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Kc S, Nguyen KH, Nicholson V, Walgren A, Trent T, Gollub E, Ramero S, Holehouse AS, Sukenik S, Boothby TC. Disordered proteins interact with the chemical environment to tune their protective function during drying. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582506. [PMID: 38464187 PMCID: PMC10925285 DOI: 10.1101/2024.02.28.582506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The conformational ensemble and function of intrinsically disordered proteins (IDPs) are sensitive to their solution environment. The inherent malleability of disordered proteins combined with the exposure of their residues accounts for this sensitivity. One context in which IDPs play important roles that is concomitant with massive changes to the intracellular environment is during desiccation (extreme drying). The ability of organisms to survive desiccation has long been linked to the accumulation of high levels of cosolutes such as trehalose or sucrose as well as the enrichment of IDPs, such as late embryogenesis abundant (LEA) proteins or cytoplasmic abundant heat soluble (CAHS) proteins. Despite knowing that IDPs play important roles and are co-enriched alongside endogenous, species-specific cosolutes during desiccation, little is known mechanistically about how IDP-cosolute interactions influence desiccation tolerance. Here, we test the notion that the protective function of desiccation-related IDPs is enhanced through conformational changes induced by endogenous cosolutes. We find that desiccation-related IDPs derived from four different organisms spanning two LEA protein families and the CAHS protein family, synergize best with endogenous cosolutes during drying to promote desiccation protection. Yet the structural parameters of protective IDPs do not correlate with synergy for either CAHS or LEA proteins. We further demonstrate that for CAHS, but not LEA proteins, synergy is related to self-assembly and the formation of a gel. Our results suggest that functional synergy between IDPs and endogenous cosolutes is a convergent desiccation protection strategy seen among different IDP families and organisms, yet, the mechanisms underlying this synergy differ between IDP families.
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Galas S, Le Goff E, Cazevieille C, Tanaka A, Cuq P, Baghdiguian S, Kunieda T, Godefroy N, Richaud M. A comparative ultrastructure study of the tardigrade Ramazzottius varieornatus in the hydrated state, after desiccation and during the process of rehydration. PLoS One 2024; 19:e0302552. [PMID: 38843161 PMCID: PMC11156355 DOI: 10.1371/journal.pone.0302552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 04/07/2024] [Indexed: 06/09/2024] Open
Abstract
Tardigrades can survive hostile environments such as desiccation by adopting a state of anhydrobiosis. Numerous tardigrade species have been described thus far, and recent genome and transcriptome analyses revealed that several distinct strategies were employed to cope with harsh environments depending on the evolutionary lineages. Detailed analyses at the cellular and subcellular levels are essential to complete these data. In this work, we analyzed a tardigrade species that can withstand rapid dehydration, Ramazzottius varieornatus. Surprisingly, we noted an absence of the anhydrobiotic-specific extracellular structure previously described for the Hypsibius exemplaris species. Both Ramazzottius varieornatus and Hypsibius exemplaris belong to the same evolutionary class of Eutardigrada. Nevertheless, our observations reveal discrepancies in the anhydrobiotic structures correlated with the variation in the anhydrobiotic mechanisms.
