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Weng YM, Kavanaugh DH, Schoville SD. Evidence for Admixture and Rapid Evolution During Glacial Climate Change in an Alpine Specialist. Mol Biol Evol 2024; 41:msae130. [PMID: 38935588 PMCID: PMC11247348 DOI: 10.1093/molbev/msae130] [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: 12/05/2023] [Revised: 05/30/2024] [Accepted: 06/14/2024] [Indexed: 06/29/2024] Open
Abstract
The pace of current climate change is expected to be problematic for alpine flora and fauna, as their adaptive capacity may be limited by small population size. Yet, despite substantial genetic drift following post-glacial recolonization of alpine habitats, alpine species are notable for their success surviving in highly heterogeneous environments. Population genomic analyses demonstrating how alpine species have adapted to novel environments with limited genetic diversity remain rare, yet are important in understanding the potential for species to respond to contemporary climate change. In this study, we explored the evolutionary history of alpine ground beetles in the Nebria ingens complex, including the demographic and adaptive changes that followed the last glacier retreat. We first tested alternative models of evolutionary divergence in the species complex. Using millions of genome-wide SNP markers from hundreds of beetles, we found evidence that the N. ingens complex has been formed by past admixture of lineages responding to glacial cycles. Recolonization of alpine sites involved a distributional range shift to higher elevation, which was accompanied by a reduction in suitable habitat and the emergence of complex spatial genetic structure. We tested several possible genetic pathways involved in adaptation to heterogeneous local environments using genome scan and genotype-environment association approaches. From the identified genes, we found enriched functions associated with abiotic stress responses, with strong evidence for adaptation to hypoxia-related pathways. The results demonstrate that despite rapid demographic change, alpine beetles in the N. ingens complex underwent rapid physiological evolution.
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Affiliation(s)
- Yi-Ming Weng
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
- Okinawa Institute of Science and Technology, Graduate University, Okinawa, Japan
| | - David H Kavanaugh
- California Academy of Sciences, Department of Entomology, San Francisco, CA, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
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2
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Belott CJ, Gusev OA, Kikawada T, Menze MA. Membraneless and membrane-bound organelles in an anhydrobiotic cell line are protected from desiccation-induced damage. Cell Stress Chaperones 2024; 29:425-436. [PMID: 38608858 PMCID: PMC11061232 DOI: 10.1016/j.cstres.2024.04.002] [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: 12/29/2023] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
Anhydrobiotic species can survive virtually complete water loss by entering a reversible ametabolic glassy state that may persist for years in ambient conditions. The Pv11 cell line was derived from the egg mass of the anhydrobiotic midge, Polypedilum vanderplanki, and is currently the only available anhydrobiotic cell line. Our results demonstrate that the necessary preconditioning for Pv11 cells to enter anhydrobiosis causes autophagy and reduces mitochondrial respiration by over 70%. We speculate that reorganizing cellular bioenergetics to create and conserve energy stores may be valuable to successfully recover after rehydration. Furthermore, mitochondria in preconditioned cells lose their membrane potential during desiccation but rapidly restore it within 30 min upon rehydration, demonstrating that the inner mitochondrial membrane integrity is well-preserved. Strikingly, the nucleolus remains visible immediately upon rehydration in preconditioned cells while absent in control cells. In contrast, a preconditioning-induced membraneless organelle reformed after rehydration, demonstrating that membraneless organelles in Pv11 cells can be either stabilized or recovered. Staining the endoplasmic reticulum and the Golgi apparatus revealed that these organelles fragment during preconditioning. We hypothesize that this process reduces sheering stress caused by rapid changes in cellular volume during desiccation and rehydration. Additionally, preconditioning was found to cause the filamentous-actin (F-actin) network to disassemble significantly and reduce the fusion of adjacent plasma membranes. This study offers several exciting avenues for future studies in the animal model and Pv11 cell line that will further our understanding of anhydrobiosis and may lead to advancements in storing sensitive biologics at ambient temperatures for months or years.
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Affiliation(s)
- Clinton J Belott
- Department of Biology, University of Louisville, Louisville, KY, USA; Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan.
| | - Oleg A Gusev
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Tatarstan, Russia; Molecular Biomimetics Group, Life Improvement by Future Technologies (LIFT) Center, Moscow, Russia; Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Bunkyo-ku, Tokyo, Japan.
| | - Takahiro Kikawada
- Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan.
| | - Michael A Menze
- Department of Biology, University of Louisville, Louisville, KY, USA
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3
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Sogame Y, Ogata M, Hakozaki S, Saito Y, Suzuki T, Saito R, Suizu F, Watanabe K. α,β-trehalose, an intracellular substance in resting cyst of colpodid ciliates as a key to environmental tolerances. Biochem Biophys Res Commun 2024; 716:149971. [PMID: 38697009 DOI: 10.1016/j.bbrc.2024.149971] [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: 02/27/2024] [Revised: 04/07/2024] [Accepted: 04/17/2024] [Indexed: 05/04/2024]
Abstract
α,α-trehalose is a well-known sugar that plays a key role in establishing tolerance to environmental stresses in many organisms, except unicellular eukaryotes. However, almost nothing is known about α,β-trehalose, including their synthesis, function, and even presence in living organisms. In this study, we identified α,β-trehalose in the resting cyst, a dormancy cell form characterized by extreme tolerance to environmental stresses, of the ciliated protist Colpoda cucullus, using high-performance liquid chromatography (HPLC), and a proton nuclear magnetic resonance (1H NMR). Gene expression analysis revealed that the expression of trehalose-6-phosphate synthase (TPS), glycosyltransferase (GT), alpha-amylase (AMY), and trehalose transporter 1 (TRET1), were up-regulated in encystment, while the expression of α-glucosidase 2 (AG2) and trehalase (TREH) was up-regulated in excystment. These results suggest that α,β-trehalose is synthesized during encystment process, while and contributes to extreme tolerances to environmental stressors, stored carbohydrates, and energy reserve during resting cyst and/or during excystment.
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Affiliation(s)
- Yoichiro Sogame
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Fukushima College, Iwaki, 970-8034, Japan.
| | - Makoto Ogata
- Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima, 960-1296, Japan
| | - Shuntaro Hakozaki
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Fukushima College, Iwaki, 970-8034, Japan
| | - Yuta Saito
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Fukushima College, Iwaki, 970-8034, Japan
| | - Tomohiro Suzuki
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, 321-8505, Japan
| | - Ryota Saito
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Fukushima College, Iwaki, 970-8034, Japan
| | - Futoshi Suizu
- Molecular Oncologic Pathology, Department of Pathology and Host-Defense, Faculty of Medicine, Kagawa University, Takamatsu, 761-0793, Japan
| | - Kozo Watanabe
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, 790-8577, Japan
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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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Cornette R, Indo HP, Iwata KI, Hagiwara-Komoda Y, Nakahara Y, Gusev O, Kikawada T, Okuda T, Majima HJ. Oxidative stress is an essential factor for the induction of anhydrobiosis in the desiccation-tolerant midge, Polypedilum vanderplanki (Diptera, Chironomidae). Mitochondrion 2023; 73:84-94. [PMID: 37956777 DOI: 10.1016/j.mito.2023.11.002] [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: 04/11/2023] [Revised: 10/06/2023] [Accepted: 11/09/2023] [Indexed: 11/15/2023]
Abstract
The sleeping chironomid (Polypedilum vanderplanki) is the only insect capable of surviving complete desiccation in an ametabolic state called anhydrobiosis. Here, we focused on the role of oxidative stress and we observed the production of reactive oxygen species (ROS) in desiccating larvae and in those exposed to salinity stress. Oxidative stress occurs to some extent in desiccating larvae, inducing carbonylation of proteins. Oxidative stress overcomes the antioxidant defenses of the larvae during the first hour following rehydration of anhydrobiotic larvae. It facilitates the oxidation of DNA and cell membrane lipids; however, these damages are quickly repaired after a few hours. In addition to its deleterious effects, we demonstrated that artificial exposure to oxidative stress could induce a response similar to desiccation stress, at the transcriptome and protein levels. Furthermore, the response of anhydrobiosis-related genes to desiccation and salinity stress was inhibited by antioxidant treatment. Thus, we conclude that oxidative stress is an essential trigger for inducing the expression of protective genes during the onset of anhydrobiosis in desiccating of P. vanderplanki larvae.
