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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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2
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Swamy CSUS, Boothby TC. Surviving extreme radiation. eLife 2024; 13:e100219. [PMID: 38963418 PMCID: PMC11223764 DOI: 10.7554/elife.100219] [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] [Indexed: 07/05/2024] Open
Abstract
Tiny animals known as tardigrades use a combination of DNA repair machinery and a novel protein to mend their genome after intense ionizing radiation.
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Affiliation(s)
| | - Thomas C Boothby
- Department of Molecular Biology, University of WyomingLaramieUnited States
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3
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Smith FW, Game M, Mapalo MA, Chavarria RA, Harrison TR, Janssen R. Developmental and genomic insight into the origin of the tardigrade body plan. Evol Dev 2024; 26:e12457. [PMID: 37721221 DOI: 10.1111/ede.12457] [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: 05/05/2023] [Revised: 08/11/2023] [Accepted: 08/29/2023] [Indexed: 09/19/2023]
Abstract
Tardigrada is an ancient lineage of miniaturized animals. As an outgroup of the well-studied Arthropoda and Onychophora, studies of tardigrades hold the potential to reveal important insights into body plan evolution in Panarthropoda. Previous studies have revealed interesting facets of tardigrade development and genomics that suggest that a highly compact body plan is a derived condition of this lineage, rather than it representing an ancestral state of Panarthropoda. This conclusion was based on studies of several species from Eutardigrada. We review these studies and expand on them by analyzing the publicly available genome and transcriptome assemblies of Echiniscus testudo, a representative of Heterotardigrada. These new analyses allow us to phylogenetically reconstruct important features of genome evolution in Tardigrada. We use available data from tardigrades to interrogate several recent models of body plan evolution in Panarthropoda. Although anterior segments of panarthropods are highly diverse in terms of anatomy and development, both within individuals and between species, we conclude that a simple one-to-one alignment of anterior segments across Panarthropoda is the best available model of segmental homology. In addition to providing important insight into body plan diversification within Panarthropoda, we speculate that studies of tardigrades may reveal generalizable pathways to miniaturization.
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Affiliation(s)
- Frank W Smith
- Biology Department, University of North Florida, Jacksonville, Florida, USA
| | - Mandy Game
- Biology Department, University of North Florida, Jacksonville, Florida, USA
| | - Marc A Mapalo
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Raul A Chavarria
- Biology Department, University of North Florida, Jacksonville, Florida, USA
| | - Taylor R Harrison
- Biology Department, University of North Florida, Jacksonville, Florida, USA
| | - Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Uppsala University, Uppsala, Sweden
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4
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Geng F, Zhong L, Yang T, Chen J, Yang P, Jiang F, Yan T, Song B, Yu Z, Yu D, Zhang J, Cao J, Zhang S. A Frog Skin-Derived Peptide Targeting SCD1 Exerts Radioprotective Effects Against Skin Injury by Inhibiting STING-Mediated Inflammation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306253. [PMID: 38582510 PMCID: PMC11220654 DOI: 10.1002/advs.202306253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 03/22/2024] [Indexed: 04/08/2024]
Abstract
The extensive application of nuclear technology has increased the potential of uncontrolled radiation exposure to the public. Since skin is the largest organ, radiation-induced skin injury remains a serious medical concern. Organisms evolutionally develop distinct strategies to protect against environment insults and the related research may bring novel insights into therapeutics development. Here, 26 increased peptides are identified in skin tissues of frogs (Pelophylax nigromaculatus) exposed to electron beams, among which four promoted the wound healing of irradiated skin in rats. Specifically, radiation-induced frog skin peptide-2 (RIFSP-2), from histone proteolysis exerted membrane permeability property, maintained cellular homeostasis, and reduced pyroptosis of irradiated cells with decreased TBK1 phosphorylation. Subsequently, stearyl-CoA desaturase 1 (SCD1) is identified, a critical enzyme in biogenesis of monounsaturated fatty acids (MUFAs) as a direct target of RIFSP-2 based on streptavidin-biotin system. The lipidomic analysis further assured the restrain of MUFAs biogenesis by RIFSP-2 following radiation. Moreover, the decreased MUFA limited radiation-induced and STING-mediated inflammation response. In addition, genetic depletion or pharmacological inhibition of STING counteracted the decreased pyroptosis by RIFSP-2 and retarded tissue repair process. Altogether, RIFSP-2 restrains radiation-induced activation of SCD1-MUFA-STING axis. Thus, the stress-induced amphibian peptides can be a bountiful source of novel radiation mitigators.
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Affiliation(s)
- Fenghao Geng
- Laboratory of Radiation MedicineWest China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengdu610041China
- Laboratory of Radiation MedicineWest China Second University HospitalSichuan UniversityChengdu610041China
- Radiation Medicine Department of Institute of Preventive MedicineFourth Military Medical UniversityXi'an710032China
| | - Li Zhong
- School of Radiation Medicine and ProtectionState Key Laboratory of Radiation MedicineSoochow UniversitySuzhou215123China
| | - Tingyi Yang
- Laboratory of Radiation MedicineWest China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengdu610041China
| | - Jianhui Chen
- Laboratory of Radiation MedicineWest China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengdu610041China
| | - Ping Yang
- Laboratory of Radiation MedicineWest China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengdu610041China
| | - Fengdi Jiang
- Laboratory of Radiation MedicineWest China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengdu610041China
| | - Tao Yan
- Laboratory of Radiation MedicineWest China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengdu610041China
| | - Bin Song
- Laboratory of Radiation MedicineWest China Second University HospitalSichuan UniversityChengdu610041China
| | - Zuxiang Yu
- Laboratory of Radiation MedicineWest China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengdu610041China
| | - Daojiang Yu
- The Second Affiliated Hospital of Chengdu Medical CollegeChina National Nuclear Corporation 416 HospitalChengdu610051China
| | - Jie Zhang
- Radiation Medicine Department of Institute of Preventive MedicineFourth Military Medical UniversityXi'an710032China
| | - Jianping Cao
- School of Radiation Medicine and ProtectionState Key Laboratory of Radiation MedicineSoochow UniversitySuzhou215123China
| | - Shuyu Zhang
- Laboratory of Radiation MedicineWest China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengdu610041China
- Laboratory of Radiation MedicineWest China Second University HospitalSichuan UniversityChengdu610041China
- The Second Affiliated Hospital of Chengdu Medical CollegeChina National Nuclear Corporation 416 HospitalChengdu610051China
- NHC Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital)Mianyang621099China
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5
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Sugiura K, Yoshida Y, Hayashi K, Arakawa K, Kunieda T, Matsumoto M. Sexual dimorphism in the tardigrade Paramacrobiotus metropolitanus transcriptome. ZOOLOGICAL LETTERS 2024; 10:11. [PMID: 38902818 PMCID: PMC11191345 DOI: 10.1186/s40851-024-00233-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/14/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND In gonochoristic animals, the sex determination pathway induces different morphological and behavioral features that can be observed between sexes, a condition known as sexual dimorphism. While many components of this sex differentiation cascade show high levels of diversity, factors such as the Doublesex-Mab-3-Related Transcription factor (DMRT) are widely conserved across animal taxa. Species of the phylum Tardigrada exhibit remarkable diversity in morphology and behavior between sexes, suggesting a pathway regulating this dimorphism. Despite the wealth of genomic and zoological knowledge accumulated in recent studies, the sexual differences in tardigrades genomes have not been identified. In the present study, we focused on the gonochoristic species Paramacrobiotus metropolitanus and employed omics analyses to unravel the molecular basis of sexual dimorphism. RESULTS Transcriptome analysis between sex-identified specimens revealed numerous differentially expressed genes, of which approximately 2,000 male-biased genes were focused on 29 non-male-specific genomic loci. From these regions, we identified two Macrobiotidae family specific DMRT paralogs, which were significantly upregulated in males and lacked sex specific splicing variants. Furthermore, phylogenetic analysis indicated all tardigrade genomes lack the doublesex ortholog, suggesting doublesex emerged after the divergence of Tardigrada. In contrast to sex-specific expression, no evidence of genomic differences between the sexes was found. We also identified several anhydrobiosis genes that exhibit sex-biased expression, suggesting a possible mechanism for protection of sex-specific tissues against extreme stress. CONCLUSIONS This study provides a comprehensive analysis for analyzing the genetic differences between sexes in tardigrades. The existence of male-biased, but not male-specific, genomic loci and identification of the family specific male-biased DMRT subfamily provides the foundation for understanding the sex determination cascade. In addition, sex-biased expression of several tardigrade-specific genes which are involved their stress tolerance suggests a potential role in protecting sex-specific tissue and gametes.
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Affiliation(s)
- Kenta Sugiura
- Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku, Yokohama, Kanagawa, 223-8522, Japan
| | - Yuki Yoshida
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Kohei Hayashi
- Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku, Yokohama, Kanagawa, 223-8522, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, 403-1 Nihonkoku, Daihoji, Tsuruoka, Yamagata, 997-0017, Japan
- Exploratory Research Center On Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Takekazu Kunieda
- Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Midori Matsumoto
- Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku, Yokohama, Kanagawa, 223-8522, Japan.
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6
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Galas S, Le Goff E, Cazevieille C, Tanaka A, Cuq P, Baghdiguian S, Kunieda T, Godefroy N, Richaud M. A comparative ultrastructure study of the tardigrade Ramazzottius varieornatus in the hydrated state, after desiccation and during the process of rehydration. PLoS One 2024; 19:e0302552. [PMID: 38843161 PMCID: PMC11156355 DOI: 10.1371/journal.pone.0302552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 04/07/2024] [Indexed: 06/09/2024] Open
Abstract
Tardigrades can survive hostile environments such as desiccation by adopting a state of anhydrobiosis. Numerous tardigrade species have been described thus far, and recent genome and transcriptome analyses revealed that several distinct strategies were employed to cope with harsh environments depending on the evolutionary lineages. Detailed analyses at the cellular and subcellular levels are essential to complete these data. In this work, we analyzed a tardigrade species that can withstand rapid dehydration, Ramazzottius varieornatus. Surprisingly, we noted an absence of the anhydrobiotic-specific extracellular structure previously described for the Hypsibius exemplaris species. Both Ramazzottius varieornatus and Hypsibius exemplaris belong to the same evolutionary class of Eutardigrada. Nevertheless, our observations reveal discrepancies in the anhydrobiotic structures correlated with the variation in the anhydrobiotic mechanisms.
