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Sadowska-Bartosz I, Bartosz G. Antioxidant Defense in the Toughest Animals on the Earth: Its Contribution to the Extreme Resistance of Tardigrades. Int J Mol Sci 2024; 25:8393. [PMID: 39125965 PMCID: PMC11313143 DOI: 10.3390/ijms25158393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 07/23/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Tardigrades are unique among animals in their resistance to dehydration, mainly due to anhydrobiosis and tun formation. They are also very resistant to high-energy radiation, low and high temperatures, low and high pressure, and various chemical agents, Interestingly, they are resistant to ionizing radiation both in the hydrated and dehydrated states to a similar extent. They are able to survive in the cosmic space. Apparently, many mechanisms contribute to the resistance of tardigrades to harmful factors, including the presence of trehalose (though not common to all tardigrades), heat shock proteins, late embryogenesis-abundant proteins, tardigrade-unique proteins, DNA repair proteins, proteins directly protecting DNA (Dsup and TDR1), and efficient antioxidant system. Antioxidant enzymes and small-molecular-weight antioxidants are an important element in the tardigrade resistance. The levels and activities of many antioxidant proteins is elevated by anhydrobiosis and UV radiation; one explanation for their induction during dehydration is provided by the theory of "preparation for oxidative stress", which occurs during rehydration. Genes coding for some antioxidant proteins are expanded in tardigrades; some genes (especially those coding for catalases) were hypothesized to be of bacterial origin, acquired by horizontal gene transfer. An interesting antioxidant protein found in tardigrades is the new Mn-dependent peroxidase.
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Affiliation(s)
- Izabela Sadowska-Bartosz
- Laboratory of Analytical Biochemistry, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszów, 4 Zelwerowicza Street, 35-601 Rzeszow, Poland;
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Yoshida Y, Hirayama A, Arakawa K. Transcriptome analysis of the tardigrade Hypsibius exemplaris exposed to the DNA-damaging agent bleomycin. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2024; 100:414-428. [PMID: 38839369 DOI: 10.2183/pjab.pjab.100.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Tardigrades are microscopic animals that are renowned for their capabilities of tolerating near-complete desiccation by entering an ametabolic state called anhydrobiosis. However, many species also show high tolerance against radiation in the active state as well, suggesting cross-tolerance via the anhydrobiosis mechanism. Previous studies utilized indirect DNA damaging agents to identify core components of the cross-tolerance machinery in species with high anhydrobiosis capacities. However, it was difficult to distinguish whether transcriptomic changes were specific to DNA damage or mutual with anhydrobiosis. To this end, we performed transcriptome analysis on bleomycin-exposed Hypsibius exemplaris. We observed induction of several tardigrade-specific gene families, including a previously identified novel anti-oxidative stress family, which may be a core component of the cross-tolerance mechanism. We also identified enrichment of the tryptophan metabolism pathway, for which metabolomic analysis suggested engagement of this pathway in stress tolerance. These results provide several candidates for the core component of cross-tolerance, as well as possible anhydrobiosis machinery.
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Affiliation(s)
- Yuki Yoshida
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, Japan
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Anoud M, Delagoutte E, Helleu Q, Brion A, Duvernois-Berthet E, As M, Marques X, Lamribet K, Senamaud-Beaufort C, Jourdren L, Adrait A, Heinrich S, Toutirais G, Hamlaoui S, Gropplero G, Giovannini I, Ponger L, Geze M, Blugeon C, Couté Y, Guidetti R, Rebecchi L, Giovannangeli C, De Cian A, Concordet JP. Comparative transcriptomics reveal a novel tardigrade-specific DNA-binding protein induced in response to ionizing radiation. eLife 2024; 13:RP92621. [PMID: 38980300 PMCID: PMC11233135 DOI: 10.7554/elife.92621] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024] Open
Abstract
Tardigrades are microscopic animals renowned for their ability to withstand extreme conditions, including high doses of ionizing radiation (IR). To better understand their radio-resistance, we first characterized induction and repair of DNA double- and single-strand breaks after exposure to IR in the model species Hypsibius exemplaris. Importantly, we found that the rate of single-strand breaks induced was roughly equivalent to that in human cells, suggesting that DNA repair plays a predominant role in tardigrades' radio-resistance. To identify novel tardigrade-specific genes involved, we next conducted a comparative transcriptomics analysis across three different species. In all three species, many DNA repair genes were among the most strongly overexpressed genes alongside a novel tardigrade-specific gene, which we named Tardigrade DNA damage Response 1 (TDR1). We found that TDR1 protein interacts with DNA and forms aggregates at high concentration suggesting it may condensate DNA and preserve chromosome organization until DNA repair is accomplished. Remarkably, when expressed in human cells, TDR1 improved resistance to Bleomycin, a radiomimetic drug. Based on these findings, we propose that TDR1 is a novel tardigrade-specific gene conferring resistance to IR. Our study sheds light on mechanisms of DNA repair helping cope with high levels of DNA damage inflicted by IR.