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Affiliation(s)
- Richard Cornette
- Anhydrobiosis Research Group, Division of Biomaterial Sciences, Institute of Agrobiological Sciences, NARO, 1-2 Owashi, Tsukuba, Ibaraki 305-8634 Japan.
| | - Hiroko P Indo
- Department of Oncology, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Ken-Ichi Iwata
- Anhydrobiosis Research Group, Division of Biomaterial Sciences, Institute of Agrobiological Sciences, NARO, 1-2 Owashi, Tsukuba, Ibaraki 305-8634 Japan
| | - Yuka Hagiwara-Komoda
- Anhydrobiosis Research Group, Division of Biomaterial Sciences, Institute of Agrobiological Sciences, NARO, 1-2 Owashi, Tsukuba, Ibaraki 305-8634 Japan; Department of Sustainable Agriculture, Rakuno Gakuen University, Ebetsu, Hokkaido 069-8501, Japan
| | - Yuichi Nakahara
- Anhydrobiosis Research Group, Division of Biomaterial Sciences, Institute of Agrobiological Sciences, NARO, 1-2 Owashi, Tsukuba, Ibaraki 305-8634 Japan; Rimco., Ltd, 12-75 Suzaki, Uruma, Okinawa 904-2234, Japan
| | - Oleg Gusev
- Intractable Disease Research Center, Juntendo University School of Medicine, Tokyo, Japan; Regulatory Genomics Research Center, Institute of Fundamental Biology and Medicine, Kazan Federal University, Kazan, 420008 Russia
| | - Takahiro Kikawada
- Anhydrobiosis Research Group, Division of Biomaterial Sciences, Institute of Agrobiological Sciences, NARO, 1-2 Owashi, Tsukuba, Ibaraki 305-8634 Japan
| | - Takashi Okuda
- Anhydrobiosis Research Group, Division of Biomaterial Sciences, Institute of Agrobiological Sciences, NARO, 1-2 Owashi, Tsukuba, Ibaraki 305-8634 Japan; NEMLI PROJECT LLC, 2756 Okijuku, Tsuchiura, Ibaraki, Japan
| | - Hideyuki J Majima
- Department of Oncology, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan; Biomedical Sciences, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand; Research Excellence Center for Innovation and Health Products (RECIHP), School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand.
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Deciphering the mechanism of anhydrobiosis in the entomopathogenic nematode Heterorhabditis indica through comparative transcriptomics. PLoS One 2022; 17:e0275342. [PMID: 36301967 PMCID: PMC9612587 DOI: 10.1371/journal.pone.0275342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 09/14/2022] [Indexed: 11/07/2022] Open
Abstract
The entomopathogenic nematode, Heterorhabditis indica, is a popular biocontrol agent of high commercial significance. It possesses tremendous genetic architecture to survive desiccation stress by undergoing anhydrobiosis to increase its lifespan-an attribute exploited in the formulation technology. The comparative transcriptome of unstressed and anhydrobiotic H. indica revealed several previously concealed metabolic events crucial for adapting towards the moisture stress. During the induction of anhydrobiosis in the infective juveniles (IJ), 1584 transcripts were upregulated and 340 downregulated. As a strategy towards anhydrobiotic survival, the IJ showed activation of several genes critical to antioxidant defense, detoxification pathways, signal transduction, unfolded protein response and molecular chaperones and ubiquitin-proteasome system. Differential expression of several genes involved in gluconeogenesis - β-oxidation of fatty acids, glyoxylate pathway; glyceroneogenesis; fatty acid biosynthesis; amino-acid metabolism - shikimate pathway, sachharopine pathway, kyneurine pathway, lysine biosynthesis; one-carbon metabolism-polyamine pathway, transsulfuration pathway, folate cycle, methionine cycle, nucleotide biosynthesis; mevalonate pathway; and glyceraldehyde-3-phosphate dehydrogenase were also observed. We report the role of shikimate pathway, sachharopine pathway and glyceroneogenesis in anhydrobiotes, and seven classes of repeat proteins, specifically in H. indica for the first time. These results provide insights into anhydrobiotic survival strategies which can be utilized to strengthen the development of novel formulations with enhanced and sustained shelf-life.
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Deciphering the Biological Enigma-Genomic Evolution Underlying Anhydrobiosis in the Phylum Tardigrada and the Chironomid Polypedilum vanderplanki. INSECTS 2022; 13:insects13060557. [PMID: 35735894 PMCID: PMC9224920 DOI: 10.3390/insects13060557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/13/2022] [Accepted: 06/17/2022] [Indexed: 02/04/2023]
Abstract
Anhydrobiosis, an ametabolic dehydrated state triggered by water loss, is observed in several invertebrate lineages. Anhydrobiotes revive when rehydrated, and seem not to suffer the ultimately lethal cell damage that results from severe loss of water in other organisms. Here, we review the biochemical and genomic evidence that has revealed the protectant molecules, repair systems, and maintenance pathways associated with anhydrobiosis. We then introduce two lineages in which anhydrobiosis has evolved independently: Tardigrada, where anhydrobiosis characterizes many species within the phylum, and the genus Polypedilum, where anhydrobiosis occurs in only two species. Finally, we discuss the complexity of the evolution of anhydrobiosis within invertebrates based on current knowledge, and propose perspectives to enhance the understanding of anhydrobiosis.
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Giovannini I, Corsetto PA, Altiero T, Montorfano G, Guidetti R, Rizzo AM, Rebecchi L. Antioxidant Response during the Kinetics of Anhydrobiosis in Two Eutardigrade Species. Life (Basel) 2022; 12:life12060817. [PMID: 35743848 PMCID: PMC9225123 DOI: 10.3390/life12060817] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/23/2022] [Accepted: 05/26/2022] [Indexed: 11/16/2022] Open
Abstract
Anhydrobiosis, a peculiar adaptive strategy existing in nature, is a reversible capability of organisms to tolerate a severe loss of their body water when their surrounding habitat is drying out. In the anhydrobiotic state, an organism lacks all dynamic features of living beings since an ongoing metabolism is absent. The depletion of water in the anhydrobiotic state increases the ionic concentration and the production of reactive oxygen species (ROS). An imbalance between the increased production of ROS and the limited action of antioxidant defences is a source of biomolecular damage and can lead to oxidative stress. The deleterious effects of oxidative stress were demonstrated in anhydrobiotic unicellular and multicellular organisms, which counteract the effects using efficient antioxidant machinery, mainly represented by ROS scavenger enzymes. To gain insights into the dynamics of antioxidant patterns during the kinetics of the anhydrobiosis of two tardigrade species, Paramacrobiotus spatialis and Acutuncus antarcticus, we investigated the activity of enzymatic antioxidants (catalase, superoxide dismutase, glutathione peroxidase, and glutathione reductase) and the amount of non-enzymatic antioxidants (glutathione) in the course of rehydration. In P. spatialis, the activity of catalase increases during dehydration and decreases during rehydration, whereas in A. antarcticus, the activity of superoxide dismutase decreases during desiccation and increases during rehydration. Genomic varieties, different habitats and geographical regions, different diets, and diverse evolutionary lineages may have led to the specialization of antioxidant strategies in the two species.
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Affiliation(s)
- Ilaria Giovannini
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (I.G.); (R.G.)
| | - Paola Antonia Corsetto
- Department of Pharmacological and Biomolecular Sciences, University of Milan, 20122 Milan, Italy; (P.A.C.); (G.M.)
| | - Tiziana Altiero
- Department of Education and Humanities, University of Modena and Reggio Emilia, 42121 Reggio Emilia, Italy;
| | - Gigliola Montorfano
- Department of Pharmacological and Biomolecular Sciences, University of Milan, 20122 Milan, Italy; (P.A.C.); (G.M.)
| | - Roberto Guidetti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (I.G.); (R.G.)
| | - Angela Maria Rizzo
- Department of Pharmacological and Biomolecular Sciences, University of Milan, 20122 Milan, Italy; (P.A.C.); (G.M.)
- Correspondence: (A.M.R.); (L.R.); Tel.: +39-02503-1777 (A.M.R.); +39-0592055553 (L.R.)
| | - Lorena Rebecchi
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (I.G.); (R.G.)
- Correspondence: (A.M.R.); (L.R.); Tel.: +39-02503-1777 (A.M.R.); +39-0592055553 (L.R.)
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Park K, Kwak IS. Multi-Level Gene Expression in Response to Environmental Stress in Aquatic Invertebrate Chironomids: Potential Applications in Water Quality Monitoring. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2021; 259:77-122. [PMID: 34661753 DOI: 10.1007/398_2021_79] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In freshwater ecosystems, aquatic invertebrates are influenced continuously by both physical stress and xenobiotics. Chironomids (Diptera; Chironomidae), or non-biting midges, are the most diverse and abundant invertebrates in freshwater habitats. They are a fundamental link in food chains of aquatic ecosystems. Chironomid larvae tolerate stress factors in their environments via various physiological processes. At the molecular level, environmental pollutants induce multi-level gene responses in Chironomus that regulate cellular protection through the activation of defense processes. This paper reviews literature on the transcriptional responses of biomarker genes to environmental stress in chironomids at the molecular level, in studies conducted from 1991 to 2020 (120 selected literatures of 374 results with the keywords "Chironomus and gene expression" by PubMed search tool). According to these studies, transcriptional responses in chironomids vary depending on the type of stress factor and defensive responses associated with antioxidant activity, the endocrine system, detoxification, homeostasis and stress response, energy metabolism, ribosomal machinery, apoptosis, DNA repair, and epigenetics. These data could provide a comprehensive overview of how Chironomus species respond to pollutants in aquatic environments. Furthermore, the transcriptomic data could facilitate the development of genetic tools for water quality and environmental monitoring based on resident chironomid species.