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Affiliation(s)
- Simon Galas
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | - Emilie Le Goff
- ISEM, University of Montpellier, CNRS, IRD, Montpellier, France
| | | | - Akihiro Tanaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Pierre Cuq
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | | | - Takekazu Kunieda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Nelly Godefroy
- ISEM, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Myriam Richaud
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
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7
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Kondo K, Tanaka A, Kunieda T. Single-step generation of homozygous knockout/knock-in individuals in an extremotolerant parthenogenetic tardigrade using DIPA-CRISPR. PLoS Genet 2024; 20:e1011298. [PMID: 38870088 PMCID: PMC11175437 DOI: 10.1371/journal.pgen.1011298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 05/10/2024] [Indexed: 06/15/2024] Open
Abstract
Tardigrades are small aquatic invertebrates known for their remarkable tolerance to diverse extreme stresses. To elucidate the in vivo mechanisms underlying this extraordinary resilience, methods for genetically manipulating tardigrades have long been desired. Despite our prior success in somatic cell gene editing by microinjecting Cas9 ribonucleoproteins (RNPs) into the body cavity of tardigrades, the generation of gene-edited individuals remained elusive. In this study, employing an extremotolerant parthenogenetic tardigrade species, Ramazzottius varieornatus, we established conditions that led to the generation of gene-edited tardigrade individuals. Drawing inspiration from the direct parental CRISPR (DIPA-CRISPR) technique employed in several insects, we simply injected a concentrated Cas9 RNP solution into the body cavity of parental females shortly before their initial oviposition. This approach yielded gene-edited G0 progeny. Notably, only a single allele was predominantly detected at the target locus for each G0 individual, indicative of homozygous mutations. By co-injecting single-stranded oligodeoxynucleotides (ssODNs) with Cas9 RNPs, we achieved the generation of homozygously knocked-in G0 progeny, and these edited alleles were inherited by G1/G2 progeny. This is the first example of heritable gene editing in the entire phylum of Tardigrada. This establishment of a straightforward method for generating homozygous knockout/knock-in individuals not only facilitates in vivo analyses of the molecular mechanisms underpinning extreme tolerance, but also opens up avenues for exploring various topics, including Evo-Devo, in tardigrades.
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Affiliation(s)
- Koyuki Kondo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, Tsudanuma, Narashino, Chiba, Japan
| | - Akihiro Tanaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Takekazu Kunieda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
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8
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Surmacz B, Stec D, Prus-Frankowska M, Buczek M, Michalczyk Ł, Łukasik P. Pinpointing the microbiota of tardigrades: What is really there? Environ Microbiol 2024; 26:e16659. [PMID: 38899728 DOI: 10.1111/1462-2920.16659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/09/2024] [Indexed: 06/21/2024]
Abstract
Microbiota are considered significant in the biology of tardigrades, yet their diversity and distribution remain largely unexplored. This is partly due to the methodological challenges associated with studying the microbiota of small organisms that inhabit microbe-rich environments. In our study, we characterized the microbiota of 31 species of cultured tardigrades using 16S rRNA amplicon sequencing. We employed various sample preparation strategies and multiple types of controls and estimated the number of microbes in samples using synthetic DNA spike-ins. We also reanalysed data from previous tardigrade microbiome studies. Our findings suggest that the microbial communities of cultured tardigrades are predominantly composed of bacterial genotypes originating from food, medium, or reagents. Despite numerous experiments, we found it challenging to identify strains that were enriched in certain tardigrades, which would have indicated likely symbiotic associations. Putative tardigrade-associated microbes rarely constituted more than 20% of the datasets, although some matched symbionts identified in other studies. We also uncovered serious contamination issues in previous tardigrade microbiome studies, casting doubt on some of their conclusions. We concluded that tardigrades are not universally dependent on specialized microbes. Our work underscores the need for rigorous safeguards in studies of the microbiota of microscopic organisms and serves as a cautionary tale for studies involving samples with low microbiome abundance.
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Affiliation(s)
- Bartłomiej Surmacz
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Department of Invertebrate Evolution, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Daniel Stec
- Department of Invertebrate Evolution, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Monika Prus-Frankowska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Mateusz Buczek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Łukasz Michalczyk
- Department of Invertebrate Evolution, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Piotr Łukasik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
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9
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Zhang J, Shirakashi R. Measurement of the rotational relaxation time of intracellular water in dried yeast and Jurkat cells by near infrared spectroscopy. Biochem Biophys Res Commun 2024; 710:149857. [PMID: 38583232 DOI: 10.1016/j.bbrc.2024.149857] [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: 02/25/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/09/2024]
Abstract
Molecular mobility of intracellular water is a crucial parameter in the study of the mechanism of desiccation tolerance. As one of the parameters that reflecting molecular mobility, the viscosity of intracellular water has been found intimately related with the protection of the phospholipid membrane because it quantifies the diffusion ability of water and mass in the intracellular environment. In this work we measured the intracellular water relaxation time, which can be translated into water viscosity, by using a previously established NIR-dielectric method to monitor the drying process of baker's yeast and Jurkat cells with different desiccation tolerance. We found that intracellular saccharide can significantly decrease the intracellular water viscosity. Also, the intracellular water diffusion coefficient obtained from this method were found in good agreement with other reports.
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Affiliation(s)
- Junkai Zhang
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro City, Tokyo, 153-8505, Japan.
| | - Ryo Shirakashi
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro City, Tokyo, 153-8505, Japan
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10
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Rolsma JL, Darch W, Higgins NC, Morgan JT. The tardigrade-derived mitochondrial abundant heat soluble protein improves adipose-derived stem cell survival against representative stressors. Sci Rep 2024; 14:11834. [PMID: 38783150 PMCID: PMC11116449 DOI: 10.1038/s41598-024-62693-w] [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: 03/14/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024] Open
Abstract
Human adipose-derived stem cell (ASC) grafts have emerged as a powerful tool in regenerative medicine. However, ASC therapeutic potential is hindered by stressors throughout their use. Here we demonstrate the transgenic expression of the tardigrade-derived mitochondrial abundant heat soluble (MAHS) protein for improved ASC resistance to metabolic, mitochondrial, and injection shear stress. In vitro, MAHS-expressing ASCs demonstrate up to 61% increased cell survival following 72 h of incubation in phosphate buffered saline containing 20% media. Following up to 3.5% DMSO exposure for up to 72 h, a 14-49% increase in MAHS-expressing ASC survival was observed. Further, MAHS expression in ASCs is associated with up to 39% improved cell viability following injection through clinically relevant 27-, 32-, and 34-gauge needles. Our results reveal that MAHS expression in ASCs supports survival in response to a variety of common stressors associated with regenerative therapies, thereby motivating further investigation into MAHS as an agent for stem cell stress resistance. However, differentiation capacity in MAHS-expressing ASCs appears to be skewed in favor of osteogenesis over adipogenesis. Specifically, activity of the early bone formation marker alkaline phosphatase is increased by 74% in MAHS-expressing ASCs following 14 days in osteogenic media. Conversely, positive area of the neutral lipid droplet marker BODIPY is decreased by up to 10% in MAHS-transgenic ASCs following 14 days in adipogenic media. Interestingly, media supplementation with up to 40 mM glucose is sufficient to restore adipogenic differentiation within 14 days, prompting further analysis of mechanisms underlying interference between MAHS and differentiation processes.
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Affiliation(s)
- Jordan L Rolsma
- Department of Bioengineering, University of California, 900 University Ave, Riverside, CA, 92521, USA
| | - William Darch
- Department of Bioengineering, University of California, 900 University Ave, Riverside, CA, 92521, USA
| | - Nicholas C Higgins
- Department of Bioengineering, University of California, 900 University Ave, Riverside, CA, 92521, USA
| | - Joshua T Morgan
- Department of Bioengineering, University of California, 900 University Ave, Riverside, CA, 92521, USA.
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11
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Rolland SGM, Memar N, Gartner A. Tardigrades: Trained to be hardy in the face of DNA damage. Curr Biol 2024; 34:R504-R507. [PMID: 38772339 DOI: 10.1016/j.cub.2024.04.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Tardigrades withstand ionizing irradiation levels ∼500 times higher than humans can tolerate. Two recent papers shed light on how this might be achieved - via the transcriptional induction of DNA repair genes, the induction of a radioprotective DNA-binding protein, and possibly also the heightened capacity of repair proteins.
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Affiliation(s)
- Stéphane G M Rolland
- Center for Genomic Integrity, Institute for Basic Science, UNIST-gil 50, Ulsan 44919, Republic of Korea
| | - Nadin Memar
- Center for Genomic Integrity, Institute for Basic Science, UNIST-gil 50, Ulsan 44919, Republic of Korea
| | - Anton Gartner
- Center for Genomic Integrity, Institute for Basic Science, UNIST-gil 50, Ulsan 44919, Republic of Korea; Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Graduate School for Health Sciences and Technology, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
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12
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Del Casino C, Conti V, Licata S, Cai G, Cantore A, Ricci C, Cantara S. Mitigation of UV-B Radiation Stress in Tobacco Pollen by Expression of the Tardigrade Damage Suppressor Protein (Dsup). Cells 2024; 13:840. [PMID: 38786062 PMCID: PMC11119994 DOI: 10.3390/cells13100840] [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: 03/24/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Pollen, the male gametophyte of seed plants, is extremely sensitive to UV light, which may prevent fertilization. As a result, strategies to improve plant resistance to solar ultraviolet (UV) radiation are required. The tardigrade damage suppressor protein (Dsup) is a putative DNA-binding protein that enables tardigrades to tolerate harsh environmental conditions, including UV radiation, and was therefore considered as a candidate for reducing the effects of UV exposure on pollen. Tobacco pollen was genetically engineered to express Dsup and then exposed to UV-B radiation to determine the effectiveness of the protein in increasing pollen resistance. To establish the preventive role of Dsup against UV-B stress, we carried out extensive investigations into pollen viability, germination rate, pollen tube length, male germ unit position, callose plug development, marker protein content, and antioxidant capacity. The results indicated that UV-B stress has a significant negative impact on both pollen grain and pollen tube growth. However, Dsup expression increased the antioxidant levels and reversed some of the UV-B-induced changes to pollen, restoring the proper distance between the tip and the last callose plug formed, as well as pollen tube length, tubulin, and HSP70 levels. Therefore, the expression of heterologous Dsup in pollen may provide the plant male gametophyte with enhanced responses to UV-B stress and protection against harmful environmental radiation.
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Affiliation(s)
- Cecilia Del Casino
- Dipartimento di Scienze della Vita, University of Siena, via Mattioli 4, 53100 Siena, Italy; (C.D.C.); (S.L.)
| | - Veronica Conti
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, via Irnerio 42, 40126 Bologna, Italy;
| | - Silvia Licata
- Dipartimento di Scienze della Vita, University of Siena, via Mattioli 4, 53100 Siena, Italy; (C.D.C.); (S.L.)
| | - Giampiero Cai
- Dipartimento di Scienze della Vita, University of Siena, via Mattioli 4, 53100 Siena, Italy; (C.D.C.); (S.L.)
| | - Anna Cantore
- Department of Medical, Surgical and Neurological Sciences, University of Siena, Viale Bracci, 53100 Siena, Italy; (A.C.); (C.R.); (S.C.)
| | - Claudia Ricci
- Department of Medical, Surgical and Neurological Sciences, University of Siena, Viale Bracci, 53100 Siena, Italy; (A.C.); (C.R.); (S.C.)
| | - Silvia Cantara
- Department of Medical, Surgical and Neurological Sciences, University of Siena, Viale Bracci, 53100 Siena, Italy; (A.C.); (C.R.); (S.C.)
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13
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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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14
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Zarubin M, Andreev E, Kravchenko E, Pinaeva U, Nechaev A, Apel P. Developing tardigrade-inspired material: Track membranes functionalized with Dsup protein for cell-free DNA isolation. Biotechnol Prog 2024:e3478. [PMID: 38699905 DOI: 10.1002/btpr.3478] [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: 11/29/2023] [Revised: 04/09/2024] [Accepted: 04/24/2024] [Indexed: 05/05/2024]
Abstract
When developing functionalized biomaterials, the proteins from extremophilic organisms, in particular unique tardigrade disordered proteins, are of great value. The damage suppressor protein (Dsup), initially discovered in the tardigrade Ramazzottius varieornatus and found to be an efficient DNA protector under oxidative and irradiation stress, has been hypothesized to possess a good potential for the development of the material, which can isolate cell-free DNA. With this in mind, DNA-nonadsorbing polyethylene terephthalate track membranes have been functionalized using the Dsup protein via covalent bonding with glutaraldehyde. The filtration experiments have verified the ability of track membranes with the immobilized Dsup protein to adsorb cell-free DNA, with an accumulation capacity of 70 ± 19 mg m-2. The resulting track membrane-based biomaterial might be used in various devices for filtration and separation of cell-free DNA molecules from biological solutions and environmental samples, and also for their accumulation, storage, and further manipulation.