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Affiliation(s)
- Marwan Anoud
- Département AVIV, MNHN, CNRS UMR7196, INSERM U1154ParisFrance
- Université Paris-SaclayOrsayFrance
| | | | - Quentin Helleu
- Département AVIV, MNHN, CNRS UMR7196, INSERM U1154ParisFrance
| | - Alice Brion
- Département AVIV, MNHN, CNRS UMR7196, INSERM U1154ParisFrance
| | | | - Marie As
- Département AVIV, MNHN, CNRS UMR7196, INSERM U1154ParisFrance
| | - Xavier Marques
- Département AVIV, MNHN, CNRS UMR7196, INSERM U1154ParisFrance
- CeMIM, MNHN, CNRS UMR7245ParisFrance
| | | | - Catherine Senamaud-Beaufort
- Génomique ENS, Institut de Biologie de l’ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSLParisFrance
| | - Laurent Jourdren
- Génomique ENS, Institut de Biologie de l’ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSLParisFrance
| | - Annie Adrait
- Univ. Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, CEAGrenobleFrance
| | - Sophie Heinrich
- Institut Curie, Inserm U1021-CNRS UMR 3347, Université Paris-Saclay, Université PSLOrsay CedexFrance
- Plateforme RADEXP, Institut CurieOrsayFrance
| | | | | | | | - Ilaria Giovannini
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
- NBFC, National Biodiversity Future CenterPalermoItaly
| | - Loic Ponger
- Département AVIV, MNHN, CNRS UMR7196, INSERM U1154ParisFrance
| | - Marc Geze
- CeMIM, MNHN, CNRS UMR7245ParisFrance
| | - Corinne Blugeon
- Génomique ENS, Institut de Biologie de l’ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSLParisFrance
| | - Yohann Couté
- Univ. Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, CEAGrenobleFrance
| | - Roberto Guidetti
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
- NBFC, National Biodiversity Future CenterPalermoItaly
| | - Lorena Rebecchi
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
- NBFC, National Biodiversity Future CenterPalermoItaly
| | | | - Anne De Cian
- Département AVIV, MNHN, CNRS UMR7196, INSERM U1154ParisFrance
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Clark-Hachtel CM, Hibshman JD, De Buysscher T, Stair ER, Hicks LM, Goldstein B. The tardigrade Hypsibius exemplaris dramatically upregulates DNA repair pathway genes in response to ionizing radiation. Curr Biol 2024; 34:1819-1830.e6. [PMID: 38614079 PMCID: PMC11078613 DOI: 10.1016/j.cub.2024.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/19/2024] [Accepted: 03/13/2024] [Indexed: 04/15/2024]
Abstract
Tardigrades can survive remarkable doses of ionizing radiation, up to about 1,000 times the lethal dose for humans. How they do so is incompletely understood. We found that the tardigrade Hypsibius exemplaris suffers DNA damage upon gamma irradiation, but the damage is repaired. We show that this species has a specific and robust response to ionizing radiation: irradiation induces a rapid upregulation of many DNA repair genes. This upregulation is unexpectedly extreme-making some DNA repair transcripts among the most abundant transcripts in the animal. By expressing tardigrade genes in bacteria, we validate that increased expression of some repair genes can suffice to increase radiation tolerance. We show that at least one such gene is important in vivo for tardigrade radiation tolerance. We hypothesize that the tardigrades' ability to sense ionizing radiation and massively upregulate specific DNA repair pathway genes may represent an evolved solution for maintaining DNA integrity.