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Affiliation(s)
- Kiyun Park
- Fisheries Science Institute, Chonnam National University, Yeosu, South Korea
| | - Ihn-Sil Kwak
- Department of Ocean Integrated Science and Fisheries Science Institute, Chonnam National University, Yeosu, South Korea.
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10
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Combined metabolome and transcriptome analysis reveals key components of complete desiccation tolerance in an anhydrobiotic insect. Proc Natl Acad Sci U S A 2020; 117:19209-19220. [PMID: 32723826 PMCID: PMC7431039 DOI: 10.1073/pnas.2003650117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Anhydrobiosis is a reversible ametabolic state that occurs in response to severe desiccation. The largest anhydrobiotic animal known is the larva of the African chironomid Polypedilum vanderplanki. Here, we investigated how the metabolism of larvae changes during the desiccation–rehydration cycle and how simple biochemical processes determine viability of the chironomid. Major findings suggest that, in addition to its known anhydroprotectant role, trehalose acts as a major source of energy for rehydration. Citrate and adenosine monophosphate, accumulated in the dry state, allow rapid resumption of metabolism during the recovery phase. Finally, metabolic waste is stored as stable or nontoxic compounds such as allantoin, xanthurenic acid, or ophthalmic acid that may also act as antioxidants. Some organisms have evolved a survival strategy to withstand severe dehydration in an ametabolic state, called anhydrobiosis. The only known example of anhydrobiosis among insects is observed in larvae of the chironomid Polypedilum vanderplanki. Recent studies have led to a better understanding of the molecular mechanisms underlying anhydrobiosis and the action of specific protective proteins. However, gene regulation alone cannot explain the rapid biochemical reactions and independent metabolic changes that are expected to sustain anhydrobiosis. For this reason, we conducted a comprehensive comparative metabolome–transcriptome analysis in the larvae. We showed that anhydrobiotic larvae adopt a unique metabolic strategy to cope with complete desiccation and, in particular, to allow recovery after rehydration. We argue that trehalose, previously known for its anhydroprotective properties, plays additional vital roles, providing both the principal source of energy and also the restoration of antioxidant potential via the pentose phosphate pathway during the early stages of rehydration. Thus, larval viability might be directly dependent on the total amount of carbohydrate (glycogen and trehalose). Furthermore, in the anhydrobiotic state, energy is stored as accumulated citrate and adenosine monophosphate, allowing rapid reactivation of the citric acid cycle and mitochondrial activity immediately after rehydration, before glycolysis is fully functional. Other specific adaptations to desiccation include potential antioxidants (e.g., ophthalmic acid) and measures to avoid the accumulation of toxic waste metabolites by converting these to stable and inert counterparts (e.g., xanthurenic acid and allantoin). Finally, we confirmed that these metabolic adaptations correlate with unique organization and expression of the corresponding enzyme genes.
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11
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Yamada TG, Hiki Y, Hiroi NF, Shagimardanova E, Gusev O, Cornette R, Kikawada T, Funahashi A. Identification of a master transcription factor and a regulatory mechanism for desiccation tolerance in the anhydrobiotic cell line Pv11. PLoS One 2020; 15:e0230218. [PMID: 32191739 PMCID: PMC7082025 DOI: 10.1371/journal.pone.0230218] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 02/24/2020] [Indexed: 01/10/2023] Open
Abstract
Water is essential for living organisms. Terrestrial organisms are incessantly exposed to the stress of losing water, desiccation stress. Avoiding the mortality caused by desiccation stress, many organisms acquired molecular mechanisms to tolerate desiccation. Larvae of the African midge, Polypedilum vanderplanki, and its embryonic cell line Pv11 tolerate desiccation stress by entering an ametabolic state, anhydrobiosis, and return to active life after rehydration. The genes related to desiccation tolerance have been comprehensively analyzed, but transcriptional regulatory mechanisms to induce these genes after desiccation or rehydration remain unclear. Here, we comprehensively analyzed the gene regulatory network in Pv11 cells and compared it with that of Drosophila melanogaster, a desiccation sensitive species. We demonstrated that nuclear transcription factor Y subunit gamma-like, which is important for drought stress tolerance in plants, and its transcriptional regulation of downstream positive feedback loops have a pivotal role in regulating various anhydrobiosis-related genes. This study provides an initial insight into the systemic mechanism of desiccation tolerance.
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Affiliation(s)
- Takahiro G. Yamada
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan
| | - Yusuke Hiki
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan
| | - Noriko F. Hiroi
- Faculty of Pharmaceutical Science, Sanyo-Onoda City University, Sanyo-Onoda, Yamaguchi, Japan
| | | | - Oleg Gusev
- Kazan Federal University, Kazan, Russia
- RIKEN Cluster for Science, Technology and Innovation Hub, RIKEN, Yokohama, Kanagawa, Japan
| | - Richard Cornette
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Takahiro Kikawada
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
- * E-mail: (TK); (AF)
| | - Akira Funahashi
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan
- * E-mail: (TK); (AF)
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12
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Zhou Y, Li X, Katsuma S, Xu Y, Shi L, Shimada T, Wang H. Duplication and diversification of trehalase confers evolutionary advantages on lepidopteran insects. Mol Ecol 2019; 28:5282-5298. [PMID: 31674075 DOI: 10.1111/mec.15291] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 10/23/2019] [Indexed: 01/06/2023]
Abstract
Gene duplication provides a major source of new genes for evolutionary novelty and ecological adaptation. However, the maintenance of duplicated genes and their relevance to adaptive evolution has long been debated. Insect trehalase (Treh) plays key roles in energy metabolism, growth, and stress recovery. Here, we show that the duplication of Treh in Lepidoptera (butterflies and moths) is linked with their adaptation to various environmental stresses. Generally, two Treh genes are present in insects: Treh1 and Treh2. We report three distinct forms of Treh in lepidopteran insects, where Treh1 was duplicated into two gene clusters (Treh1a and Treh1b). These gene clusters differ in gene expression patterns, enzymatic properties, and subcellular localizations, suggesting that the enzymes probably underwent sub- and/or neofunctionalization in the lepidopteran insects. Interestingly, selective pressure analysis provided significant evidence of positive selection on duplicate Treh1b gene in lepidopteran insect lineages. Most positively selected sites were located in the alpha-helical region, and several sites were close to the trehalose binding and catalytic sites. Subcellular adaptation of duplicate Treh1b driven by positive selection appears to have occurred as a result of selected changes in specific sequences, allowing for rapid reprogramming of duplicated Treh during evolution. Our results suggest that gene duplication of Treh and subsequent functional diversification could increase the survival rate of lepidopteran insects through various regulations of intracellular trehalose levels, facilitating their adaptation to diverse habitats. This study provides evidence regarding the mechanism by which gene family expansion can contribute to species adaptation through gene duplication and subsequent functional diversification.
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Affiliation(s)
- Yanyan Zhou
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Xiaotong Li
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Susumu Katsuma
- Laboratory of Insect Genetics and Bioscience, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Yusong Xu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Liangen Shi
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Toru Shimada
- Laboratory of Insect Genetics and Bioscience, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Huabing Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, China
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13
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Schiffer PH, Danchin EGJ, Burnell AM, Creevey CJ, Wong S, Dix I, O'Mahony G, Culleton BA, Rancurel C, Stier G, Martínez-Salazar EA, Marconi A, Trivedi U, Kroiher M, Thorne MAS, Schierenberg E, Wiehe T, Blaxter M. Signatures of the Evolution of Parthenogenesis and Cryptobiosis in the Genomes of Panagrolaimid Nematodes. iScience 2019; 21:587-602. [PMID: 31759330 PMCID: PMC6889759 DOI: 10.1016/j.isci.2019.10.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 07/17/2019] [Accepted: 10/21/2019] [Indexed: 12/12/2022] Open
Abstract
Most animal species reproduce sexually and fully parthenogenetic lineages are usually short lived in evolution. Still, parthenogenesis may be advantageous as it avoids the cost of sex and permits colonization by single individuals. Panagrolaimid nematodes have colonized environments ranging from arid deserts to Arctic and Antarctic biomes. Many are obligatory meiotic parthenogens, and most have cryptobiotic abilities, being able to survive repeated cycles of complete desiccation and freezing. To identify systems that may contribute to these striking abilities, we sequenced and compared the genomes and transcriptomes of parthenogenetic and outcrossing panagrolaimid species, including cryptobionts and non-cryptobionts. The parthenogens are triploids, most likely originating through hybridization. Adaptation to cryptobiosis shaped the genomes of panagrolaimid nematodes and is associated with the expansion of gene families and signatures of selection on genes involved in cryptobiosis. All panagrolaimids have acquired genes through horizontal gene transfer, some of which are likely to contribute to cryptobiosis.