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Affiliation(s)
- Mikhail Zarubin
- Dzhelepov Laboratory of Nuclear Problems, International Intergovernmental Organization Joint Institute for Nuclear Research (DLNP JINR), Dubna, Russia
| | - Evgeny Andreev
- Flerov Laboratory of Nuclear Reactions, International Intergovernmental Organization Joint Institute for Nuclear Research (FLNR JINR), Dubna, Russia
| | - Elena Kravchenko
- Dzhelepov Laboratory of Nuclear Problems, International Intergovernmental Organization Joint Institute for Nuclear Research (DLNP JINR), Dubna, Russia
| | - Uliana Pinaeva
- Flerov Laboratory of Nuclear Reactions, International Intergovernmental Organization Joint Institute for Nuclear Research (FLNR JINR), Dubna, Russia
| | - Alexander Nechaev
- Flerov Laboratory of Nuclear Reactions, International Intergovernmental Organization Joint Institute for Nuclear Research (FLNR JINR), Dubna, Russia
| | - Pavel Apel
- Flerov Laboratory of Nuclear Reactions, International Intergovernmental Organization Joint Institute for Nuclear Research (FLNR JINR), Dubna, Russia
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15
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Wilson CG, Pieszko T, Nowell RW, Barraclough TG. Recombination in bdelloid rotifer genomes: asexuality, transfer and stress. Trends Genet 2024; 40:422-436. [PMID: 38458877 DOI: 10.1016/j.tig.2024.02.001] [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: 11/03/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 03/10/2024]
Abstract
Bdelloid rotifers constitute a class of microscopic animals living in freshwater habitats worldwide. Several strange features of bdelloids have drawn attention: their ability to tolerate desiccation and other stresses, a lack of reported males across the clade despite centuries of study, and unusually high numbers of horizontally acquired, non-metazoan genes. Genome sequencing is transforming our understanding of their lifestyle and its consequences, while in turn providing wider insights about recombination and genome organisation in animals. Many questions remain, not least how to reconcile apparent genomic signatures of sex with the continued absence of reported males, why bdelloids have so many horizontally acquired genes, and how their remarkable ability to survive stress interacts with recombination and other genomic processes.
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Affiliation(s)
- Christopher G Wilson
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK.
| | - Tymoteusz Pieszko
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - Reuben W Nowell
- Institute of Ecology and Evolution, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; Biological and Environmental Sciences, School of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
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16
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Kirk MJ, Xu C, Rothman JH. Single-animal, single-tube RNA extraction for quantitative analysis of transcripts in the tardigrade Hypsibius exemplaris. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585302. [PMID: 38559134 PMCID: PMC10979942 DOI: 10.1101/2024.03.15.585302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The tardigrade Hypsibius exemplaris is an emerging model organism renowned for its ability to survive environmental extremes.1-3 To explore the molecular mechanisms and genetic basis of such extremotolerance, many studies rely on transcriptional profiling4, 5 and RNA interference (RNAi)6 to define molecular targets. Such studies require efficient, accurate, and robust RNA extraction methods; however, obtaining high-quality quantitative levels of RNA from H. exemplaris has been challenging6, 7. Possessing a layer of firm chitinous cuticle, tardigrade tissues are difficult to disrupt by chemical or mechanical means8. Here we present an efficient single-tardigrade, single-tube RNA extraction method (STST) that not only reliably isolates RNA from individual tardigrades but dramatically reduces the time required for extraction. We show that this RNA extraction method yields robust quantities of cDNA and can be used to amplify multiple transcripts by qRT-PCR. To validate the method, we use it to compare dynamic changes in expression of genes encoding two heat-shock-regulated proteins, Heat-Shock Protein 70 β2 (HSP70β2) and Heat-Shock Protein 90α (HSP90α) by quantifying their expression levels in heat-exposed and cold-exposed individuals using qRT-PCR across long-term and short-term heat stressors. Our method effectively complements existing bulk RNA extraction methods7, permitting rapid examination of individual tardigrade transcriptional data and quantification of phenotypic variations in expression profiles amongst individuals.
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Affiliation(s)
- Molly J. Kirk
- Department of Molecular Cellular and Developmental Biology University of California, Santa Barbara, Santa Barbara, CA
| | - Chaoming Xu
- Department of Molecular Cellular and Developmental Biology University of California, Santa Barbara, Santa Barbara, CA
| | - Joel H. Rothman
- Department of Molecular Cellular and Developmental Biology University of California, Santa Barbara, Santa Barbara, CA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA
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17
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Urban JM, Bateman JR, Garza KR, Borden J, Jain J, Brown A, Thach BJ, Bliss JE, Gerbi SA. Bradysia (Sciara) coprophila larvae up-regulate DNA repair pathways and down-regulate developmental regulators in response to ionizing radiation. Genetics 2024; 226:iyad208. [PMID: 38066617 PMCID: PMC10917502 DOI: 10.1093/genetics/iyad208] [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: 10/04/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/21/2023] Open
Abstract
The level of resistance to radiation and the developmental and molecular responses can vary between species, and even between developmental stages of one species. For flies (order: Diptera), prior studies concluded that the fungus gnat Bradysia (Sciara) coprophila (sub-order: Nematocera) is more resistant to irradiation-induced mutations that cause visible phenotypes than the fruit fly Drosophila melanogaster (sub-order: Brachycera). Therefore, we characterized the effects of and level of resistance to ionizing radiation on B. coprophila throughout its life cycle. Our data show that B. coprophila embryos are highly sensitive to even low doses of gamma-irradiation, whereas late-stage larvae can tolerate up to 80 Gy (compared to 40 Gy for D. melanogaster) and still retain their ability to develop to adulthood, though with a developmental delay. To survey the genes involved in the early transcriptional response to irradiation of B. coprophila larvae, we compared larval RNA-seq profiles with and without radiation treatment. The up-regulated genes were enriched for DNA damage response genes, including those involved in DNA repair, cell cycle arrest, and apoptosis, whereas the down-regulated genes were enriched for developmental regulators, consistent with the developmental delay of irradiated larvae. Interestingly, members of the PARP and AGO families were highly up-regulated in the B. coprophila radiation response. We compared the transcriptome responses in B. coprophila to the transcriptome responses in D. melanogaster from 3 previous studies: whereas pathway responses are highly conserved, specific gene responses are less so. Our study lays the groundwork for future work on the radiation responses in Diptera.
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Affiliation(s)
- John M Urban
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, RI 02912, USA
- Department of Embryology, Carnegie Institution for Science, Howard Hughes Medical Institute Research Laboratories, 3520 San Martin Drive, Baltimore, MD 21218, USA
| | - Jack R Bateman
- Biology Department, Bowdoin College, Brunswick, ME 04011, USA
| | - Kodie R Garza
- Biology Department, Bowdoin College, Brunswick, ME 04011, USA
| | - Julia Borden
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, RI 02912, USA
| | - Jaison Jain
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, RI 02912, USA
| | - Alexia Brown
- Biology Department, Bowdoin College, Brunswick, ME 04011, USA
| | - Bethany J Thach
- Biology Department, Bowdoin College, Brunswick, ME 04011, USA
| | - Jacob E Bliss
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, RI 02912, USA
| | - Susan A Gerbi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, RI 02912, USA
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18
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Lacerda AL, Frias J, Pedrotti ML. Tardigrades in the marine plastisphere: New hitchhikers surfing plastics. MARINE POLLUTION BULLETIN 2024; 200:116071. [PMID: 38290365 DOI: 10.1016/j.marpolbul.2024.116071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/19/2024] [Accepted: 01/20/2024] [Indexed: 02/01/2024]
Abstract
Tardigrades are remarkable microorganisms known for their extraordinary resilience in diverse environments, including extreme conditions such as outer space. They are known for their interactions with natural substrates in terrestrial and aquatic systems, but have remained largely unexplored in relation to marine plastics. This study aims to investigate the colonization of plastics, ranging from fossil fuel-based to bioplastics, in the coastal zones of four countries (Brazil, Ireland, France and Italy). Here, we report the first documented occurrence of tardigrades colonizing plastic substrates. We identified five amplicon sequence variants (ASVs) belonging to the Tardigrada phylum, specifically in a post-consumer polypropylene, in the coastal zone of Galway, Ireland. This discovery raises questions about the characteristics of different plastics influencing on tardigrades' adhesion. Tardigrades hitchhiking on plastics in the oceans could expand their habitat range, possibly displacing native species and altering trophic interactions, with potential consequences for the overall biodiversity.
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Affiliation(s)
- Ana Luzia Lacerda
- Laboratoire d'Océanographie de Villefranche sur mer (LOV), UPMC Université Paris 06, CNRS UMR 7093, Sorbonne Université, Villefranche sur Mer, France.
| | - João Frias
- Marine and Freshwater Research Centre, Atlantic Technological University, Dublin Road, Galway H91 T8NW, Ireland
| | - Maria Luiza Pedrotti
- Laboratoire d'Océanographie de Villefranche sur mer (LOV), UPMC Université Paris 06, CNRS UMR 7093, Sorbonne Université, Villefranche sur Mer, France
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19
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Esquirol L, Newman J, Nebl T, Scott C, Vickers C, Sainsbury F, Peat TS. Characterization of novel mevalonate kinases from the tardigrade Ramazzottius varieornatus and the psychrophilic archaeon Methanococcoides burtonii. Acta Crystallogr D Struct Biol 2024; 80:203-215. [PMID: 38411551 PMCID: PMC10910542 DOI: 10.1107/s2059798324001360] [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: 11/29/2023] [Accepted: 02/12/2024] [Indexed: 02/28/2024] Open
Abstract
Mevalonate kinase is central to the isoprenoid biosynthesis pathway. Here, high-resolution X-ray crystal structures of two mevalonate kinases are presented: a eukaryotic protein from Ramazzottius varieornatus and an archaeal protein from Methanococcoides burtonii. Both enzymes possess the highly conserved motifs of the GHMP enzyme superfamily, with notable differences between the two enzymes in the N-terminal part of the structures. Biochemical characterization of the two enzymes revealed major differences in their sensitivity to geranyl pyrophosphate and farnesyl pyrophosphate, and in their thermal stabilities. This work adds to the understanding of the structural basis of enzyme inhibition and thermostability in mevalonate kinases.