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Affiliation(s)
- Courtney M Clark-Hachtel
- Biology Department, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Biology Department, The University of North Carolina at Asheville, Asheville, NC 28804, USA.
| | - Jonathan D Hibshman
- Biology Department, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tristan De Buysscher
- Biology Department, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Bioinformatics & Analytics Research Collaborative, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Evan R Stair
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Leslie M Hicks
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bob Goldstein
- Biology Department, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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5
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Nicolas E, Simion P, Guérineau M, Terwagne M, Colinet M, Virgo J, Lingurski M, Boutsen A, Dieu M, Hallet B, Van Doninck K. Horizontal acquisition of a DNA ligase improves DNA damage tolerance in eukaryotes. Nat Commun 2023; 14:7638. [PMID: 37993452 PMCID: PMC10665377 DOI: 10.1038/s41467-023-43075-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/30/2023] [Indexed: 11/24/2023] Open
Abstract
Bdelloid rotifers are part of the restricted circle of multicellular animals that can withstand a wide range of genotoxic stresses at any stage of their life cycle. In this study, bdelloid rotifer Adineta vaga is used as a model to decipher the molecular basis of their extreme tolerance. Proteomic analysis shows that a specific DNA ligase, different from those usually involved in DNA repair in eukaryotes, is strongly over-represented upon ionizing radiation. A phylogenetic analysis reveals its orthology to prokaryotic DNA ligase E, and its horizontal acquisition by bdelloid rotifers and plausibly other eukaryotes. The fungus Mortierella verticillata, having a single copy of this DNA Ligase E homolog, also exhibits an increased radiation tolerance with an over-expression of this DNA ligase E following X-ray exposure. We also provide evidence that A. vaga ligase E is a major contributor of DNA breaks ligation activity, which is a common step of all important DNA repair pathways. Consistently, its heterologous expression in human cell lines significantly improves their radio-tolerance. Overall, this study highlights the potential of horizontal gene transfers in eukaryotes, and their contribution to the adaptation to extreme conditions.
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Affiliation(s)
- Emilien Nicolas
- Université Libre de Bruxelles, Molecular Biology and Evolution, Brussels, 1050, Belgium.
| | - Paul Simion
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
- Université de Rennes, Ecosystèmes, biodiversité, évolution (ECOBIO UMR 6553), CNRS, Rennes, France
| | - Marc Guérineau
- Université Libre de Bruxelles, Molecular Biology and Evolution, Brussels, 1050, Belgium
| | - Matthieu Terwagne
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
| | - Mathilde Colinet
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
| | - Julie Virgo
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
| | - Maxime Lingurski
- Université Libre de Bruxelles, Molecular Biology and Evolution, Brussels, 1050, Belgium
| | - Anaïs Boutsen
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
| | - Marc Dieu
- Université de Namur, MaSUN-mass spectrometry facility, Namur, 5000, Belgium
| | - Bernard Hallet
- Université Catholique de Louvain, Louvain Institute of Biomolecular Science and Technology, Louvain-la-Neuve, 1348, Belgium.
| | - Karine Van Doninck
- Université Libre de Bruxelles, Molecular Biology and Evolution, Brussels, 1050, Belgium.
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium.
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Hvidepil LKB, Møbjerg N. New insights into osmobiosis and chemobiosis in tardigrades. Front Physiol 2023; 14:1274522. [PMID: 37929212 PMCID: PMC10620314 DOI: 10.3389/fphys.2023.1274522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023] Open
Abstract
Tardigrades are renowned for their ability to enter the extremotolerant state of latent life known as cryptobiosis. While it is widely accepted that cryptobiosis can be induced by freezing (cryobiosis) and by desiccation (anhydrobiosis), the latter involving formation of a so-called tun, the exact mechanisms underlying the state-as well as the significance of other cryptobiosis inducing factors-remain ambiguous. Here, we focus on osmotic and chemical stress tolerance in the marine tidal tardigrade Echiniscoides sigismundi. We show that E. sigismundi enters the tun state following exposure to saturated seawater and upon exposure to locality seawater containing the mitochondrial uncoupler DNP. The latter experiments provide evidence of osmobiosis and chemobiosis, i.e., cryptobiosis induced by high levels of osmolytes and toxicants, respectively. A small decrease in survival was observed following simultaneous exposure to DNP and saturated seawater indicating that the tardigrades may not be entirely ametabolic while in the osmobiotic tun. The tardigrades easily handle exposure to ultrapure water, but hypo-osmotic shock impairs tun formation and when exposed to ultrapure water the tardigrades do not tolerate DNP, indicating that tolerance towards dilute solutions involves energy-consuming processes. We discuss our data in relation to earlier and more contemporary studies on cryptobiosis and we argue that osmobiosis should be defined as a state of cryptobiosis induced by high external osmotic pressure. Our investigation supports the hypothesis that the mechanisms underlying osmobiosis and anhydrobiosis are overlapping and that osmobiosis likely represents the evolutionary forerunner of cryptobiosis forms that involve body water deprivation.