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Affiliation(s)
- Philipp H Schiffer
- CLOE, Department for Biosciences, University College London, London, UK; Zoologisches Institut, Universität zu Köln, 50674 Köln, Germany; Institut für Genetik, Universität zu Köln, 50674 Köln, Germany.
| | | | - Ann M Burnell
- Maynooth University Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
| | | | - Simon Wong
- Irish Centre for High-End Computing, Tower Building, Trinity Technology & Enterprise Campus, Grand Canal Quay, Dublin D02 HP83, Ireland
| | - Ilona Dix
- Maynooth University Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
| | - Georgina O'Mahony
- Maynooth University Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
| | - Bridget A Culleton
- Maynooth University Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland; Megazyme, Bray Business Park, Bray, Co. Wicklow A98 YV29, Ireland
| | | | - Gary Stier
- Zoologisches Institut, Universität zu Köln, 50674 Köln, Germany
| | - Elizabeth A Martínez-Salazar
- Unidad Académica de Ciencias Biológicas, Laboratorio de Colecciones Biológicas y Sistemática Molecular, Universidad Autónoma de Zacatecas, Zacatecas, México
| | - Aleksandra Marconi
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Urmi Trivedi
- Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Michael Kroiher
- Zoologisches Institut, Universität zu Köln, 50674 Köln, Germany
| | - Michael A S Thorne
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | | | - Thomas Wiehe
- Institut für Genetik, Universität zu Köln, 50674 Köln, Germany
| | - Mark Blaxter
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3FL, UK; Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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14
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Exploring dry storage as an alternative biobanking strategy inspired by Nature. Theriogenology 2019; 126:17-27. [DOI: 10.1016/j.theriogenology.2018.11.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/20/2018] [Accepted: 11/25/2018] [Indexed: 12/13/2022]
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15
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Kim J, Fukuda Y, Inoue T. Crystal structure of Kumaglobin: a hexacoordinated heme protein from an anhydrobiotic tardigrade,
Ramazzottius varieornatus. FEBS J 2018; 286:1287-1304. [DOI: 10.1111/febs.14713] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 09/28/2018] [Accepted: 11/29/2018] [Indexed: 01/05/2023]
Affiliation(s)
- JeeEun Kim
- Department of Applied Chemistry Graduate School of Engineering Osaka University Suita Japan
| | - Yohta Fukuda
- Department of Applied Chemistry Graduate School of Engineering Osaka University Suita Japan
| | - Tsuyoshi Inoue
- Department of Applied Chemistry Graduate School of Engineering Osaka University Suita Japan
- Graduate School of Pharmaceutical Science Suita Japan
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16
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Janis B, Belott C, Menze MA. Role of Intrinsic Disorder in Animal Desiccation Tolerance. Proteomics 2018; 18:e1800067. [DOI: 10.1002/pmic.201800067] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/10/2018] [Indexed: 11/12/2022]
Affiliation(s)
- Brett Janis
- Department of Biology University of Louisville Louisville KY 40292 USA
| | - Clinton Belott
- Department of Biology University of Louisville Louisville KY 40292 USA
| | - Michael A. Menze
- Department of Biology University of Louisville Louisville KY 40292 USA
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17
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Nesmelov A, Cornette R, Gusev O, Kikawada T. The Antioxidant System in the Anhydrobiotic Midge as an Essential, Adaptive Mechanism for Desiccation Survival. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1081:259-270. [PMID: 30288714 DOI: 10.1007/978-981-13-1244-1_14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
One of the major damaging factors for living organisms experiencing water insufficiency is oxidative stress. Loss of water causes a dramatic increase in the production of reactive oxygen species (ROS). Thus, the ability for some organisms to survive almost complete desiccation (called anhydrobiosis) is tightly related to the ability to overcome extraordinary oxidative stress. The most complex anhydrobiotic organism known is the larva of the chironomid Polypedilum vanderplanki. Its antioxidant system shows remarkable features, such as an expansion of antioxidant genes, their overexpression, as well as the absence or low expression of enzymes required for the synthesis of ascorbate and glutathione and their antioxidant function. In this chapter, we summarize existing data about the antioxidant system of this insect, which is able to cope with substantial oxidative damage, even in an intracellular environment that is severely disturbed due to water loss.
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Affiliation(s)
| | - Richard Cornette
- Molecular Biomimetics Research Unit, Institute of Agrobiological Sciences, NARO, Tsukuba, Japan
| | - Oleg Gusev
- Kazan Federal University, Kazan, Russia
- RIKEN Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | - Takahiro Kikawada
- Molecular Biomimetics Research Unit, Institute of Agrobiological Sciences, NARO, Tsukuba, Japan.
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
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18
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Involvement of Heat Shock Proteins in Invertebrate Anhydrobiosis. HEAT SHOCK PROTEINS AND STRESS 2018. [DOI: 10.1007/978-3-319-90725-3_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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19
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Evangelista CCS, Guidelli GV, Borges G, Araujo TF, Souza TAJD, Neves UPDC, Tunnacliffe A, Pereira TC. Multiple genes contribute to anhydrobiosis (tolerance to extreme desiccation) in the nematode Panagrolaimus superbus. Genet Mol Biol 2017; 40:790-802. [PMID: 29111563 PMCID: PMC5738622 DOI: 10.1590/1678-4685-gmb-2017-0030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 07/20/2017] [Indexed: 11/21/2022] Open
Abstract
The molecular basis of anhydrobiosis, the state of suspended animation entered by some species during extreme desiccation, is still poorly understood despite a number of transcriptome and proteome studies. We therefore conducted functional screening by RNA interference (RNAi) for genes involved in anhydrobiosis in the holo-anhydrobiotic nematode Panagrolaimus superbus. A new method of survival analysis, based on staining, and proof-of-principle RNAi experiments confirmed a role for genes involved in oxidative stress tolerance, while a novel medium-scale RNAi workflow identified a further 40 anhydrobiosis-associated genes, including several involved in proteostasis, DNA repair and signal transduction pathways. This suggests that multiple genes contribute to anhydrobiosis in P. superbus.
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Affiliation(s)
- Cláudia Carolina Silva Evangelista
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil.,Programa de Pós-Graduação em Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Giovanna Vieira Guidelli
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Gustavo Borges
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Thais Fenz Araujo
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Tiago Alves Jorge de Souza
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil.,Programa de Pós-Graduação em Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Ubiraci Pereira da Costa Neves
- Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Alan Tunnacliffe
- Deptartment of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Tiago Campos Pereira
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil.,Programa de Pós-Graduação em Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil
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20
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Sogame Y, Kikawada T. Current findings on the molecular mechanisms underlying anhydrobiosis in Polypedilum vanderplanki. CURRENT OPINION IN INSECT SCIENCE 2017; 19:16-21. [PMID: 28521938 DOI: 10.1016/j.cois.2016.10.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 10/20/2016] [Accepted: 10/24/2016] [Indexed: 06/07/2023]
Abstract
Water is an essential molecule for living organisms. However, some organisms can survive in environments which receive no rainfall for months and in which ordinary life cannot survive. How do they endure the extended dry season? The sleeping chironomid Polypedilum vanderplanki, which inhabits sub-Saharan Africa, exhibits extreme tolerance to complete desiccation, a process termed anhydrobiosis. During anhydrobiosis these organisms dry up and entirely shut down their metabolism. However, when the dried larvae are immersed in water, their metabolism is resumed. Interestingly, anhydrobiosis allows these organisms to tolerate not only desiccation but also high and low temperatures, the absence of oxygen, radiation, and chemical stresses. Here, we describe the mechanisms by which P. vanderplanki achieves anhydrobiosis revealed in our recent research.
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Affiliation(s)
- Yoichiro Sogame
- Institute of Agrobiological Sciences, National Institute of Agriculture and Food Research Organization, Japan
| | - Takahiro Kikawada
- Institute of Agrobiological Sciences, National Institute of Agriculture and Food Research Organization, Japan; Institute of Fundamental Medicine and Biology, Kazan Federal University, Russia; Graduate School of Frontier Sciences, University of Tokyo, Japan.