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Affiliation(s)
- Lygie Esquirol
- Environment, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Janet Newman
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Tom Nebl
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Colin Scott
- Environment, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT 2601, Australia
- Advanced Engineering Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Claudia Vickers
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
- Synbio Future Science Platform, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT 2601, Australia
- Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Frank Sainsbury
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
- Synbio Future Science Platform, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Thomas S. Peat
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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Kayastha P, Wieczorkiewicz F, Pujol M, Robinson A, Michalak M, Kaczmarek Ł, Poprawa I. Elevated external temperature affects cell ultrastructure and heat shock proteins (HSPs) in Paramacrobiotus experimentalis Kaczmarek, Mioduchowska, Poprawa, & Roszkowska, 2020. Sci Rep 2024; 14:5097. [PMID: 38429316 PMCID: PMC10907573 DOI: 10.1038/s41598-024-55295-z] [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: 07/25/2023] [Accepted: 02/22/2024] [Indexed: 03/03/2024] Open
Abstract
Increasing temperature influences the habitats of various organisms, including microscopic invertebrates. To gain insight into temperature-dependent changes in tardigrades, we isolated storage cells exposed to various temperatures and conducted biochemical and ultrastructural analysis in active and tun-state Paramacrobiotus experimentalis Kaczmarek, Mioduchowska, Poprawa, & Roszkowska, 2020. The abundance of heat shock proteins (HSPs) and ultrastructure of the storage cells were examined at different temperatures (20 °C, 30 °C, 35 °C, 37 °C, 40 °C, and 42 °C) in storage cells isolated from active specimens of Pam. experimentalis. In the active animals, upon increase in external temperature, we observed an increase in the levels of HSPs (HSP27, HSP60, and HSP70). Furthermore, the number of ultrastructural changes in storage cells increased with increasing temperature. Cellular organelles, such as mitochondria and the rough endoplasmic reticulum, gradually degenerated. At 42 °C, cell death occurred by necrosis. Apart from the higher electron density of the karyoplasm and the accumulation of electron-dense material in some mitochondria (at 42 °C), almost no changes were observed in the ultrastructure of tun storage cells exposed to different temperatures. We concluded that desiccated (tun-state) are resistant to high temperatures, but not active tardigrades (survival rates of tuns after 24 h of rehydration: 93.3% at 20 °C, 60.0% at 35 °C, 33.3% at 37 °C, 33.3% at 40 °C, and 20.0% at 42 °C).
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Affiliation(s)
- Pushpalata Kayastha
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
| | - Filip Wieczorkiewicz
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007, Katowice, Poland
| | - Myriam Pujol
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Alison Robinson
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Marek Michalak
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Łukasz Kaczmarek
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Izabela Poprawa
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007, Katowice, Poland.
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Al-Ansari M, Fitzsimons T, Wei W, Goldberg MW, Kunieda T, Quinlan RA. The major inducible small heat shock protein HSP20-3 in the tardigrade Ramazzottius varieornatus forms filament-like structures and is an active chaperone. Cell Stress Chaperones 2024; 29:51-65. [PMID: 38330543 PMCID: PMC10939073 DOI: 10.1016/j.cstres.2023.12.001] [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: 11/28/2023] [Accepted: 12/03/2023] [Indexed: 02/10/2024] Open
Abstract
The tardigrade Ramazzottius varieornatus has remarkable resilience to a range of environmental stresses. In this study, we have characterised two members of the small heat shock protein (sHSP) family in R. varieornatus, HSP20-3 and HSP20-6. These are the most highly upregulated sHSPs in response to a 24 h heat shock at 35 0C of adult tardigrades with HSP20-3 being one of the most highly upregulated gene in the whole transcriptome. Both R. varieornatus sHSPs and the human sHSP, CRYAB (HSPB5), were produced recombinantly for comparative structure-function studies. HSP20-3 exhibited a superior chaperone activity than human CRYAB in a heat-induced protein aggregation assay. Both tardigrade sHSPs also formed larger oligomers than CRYAB as assessed by size exclusion chromatography and transmission electron microscopy of negatively stained samples. Whilst both HSP20-3 and HSP20-6 formed particles that were variable in size and larger than the particles formed by CRYAB, only HSP20-3 formed filament-like structures. The particles and filament-like structures formed by HSP20-3 appear inter-related as the filament-like structures often had particles located at their ends. Sequence analyses identified two unique features; an insertion in the middle region of the N-terminal domain (NTD) and preceding the critical-sequence identified in CRYAB, as well as a repeated QNTN-motif located in the C-terminal domain of HSP20-3. The NTD insertion is expected to affect protein-protein interactions and subunit oligomerisation. Removal of the repeated QNTN-motif abolished HSP20-3 chaperone activity and also affected the assembly of the filament-like structures. We discuss the potential contribution of HSP20-3 to protein condensate formation.
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Affiliation(s)
- Mohammad Al-Ansari
- Department of Biosciences, Upper Mountjoy Science Site, University of Durham, Durham DH1 3LE, UK; Department of Biochemistry, Health Sciences Centre, Kuwait University, Kuwait
| | - Taylor Fitzsimons
- Department of Biosciences, Upper Mountjoy Science Site, University of Durham, Durham DH1 3LE, UK
| | - Wenbin Wei
- Department of Biosciences, Upper Mountjoy Science Site, University of Durham, Durham DH1 3LE, UK.
| | - Martin W Goldberg
- Department of Biosciences, Upper Mountjoy Science Site, University of Durham, Durham DH1 3LE, UK
| | - Takekazu Kunieda
- Department of Biological Sciences, The University of Tokyo, Japan
| | - Roy A Quinlan
- Department of Biosciences, Upper Mountjoy Science Site, University of Durham, Durham DH1 3LE, UK; Department of Biological Structure, University of Washington, Seattle, WA 98195, USA.
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22
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Moris VC, Bruneau L, Berthe J, Heuskin AC, Penninckx S, Ritter S, Weber U, Durante M, Danchin EGJ, Hespeels B, Doninck KV. Ionizing radiation responses appear incidental to desiccation responses in the bdelloid rotifer Adineta vaga. BMC Biol 2024; 22:11. [PMID: 38273318 PMCID: PMC10809525 DOI: 10.1186/s12915-023-01807-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND The remarkable resistance to ionizing radiation found in anhydrobiotic organisms, such as some bacteria, tardigrades, and bdelloid rotifers has been hypothesized to be incidental to their desiccation resistance. Both stresses produce reactive oxygen species and cause damage to DNA and other macromolecules. However, this hypothesis has only been investigated in a few species. RESULTS In this study, we analyzed the transcriptomic response of the bdelloid rotifer Adineta vaga to desiccation and to low- (X-rays) and high- (Fe) LET radiation to highlight the molecular and genetic mechanisms triggered by both stresses. We identified numerous genes encoding antioxidants, but also chaperones, that are constitutively highly expressed, which may contribute to the protection of proteins against oxidative stress during desiccation and ionizing radiation. We also detected a transcriptomic response common to desiccation and ionizing radiation with the over-expression of genes mainly involved in DNA repair and protein modifications but also genes with unknown functions that were bdelloid-specific. A distinct transcriptomic response specific to rehydration was also found, with the over-expression of genes mainly encoding Late Embryogenesis Abundant proteins, specific heat shock proteins, and glucose repressive proteins. CONCLUSIONS These results suggest that the extreme resistance of bdelloid rotifers to radiation might indeed be a consequence of their capacity to resist complete desiccation. This study paves the way to functional genetic experiments on A. vaga targeting promising candidate proteins playing central roles in radiation and desiccation resistance.
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Affiliation(s)
- Victoria C Moris
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium.
- Laboratory of Molecular Biology & Evolution (MBE), Department of Biology, Université Libre de Bruxelles, 1000, Brussels, Belgium.
| | - Lucie Bruneau
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Jérémy Berthe
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Anne-Catherine Heuskin
- Namur Research Institute for Life Sciences (NARILIS), Laboratory of Analysis By Nuclear Reactions (LARN), University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Sébastien Penninckx
- Medical Physics Department, Institut Jules Bordet - Université Libre de Bruxelles, 90 Rue Meylemeersch, 1070, Brussels, Belgium
| | - Sylvia Ritter
- Biophysics Department, GSI Helmholtzzentrum Für Schwerionenforschung, Darmstadt, Germany
| | - Uli Weber
- Biophysics Department, GSI Helmholtzzentrum Für Schwerionenforschung, Darmstadt, Germany
| | - Marco Durante
- Biophysics Department, GSI Helmholtzzentrum Für Schwerionenforschung, Darmstadt, Germany
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Etienne G J Danchin
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 06903, Sophia Antipolis, France
| | - Boris Hespeels
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Karine Van Doninck
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
- Laboratory of Molecular Biology & Evolution (MBE), Department of Biology, Université Libre de Bruxelles, 1000, Brussels, Belgium
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23
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Panier S, Wang S, Schumacher B. Genome Instability and DNA Repair in Somatic and Reproductive Aging. ANNUAL REVIEW OF PATHOLOGY 2024; 19:261-290. [PMID: 37832947 DOI: 10.1146/annurev-pathmechdis-051122-093128] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Genetic material is constantly subjected to genotoxic insults and is critically dependent on DNA repair. Genome maintenance mechanisms differ in somatic and germ cells as the soma only requires maintenance during an individual's lifespan, while the germline indefinitely perpetuates its genetic information. DNA lesions are recognized and repaired by mechanistically highly diverse repair machineries. The DNA damage response impinges on a vast array of homeostatic processes and can ultimately result in cell fate changes such as apoptosis or cellular senescence. DNA damage causally contributes to the aging process and aging-associated diseases, most prominently cancer. By causing mutations, DNA damage in germ cells can lead to genetic diseases and impact the evolutionary trajectory of a species. The mechanisms ensuring tight control of germline DNA repair could be highly instructive in defining strategies for improved somatic DNA repair. They may provide future interventions to maintain health and prevent disease during aging.
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Affiliation(s)
- Stephanie Panier
- Institute for Genome Stability in Aging and Disease and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital of Cologne, Cologne, Germany;
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Siyao Wang
- Institute for Genome Stability in Aging and Disease and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital of Cologne, Cologne, Germany;
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital of Cologne, Cologne, Germany;
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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24
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Smythers AL, Joseph KM, O'Dell HM, Clark TA, Crislip JR, Flinn BB, Daughtridge MH, Stair ER, Mubarek SN, Lewis HC, Salas AA, Hnilica ME, Kolling DRJ, Hicks LM. Chemobiosis reveals tardigrade tun formation is dependent on reversible cysteine oxidation. PLoS One 2024; 19:e0295062. [PMID: 38232097 DOI: 10.1371/journal.pone.0295062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/14/2023] [Indexed: 01/19/2024] Open
Abstract
Tardigrades, commonly known as 'waterbears', are eight-legged microscopic invertebrates renowned for their ability to withstand extreme stressors, including high osmotic pressure, freezing temperatures, and complete desiccation. Limb retraction and substantial decreases to their internal water stores results in the tun state, greatly increasing their ability to survive. Emergence from the tun state and/or activity regain follows stress removal, where resumption of life cycle occurs as if stasis never occurred. However, the mechanism(s) through which tardigrades initiate tun formation is yet to be uncovered. Herein, we use chemobiosis to demonstrate that tardigrade tun formation is mediated by reactive oxygen species (ROS). We further reveal that tuns are dependent on reversible cysteine oxidation, and that this reversible cysteine oxidation is facilitated by the release of intracellular reactive oxygen species (ROS). We provide the first empirical evidence of chemobiosis and map the initiation and survival of tardigrades via osmobiosis, chemobiosis, and cryobiosis. In vivo electron paramagnetic spectrometry suggests an intracellular release of reactive oxygen species following stress induction; when this release is quenched through the application of exogenous antioxidants, the tardigrades can no longer survive osmotic stress. Together, this work suggests a conserved dependence of reversible cysteine oxidation across distinct tardigrade cryptobioses.