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Affiliation(s)
| | - Nadja Møbjerg
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
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Tanaka Y, Ma D, Amaya S, Aishan Y, Shen Y, Funano SI, Tang T, Hosokawa Y, Gusev O, Okuda T, Kikawada T, Yalikun Y. Anhydrobiotic chironomid larval motion-based multi-sensing microdevice for the exploration of survivable locations. iScience 2022; 25:104639. [PMID: 36039361 PMCID: PMC9418600 DOI: 10.1016/j.isci.2022.104639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/31/2022] [Accepted: 06/14/2022] [Indexed: 11/30/2022] Open
Abstract
African chironomid (Polypedilum vanderplanki) larvae can suspend their metabolism by undergoing severe desiccation and then resume this activity by simple rehydration. We present a microdevice using interdigital comb electrodes to detect the larval motion using the natural surface charge of the living larvae in water. The larvae were most active 2 h after soaking them in water at 30°C; they exhibited motions with 2 Hz frequency. This was comparable to the signal obtained from the microdevice via fast Fourier transform (FFT) processing. The amplitude of the voltage and current were 0.11 mV and 730 nA, respectively. They would be enough to be detected by a low power consumption microcomputer. Temperature and pH sensing were demonstrated by detecting the vital motions of the revived larvae under different conditions. This multi-functional biosensor will be a useful microdevice to search for survivable locations under extreme environmental conditions like those on other planets. A biosensor using anhydrobiotic chironomid larva was created Interdigital comb electrodes were fabricated to detect the larvae motion Multi-parameters such as temperature or pH can be detected The device can search survivable locations under extreme environmental conditions
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Affiliation(s)
- Yo Tanaka
- Center for Biosystems Dynamics Research (BDR), RIKEN, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
- Corresponding author
| | - Doudou Ma
- Center for Biosystems Dynamics Research (BDR), RIKEN, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Satoshi Amaya
- Center for Biosystems Dynamics Research (BDR), RIKEN, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yusufu Aishan
- Center for Biosystems Dynamics Research (BDR), RIKEN, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yigang Shen
- Center for Biosystems Dynamics Research (BDR), RIKEN, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shun-ichi Funano
- Center for Biosystems Dynamics Research (BDR), RIKEN, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tao Tang
- Graduate School of Nara Institute of Science and Technology, 8916-5 Takayamacho, Ikoma, Nara 630-0192, Japan
| | - Yoichiroh Hosokawa
- Graduate School of Nara Institute of Science and Technology, 8916-5 Takayamacho, Ikoma, Nara 630-0192, Japan
| | - Oleg Gusev
- RIKEN Cluster for Science, Technology and Innovation Hub (RCSTI), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Takashi Okuda
- Institute of Agrobiological Sciences, NARO, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Takahiro Kikawada
- Institute of Agrobiological Sciences, NARO, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Yaxiaer Yalikun
- Center for Biosystems Dynamics Research (BDR), RIKEN, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
- Graduate School of Nara Institute of Science and Technology, 8916-5 Takayamacho, Ikoma, Nara 630-0192, Japan
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Yoshida Y, Tanaka S. Deciphering the Biological Enigma-Genomic Evolution Underlying Anhydrobiosis in the Phylum Tardigrada and the Chironomid Polypedilum vanderplanki. INSECTS 2022; 13:557. [PMID: 35735894 PMCID: PMC9224920 DOI: 10.3390/insects13060557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/13/2022] [Accepted: 06/17/2022] [Indexed: 02/04/2023]
Abstract
Anhydrobiosis, an ametabolic dehydrated state triggered by water loss, is observed in several invertebrate lineages. Anhydrobiotes revive when rehydrated, and seem not to suffer the ultimately lethal cell damage that results from severe loss of water in other organisms. Here, we review the biochemical and genomic evidence that has revealed the protectant molecules, repair systems, and maintenance pathways associated with anhydrobiosis. We then introduce two lineages in which anhydrobiosis has evolved independently: Tardigrada, where anhydrobiosis characterizes many species within the phylum, and the genus Polypedilum, where anhydrobiosis occurs in only two species. Finally, we discuss the complexity of the evolution of anhydrobiosis within invertebrates based on current knowledge, and propose perspectives to enhance the understanding of anhydrobiosis.