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21
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Tsubota T, Yamamoto K, Mita K, Sezutsu H. Gene expression analysis in the larval silk gland of the eri silkworm Samia ricini. INSECT SCIENCE 2016; 23:791-804. [PMID: 26178074 DOI: 10.1111/1744-7917.12251] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/23/2015] [Indexed: 06/04/2023]
Abstract
Insects produce silk for a range of purposes. In the Lepidoptera, silk is utilized as a material for cocoon production and serves to protect larvae from adverse environmental conditions or predators. Species in the Saturniidae family produce an especially wide variety of cocoons, for example, large, golden colored cocoons and those with many small holes. Although gene expression in the silk gland of the domestic silkworm (Bombyx mori L.) has been extensively studied, considerably fewer investigations have focused on members of the saturniid family. Here, we established expression sequence tags from the silk gland of the eri silkworm (Samia ricini), a saturniid species, and used these to analyze gene expression. Although we identified the fibroin heavy chain gene in the established library, genes for other major silk proteins, such as fibroin light chain and fibrohexamerin, were absent. This finding is consistent with previous reports that these latter proteins are lacking in saturniid silk. Recently, a series of fibrohexamerin-like genes were identified in the Bombyx genome. We used this information to conduct a detailed analysis of the library established here. This analysis identified putative homologues of these genes. We also found several genes encoding small silk protein molecules that are also present in the silk of other Lepidoptera. Gene expression patterns were compared between eri and domestic silkworm, and both conserved and nonconserved expression patterns were identified for the tested genes. Such differential gene expression might be one of the major causes of the differences in silk properties between these species. We believe that our study can be of value as a basic catalogue for silk gland gene expression, which will yield to the further understanding of silk evolution.
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Affiliation(s)
- Takuya Tsubota
- Transgenic Silkworm Research Unit, National Institute of Agrobiological Sciences, Ibaraki, 305-8634, Japan
| | - Kimiko Yamamoto
- Insect Genome Research Unit, National Institute of Agrobiological Sciences, Ibaraki, 305-8634, Japan
| | - Kazuei Mita
- Insect Genome Research Unit, National Institute of Agrobiological Sciences, Ibaraki, 305-8634, Japan
| | - Hideki Sezutsu
- Transgenic Silkworm Research Unit, National Institute of Agrobiological Sciences, Ibaraki, 305-8634, Japan
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22
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Ryabova A, Mukae K, Cherkasov A, Cornette R, Shagimardanova E, Sakashita T, Okuda T, Kikawada T, Gusev O. Genetic background of enhanced radioresistance in an anhydrobiotic insect: transcriptional response to ionizing radiations and desiccation. Extremophiles 2016; 21:109-120. [PMID: 27807620 DOI: 10.1007/s00792-016-0888-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/20/2016] [Indexed: 01/02/2023]
Abstract
It is assumed that resistance to ionizing radiation, as well as cross-resistance to other abiotic stresses, is a side effect of the evolutionary-based adaptation of anhydrobiotic animals to dehydration stress. Larvae of Polypedilum vanderplanki can withstand prolonged desiccation as well as high doses of ionizing radiation exposure. For a further understanding of the mechanisms of cross-tolerance to both types of stress exposure, we profiled genome-wide mRNA expression patterns using microarray techniques on the chironomid larvae collected at different stages of desiccation and after exposure to two types of ionizing radiation-70 Gy of high-linear energy transfer (LET) ions (4He) and the same dose of low-LET radiation (gamma rays). In expression profiles, a wide transcriptional response to desiccation stress that much exceeded the amount of up-regulated transcripts to irradiation exposure was observed. An extensive group of coincidently up-regulated overlapped transcripts in response to desiccation and ionizing radiation was found. Among this, overlapped set of transcripts was indicated anhydrobiosis-related genes: antioxidants, late embryogenesis abundant (LEA) proteins, and heat-shock proteins. The most overexpressed group was that of protein-L-isoaspartate/D-aspartate O-methyltransferase (PIMT), while probes, corresponding to LEA proteins, were the most represented. Performed functional analysis showed strongly enriched gene ontology terms associated with protein methylation. In addition, active processes of DNA repair were detected. We assume that the cross-tolerance of the sleeping chironomid to both desiccation and irradiation exposure comes from a complex mechanism of adaptation to anhydrobiosis.
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Affiliation(s)
- Alina Ryabova
- Institute of Fundamental Biology and Medicine, Kazan Federal University, Kazan, Russia
| | - Kyosuke Mukae
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan.,Anhydrobiosis Research Group, Institute of Agrobiological Sciences, NARO, Tsukuba, Japan
| | - Alexander Cherkasov
- Institute of Fundamental Biology and Medicine, Kazan Federal University, Kazan, Russia
| | - Richard Cornette
- Anhydrobiosis Research Group, Institute of Agrobiological Sciences, NARO, Tsukuba, Japan
| | - Elena Shagimardanova
- Institute of Fundamental Biology and Medicine, Kazan Federal University, Kazan, Russia
| | - Tetsuya Sakashita
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology, Takasaki, Japan
| | - Takashi Okuda
- Anhydrobiosis Research Group, Institute of Agrobiological Sciences, NARO, Tsukuba, Japan
| | - Takahiro Kikawada
- Anhydrobiosis Research Group, Institute of Agrobiological Sciences, NARO, Tsukuba, Japan. .,Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.
| | - Oleg Gusev
- Institute of Fundamental Biology and Medicine, Kazan Federal University, Kazan, Russia. .,Anhydrobiosis Research Group, Institute of Agrobiological Sciences, NARO, Tsukuba, Japan. .,Center for Life Science Technologies, RIKEN, Yokohama, Japan. .,RIKEN Innovation Center, RIKEN, Yokohama, Japan.
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23
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Sogame Y, Okada J, Kikuta S, Miyata Y, Cornette R, Gusev O, Kikawada T. Establishment of gene transfer and gene silencing methods in a desiccation-tolerant cell line, Pv11. Extremophiles 2016; 21:65-72. [PMID: 27757696 DOI: 10.1007/s00792-016-0880-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/04/2016] [Indexed: 11/26/2022]
Abstract
Larvae of the African midge Polypedilum vanderplanki show extreme desiccation tolerance, known as anhydrobiosis. Recently, the cultured cell line Pv11 was derived from this species; Pv11 cells can be preserved in the dry state for over 6 months and retain their proliferation potential. Here, we attempted to expand the use of Pv11 cells as a model to investigate the mechanisms underlying anhydrobiosis in P. vanderplanki. A newly developed vector comprising a constitutive promoter for the PvGapdh gene allowed the expression of exogenous proteins in Pv11 cells. Using this vector, a stable Pv11 cell line expressing green fluorescence protein (GFP) was established and retained desiccation tolerance. Gene silencing with GFP-specific siRNAs significantly suppressed GFP expression to approximately 7.5-34.6% of that in the non-siRNA-transfected GFP stable line. Establishment of these functional assays will enable Pv11 cells to be utilized as an effective tool to investigate the molecular mechanisms underlying anhydrobiosis.
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Affiliation(s)
- Yoichiro Sogame
- Anhydrobiosis Research Group, Molecular Biomimetics Research Unit, Institute of Agrobiological Sciences, NARO (NIAS), Tsukuba, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Jun Okada
- Anhydrobiosis Research Group, Molecular Biomimetics Research Unit, Institute of Agrobiological Sciences, NARO (NIAS), Tsukuba, Japan
| | - Shingo Kikuta
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Yugo Miyata
- Anhydrobiosis Research Group, Molecular Biomimetics Research Unit, Institute of Agrobiological Sciences, NARO (NIAS), Tsukuba, Japan
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama, Japan
| | - Richard Cornette
- Anhydrobiosis Research Group, Molecular Biomimetics Research Unit, Institute of Agrobiological Sciences, NARO (NIAS), Tsukuba, Japan
| | - Oleg Gusev
- Institute of Fundamental Biology and Medicine, Kazan Federal University, Kazan, Russia
- Division of Genomic Technologies, Center for Life Science Technologies, RIKEN, Yokohama, Japan
- Preventive Medicine and Diagnosis Innovation Program, Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | - Takahiro Kikawada
- Anhydrobiosis Research Group, Molecular Biomimetics Research Unit, Institute of Agrobiological Sciences, NARO (NIAS), Tsukuba, Japan.
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.