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Affiliation(s)
- Simon Galas
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | - Emilie Le Goff
- ISEM, University of Montpellier, CNRS, IRD, Montpellier, France
| | | | - Akihiro Tanaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Pierre Cuq
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | | | - Takekazu Kunieda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Nelly Godefroy
- ISEM, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Myriam Richaud
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
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3
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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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4
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Sanchez‐Martinez S, Nguyen K, Biswas S, Nicholson V, Romanyuk AV, Ramirez J, Kc S, Akter A, Childs C, Meese EK, Usher ET, Ginell GM, Yu F, Gollub E, Malferrari M, Francia F, Venturoli G, Martin EW, Caporaletti F, Giubertoni G, Woutersen S, Sukenik S, Woolfson DN, Holehouse AS, Boothby TC. Labile assembly of a tardigrade protein induces biostasis. Protein Sci 2024; 33:e4941. [PMID: 38501490 PMCID: PMC10949331 DOI: 10.1002/pro.4941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/01/2024] [Accepted: 02/09/2024] [Indexed: 03/20/2024]
Abstract
Tardigrades are microscopic animals that survive desiccation by inducing biostasis. To survive drying tardigrades rely on intrinsically disordered CAHS proteins, which also function to prevent perturbations induced by drying in vitro and in heterologous systems. CAHS proteins have been shown to form gels both in vitro and in vivo, which has been speculated to be linked to their protective capacity. However, the sequence features and mechanisms underlying gel formation and the necessity of gelation for protection have not been demonstrated. Here we report a mechanism of fibrillization and gelation for CAHS D similar to that of intermediate filament assembly. We show that in vitro, gelation restricts molecular motion, immobilizing and protecting labile material from the harmful effects of drying. In vivo, we observe that CAHS D forms fibrillar networks during osmotic stress. Fibrillar networking of CAHS D improves survival of osmotically shocked cells. We observe two emergent properties associated with fibrillization; (i) prevention of cell volume change and (ii) reduction of metabolic activity during osmotic shock. We find that there is no significant correlation between maintenance of cell volume and survival, while there is a significant correlation between reduced metabolism and survival. Importantly, CAHS D's fibrillar network formation is reversible and metabolic rates return to control levels after CAHS fibers are resolved. This work provides insights into how tardigrades induce reversible biostasis through the self-assembly of labile CAHS gels.
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Affiliation(s)
| | - K. Nguyen
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - S. Biswas
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - V. Nicholson
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - A. V. Romanyuk
- School of ChemistryUniversity of BristolBristolUK
- Max Planck‐Bristol Centre for Minimal BiologyUniversity of BristolBristolUK
| | - J. Ramirez
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - S. Kc
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - A. Akter
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - C. Childs
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - E. K. Meese
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - E. T. Usher
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSt. LouisMissouriUSA
- Center for Biomolecular CondensatesWashington University in St. LouisSt. LouisMissouriUSA
| | - G. M. Ginell
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSt. LouisMissouriUSA
- Center for Biomolecular CondensatesWashington University in St. LouisSt. LouisMissouriUSA
| | - F. Yu
- Quantitative Systems Biology ProgramUniversity of California MercedMercedCaliforniaUSA
| | - E. Gollub
- Department of Chemistry and BiochemistryUniversity of California MercedMercedCaliforniaUSA
| | - M. Malferrari
- Dipartimento di Chimica “Giacomo Ciamician”Università di BolognaBolognaItaly
| | - F. Francia
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di Farmacia e Biotecnologie, FaBiTUniversità di BolognaBolognaItaly
| | - G. Venturoli
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di Farmacia e Biotecnologie, FaBiTUniversità di BolognaBolognaItaly
- Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), c/o Dipartimento di Fisica e Astronomia (DIFA)Università di BolognaBolognaItaly
| | - E. W. Martin
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTennesseeUSA
| | - F. Caporaletti
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - G. Giubertoni
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - S. Woutersen
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - S. Sukenik
- Quantitative Systems Biology ProgramUniversity of California MercedMercedCaliforniaUSA
- Department of Chemistry and BiochemistryUniversity of California MercedMercedCaliforniaUSA
| | - D. N. Woolfson
- School of ChemistryUniversity of BristolBristolUK
- Max Planck‐Bristol Centre for Minimal BiologyUniversity of BristolBristolUK
- School of BiochemistryUniversity of Bristol, Biomedical Sciences BuildingBristolUK
| | - A. S. Holehouse
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSt. LouisMissouriUSA
- Center for Biomolecular CondensatesWashington University in St. LouisSt. LouisMissouriUSA
| | - T. C. Boothby
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