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Affiliation(s)
- Yuki Yoshida
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Sae Tanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Institute for Advanced Biosciences, Keio University, 341-1 Mizukami, Tsuruoka 997-0052, Japan
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Yoshida Y, Satoh T, Ota C, Tanaka S, Horikawa DD, Tomita M, Kato K, Arakawa K. Time-series transcriptomic screening of factors contributing to the cross-tolerance to UV radiation and anhydrobiosis in tardigrades. BMC Genomics 2022; 23:405. [PMID: 35643424 PMCID: PMC9145152 DOI: 10.1186/s12864-022-08642-1] [Citation(s) in RCA: 2] [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: 07/14/2021] [Accepted: 05/18/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Tardigrades are microscopic animals that are capable of tolerating extreme environments by entering a desiccated state of suspended animation known as anhydrobiosis. While antioxidative stress proteins, antiapoptotic pathways and tardigrade-specific intrinsically disordered proteins have been implicated in the anhydrobiotic machinery, conservation of these mechanisms is not universal within the phylum Tardigrada, suggesting the existence of overlooked components. RESULTS Here, we show that a novel Mn-dependent peroxidase is an important factor in tardigrade anhydrobiosis. Through time-series transcriptome analysis of Ramazzottius varieornatus specimens exposed to ultraviolet light and comparison with anhydrobiosis entry, we first identified several novel gene families without similarity to existing sequences that are induced rapidly after stress exposure. Among these, a single gene family with multiple orthologs that is highly conserved within the phylum Tardigrada and enhances oxidative stress tolerance when expressed in human cells was identified. Crystallographic study of this protein suggested Zn or Mn binding at the active site, and we further confirmed that this protein has Mn-dependent peroxidase activity in vitro. CONCLUSIONS Our results demonstrated novel mechanisms for coping with oxidative stress that may be a fundamental mechanism of anhydrobiosis in tardigrades. Furthermore, localization of these sets of proteins mainly in the Golgi apparatus suggests an indispensable role of the Golgi stress response in desiccation tolerance.
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Affiliation(s)
- Yuki Yoshida
- Institute for Advanced Biosciences, Keio University, Nihonkoku, 403-1, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa, 252-0882, Japan
| | - Tadashi Satoh
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho, Nagoya, 467-8603, Japan
| | - Chise Ota
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho, Nagoya, 467-8603, Japan
| | - Sae Tanaka
- Exploratory Research Center On Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Daiki D Horikawa
- Institute for Advanced Biosciences, Keio University, Nihonkoku, 403-1, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa, 252-0882, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Nihonkoku, 403-1, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa, 252-0882, Japan
| | - Koichi Kato
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho, Nagoya, 467-8603, Japan
- Exploratory Research Center On Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Nihonkoku, 403-1, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan.
- Systems Biology Program, Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa, 252-0882, Japan.
- Exploratory Research Center On Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
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10
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Abstract
Tardigrades are ubiquitous meiofauna that are especially renowned for their exceptional extremotolerance to various adverse environments, including pressure, temperature, and even ionizing radiation. This is achieved through a reversible halt of metabolism triggered by desiccation, a phenomenon called anhydrobiosis. Recent establishment of genome resources for two tardigrades, Hypsibius exemplaris and Ramazzottius varieornatus, accelerated research to uncover the molecular mechanisms behind anhydrobiosis, leading to the discovery of many tardigrade-unique proteins. This review focuses on the history, methods, discoveries, and current state and challenges regarding tardigrade genomics, with an emphasis on molecular anhydrobiology. Remaining questions and future perspectives regarding prospective approaches to fully elucidate the molecular machinery of this complex phenomenon are discussed.