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24
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How widespread is preparation for oxidative stress in the animal kingdom? Comp Biochem Physiol A Mol Integr Physiol 2016; 200:64-78. [DOI: 10.1016/j.cbpa.2016.01.023] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/26/2016] [Accepted: 01/29/2016] [Indexed: 11/19/2022]
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25
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Air-dried cells from the anhydrobiotic insect, Polypedilum vanderplanki, can survive long term preservation at room temperature and retain proliferation potential after rehydration. Cryobiology 2016; 73:93-8. [PMID: 27207249 DOI: 10.1016/j.cryobiol.2016.05.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 04/28/2016] [Accepted: 05/16/2016] [Indexed: 12/31/2022]
Abstract
Pv11, a cell line derived from the anhydrobiotic insect, Polypedilum vanderplanki, was preserved in a dry form (only 6% residual moisture) at room temperature for up to 251 days and restarted proliferating after rehydration. A previous study already reported survival of Pv11 cells after desiccation, but without subsequent proliferation. Here, the protocol was improved to increase survival and achieve proliferation of Pv11 cells after dry storage. The method basically included preincubation, desiccation and rehydration processes and each step was investigated. So far, preincubation in a 600 mM trehalose solution for 48 h before dehydration was the most favourable preconditioning to achieve successful dry preservation of Pv11 cells, allowing about 16% of survival after rehydration and subsequent cell proliferation. Although the simple air-dry method established for Pv11 cells here was not applicable for successful dry-preservation of other insect cell lines, Pv11 is the first dry-preservable animal cell line and will surely contribute not only to basic but also applied sciences.
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Thorat L, Mani KP, Thangaraj P, Chatterjee S, Nath BB. Downregulation of dTps1 in Drosophila melanogaster larvae confirms involvement of trehalose in redox regulation following desiccation. Cell Stress Chaperones 2016; 21:285-94. [PMID: 26577464 PMCID: PMC4786531 DOI: 10.1007/s12192-015-0658-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/28/2015] [Accepted: 11/03/2015] [Indexed: 02/01/2023] Open
Abstract
As a survival strategy to environmental water deficits, desiccation-tolerant organisms are commonly known for their ability to recruit stress-protective biomolecules such as trehalose. We have previously reported the pivotal role of trehalose in larval desiccation tolerance in Drosophila melanogaster. Trehalose has emerged as a versatile molecule, serving mainly as energy source in insects and also being a stress protectant. While several recent reports have revealed the unconventional role of trehalose in scavenging reactive oxygen species in yeast and plants, this aspect has not received much attention in animals. We examined the status of desiccation-induced generation of reactive oxygen species in D. melanogaster larvae and the possible involvement of trehalose in ameliorating the harmful consequences thereof. Insect trehalose synthesis is governed by the enzyme trehalose 6-phosphate synthase 1 (TPS1). Using the ubiquitous da-GAL4-driven expression of the dTps1-RNAi transgene, we generated dTps1-downregulated Drosophila larvae possessing depleted levels of dTps1 transcripts. This resulted in the inability of the larvae for trehalose synthesis, thereby allowing us to elucidate the significance of trehalose in the regulation of desiccation-responsive redox homeostasis. Furthermore, the results from molecular genetics studies, biochemical assays, electron spin resonance analyses and a simple, non-invasive method of whole larval live imaging suggested that trehalose in collaboration with superoxide dismutase (SOD) is involved in the maintenance of redox state in D. melanogaster.
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Affiliation(s)
- Leena Thorat
- UGC-Centre for Advanced Studies, Stress Biology Research Laboratory, Department of Zoology, Savitribai Phule Pune University, Pune, 411007, India
| | - Krishna-Priya Mani
- AU-KBC Research Centre, MIT Campus of Anna University, Chennai, Tamil Nadu, 600044, India
| | - Pradeep Thangaraj
- AU-KBC Research Centre, MIT Campus of Anna University, Chennai, Tamil Nadu, 600044, India
| | - Suvro Chatterjee
- AU-KBC Research Centre, MIT Campus of Anna University, Chennai, Tamil Nadu, 600044, India
- Department of Biotechnology, Anna University, Chennai, Tamil Nadu, 600044, India
| | - Bimalendu B Nath
- UGC-Centre for Advanced Studies, Stress Biology Research Laboratory, Department of Zoology, Savitribai Phule Pune University, Pune, 411007, India.
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Deviatiiarov R, Kikawada T, Gusev O. The complete mitochondrial genome of an anhydrobiotic midge Polypedilum vanderplanki (Chironomidae, Diptera). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:218-220. [PMID: 26711887 DOI: 10.3109/19401736.2015.1115849] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this work, we describe a complete mitochondrial genome of chironomid Polypedilum vanderplanki. In spite of unique ecology of this species, the larvae are able to survive years of complete desiccation; the circular mitochondrial genome keeps basic structure and consists of 13 protein-coding genes, 2 rRNA, and 22 tRNA genes, and has a total length of 16 060 bp. Low GC level, small regulatory region, and unusually high number and length of non-coding spacers are the main determined features.
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Affiliation(s)
- Ruslan Deviatiiarov
- a Institute of Fundamental Medicine and Biology, Kazan Federal University , Kazan , Russia.,b Division of Genomic Technologies , RIKEN Center for Life Science Technologies , Yokohama , Kanagawa , Japan
| | - Takahiro Kikawada
- c National Institute of Agrobiological Sciences (NIAS) , Tsukuba , Japan
| | - Oleg Gusev
- a Institute of Fundamental Medicine and Biology, Kazan Federal University , Kazan , Russia.,b Division of Genomic Technologies , RIKEN Center for Life Science Technologies , Yokohama , Kanagawa , Japan.,d Preventive Medicine & Diagnosis Innovation Program , RIKEN Center of Life Science Technologies , Yokohama , Kanagawa , Japan
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Cornette R, Gusev O, Nakahara Y, Shimura S, Kikawada T, Okuda T. Chironomid Midges (Diptera, Chironomidae) Show Extremely Small Genome Sizes. Zoolog Sci 2015; 32:248-54. [DOI: 10.2108/zs140166] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Petrova NA, Cornette R, Shimura S, Gusev OA, Pemba D, Kikawada T, Zhirov SV, Okuda T. Karyotypical characteristics of two allopatric African populations of anhydrobiotic Polypedilum Kieffer, 1912 (Diptera, Chironomidae) originating from Nigeria and Malawi. COMPARATIVE CYTOGENETICS 2015; 9:173-88. [PMID: 26140160 PMCID: PMC4488965 DOI: 10.3897/compcytogen.v9i2.9104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/10/2015] [Indexed: 05/26/2023]
Abstract
The African chironomid Polypedilumvanderplanki Hinton, 1951 is the only chironomid able to withstand almost complete desiccation in an ametabolic state known as anhydrobiosis. The karyotypes of two allopatric populations of this anhydrobiotic chironomid, one from Nigeria and another from Malawi, were described according to the polytene giant chromosomes. The karyotype from the Nigerian population was presented as the reference chromosome map for Polypedilumvanderplanki. Both populations, Nigerian and Malawian, showed the same number of chromosomes (2n=8), but important differences were found in the band sequences of polytene chromosomes, and in the number and the arrangement of active regions between the two populations. Such important differences raise the possibility that the Malawian population could constitute a distinct new species of anhydrobiotic chironomid.
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Affiliation(s)
- Ninel A Petrova
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, St. Petersburg 199034, Russia
| | - Richard Cornette
- National Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Sachiko Shimura
- National Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Oleg A Gusev
- National Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634, Japan ; Institute of Fundamental Biology and Medicine, Kazan Federal University, Kremlevskaya ul., 18, Kazan, 420008 Russia
| | - Dylo Pemba
- Biological Sciences Department Chancellor college, University of Malawi, P.O.Box 280, Zomba, Malawi
| | - Takahiro Kikawada
- National Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Sergey V Zhirov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, St. Petersburg 199034, Russia
| | - Takashi Okuda
- National Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634, Japan
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Toxopeus J, Warner AH, MacRae TH. Group 1 LEA proteins contribute to the desiccation and freeze tolerance of Artemia franciscana embryos during diapause. Cell Stress Chaperones 2014; 19:939-48. [PMID: 24846336 PMCID: PMC4389855 DOI: 10.1007/s12192-014-0518-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/08/2014] [Accepted: 05/09/2014] [Indexed: 11/26/2022] Open
Abstract
Water loss either by desiccation or freezing causes multiple forms of cellular damage. The encysted embryos (cysts) of the crustacean Artemia franciscana have several molecular mechanisms to enable anhydrobiosis-life without water-during diapause. To better understand how cysts survive reduced hydration, group 1 late embryogenesis abundant (LEA) proteins, hydrophilic unstructured proteins that accumulate in the stress-tolerant cysts of A. franciscana, were knocked down using RNA interference (RNAi). Embryos lacking group 1 LEA proteins showed significantly lower survival than control embryos after desiccation and freezing, or freezing alone, demonstrating a role for group 1 LEA proteins in A. franciscana tolerance of low water conditions. In contrast, regardless of group 1 LEA protein presence, cysts responded similarly to hydrogen peroxide (H2O2) exposure, indicating little to no function for these proteins in diapause termination. This is the first in vivo study of group 1 LEA proteins in an animal and it contributes to the fundamental understanding of these proteins. Knowing how LEA proteins protect A. franciscana cysts from desiccation and freezing may have applied significance in aquaculture, where Artemia is an important feed source, and in the cryopreservation of cells for therapeutic applications.
