically clustered in a clade separate from other species of Turritopsis. The genetic distance between T. sp.5 and the Japanese species T. sp.2 is the shortest, when measured by the Kimura 2-Parameter metric, and the distance to the New Zealand species T. rubra is the largest. An experimental assay on the induction of reverse development in this species was initiated by cutting medusae into upper and lower parts. We show, for the first time, that the two dissected parts have significantly different potentials to transform into polyps. Also, a series of morphological changes of the reversed life cycle can be recognised, including medusa stage, contraction stage I, contraction stage II, cyst, cyst with stolons, and polyp. The discovery of species capable of reverse ontogeny caused by unfavorable conditions adds to the available systems with which to study the cell types that contribute to the developmental reversal and the molecular mechanisms of the directional determination of ontogeny.
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Affiliation(s)
- Jun-Yuan Li
- Department of Life Sciences, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China.,College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Dong-Hui Guo
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Peng-Cheng Wu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Li-Sheng He
- Department of Life Sciences, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
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