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Affiliation(s)
- Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Daishouji, Tsuruoka, Yamagata, Japan; .,Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan.,Graduate School of Media and Governance, Systems Biology Program, Keio University, Fujisawa, Kanagawa, Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan
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11
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Murai Y, Yagi-Utsumi M, Fujiwara M, Tanaka S, Tomita M, Kato K, Arakawa K. Multiomics study of a heterotardigrade, Echinisicus testudo, suggests the possibility of convergent evolution of abundant heat-soluble proteins in Tardigrada. BMC Genomics 2021; 22:813. [PMID: 34763673 PMCID: PMC8582207 DOI: 10.1186/s12864-021-08131-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 10/28/2021] [Indexed: 11/13/2022] Open
Abstract
Background Many limno-terrestrial tardigrades can enter an ametabolic state, known as anhydrobiosis, upon desiccation, in which the animals can withstand extreme environments. Through genomics studies, molecular components of anhydrobiosis are beginning to be elucidated, such as the expansion of oxidative stress response genes, loss of stress signaling pathways, and gain of tardigrade-specific heat-soluble protein families designated CAHS and SAHS. However, to date, studies have predominantly investigated the class Eutardigrada, and molecular mechanisms in the remaining class, Heterotardigrada, still remains elusive. To address this gap in the research, we report a multiomics study of the heterotardigrade Echiniscus testudo, one of the most desiccation-tolerant species which is not yet culturable in laboratory conditions. Results In order to elucidate the molecular basis of anhydrobiosis in E. testudo, we employed a multi-omics strategy encompassing genome sequencing, differential transcriptomics, and proteomics. Using ultra-low input library sequencing protocol from a single specimen, we sequenced and assembled the 153.7 Mbp genome annotated using RNA-Seq data. None of the previously identified tardigrade-specific abundant heat-soluble genes was conserved, while the loss and expansion of existing pathways were partly shared. Furthermore, we identified two families novel abundant heat-soluble proteins, which we named E. testudo Abundant Heat Soluble (EtAHS), that are predicted to contain large stretches of disordered regions. Likewise the AHS families in eutardigrada, EtAHS shows structural changes from random coil to alphahelix as the water content was decreased in vitro. These characteristics of EtAHS proteins are analogous to those of CAHS in eutardigrades, while there is no conservation at the sequence level. Conclusions Our results suggest that Heterotardigrada have partly shared but distinct anhydrobiosis machinery compared with Eutardigrada, possibly due to convergent evolution within Tardigrada. (276/350). Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08131-x.
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Affiliation(s)
- Yumi Murai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, Japan
| | - Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Masayuki Fujiwara
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, Japan
| | - Sae Tanaka
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan. .,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, Japan. .,Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan. .,Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan.
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12
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Paithankar JG, Ghodke TS, Patil RK. Insight into the evolutionary profile of radio-resistance among insects having intrinsically evolved defence against radiation toxicity. Int J Radiat Biol 2021; 98:1012-1024. [PMID: 33264042 DOI: 10.1080/09553002.2020.1859153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Ionizing radiation (IR) has wide-ranging applications in various fields. In agriculture, pest control is one of the important applications, because insect pests have become a threat to the global agriculture industry. IR are used routinely to prevent crop loss and to protect stored food commodities. Radio-sterilization and disinfestation treatments are commonly used procedures for insect pest control. From various studies on insect radio-sterilization and disinfestation, it has been established that compared to vertebrates' insects have high levels of radiation resistance. Therefore, to achieve adequate radio-sterilization/disinfestation; exposure to high doses of IR is necessary. However, studies over decades made a presumption that radiation resistance is general among insects. Recent studies have shown that some insect orders are having high IR resistance and some insect orders are sensitive to IR. These studies have clarified that radiation resistance is not uniform throughout insect class. The present review is an attempt to insight at the evolutionary profile of insect species studied for radio-sterilization and disinfestation treatment and are having the trait of radio-resistance. From various studies on insect radiation resistance and after phylogenetic analysis of insect species it appears that the evolutionary near species have drastically different levels of radio-resistance and trait of radiation resistance appears to be independent of insect evolution.