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Affiliation(s)
- Jantina Toxopeus
- />Department of Biology, Dalhousie University, 1355 Oxford St., Halifax, NS B3H 4R2 Canada
| | - Alden H. Warner
- />Department of Biological Sciences, University of Windsor, Windsor, ON N9B 3P4 Canada
| | - Thomas H. MacRae
- />Department of Biology, Dalhousie University, 1355 Oxford St., Halifax, NS B3H 4R2 Canada
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Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge. Nat Commun 2014; 5:4784. [PMID: 25216354 PMCID: PMC4175575 DOI: 10.1038/ncomms5784] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 07/23/2014] [Indexed: 11/24/2022] Open
Abstract
Anhydrobiosis represents an extreme example of tolerance adaptation to water loss, where an organism can survive in an ametabolic state until water returns. Here we report the first comparative analysis examining the genomic background of extreme desiccation tolerance, which is exclusively found in larvae of the only anhydrobiotic insect, Polypedilum vanderplanki. We compare the genomes of P. vanderplanki and a congeneric desiccation-sensitive midge P. nubifer. We determine that the genome of the anhydrobiotic species specifically contains clusters of multi-copy genes with products that act as molecular shields. In addition, the genome possesses several groups of genes with high similarity to known protective proteins. However, these genes are located in distinct paralogous clusters in the genome apart from the classical orthologues of the corresponding genes shared by both chironomids and other insects. The transcripts of these clustered paralogues contribute to a large majority of the mRNA pool in the desiccating larvae and most likely define successful anhydrobiosis. Comparison of expression patterns of orthologues between two chironomid species provides evidence for the existence of desiccation-specific gene expression systems in P. vanderplanki. The African chironomid midge, Polypedilum vanderplanki, is able to withstand extreme desiccation. Here the authors sequence the genomes of a desiccation-tolerant and desiccation-sensitive species of chironomid midge and pinpoint genes that may have a role in conferring resistance to desiccation.
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Compact genome of the Antarctic midge is likely an adaptation to an extreme environment. Nat Commun 2014; 5:4611. [PMID: 25118180 PMCID: PMC4164542 DOI: 10.1038/ncomms5611] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 07/08/2014] [Indexed: 12/30/2022] Open
Abstract
The midge, Belgica antarctica, is the only insect endemic to Antarctica, and thus it offers a powerful model for probing responses to extreme temperatures, freeze tolerance, dehydration, osmotic stress, ultraviolet radiation and other forms of environmental stress. Here we present the first genome assembly of an extremophile, the first dipteran in the family Chironomidae, and the first Antarctic eukaryote to be sequenced. At 99 megabases, B. antarctica has the smallest insect genome sequenced thus far. Although it has a similar number of genes as other Diptera, the midge genome has very low repeat density and a reduction in intron length. Environmental extremes appear to constrain genome architecture, not gene content. The few transposable elements present are mainly ancient, inactive retroelements. An abundance of genes associated with development, regulation of metabolism and responses to external stimuli may reflect adaptations for surviving in this harsh environment.
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Wang C, Grohme MA, Mali B, Schill RO, Frohme M. Towards decrypting cryptobiosis--analyzing anhydrobiosis in the tardigrade Milnesium tardigradum using transcriptome sequencing. PLoS One 2014; 9:e92663. [PMID: 24651535 PMCID: PMC3961413 DOI: 10.1371/journal.pone.0092663] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 02/25/2014] [Indexed: 11/18/2022] Open
Abstract
Background Many tardigrade species are capable of anhydrobiosis; however, mechanisms underlying their extreme desiccation resistance remain elusive. This study attempts to quantify the anhydrobiotic transcriptome of the limno-terrestrial tardigrade Milnesium tardigradum. Results A prerequisite for differential gene expression analysis was the generation of a reference hybrid transcriptome atlas by assembly of Sanger, 454 and Illumina sequence data. The final assembly yielded 79,064 contigs (>100 bp) after removal of ribosomal RNAs. Around 50% of them could be annotated by SwissProt and NCBI non-redundant protein sequences. Analysis using CEGMA predicted 232 (93.5%) out of the 248 highly conserved eukaryotic genes in the assembly. We used this reference transcriptome for mapping and quantifying the expression of transcripts regulated under anhdydrobiosis in a time-series during dehydration and rehydration. 834 of the transcripts were found to be differentially expressed in a single stage (dehydration/inactive tun/rehydration) and 184 were overlapping in two stages while 74 were differentially expressed in all three stages. We have found interesting patterns of differentially expressed transcripts that are in concordance with a common hypothesis of metabolic shutdown during anhydrobiosis. This included down-regulation of several proteins of the DNA replication and translational machinery and protein degradation. Among others, heat shock proteins Hsp27 and Hsp30c were up-regulated in response to dehydration and rehydration. In addition, we observed up-regulation of ployubiquitin-B upon rehydration together with a higher expression level of several DNA repair proteins during rehydration than in the dehydration stage. Conclusions Most of the transcripts identified to be differentially expressed had distinct cellular function. Our data suggest a concerted molecular adaptation in M. tardigradum that permits extreme forms of ametabolic states such as anhydrobiosis. It is temping to surmise that the desiccation tolerance of tradigrades can be achieved by a constitutive cellular protection system, probably in conjunction with other mechanisms such as rehydration-induced cellular repair.
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Affiliation(s)
- Chong Wang
- Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
- * E-mail:
| | - Markus A. Grohme
- Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
| | - Brahim Mali
- Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
| | - Ralph O. Schill
- Biological Institute, Zoology, University of Stuttgart, Stuttgart, Germany
| | - Marcus Frohme
- Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
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Hatanaka R, Hagiwara-Komoda Y, Furuki T, Kanamori Y, Fujita M, Cornette R, Sakurai M, Okuda T, Kikawada T. An abundant LEA protein in the anhydrobiotic midge, PvLEA4, acts as a molecular shield by limiting growth of aggregating protein particles. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 43:1055-1067. [PMID: 23978448 DOI: 10.1016/j.ibmb.2013.08.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 08/12/2013] [Accepted: 08/12/2013] [Indexed: 06/02/2023]
Abstract
LEA proteins are found in anhydrobiotes and are thought to be associated with the acquisition of desiccation tolerance. The sleeping chironomid Polypedilum vanderplanki, which can survive in an almost completely desiccated state throughout the larval stage, accumulates LEA proteins in response to desiccation and high salinity conditions. However, the biochemical functions of these proteins remain unclear. Here, we report the characterization of a novel chironomid LEA protein, PvLEA4, which is the most highly accumulated LEA protein in desiccated larvae. Cytoplasmic-soluble PvLEA4 showed many typical characteristics of group 3 LEA proteins (G3LEAs), such as desiccation-inducible accumulation, high hydrophilicity, folding into α-helices on drying, and the ability to reduce aggregation of dehydration-sensitive proteins. This last property of LEA proteins has been termed molecular shield function. To further investigate the molecular shield activity of PvLEA4, we introduced two distinct methods, turbidity measurement and dynamic light scattering (DLS). Turbidity measurements demonstrated that both PvLEA4, and BSA as a positive control, reduced aggregation in α-casein subjected to desiccation and rehydration. However, DLS experiments showed that a small amount of BSA relative to α-casein increased aggregate particle size, whereas PvLEA4 decreased particle size in a dose-dependent manner. Trehalose, which is the main heamolymph sugar in most insects but also a protectant as a chemical chaperone in the sleeping chironomid, has less effect on the limitation of aggregate formation. This analysis suggests that molecular shield proteins function by limiting the growth of protein aggregates during drying and that PvLEA4 counteracts protein aggregation in the desiccation-tolerant larvae of the sleeping chironomid.
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Affiliation(s)
- Rie Hatanaka
- Insect Mimetics Research Unit, Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8634, Japan
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Gene expression changes governing extreme dehydration tolerance in an Antarctic insect. Proc Natl Acad Sci U S A 2012. [PMID: 23197828 DOI: 10.1073/pnas.1218661109] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Among terrestrial organisms, arthropods are especially susceptible to dehydration, given their small body size and high surface area to volume ratio. This challenge is particularly acute for polar arthropods that face near-constant desiccating conditions, as water is frozen and thus unavailable for much of the year. The molecular mechanisms that govern extreme dehydration tolerance in insects remain largely undefined. In this study, we used RNA sequencing to quantify transcriptional mechanisms of extreme dehydration tolerance in the Antarctic midge, Belgica antarctica, the world's southernmost insect and only insect endemic to Antarctica. Larvae of B. antarctica are remarkably tolerant of dehydration, surviving losses up to 70% of their body water. Gene expression changes in response to dehydration indicated up-regulation of cellular recycling pathways including the ubiquitin-mediated proteasome and autophagy, with concurrent down-regulation of genes involved in general metabolism and ATP production. Metabolomics results revealed shifts in metabolite pools that correlated closely with changes in gene expression, indicating that coordinated changes in gene expression and metabolism are a critical component of the dehydration response. Finally, using comparative genomics, we compared our gene expression results with a transcriptomic dataset for the Arctic collembolan, Megaphorura arctica. Although B. antarctica and M. arctica are adapted to similar environments, our analysis indicated very little overlap in expression profiles between these two arthropods. Whereas several orthologous genes showed similar expression patterns, transcriptional changes were largely species specific, indicating these polar arthropods have developed distinct transcriptional mechanisms to cope with similar desiccating conditions.