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Biswas S, Gollub E, Yu F, Ginell G, Holehouse A, Sukenik S, Boothby TC. Helicity of a tardigrade disordered protein contributes to its protective function during desiccation. Protein Sci 2024; 33:e4872. [PMID: 38114424 PMCID: PMC10804681 DOI: 10.1002/pro.4872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/30/2023] [Accepted: 12/12/2023] [Indexed: 12/21/2023]
Abstract
To survive extreme drying (anhydrobiosis), many organisms, spanning every kingdom of life, accumulate intrinsically disordered proteins (IDPs). For decades, the ability of anhydrobiosis-related IDPs to form transient amphipathic helices has been suggested to be important for promoting desiccation tolerance. However, evidence empirically supporting the necessity and/or sufficiency of helicity in mediating anhydrobiosis is lacking. Here, we demonstrate that the linker region of CAHS D, a desiccation-related IDP from the tardigrade Hypsibius exemplaris, that contains significant helical structure, is the protective portion of this protein. Perturbing the sequence composition and grammar of the linker region of CAHS D, through the insertion of helix-breaking prolines, modulating the identity of charged residues, or replacement of hydrophobic amino acids with serine or glycine residues results in variants with different degrees of helical structure. Importantly, correlation of protective capacity and helical content in variants generated through different helix perturbing modalities does not show as strong a trend, suggesting that while helicity is important, it is not the only property that makes a protein protective during desiccation. These results provide direct evidence for the decades-old theory that helicity of desiccation-related IDPs is linked to their anhydrobiotic capacity.
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Affiliation(s)
- Sourav Biswas
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - Edith Gollub
- Department of Chemistry and BiochemistryUniversity of California, MercedMercedCaliforniaUSA
- Quantitative Systems Biology ProgramUniversity of California MercedMercedCaliforniaUSA
| | - Feng Yu
- Department of Chemistry and BiochemistryUniversity of California, MercedMercedCaliforniaUSA
- Quantitative Systems Biology ProgramUniversity of California MercedMercedCaliforniaUSA
| | - Garrett Ginell
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSt. LouisMissouriUSA
- Center for Biomolecular CondensatesWashington University in St. LouisSt. LouisMissouriUSA
| | - Alex Holehouse
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSt. LouisMissouriUSA
- Center for Biomolecular CondensatesWashington University in St. LouisSt. LouisMissouriUSA
| | - Shahar Sukenik
- Department of Chemistry and BiochemistryUniversity of California, MercedMercedCaliforniaUSA
- Quantitative Systems Biology ProgramUniversity of California MercedMercedCaliforniaUSA
| | - Thomas C. Boothby
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
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6
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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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7
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Ramirez JF, Kumara U, Arulsamy N, Boothby TC. Water content, transition temperature and fragility influence protection and anhydrobiotic capacity. BBA ADVANCES 2024; 5:100115. [PMID: 38318251 PMCID: PMC10840120 DOI: 10.1016/j.bbadva.2024.100115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Abstract
Water is essential for metabolism and all life processes. Despite this, many organisms distributed across the kingdoms of life survive near-complete desiccation or anhydrobiosis. Increased intracellular viscosity, leading to the formation of a vitrified state is necessary, but not sufficient, for survival while dry. What properties of a vitrified system make it desiccation-tolerant or -sensitive are unknown. We have analyzed 18 different in vitro vitrified systems, composed of one of three protective disaccharides (trehalose, sucrose, or maltose) and glycerol, quantifying their enzyme-protective capacity and their material properties in a dry state. Protection conferred by mixtures containing maltose correlates strongly with increased water content, increased glass-transition temperature, and reduced glass former fragility, while the protection of glasses formed with sucrose correlates with increased glass transition temperature and the protection conferred by trehalose glasses correlates with reduced glass former fragility. Thus, in vitro different vitrified sugars confer protection through distinct material properties. Next, we examined the material properties of a dry desiccation tolerant and intolerant life stage from three different organisms. The dried desiccation tolerant life stage of all organisms had an increased glass transition temperature and reduced glass former fragility relative to its dried desiccation intolerant life stage. These results suggest in nature organismal desiccation tolerance relies on a combination of various material properties. This study advances our understanding of how protective and non-protective glasses differ in terms of material properties that promote anhydrobiosis. This knowledge presents avenues to develop novel stabilization technologies for pharmaceuticals that currently rely on the cold-chain. Statement of significance For the past three decades the anhydrobiosis field has lived with a paradox, while vitrification is necessary for survival in the dry state, it is not sufficient. Understanding what property(s) distinguishes a desiccation tolerant from an intolerant vitrified system and how anhydrobiotic organisms survive drying is one of the enduring mysteries of organismal physiology. Here we show in vitro the enzyme-protective capacity of different vitrifying sugars can be correlated with distinct material properties. However, in vivo, diverse desiccation tolerant organisms appear to combine these material properties to promote their survival in a dry state.