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Affiliation(s)
- Jagdish Gopal Paithankar
- Division of Environmental Health and Toxicology, Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Mangalore, India
| | - Tanhaji Sandu Ghodke
- Centre for Applications of Radioisotopes and Radiation Technology (CARRT), Mangalore University, Mangalore, India.,Department of Applied Zoology, Mangalore University, Mangalore, India
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13
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Differential mechanisms of tolerance to extreme environmental conditions in tardigrades. Sci Rep 2019; 9:14938. [PMID: 31624306 PMCID: PMC6797769 DOI: 10.1038/s41598-019-51471-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 09/29/2019] [Indexed: 01/17/2023] Open
Abstract
Tardigrades, also known as water bears, are small aquatic animals that inhabit marine, fresh water or limno-terrestrial environments. While all tardigrades require surrounding water to grow and reproduce, species living in limno-terrestrial environments (e.g. Ramazzottius varieornatus) are able to undergo almost complete dehydration by entering an arrested state known as anhydrobiosis, which allows them to tolerate ionic radiation, extreme temperatures and intense pressure. Previous studies based on comparison of the genomes of R. varieornatus and Hypsibius dujardini - a less tolerant tardigrade - have pointed to potential mechanisms that may partially contribute to their remarkable ability to resist extreme physical conditions. In this work, we have further annotated the genomes of both tardigrades using a guided approach in search for novel mechanisms underlying the extremotolerance of R. varieornatus. We have found specific amplifications of several genes, including MRE11 and XPC, and numerous missense variants exclusive of R. varieornatus in CHEK1, POLK, UNG and TERT, all of them involved in important pathways for DNA repair and telomere maintenance. Taken collectively, these results point to genomic features that may contribute to the enhanced ability to resist extreme environmental conditions shown by R. varieornatus.
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14
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Jönsson KI. Radiation Tolerance in Tardigrades: Current Knowledge and Potential Applications in Medicine. Cancers (Basel) 2019; 11:E1333. [PMID: 31505739 PMCID: PMC6770827 DOI: 10.3390/cancers11091333] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 11/17/2022] Open
Abstract
Tardigrades represent a phylum of very small aquatic animals in which many species have evolved adaptations to survive under extreme environmental conditions, such as desiccation and freezing. Studies on several species have documented that tardigrades also belong to the most radiation-tolerant animals on Earth. This paper gives an overview of our current knowledge on radiation tolerance of tardigrades, with respect to dose-responses, developmental stages, and different radiation sources. The molecular mechanisms behind radiation tolerance in tardigrades are still largely unknown, but omics studies suggest that both mechanisms related to the avoidance of DNA damage and mechanisms of DNA repair are involved. The potential of tardigrades to provide knowledge of importance for medical sciences has long been recognized, but it is not until recently that more apparent evidence of such potential has appeared. Recent studies show that stress-related tardigrade genes may be transfected to human cells and provide increased tolerance to osmotic stress and ionizing radiation. With the recent sequencing of the tardigrade genome, more studies applying tardigrade omics to relevant aspects of human medicine are expected. In particular, the cancer research field has potential to learn from studies on tardigrades about molecular mechanisms evolved to maintain genome integrity.
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Affiliation(s)
- K Ingemar Jönsson
- Department of Environmental Science and Bioscience, Kristianstad University, 291 88 Kristianstad, Sweden.
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15
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Sugiura K, Minato H, Suzuki AC, Arakawa K, Kunieda T, Matsumoto M. Comparison of Sexual Reproductive Behaviors in Two Species of Macrobiotidae (Tardigrada: Eutardigrada). Zoolog Sci 2019; 36:120-127. [DOI: 10.2108/zs180103] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/10/2018] [Indexed: 11/17/2022]
Affiliation(s)
- Kenta Sugiura
- School of Fundamental Science and Technology, Graduate School of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama-shi, Kanagawa 223-8522, Japan
| | - Hiroki Minato
- School of Fundamental Science and Technology, Graduate School of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama-shi, Kanagawa 223-8522, Japan
| | - Atsushi C. Suzuki
- Department of Biology, School of Medicine, Keio University, 4-1-1 Hiyoshi, Kohoku-ku, Yokohama-shi, Kanagawa 223-8521, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, 14-1, Baba-cho, Tsuruoka-shi, Yamagata 997-0035, Japan
| | - Takekazu Kunieda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Midori Matsumoto
- School of Fundamental Science and Technology, Graduate School of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama-shi, Kanagawa 223-8522, Japan
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16
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Costantini D, Borremans B. The linear no-threshold model is less realistic than threshold or hormesis-based models: An evolutionary perspective. Chem Biol Interact 2018; 301:26-33. [PMID: 30342016 DOI: 10.1016/j.cbi.2018.10.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/12/2018] [Accepted: 10/16/2018] [Indexed: 12/30/2022]
Abstract
The linear no-threshold (LNT) risk model is the current human health risk assessment paradigm. This model states that adverse stochastic biological responses to high levels of a stressor can be used to estimate the response to low or moderate levels of that stressor. In recent years the validity of the LNT risk model has increasingly been questioned because of the recurring observation that an organism's response to high stressor doses differs from that to low doses. This raises important questions about the biological and evolutionary validity of the LNT model. In this review we reiterate that the LNT model as applied to stochastic biological effects of low and moderate stressor levels has less biological validity than threshold or, particularly, hormetic models. In so doing, we rely heavily on literature from disciplines like ecophysiology or evolutionary ecology showing how exposure to moderate amounts of stress can have severe impacts on phenotype and organism reproductive fitness. We present a mathematical model that illustrates and explores the hypothetical conditions that make a particular kind of hormesis (conditioning hormesis) ecologically and evolutionarily plausible.