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GAPDH in anesthesia. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 985:269-91. [PMID: 22851453 DOI: 10.1007/978-94-007-4716-6_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Thus far, two independent laboratories have shown that inhaled anesthetics directly affect GAPDH structure and function. Additionally, it has been demonstrated that GAPDH normally regulates the function of GABA (type A) receptor. In light of these literature observations and some less direct findings, there is a discussion on the putative role of GAPDH in anesthesia. The binding site of inhaled anesthetics is described from literature reports on model proteins, such as human serum albumin and apoferritin. In addition to the expected hydrophobic residues that occupy the binding cavity, there are hydrophilic residues at or in very close proximity to the site of anesthetic binding. A putative binding site in the bacterial analog of the human GABA (type A) receptor is also described. Additionally, GAPDH may also play a role in anesthetic preconditioning, a phenomenon that confers protection of cells and tissues to future challenges by noxious stimuli. The central thesis regarding this paradigm is that inhaled anesthetics evoke an intra-molecular protein dehydration that is recognized by the cell, eliciting a very specific burst of chaperone gene expression. The chaperones that are implicated are associated with conferring protection against dehydration-induced protein aggregation.
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Storey KB, Storey JM. Insect cold hardiness: metabolic, gene, and protein adaptation1This review is part of a virtual symposium on recent advances in understanding a variety of complex regulatory processes in insect physiology and endocrinology, including development, metabolism, cold hardiness, food intake and digestion, and diuresis, through the use of omics technologies in the postgenomic era. CAN J ZOOL 2012. [DOI: 10.1139/z2012-011] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Winter survival for thousands of species of insects relies on adaptive strategies for cold hardiness. Two basic mechanisms are widely used (freeze avoidance by deep supercooling and freeze tolerance where insects endure ice formation in extracellular fluid spaces), whereas additional strategies (cryoprotective dehydration, vitrification) are also used by some polar species in extreme environments. This review assesses recent research on the biochemical adaptations that support insect cold hardiness. We examine new information about the regulation of cryoprotectant biosynthesis, mechanisms of metabolic rate depression, role of aquaporins in water and glycerol movement, and cell preservation strategies (chaperones, antioxidant defenses and metal binding proteins, mitochondrial suppression) for survival over the winter. We also review the new information coming from the use of genomic and proteomic screening methods that are greatly widening the scope for discovery of genes and proteins that support winter survival.
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Affiliation(s)
- Kenneth B. Storey
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Janet M. Storey
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
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Ferns JE, Theisen CS, Fibuch EE, Seidler NW. Protection against protein aggregation by alpha-crystallin as a mechanism of preconditioning. Neurochem Res 2011; 37:244-52. [PMID: 21984199 DOI: 10.1007/s11064-011-0601-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 09/01/2011] [Accepted: 09/09/2011] [Indexed: 11/29/2022]
Abstract
Anesthetic preconditioning occurs when cells previously exposed to inhaled anesthetics are protected against subsequent injury. We hypothesize that inhaled anesthetics may cause slight protein misfolding that involves site-specific dehydration, stimulating cytoprotective mechanisms. Human neuroblastoma cells were exposed to ethanol (as the dehydration agent) followed by quantitative analysis of the expression of five heat shock genes: DNAJC5G, CRYAA, HSPB2, HSF4 and HSF2. There was an ethanol-induced upregulation of all genes except HSF4, similar to previous observations using isoflurane. CRYAA (the gene for alphaA-crystallin) exhibited a 23.19 and 17.15-fold increase at 24 and 48 h post ethanol exposure, respectively. Additionally, we exposed glyceraldehyde 3-phosphate dehydrogenase to ethanol, which altered oligomeric subspecies and caused protein aggregation in a concentration-dependent manner. Ethanol-mediated dehydration-induced protein aggregation was prevented by incubation with alpha-crystallin. These data indicate that ethanol mimics the effects of isoflurane presumably through a cellular preconditioning mechanism that involves dehydration-induced protein aggregation.
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Affiliation(s)
- Jonathan E Ferns
- Department of Anesthesiology, University of Missouri-Kansas City School of Medicine, 4401 Wornall Road, Kansas City, MO 64111, USA
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Cornette R, Kikawada T. The induction of anhydrobiosis in the sleeping chironomid: current status of our knowledge. IUBMB Life 2011; 63:419-29. [PMID: 21547992 DOI: 10.1002/iub.463] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 03/09/2011] [Indexed: 01/09/2023]
Abstract
An African chironomid, Polypedilum vanderplanki, is the only insect known to be capable of extreme desiccation tolerance, or anhydrobiosis. In the 1950s and 1960s, Hinton strenuously studied anhydrobiosis in this insect from a physiological standpoint; however, nobody has afterward investigated the phenomenon. In 2000, research on mechanisms underlying anhydrobiosis was resumed due to successful establishment of a rearing system for P. vanderplanki. This review is focused on the latest findings on the physiological and molecular mechanisms underlying the induction of anhydrobiosis in P. vanderplanki. Early experiments demonstrated that the induction of anhydrobiosis was possible in isolated tissues and independent from the control of central nervous system. However, to achieve successful anhydrobiosis, larvae need a slow regime of desiccation, allowing them to synthesize molecules, which will protect cells and tissues against the deleterious effects of dehydration. Trehalose, a nonreducing disaccharide, which accumulates in P. vanderplanki larvae up to 20% of the dry body mass, is thought to replace the water in its tissues. Similarly, highly hydrophilic proteins called the late embryogenesis abundant (LEA) proteins are expressed in huge quantities and act as a molecular shield to protect biological molecules against aggregation and denaturation. This function is shared by heat shock proteins, which are also upregulated during the desiccation process. At the same time, desiccating larvae express various antioxidant molecules and enzymes, to cope with the massive oxidative stress, which is responsible for general damage to membranes, proteins, and DNA in dehydrating cells. Finally, specific water channels, called aquaporins, accelerate dehydration, and trehalose together with LEA proteins forms a glassy matrix, which protects the biological molecules and the structural integrity of larvae in the anhydrobiotic state.
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Affiliation(s)
- Richard Cornette
- Anhydrobiosis Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8634, Japan
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Anhydrobiosis-associated nuclear DNA damage and repair in the sleeping chironomid: linkage with radioresistance. PLoS One 2010; 5:e14008. [PMID: 21103355 PMCID: PMC2982815 DOI: 10.1371/journal.pone.0014008] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Accepted: 10/28/2010] [Indexed: 11/23/2022] Open
Abstract
Anhydrobiotic chironomid larvae can withstand prolonged complete desiccation as well as other external stresses including ionizing radiation. To understand the cross-tolerance mechanism, we have analyzed the structural changes in the nuclear DNA using transmission electron microscopy and DNA comet assays in relation to anhydrobiosis and radiation. We found that dehydration causes alterations in chromatin structure and a severe fragmentation of nuclear DNA in the cells of the larvae despite successful anhydrobiosis. Furthermore, while the larvae had restored physiological activity within an hour following rehydration, nuclear DNA restoration typically took 72 to 96 h. The DNA fragmentation level and the recovery of DNA integrity in the rehydrated larvae after anhydrobiosis were similar to those of hydrated larvae irradiated with 70 Gy of high-linear energy transfer (LET) ions (4He). In contrast, low-LET radiation (gamma-rays) of the same dose caused less initial damage to the larvae, and DNA was completely repaired within within 24 h. The expression of genes encoding the DNA repair enzymes occurred upon entering anhydrobiosis and exposure to high- and low-LET radiations, indicative of DNA damage that includes double-strand breaks and their subsequent repair. The expression of antioxidant enzymes-coding genes was also elevated in the anhydrobiotic and the gamma-ray-irradiated larvae that probably functions to reduce the negative effect of reactive oxygen species upon exposure to these stresses. Indeed the mature antioxidant proteins accumulated in the dry larvae and the total activity of antioxidants increased by a 3–4 fold in association with anhydrobiosis. We conclude that one of the factors explaining the relationship between radioresistance and the ability to undergo anhydrobiosis in the sleeping chironomid could be an adaptation to desiccation-inflicted nuclear DNA damage. There were also similarities in the molecular response of the larvae to damage caused by desiccation and ionizing radiation.
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