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Affiliation(s)
- Amanda L Smythers
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Kara M Joseph
- Department of Chemistry, Marshall University, Huntington, WV, United States of America
| | - Hayden M O'Dell
- Department of Chemistry, Marshall University, Huntington, WV, United States of America
| | - Trace A Clark
- Department of Chemistry, Marshall University, Huntington, WV, United States of America
| | - Jessica R Crislip
- Department of Chemistry, Marshall University, Huntington, WV, United States of America
| | - Brendin B Flinn
- Department of Chemistry, Marshall University, Huntington, WV, United States of America
| | - Meredith H Daughtridge
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Evan R Stair
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Saher N Mubarek
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Hailey C Lewis
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Abel A Salas
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Megan E Hnilica
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Derrick R J Kolling
- Department of Chemistry, Marshall University, Huntington, WV, United States of America
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
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25
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Li S, Yang Y, Wen J, He M, Hu Q, Zhang K, Weng Q. Comparative transcriptome analysis reveals the molecular mechanism of sterility induced by irradiation of Plutella xylostella (Linnaeus). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 270:115890. [PMID: 38150750 DOI: 10.1016/j.ecoenv.2023.115890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 12/29/2023]
Abstract
Plutella xylostella (Linnaeus) is an important pest of cruciferous plants, which is harmful all over the world, causing serious economic losses, and its drug resistance is increasing rapidly. The sterile insect technique (SIT) is a green control method and does not cause resistance. In this study, transcriptomics and bioinformatics were used to explore the effects of irradiation on the reproductive function of Plutella xylostella, and the response mechanism of sterility under irradiation was initially revealed. We identified 3342 (1682 up-regulated, 1660 down-regulated), 1963 (1042 up-regulated, 921 down-regulated) and 1531 (721 up-regulated, 810 down-regulated) differentially expressed genes (DEGs) in the 200 Gy vs CK (Control Check), 400 Gy vs CK and 400 Gy vs 200 Gy groups, respectively. GO and KEGG analyses were performed for DEGs in each group. The results showed that 200 Gy activated the downstream phosphorylation pathway and inhibited the cytochrome p450 immune response mechanism. 400 Gy promoted protein decomposition and absorption pathways, autophagy pathways, etc. Down-regulated genes were concentrated in the transformation process of energy metabolizing substances such as ATP, phosphorylation signaling pathway, and insulin, while up-regulated genes were concentrated in biological regulation and metabolic processes. Eight genes in the phosphorylation pathway were selected for qRT-PCR verification, and the results showed that the phosphorylation of different dose groups was regulated in different ways. 400 Gy used positive feedback regulation, while the phosphorylation of F1 used negative feedback regulation.
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Affiliation(s)
- Shifan Li
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Yuhang Yang
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; Dazhou Vocational and Technical College, Sichuan Province, China
| | - Jiaqi Wen
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Min He
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Qiongbo Hu
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, China
| | - Ke Zhang
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Qunfang Weng
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, China.
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26
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Fleming JF, Pisani D, Arakawa K. The Evolution of Temperature and Desiccation-Related Protein Families in Tardigrada Reveals a Complex Acquisition of Extremotolerance. Genome Biol Evol 2024; 16:evad217. [PMID: 38019582 PMCID: PMC10799326 DOI: 10.1093/gbe/evad217] [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: 05/02/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023] Open
Abstract
Tardigrada is an ecdysozoan lineage famed for its resilience. Tardigrades can tolerate high doses of radiation, low-oxygen environments, desiccation, and both high and low temperatures under a dormant state called "anhydrobiosis", which is a reversible halt of metabolism upon almost complete desiccation. A large amount of research has focused on the genetic pathways related to these capabilities, and a number of genes have been identified and linked to the extremotolerant response of tardigrades. However, the history of these genes is unclear, and the origins and history of extremotolerant genes within Tardigrada remain a mystery. Here, we generate the first phylogenies of six separate protein families linked with desiccation and radiation tolerance in Tardigrada: cytosolic abundant heat-soluble protein, mitochondrial abundant heat-soluble protein, secretory abundant heat-soluble protein, meiotic recombination 11 homolog, and the newly discovered Echiniscus testudo abundant heat-soluble proteins (alpha and beta). The high number of independent gene duplications found amongst the six gene families studied suggests that tardigrades have a complex history with numerous independent adaptations to cope with aridity within the limnoterrestrial environment. Our results suggest that tardigrades likely transitioned from a marine environment to a limnoterrestrial environment only twice, once in stem Eutardigrada and once in Heterotardigrada, which explains the unique adaptations to anhydrobiosis present in both classes.
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Affiliation(s)
- James F Fleming
- Institute for Advanced Biosciences, Keio University, Tsuruoka City, Yamagata, Japan
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Davide Pisani
- Palaeobiology Research Group, School of Biological Sciences and School of Earth Sciences, University of Bristol, Bristol, United Kingdom
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka City, Yamagata, Japan
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27
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Goh KM, González-Siso MI, Sani RK. Genomics of extreme environments: unveiling the secrets of survival. Sci Rep 2023; 13:21441. [PMID: 38052842 PMCID: PMC10698157 DOI: 10.1038/s41598-023-48470-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023] Open
Affiliation(s)
- Kian Mau Goh
- Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor, Malaysia.
| | - María-Isabel González-Siso
- Facultade de Ciencias, CICA-Centro Interdisciplinar de Química e Bioloxía, Universidade da Coruña, 15071, A Coruña, Spain
| | - Rajesh K Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, 57701, USA
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28
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Ye C, Guo J, Zhou XQ, Chen DG, Liu J, Peng X, Jaremko M, Jaremko Ł, Guo T, Liu CG, Chen K. The Dsup coordinates grain development and abiotic stress in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 205:108184. [PMID: 37977025 DOI: 10.1016/j.plaphy.2023.108184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/06/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023]
Abstract
DNA damage is a serious threat to all living organisms and may be induced by environmental stressors. Previous studies have revealed that the tardigrade (Ramazzotius varieornatus) DNA damage suppressor protein Dsup has protective effects in human cells and tobacco. However, whether Dsup provides radiation damage protection more widely in crops is unclear. To explore the effects of Dsup in other crops, stable Dsup overexpression lines through Agrobacterium-mediated transformation were generated and their agronomic traits were deeply investigated. In this study, the overexpression of Dsup not only enhanced the DNA damage resistance at the seeds and seedlings stages, they also exhibited grain size enlargement and starch granule structure and cell size alteration by the scanning electron microscopy observation. Notably, the RNA-seq revealed that the Dsup plants increased radiation-related and abiotic stress-related gene expression in comparison to wild types, suggesting that Dsup is capable to coordinate normal growth and abiotic stress resistance in rice. Immunoprecipitation enrichment with liquid chromatography-tandem mass spectrometry (IP-LC-MS) assays uncovered 21 proteins preferably interacting with Dsup in plants, suggesting that Dsup binds to transcription and translation related proteins to regulate the homeostasis between DNA protection and plant development. In conclusion, our data provide a detailed agronomic analysis of Dsup plants and potential mechanisms of Dsup function in crops. Our findings provide novel insights for the breeding of crop radiation resistance.
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Affiliation(s)
- Chanjuan Ye
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetic and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agricultural and Rural Affairs, Guangzhou, 510640, China
| | - Jie Guo
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetic and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agricultural and Rural Affairs, Guangzhou, 510640, China
| | - Xin-Qiao Zhou
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetic and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agricultural and Rural Affairs, Guangzhou, 510640, China
| | - Da-Gang Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetic and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agricultural and Rural Affairs, Guangzhou, 510640, China
| | - Juan Liu
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetic and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agricultural and Rural Affairs, Guangzhou, 510640, China
| | - Xin Peng
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetic and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agricultural and Rural Affairs, Guangzhou, 510640, China
| | - Mariusz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Łukasz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Tao Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas and Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chuan-Guang Liu
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetic and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agricultural and Rural Affairs, Guangzhou, 510640, China.
| | - Ke Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetic and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agricultural and Rural Affairs, Guangzhou, 510640, China.
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29
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Kihm JH, Zawierucha K, Rho HS, Park TYS. Homology of the head sensory structures between Heterotardigrada and Eutardigrada supported in a new species of water bear (Ramazzottiidae: Ramazzottius). ZOOLOGICAL LETTERS 2023; 9:22. [PMID: 38012802 PMCID: PMC10680360 DOI: 10.1186/s40851-023-00221-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 10/05/2023] [Indexed: 11/29/2023]
Abstract
Phylum Tardigrada is represented by microscopic eight-legged panarthropods that inhabit terrestrial and marine environments. Although tardigrades are emerging model animals for areas of research including physiology, evolutionary biology, and astrobiology, knowledge of their external morphology remains insufficient. For instance, homologies between marine and terrestrial relatives largely remain unexplored. In the present study we provide detailed pictures of the head sensory organs in a new tardigrade, Ramazzottius groenlandensis sp. nov. Specimens were collected from a mixed moss and lichen sample on Ella Island, East Greenland. The new species differs from congeneric species in the presence of polygonal sculpturing on the dorsal cuticle, which is accentuated in the posterior region of the body, a lateral papilla on leg IV, and distinctive egg morphology. A Bayesian phylogenetic analysis (18S rRNA + 28S rRNA + COI) places the new species within the genus Ramazzottius with high confidence. Interestingly, the new species shows a full set of well-developed cephalic organs, which correspond to all sensory fields found in eutardigrades. Details on the full set of head organs were present only for heterotardigrades. The surface of these organs is covered with small pores, which presumably play a sensory role. This discovery suggests the homology of head sensory structures between heterotardigrades and eutardigrades, implying that the distinctive arrangement and positioning of sensory organs on the head is a plesiomorphic feature of tardigrades. Moreover, we find that the Ramazzottius oberhaeuseri morphotype forms a morphogroup, not a monophyletic species complex.
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Affiliation(s)
- Ji-Hoon Kihm
- Division of Earth Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon, 21990, Korea.
| | - Krzysztof Zawierucha
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Hyun Soo Rho
- East Sea Environmental Research Center, East Sea Research Institute, Korea Institute of Ocean Science & Technology, 48 Haeyanggwahak-gil, Uljin, Gyeongsangbuk-do, 36315, Korea
| | - Tae-Yoon S Park
- Division of Earth Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon, 21990, Korea
- Polar Sciences, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Korea
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30
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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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31
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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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32
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Porter WP, Bertz AE, Mathewson PD, Solorzano LC, Dudley PN, Bonazza R, Gebremedhin KG. Climate Spaces and Cliffs: A Novel Bovine Thermodynamic and Mass Balances Model. Animals (Basel) 2023; 13:3043. [PMID: 37835649 PMCID: PMC10572002 DOI: 10.3390/ani13193043] [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: 05/15/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/15/2023] Open
Abstract
The effects of climate change on animals are typically viewed in terms of survivability and wellbeing. In this study, we broaden that purview to include climate impacts on reproductive capability. There are not only climate spaces for daily function, but climate cliffs that represent reproductive failures in the face of climate warming. This alternative focus suggests that climate warming challenges may be more immediate and profound than initially imagined. This research describes a state-of-the-art mechanistic model, Dairy Niche Mapper (DNM), and independent validation tests. Where test data are absent, the calculated results are consistent with expected responses. Simulations of metabolic chamber conditions reveal the local steady-state impacts of climate and animal variables on milk production capacity, metabolic rate, food consumption and water needs. Simulations of a temperature humidity index (THI) show strengths and limitations of that approach. Broader time- and spatial-scale calculations applied in the western and eastern halves of the northern hemisphere identify current and future monthly latitudinal climate change impacts on milk production potential, feed and water needs in dairy cows of different sizes. Dairy Niche Mapper (DNM) was developed from a broadly tested mechanistic microclimate-animal model, Niche Mapper (NM). DNM provides an improved quantitative understanding of the complex nonlinear interactions of climate variation and dairy bovine properties' effects on current and future milk production, feed and water needs for grazing and confinement dairy operations. DNM outputs include feasible activity times, milk production and water and feed needs of different-sized Holstein cows on high-grain (confinement feeding) versus high-forage (grazing feeding) diets at three arbitrary north latitudes, 12°, 30° and 60°, for North and Central America and for Asia. These three latitudes encompass current northern hemisphere bovine production environments and possible future production locations. The greatest impacts of climate change will be in the low elevations in tropical and subtropical regions. Global regions above 30° and below 60° latitude with reliable rainfall will be least affected by current projected levels of climate change. This work provides the basis for computational animal design for guiding agricultural development via breeding programs, genetic engineering, management options including siting or the manipulation of other relevant environmental and animal variables.