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Affiliation(s)
- David Costantini
- UMR 7221 CNRS/MNHN, Muséum National d'Histoire Naturelle, Sorbonne Universités, 7 rue Cuvier, 75005, Paris, France; Behavioural Ecology & Ecophysiology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium.
| | - Benny Borremans
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 610 Charles E. Young Dr. South, Los Angeles, 90095, United States; Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium; Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BIOSTAT), Hasselt University, Agoralaan gebouw D, 3590, Diepenbeek, Belgium
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17
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Sørensen-Hygum TL, Stuart RM, Jørgensen A, Møbjerg N. Modelling extreme desiccation tolerance in a marine tardigrade. Sci Rep 2018; 8:11495. [PMID: 30065347 PMCID: PMC6068186 DOI: 10.1038/s41598-018-29824-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/18/2018] [Indexed: 11/17/2022] Open
Abstract
It has recently been argued that the enigmatic tardigrades (water bears) will endure until the sun dies, surviving any astrophysical calamities in Earth's oceans. Yet, our knowledge of stress tolerance among marine tardigrade species is very limited and most investigations revolve around species living in moist habitats on land. Here, we investigate desiccation tolerance in the cosmopolitan marine tidal tardigrade, Echiniscoides sigismundi, providing the first thorough analysis on recovery upon desiccation from seawater. We test the influence on survival of desiccation surface, time spent desiccated (up to 1 year) and initial water volume. We propose analysis methods for survival estimates, which can be used as a future platform for evaluating and analysing recovery rates in organisms subjected to extreme stress. Our data reveal that marine tidal tardigrades tolerate extremely rapid and extended periods of desiccation from seawater supporting the argument that these animals are among the toughest organisms on Earth.
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Affiliation(s)
- Thomas L Sørensen-Hygum
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Robyn M Stuart
- Data Science Laboratory, Department of Mathematical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Aslak Jørgensen
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Nadja Møbjerg
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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18
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Jönsson KI, Levine EB, Wojcik A, Haghdoost S, Harms-Ringdahl M. Environmental Adaptations: Radiation Tolerance. WATER BEARS: THE BIOLOGY OF TARDIGRADES 2018. [DOI: 10.1007/978-3-319-95702-9_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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19
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Hashimoto T, Kunieda T. DNA Protection Protein, a Novel Mechanism of Radiation Tolerance: Lessons from Tardigrades. Life (Basel) 2017; 7:life7020026. [PMID: 28617314 PMCID: PMC5492148 DOI: 10.3390/life7020026] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 06/08/2017] [Accepted: 06/12/2017] [Indexed: 01/19/2023] Open
Abstract
Genomic DNA stores all genetic information and is indispensable for maintenance of normal cellular activity and propagation. Radiation causes severe DNA lesions, including double-strand breaks, and leads to genome instability and even lethality. Regardless of the toxicity of radiation, some organisms exhibit extraordinary tolerance against radiation. These organisms are supposed to possess special mechanisms to mitigate radiation-induced DNA damages. Extensive study using radiotolerant bacteria suggested that effective protection of proteins and enhanced DNA repair system play important roles in tolerability against high-dose radiation. Recent studies using an extremotolerant animal, the tardigrade, provides new evidence that a tardigrade-unique DNA-associating protein, termed Dsup, suppresses the occurrence of DNA breaks by radiation in human-cultured cells. In this review, we provide a brief summary of the current knowledge on extremely radiotolerant animals, and present novel insights from the tardigrade research, which expand our understanding on molecular mechanism of exceptional radio-tolerability.
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Affiliation(s)
- Takuma Hashimoto
- Laboratory for Radiation Biology, School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan.
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Takekazu Kunieda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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