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Affiliation(s)
- Warren P. Porter
- Department of Integrative Biology, University of Wisconsin, Madison, WI 53706, USA; (A.E.B.); (P.D.M.)
| | - Alexa E. Bertz
- Department of Integrative Biology, University of Wisconsin, Madison, WI 53706, USA; (A.E.B.); (P.D.M.)
| | - Paul D. Mathewson
- Department of Integrative Biology, University of Wisconsin, Madison, WI 53706, USA; (A.E.B.); (P.D.M.)
| | - Luis C. Solorzano
- Adjunct Faculty, Department of Animal Science, University of Puerto Rico-Mayagüez, Mayagüez, PR 00680, USA;
| | - Peter N. Dudley
- Fisheries Collaborative Program, University of California, Santa Cruz, CA 95064, USA;
| | - Riccardo Bonazza
- Department of Mechanical Engineering, University of Wisconsin, Madison, WI 53706, USA;
| | - Kifle G. Gebremedhin
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA;
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Giovannini I, Manfrin C, Greco S, Vincenzi J, Altiero T, Guidetti R, Giulianini P, Rebecchi L. Increasing temperature-driven changes in life history traits and gene expression of an Antarctic tardigrade species. Front Physiol 2023; 14:1258932. [PMID: 37766751 PMCID: PMC10520964 DOI: 10.3389/fphys.2023.1258932] [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: 07/14/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
The Antarctic region has been experiencing some of the planet's strongest climatic changes, including an expected increase of the land temperature. The potential effects of this warming trend will lead ecosystems to a risk of losing biodiversity. Antarctic mosses and lichens host different microbial groups, micro-arthropods and meiofaunal organisms (e.g., tardigrades, rotifers). The eutardigrade Acutuncus antarcticus is considered a model animal to study the effect of increasing temperature due to global warming on Antarctic terrestrial communities. In this study, life history traits and fitness of this species are analyzed by rearing specimens at two different and increasing temperatures (5°C vs. 15°C). Moreover, the first transcriptome analysis on A. antarcticus is performed, exposing adult animals to a gradual increase of temperature (5°C, 10°C, 15°C, and 20°C) to find differentially expressed genes under short- (1 day) and long-term (15 days) heat stress. Acutuncus antarcticus specimens reared at 5°C live longer (maximum life span: 686 days), reach sexual maturity later, lay more eggs (which hatch in longer time and in lower percentage) compared with animals reared at 15°C. The fitness decreases in animals belonging to the second generation at both rearing temperatures. The short-term heat exposure leads to significant changes at transcriptomic level, with 67 differentially expressed genes. Of these, 23 upregulated genes suggest alterations of mitochondrial activity and oxido-reductive processes, and two intrinsically disordered protein genes confirm their role to cope with heat stress. The long-term exposure induces alterations limited to 14 genes, and only one annotated gene is upregulated in response to both heat stresses. The decline in transcriptomic response after a long-term exposure indicates that the changes observed in the short-term are likely due to an acclimation response. Therefore, A. antarcticus could be able to cope with increasing temperature over time, including the future conditions imposed by global climate change.
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Affiliation(s)
- Ilaria Giovannini
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Chiara Manfrin
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Samuele Greco
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Joel Vincenzi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Tiziana Altiero
- NBFC, National Biodiversity Future Center, Palermo, Italy
- Department of Education and Humanities, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Roberto Guidetti
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Piero Giulianini
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Lorena Rebecchi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
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Nagwani AK, Budka A, Łacka A, Kaczmarek Ł, Kmita H. The effect of hypomagnetic field on survival and mitochondrial functionality of active Paramacrobiotus experimentalis females and males of different age. Front Physiol 2023; 14:1253483. [PMID: 37745239 PMCID: PMC10514487 DOI: 10.3389/fphys.2023.1253483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/29/2023] [Indexed: 09/26/2023] Open
Abstract
Even for tardigrades, often called the toughest animals on Earth, a hypomagnetic field (HMF) is an extreme environment. However, studies on the effect of HMF on tardigrades and other invertebrates are scarce. Mitochondria play an important role in an organism's response to extreme conditions. The effect of HMF on the mitochondrial inner membrane potential (Δψ), a well-known marker of mitochondria functionality, shows that mitochondria are very sensitive to HMF. To measure the HMF effect on Paramacrobiotus experimentalis, we calculated the tardigrade survival rate and Δψ level after HMF treatments of different durations. We also estimated the relationship between the age and sex of the tardigrade and the HMF effect. We observed age- and sex-related differences in Δψ and found that Δψ changes after HMF treatment were dependent on its duration as well as the animal's age and sex. Furthermore, active P. experimentalis individuals displayed a high survival rate after HMF treatment. The data may contribute to the understanding of tardigrade aging and their resistance to extreme conditions including HMF, which in turn may be useful for future space explorations.
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Affiliation(s)
- Amit Kumar Nagwani
- Department of Bioenergetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Anna Budka
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Poznań, Poland
| | - Agnieszka Łacka
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Poznań, Poland
| | - Łukasz Kaczmarek
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Institute of Environmental Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Hanna Kmita
- Department of Bioenergetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznań, Poznań, Poland
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Hagelbäck P, Jönsson KI. An experimental study on tolerance to hypoxia in tardigrades. Front Physiol 2023; 14:1249773. [PMID: 37731547 PMCID: PMC10507709 DOI: 10.3389/fphys.2023.1249773] [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: 06/29/2023] [Accepted: 08/21/2023] [Indexed: 09/22/2023] Open
Abstract
Introduction: Tardigrades are small aquatic invertebrates with well documented tolerance to several environmental stresses, including desiccation, low temperature, and radiation, and an ability to survive long periods in a cryptobiotic state under arrested metabolism. Many tardigrade populations live in habitats where temporary exposure to hypoxia is expected, e.g., benthic layers or substrates that regularly undergo desiccation, but tolerance to hypoxia has so far not been thoroughly investigated in tardigrades. Method: We studied the response to exposure for hypoxia (<1 ppm) during 1-24 h in two tardigrade species, Richtersius cf. coronifer and Hypsibius exemplaris. The animals were exposed to hypoxia in their hydrated active state. Results: Survival was high in both species after the shortest exposures to hypoxia but tended to decline with longer exposures, with almost complete failure to recover after 24 h in hypoxia. R. cf. coronifer tended to be more tolerant than H. exemplaris. When oxygen level was gradually reduced from 8 to 1 ppm, behavioral responses in terms of irregular body movements were first observed at 3-4 ppm. Discussion: The study shows that both limno-terrestrial and freshwater tardigrades are able to recover after exposure to severe hypoxia, but only exposure for relatively short periods of time. It also indicates that tardigrade species have different sensitivity and response patterns to exposure to hypoxia. These results will hopefully encourage more studies on how tardigrades are affected by and respond to hypoxic conditions.
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Affiliation(s)
| | - K. Ingemar Jönsson
- Department of Environmental Science, Kristianstad University, Kristianstad, Sweden
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Arakawa K, Hirose T, Inada T, Ito T, Kai T, Oyama M, Tomari Y, Yoda T, Nakagawa S. Nondomain biopolymers: Flexible molecular strategies to acquire biological functions. Genes Cells 2023; 28:539-552. [PMID: 37249032 DOI: 10.1111/gtc.13050] [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: 04/30/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/31/2023]
Abstract
A long-standing assumption in molecular biology posits that the conservation of protein and nucleic acid sequences emphasizes the functional significance of biomolecules. These conserved sequences fold into distinct secondary and tertiary structures, enable highly specific molecular interactions, and regulate complex yet organized molecular processes within living cells. However, recent evidence suggests that biomolecules can also function through primary sequence regions that lack conservation across species or gene families. These regions typically do not form rigid structures, and their inherent flexibility is critical for their functional roles. This review examines the emerging roles and molecular mechanisms of "nondomain biomolecules," whose functions are not easily predicted due to the absence of conserved functional domains. We propose the hypothesis that both domain- and nondomain-type molecules work together to enable flexible and efficient molecular processes within the highly crowded intracellular environment.
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Grants
- 21H05273 Ministry of Education, Culture, Sports, Science and Technology
- 21H05274 Ministry of Education, Culture, Sports, Science and Technology
- 21H05275 Ministry of Education, Culture, Sports, Science and Technology
- 21H05276 Ministry of Education, Culture, Sports, Science and Technology
- 21H05277 Ministry of Education, Culture, Sports, Science and Technology
- 21H05278 Ministry of Education, Culture, Sports, Science and Technology
- 21H05279 Ministry of Education, Culture, Sports, Science and Technology
- 21H05280 Ministry of Education, Culture, Sports, Science and Technology
- 21H05281 Ministry of Education, Culture, Sports, Science and Technology
- 21H05282 Ministry of Education, Culture, Sports, Science and Technology
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Affiliation(s)
- Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tokyo, Japan
| | - Tetsuro Hirose
- RNA Biofunction Laboratory, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Toshifumi Inada
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Takuhiro Ito
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Toshie Kai
- Germline Biology Laboratory, Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Masaaki Oyama
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yukihide Tomari
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Takao Yoda
- Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
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Siddiqui R, Elmoselhi AB, Khan NA. Space medicine: gut microbiome of hardy species is a potential source to counter disorders during space travel. Future Sci OA 2023; 9:FSO868. [PMID: 37485442 PMCID: PMC10357397 DOI: 10.2144/fsoa-2023-0060] [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: 04/17/2023] [Accepted: 05/03/2023] [Indexed: 07/25/2023] Open
Abstract
It is proposed that gut microbiome of species like cockroaches may offer a potential source of novel mechanisms/molecules that can be translated into humans to safeguard astronauts against stressors of the space environment during deep space exploration missions.
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Affiliation(s)
- Ruqaiyyah Siddiqui
- College of Arts & Sciences, American University of Sharjah, University City, Sharjah, 26666, UAE
- Department of Medical Biology, Faculty of Medicine, Istinye University, Istanbul, 34010, Turkey
| | - Adel B Elmoselhi
- College of Medicine, University of Sharjah, University City, Sharjah, 27272, UAE
| | - Naveed Ahmed Khan
- Department of Medical Biology, Faculty of Medicine, Istinye University, Istanbul, 34010, Turkey
- College of Medicine, University of Sharjah, University City, Sharjah, 27272, UAE
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Aguilar R, Khan L, Arslanovic N, Birmingham K, Kasliwal K, Posnikoff S, Chakraborty U, Hickman AR, Watson R, Ezell RJ, Willis HE, Cowles MW, Garner R, Shim A, Gutierrez I, Marunde MR, Keogh MC, Tyler JK. Multivalent binding of the tardigrade Dsup protein to chromatin promotes yeast survival and longevity upon exposure to oxidative damage. RESEARCH SQUARE 2023:rs.3.rs-3182883. [PMID: 37546815 PMCID: PMC10402244 DOI: 10.21203/rs.3.rs-3182883/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Tardigrades are remarkable in their ability to survive extreme environments. The damage suppressor (Dsup) protein is thought responsible for their extreme resistance to reactive oxygen species (ROS) generated by irradiation. Here we show that expression of Ramazzottius varieornatus Dsup in Saccharomyces cerevisiae reduces oxidative DNA damage and extends the lifespan of budding yeast exposed to chronic oxidative genotoxicity. This protection from ROS requires either the Dsup HMGN-like domain or sequences C-terminal to same. Dsup associates with no apparent bias across the yeast genome, using multiple modes of nucleosome binding; the HMGN-like region interacts with both the H2A/H2B acidic patch and H3/H4 histone tails, while the C-terminal region binds DNA. These findings give precedent for engineering an organism by physically shielding its genome to promote survival and longevity in the face of oxidative damage.
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Affiliation(s)
- Rhiannon Aguilar
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
- Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | | | - Nina Arslanovic
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
| | - Kaylah Birmingham
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
- Weill Cornell Medicine, Pharmacology Graduate Program, New York, NY 10065 United States
| | - Kritika Kasliwal
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
- Weill Cornell Medicine, Biochemistry, Cellular, and Molecular Biology Graduate Program, New York, NY 10065, USA
| | - Spike Posnikoff
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
| | - Ujani Chakraborty
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
| | | | | | | | | | | | - Richard Garner
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
- Weill Cornell Medicine, Biochemistry, Cellular, and Molecular Biology Graduate Program, New York, NY 10065, USA
| | - Abraham Shim
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
- Weill Cornell Medicine, Biochemistry, Cellular, and Molecular Biology Graduate Program, New York, NY 10065, USA
| | - Ignacio Gutierrez
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
| | | | | | - Jessica K. Tyler
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
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Zarubin M, Azorskaya T, Kuldoshina O, Alekseev S, Mitrofanov S, Kravchenko E. The tardigrade Dsup protein enhances radioresistance in Drosophila melanogaster and acts as an unspecific repressor of transcription. iScience 2023; 26:106998. [PMID: 37534176 PMCID: PMC10391675 DOI: 10.1016/j.isci.2023.106998] [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: 03/18/2022] [Revised: 01/13/2023] [Accepted: 05/25/2023] [Indexed: 08/04/2023] Open
Abstract
The tardigrade-unique damage suppressor protein (Dsup) can protect DNA from ionizing radiation and reactive oxygen species (ROS). In this study, we generated Dsup-expressing lines of Drosophila melanogaster and demonstrated that Dsup increased the survival rate after γ-ray irradiation and hydrogen peroxide treatment in flies too, but reduced the level of their locomotor activity. The transcriptome analyses of Dsup-expressing lines revealed a significant number of DEGs, >99% of which were down-regulated. Moreover, Dsup could bind RNA. These findings suggest that Dsup can act not only as a DNA protector but also as a non-specific transcriptional repressor and RNA-binding protein, that may lead to disturbance of a number of biological processes in D. melanogaster. The obtained data demonstrate features of the Dsup protein action in non-tardigrade organisms and can be used to understand the impact of other unspecific DNA/RNA-binding proteins on ROS and radiation resistance, gene expression, and epigenetic processes.
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Affiliation(s)
- Mikhail Zarubin
- Dzhelepov Laboratory of Nuclear Problems, International Intergovernmental Organization Joint Institute for Nuclear Research, Dubna 141980, Russia
| | - Talyana Azorskaya
- Dzhelepov Laboratory of Nuclear Problems, International Intergovernmental Organization Joint Institute for Nuclear Research, Dubna 141980, Russia
| | - Olga Kuldoshina
- Dzhelepov Laboratory of Nuclear Problems, International Intergovernmental Organization Joint Institute for Nuclear Research, Dubna 141980, Russia
| | - Sergey Alekseev
- Flerov Laboratory of Nuclear Reactions, International Intergovernmental Organization Joint Institute for Nuclear Research, Dubna 141980, Russia
| | - Semen Mitrofanov
- Flerov Laboratory of Nuclear Reactions, International Intergovernmental Organization Joint Institute for Nuclear Research, Dubna 141980, Russia
| | - Elena Kravchenko
- Dzhelepov Laboratory of Nuclear Problems, International Intergovernmental Organization Joint Institute for Nuclear Research, Dubna 141980, Russia
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40
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Shaba E, Landi C, Marzocchi C, Vantaggiato L, Bini L, Ricci C, Cantara S. Proteomics Reveals How the Tardigrade Damage Suppressor Protein Teaches Transfected Human Cells to Survive UV-C Stress. Int J Mol Sci 2023; 24:11463. [PMID: 37511223 PMCID: PMC10380570 DOI: 10.3390/ijms241411463] [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: 05/12/2023] [Revised: 06/12/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
The genome sequencing of the tardigrade Ramazzottius varieornatus revealed a unique nucleosome-binding protein named damage suppressor (Dsup), which was discovered to be crucial for the extraordinary abilities of tardigrades in surviving extreme stresses, such as UV. Evidence in Dsup-transfected human cells suggests that Dsup mediates an overall response in DNA damage signaling, DNA repair, and cell cycle regulation, resulting in an acquired resistance to stress. Given these promising outcomes, our study attempts to provide a wider comprehension of the molecular mechanisms modulated by Dsup in human cells and to explore the Dsup-activated molecular pathways under stress. We performed a differential proteomic analysis of Dsup-transfected and control human cells under basal conditions and at 24 h recovery after exposure to UV-C. We demonstrate via enrichment and network analyses, for the first time, that even in the absence of external stimuli, and more significantly, after stress, Dsup activates mechanisms involved with the unfolded protein response, the mRNA processing and stability, cytoplasmic stress granules, the DNA damage response, and the telomere maintenance. In conclusion, our results shed new light on Dsup-mediated protective mechanisms and increases our knowledge of the molecular machineries of extraordinary protection against UV-C stress.
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Affiliation(s)
- Enxhi Shaba
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Claudia Landi
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Carlotta Marzocchi
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy
| | - Lorenza Vantaggiato
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Luca Bini
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Claudia Ricci
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy
| | - Silvia Cantara
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy
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41
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Sim KS, Inoue T. Structure of a superoxide dismutase from a tardigrade: Ramazzottius varieornatus strain YOKOZUNA-1. Acta Crystallogr F Struct Biol Commun 2023; 79:169-179. [PMID: 37358501 PMCID: PMC10327573 DOI: 10.1107/s2053230x2300523x] [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: 04/02/2023] [Accepted: 06/12/2023] [Indexed: 06/27/2023] Open
Abstract
Superoxide dismutase (SOD) is an essential and ubiquitous antioxidant protein that is widely present in biological systems. The anhydrobiotic tardigrades are some of the toughest micro-animals. They have an expanded set of genes for antioxidant proteins such as SODs. These proteins are thought to play an essential role in oxidative stress resistance in critical situations such as desiccation, although their functions at the molecular level have yet to be explored. Here, crystal structures of a copper/zinc-containing SOD (RvSOD15) from an anhydrobiotic tardigrade, Ramazzottius varieornatus strain YOKOZUNA-1, are reported. In RvSOD15, one of the histidine ligands of the catalytic copper center is replaced by a valine (Val87). The crystal structures of the wild type and the V87H mutant show that even though a histidine is placed at position 87, a nearby flexible loop can destabilize the coordination of His87 to the Cu atom. Model structures of other RvSODs were investigated and it was found that some of them are also unusual SODs, with features such as deletion of the electrostatic loop or β3 sheet and unusual metal-binding residues. These studies show that RvSOD15 and some other RvSODs may have evolved to lose the SOD function, suggesting that gene duplications of antioxidant proteins do not solely explain the high stress tolerance of anhydrobiotic tardigrades.
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Affiliation(s)
- Kee-Shin Sim
- Graduate School of Pharmaceutical Science, Osaka University, Suita City, Osaka 565-0871, Japan
| | - Tsuyoshi Inoue
- Graduate School of Pharmaceutical Science, Osaka University, Suita City, Osaka 565-0871, Japan
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42
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Escarcega RD, Patil AA, Meyer MD, Moruno-Manchon JF, Silvagnoli AD, McCullough LD, Tsvetkov AS. The Tardigrade damage suppressor protein Dsup promotes DNA damage in neurons. Mol Cell Neurosci 2023; 125:103826. [PMID: 36858083 PMCID: PMC10247392 DOI: 10.1016/j.mcn.2023.103826] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 02/18/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Tardigrades are microscopic invertebrates, which are capable of withstanding extreme environmental conditions, including high levels of radiation. A Tardigrade protein, Dsup (Damage Suppressor), protects the Tardigrade's DNA during harsh environmental stress and X-rays. When expressed in cancer cells, Dsup protects DNA from single- and double-strand breaks (DSBs) induced by radiation, increases survival of irradiated cells, and protects DNA from reactive oxygen species. These unusual properties of Dsup suggested that understanding how the protein functions may help in the design of small molecules that could protect humans during radiotherapy or space travel. Here, we investigated if Dsup is protective in cortical neurons cultured from rat embryos. We discovered that, in cortical neurons, the codon-optimized Dsup localizes to the nucleus and, surprisingly, promotes neurotoxicity, leading to neurodegeneration. Unexpectedly, we found that Dsup expression results in the formation of DNA DSBs in cultured neurons. With electron microscopy, we discovered that Dsup promotes chromatin condensation. Unlike Dsup's protective properties in cancerous cells, in neurons, Dsup promotes neurotoxicity, induces DNA damage, and rearranges chromatin. Neurons are sensitive to Dsup, and Dsup is a doubtful surrogate for DNA protection in neuronal cells.
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Affiliation(s)
- Rocio Diaz Escarcega
- Department of Neurology, The University of Texas McGovern Medical School at Houston, TX 77030, United States of America
| | - Abhijeet A Patil
- Department of Neurology, The University of Texas McGovern Medical School at Houston, TX 77030, United States of America
| | - Matthew D Meyer
- Shared Equipment Authority, Rice University, Houston, TX 77005, United States of America
| | - Jose F Moruno-Manchon
- Department of Neurology, The University of Texas McGovern Medical School at Houston, TX 77030, United States of America
| | - Alexander D Silvagnoli
- Department of Neurology, The University of Texas McGovern Medical School at Houston, TX 77030, United States of America
| | - Louise D McCullough
- Department of Neurology, The University of Texas McGovern Medical School at Houston, TX 77030, United States of America; The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, United States of America
| | - Andrey S Tsvetkov
- Department of Neurology, The University of Texas McGovern Medical School at Houston, TX 77030, United States of America; The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, United States of America; UTHealth Consortium on Aging, The University of Texas McGovern Medical School, Houston, TX 77030, United States of America.
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43
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Vandepas LE, Tassia MG, Halanych KM, Amemiya CT. Unexpected Distribution of Chitin and Chitin Synthase across Soft-Bodied Cnidarians. Biomolecules 2023; 13:biom13050777. [PMID: 37238647 DOI: 10.3390/biom13050777] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/19/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
Cnidarians are commonly recognized as sea jellies, corals, or complex colonies such as the Portuguese man-of-war. While some cnidarians possess rigid internal calcareous skeletons (e.g., corals), many are soft-bodied. Intriguingly, genes coding for the chitin-biosynthetic enzyme, chitin synthase (CHS), were recently identified in the model anemone Nematostella vectensis, a species lacking hard structures. Here we report the prevalence and diversity of CHS across Cnidaria and show that cnidarian chitin synthase genes display diverse protein domain organizations. We found that CHS is expressed in cnidarian species and/or developmental stages with no reported chitinous or rigid morphological structures. Chitin affinity histochemistry indicates that chitin is present in soft tissues of some scyphozoan and hydrozoan medusae. To further elucidate the biology of chitin in cnidarian soft tissues, we focused on CHS expression in N. vectensis. Spatial expression data show that three CHS orthologs are differentially expressed in Nematostella embryos and larvae during development, suggesting that chitin has an integral role in the biology of this species. Understanding how a non-bilaterian lineage such as Cnidaria employs chitin may provide new insight into hitherto unknown functions of polysaccharides in animals, as well as their role in the evolution of biological novelty.
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Affiliation(s)
- Lauren E Vandepas
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Michael G Tassia
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Kenneth M Halanych
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
- Departments of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC 28403, USA
| | - Chris T Amemiya
- Department of Molecular and Cell Biology, University of California at Merced, Merced, CA 95343, USA
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Vijg J, Schumacher B, Abakir A, Antonov M, Bradley C, Cagan A, Church G, Gladyshev VN, Gorbunova V, Maslov AY, Reik W, Sharifi S, Suh Y, Walsh K. Mitigating age-related somatic mutation burden. Trends Mol Med 2023:S1471-4914(23)00072-2. [PMID: 37121869 DOI: 10.1016/j.molmed.2023.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 05/02/2023]
Abstract
Genomes are inherently unstable and require constant DNA repair to maintain their genetic information. However, selective pressure has optimized repair mechanisms in somatic cells only to allow transmitting genetic information to the next generation, not to maximize sequence integrity long beyond the reproductive age. Recent studies have confirmed that somatic mutations, due to errors during genome repair and replication, accumulate in tissues and organs of humans and model organisms. Here, we describe recent advances in the quantitative analysis of somatic mutations in vivo. We also review evidence for or against a possible causal role of somatic mutations in aging. Finally, we discuss options to prevent, delay or eliminate de novo, random somatic mutations as a cause of aging.
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Affiliation(s)
- Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Center for Single-Cell Omics, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, University and University Hospital of Cologne, Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
| | - Abdulkadir Abakir
- Altos Labs Cambridge Institute of Science, Granta Park, Cambridge, UK
| | | | | | - Alex Cagan
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - George Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Alexander Y Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Wolf Reik
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK; Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK; Altos Labs Cambridge Institute of Science, Granta Park, Cambridge, UK; Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | | | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA; Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Kenneth Walsh
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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Novotná Floriančičová K, Baltzis A, Smejkal J, Czerneková M, Kaczmarek Ł, Malý J, Notredame C, Vinopal S. Phylogenetic and functional characterization of water bears (Tardigrada) tubulins. Sci Rep 2023; 13:5194. [PMID: 36997657 PMCID: PMC10063605 DOI: 10.1038/s41598-023-31992-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/21/2023] [Indexed: 04/01/2023] Open
Abstract
Tardigrades are microscopic ecdysozoans that can withstand extreme environmental conditions. Several tardigrade species undergo reversible morphological transformations and enter into cryptobiosis, which helps them to survive periods of unfavorable environmental conditions. However, the underlying molecular mechanisms of cryptobiosis are mostly unknown. Tubulins are evolutionarily conserved components of the microtubule cytoskeleton that are crucial in many cellular processes. We hypothesize that microtubules are necessary for the morphological changes associated with successful cryptobiosis. The molecular composition of the microtubule cytoskeleton in tardigrades is unknown. Therefore, we analyzed and characterized tardigrade tubulins and identified 79 tardigrade tubulin sequences in eight taxa. We found three α-, seven β-, one γ-, and one ε-tubulin isoform. To verify in silico identified tardigrade tubulins, we also isolated and sequenced nine out of ten predicted Hypsibius exemplaris tubulins. All tardigrade tubulins were localized as expected when overexpressed in mammalian cultured cells: to the microtubules or to the centrosomes. The presence of a functional ε-tubulin, clearly localized to centrioles, is attractive from a phylogenetic point of view. Although the phylogenetically close Nematoda lost their δ- and ε-tubulins, some groups of Arthropoda still possess them. Thus, our data support the current placement of tardigrades into the Panarthropoda clade.
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Affiliation(s)
- Kamila Novotná Floriančičová
- Department of Biology, Faculty of Science, J. E. Purkyně University (UJEP), Usti Nad Labem, Czech Republic
- Centre for Nanotechnology and Biotechnology, Faculty of Science, UJEP, Usti Nad Labem, Czech Republic
| | | | - Jiří Smejkal
- Centre for Nanotechnology and Biotechnology, Faculty of Science, UJEP, Usti Nad Labem, Czech Republic
| | - Michaela Czerneková
- Department of Biology, Faculty of Science, J. E. Purkyně University (UJEP), Usti Nad Labem, Czech Republic
| | - Łukasz Kaczmarek
- Department of Animal Taxonomy and Ecology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Jan Malý
- Centre for Nanotechnology and Biotechnology, Faculty of Science, UJEP, Usti Nad Labem, Czech Republic
| | - Cedric Notredame
- Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Stanislav Vinopal
- Department of Biology, Faculty of Science, J. E. Purkyně University (UJEP), Usti Nad Labem, Czech Republic.
- Centre for Nanotechnology and Biotechnology, Faculty of Science, UJEP, Usti Nad Labem, Czech Republic.
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46
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Sperling AL, Glover DM. Parthenogenesis in dipterans: a genetic perspective. Proc Biol Sci 2023; 290:20230261. [PMID: 36946111 PMCID: PMC10031431 DOI: 10.1098/rspb.2023.0261] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/28/2023] [Indexed: 03/23/2023] Open
Abstract
Parthenogenesis has been documented in almost every phylum of animals, and yet this phenomenon is largely understudied. It has particular importance in dipterans since some parthenogenetic species are also disease vectors and agricultural pests. Here, we present a catalogue of parthenogenetic dipterans, although it is likely that many more remain to be identified, and we discuss how their developmental biology and interactions with diverse environments may be linked to different types of parthenogenetic reproduction. We discuss how the advances in genetics and genomics have identified chromosomal loci associated with parthenogenesis. In particular, a polygenic cause of facultative parthenogenesis has been uncovered in Drosophila mercatorum, allowing the corresponding genetic variants to be tested for their ability to promote parthenogenesis in another species, Drosophila melanogaster. This study probably identifies just one of many routes that could be followed in the evolution of parthenogenesis. We attempt to account for why the phenomenon has evolved so many times in the dipteran order and why facultative parthenogenesis appears particularly prevalent. We also discuss the significance of coarse genomic changes, including non-disjunction, aneuploidy, and polyploidy and how, together with changes to specific genes, these might relate to both facultative and obligate parthenogenesis in dipterans and other parthenogenetic animals.
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Affiliation(s)
- A. L. Sperling
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - D. M. Glover
- Department of Genetics, University of Cambridge, Cambridge, UK
- California Institute of Technology, Pasadena, CA, USA
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47
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Heikes KL, Game M, Smith FW, Goldstein B. The embryonic origin of primordial germ cells in the tardigrade Hypsibius exemplaris. Dev Biol 2023; 497:42-58. [PMID: 36893882 DOI: 10.1016/j.ydbio.2023.02.008] [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: 01/01/2023] [Revised: 02/16/2023] [Accepted: 02/26/2023] [Indexed: 03/09/2023]
Abstract
Primordial germ cells (PGCs) give rise to gametes - cells necessary for the propagation and fertility of diverse organisms. Current understanding of PGC development is limited to the small number of organisms whose PGCs have been identified and studied. Expanding the field to include little-studied taxa and emerging model organisms is important to understand the full breadth of the evolution of PGC development. In the phylum Tardigrada, no early cell lineages have been identified to date using molecular markers. This includes the PGC lineage. Here, we describe PGC development in the model tardigrade Hypsibius exemplaris. The four earliest-internalizing cells (EICs) exhibit PGC-like behavior and nuclear morphology. The location of the EICs is enriched for mRNAs of conserved PGC markers wiwi1 (water bear piwi 1) and vasa. At early stages, both wiwi1 and vasa mRNAs are detectable uniformly in embryos, which suggests that these mRNAs do not serve as localized determinants for PGC specification. Only later are wiwi1 and vasa enriched in the EICs. Finally, we traced the cells that give rise to the four PGCs. Our results reveal the embryonic origin of the PGCs of H. exemplaris and provide the first molecular characterization of an early cell lineage in the tardigrade phylum. We anticipate that these observations will serve as a basis for characterizing the mechanisms of PGC development in this animal.
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Affiliation(s)
- Kira L Heikes
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mandy Game
- Biology Department, University of North Florida, Jacksonville, FL, USA
| | - Frank W Smith
- Biology Department, University of North Florida, Jacksonville, FL, USA
| | - Bob Goldstein
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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48
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Fleming JF. The wealth of shared resources: Improving molecular taxonomy using eDNA and public databases. ZOOL SCR 2023. [DOI: 10.1111/zsc.12591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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Microbiome and One Health: Potential of Novel Metabolites from the Gut Microbiome of Unique Species for Human Health. Microorganisms 2023; 11:microorganisms11020481. [PMID: 36838446 PMCID: PMC9958914 DOI: 10.3390/microorganisms11020481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
For thousands of years, the notion that human health and performance are concomitant with the health and diversity of the microbiome has been deliberated upon [...].
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50
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Heikes KL, Game M, Smith FW, Goldstein B. The Embryonic Origin of Primordial Germ Cells in the Tardigrade Hypsibius exemplaris. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.02.522500. [PMID: 36824831 PMCID: PMC9948961 DOI: 10.1101/2023.01.02.522500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Primordial germ cells (PGCs) give rise to gametes â€" cells necessary for the propagation and fertility of diverse organisms. Current understanding of PGC development is limited to the small number of organisms whose PGCs have been identified and studied. Expanding the field to include little-studied taxa and emerging model organisms is important to understand the full breadth of the evolution of PGC development. In the phylum Tardigrada, no early cell lineages have been identified to date using molecular markers. This includes the PGC lineage. Here, we describe PGC development in the model tardigrade Hypsibius exemplaris . The four earliest-internalizing cells (EICs) exhibit PGC-like behavior and nuclear morphology. The location of the EICs is enriched for mRNAs of conserved PGC markers wiwi1 (water bear piwi 1) and vasa . At early stages, both wiwi1 and vasa mRNAs are detectable uniformly in embryos, which suggests that these mRNAs do not serve as localized determinants for PGC specification. Only later are wiwi1 and vasa enriched in the EICs. Finally, we traced the cells that give rise to the four PGCs. Our results reveal the embryonic origin of the PGCs of H. exemplaris and provide the first molecular characterization of an early cell lineage in the tardigrade phylum. We anticipate that these observations will serve as a basis for characterizing the mechanisms of PGC development in this animal.
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Affiliation(s)
- Kira L. Heikes
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mandy Game
- Biology Department, University of North Florida, Jacksonville, FL, USA
| | - Frank W. Smith
- Biology Department, University of North Florida, Jacksonville, FL, USA
| | - Bob Goldstein
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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