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Affiliation(s)
- John F. Ramirez
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - U.G.V.S.S. Kumara
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | | | - Thomas C. Boothby
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
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8
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Morita R, Okano S, Furukawa A, Ishii K, Teramoto C, Minami Y. Analysis of the trehalose synthesis pathway of Physarum polycehalum. Biochem Biophys Res Commun 2023; 682:299-307. [PMID: 37832387 DOI: 10.1016/j.bbrc.2023.09.090] [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: 07/02/2023] [Revised: 09/20/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023]
Abstract
Desiccation is a severe survival problem for organisms. We have been studying the desiccation tolerance mechanisms in the true slime mold Physarum polycephalum. We measured the trehalose content of P. polycephalum vegetative cells (plasmodia) and drought cells (sclerotia). Surprisingly, we found that the content in sclerotia was about 473-fold greater than in the plasmodia. We then examined trehalose metabolism-related genes via RNAseq, and consequently found that trehalose 6-phosphate phosphorylase (T6pp) expression levels increased following desiccation. Next, we cloned and expressed the genes for T6pp, trehalose 6-phosphate synthase/phosphatase (Tps/Tpp), maltooligosyltrehalose trehalohydrolase (TreZ), and maltooligosyltrehalose synthase (TreY) in E. coli. Incidentally, TreY and TreZ clones have been reported in several prokaryotes, but not in eukaryotes. This report in P. polycephalum is the first evidence of their presence in a eukaryote species. Recombinant T6pp, TreY, and TreZ were purified and confirmed to be active. Our results showed that these enzymes catalyze reactions related to trehalose production, and their reaction kinetics follow the Michaelis-Menten equation. The t6pp mRNA levels of the sclerotia were about 15-fold higher than in the plasmodia. In contrast, the expression levels of TreZ and TreY showed no significant change between the sclerotia and plasmodia. Thus, T6pp is probably related to desiccation tolerance, whereas the contribution of TreY and TreZ is insufficient to account for the considerable accumulation of trehalose in sclerotia.
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Affiliation(s)
- Rihito Morita
- Department of Bioscience, Faculty of Life Science, Okayama University of Science, 1-1 Ridai-cho, Kita-ku, Okayama, 700-0005, Japan
| | - Shohei Okano
- Department of Bioscience, Faculty of Life Science, Okayama University of Science, 1-1 Ridai-cho, Kita-ku, Okayama, 700-0005, Japan
| | - Atsushi Furukawa
- Department of Bioscience, Faculty of Life Science, Okayama University of Science, 1-1 Ridai-cho, Kita-ku, Okayama, 700-0005, Japan
| | - Kazuo Ishii
- Department of Applied Information Engineering, Faculty of Engineering, Suwa University of Science, 5000-1 Toyohira, Chino-shi, Nagano, 391-0292, Japan
| | - Chise Teramoto
- Department of Bioscience, Faculty of Life Science, Okayama University of Science, 1-1 Ridai-cho, Kita-ku, Okayama, 700-0005, Japan
| | - Yoshiko Minami
- Department of Bioscience, Faculty of Life Science, Okayama University of Science, 1-1 Ridai-cho, Kita-ku, Okayama, 700-0005, Japan.
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9
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Zhou J, Horton JR, Kaur G, Chen Q, Li X, Mendoza F, Wu T, Blumenthal RM, Zhang X, Cheng X. Biochemical and structural characterization of the first-discovered metazoan DNA cytosine-N4 methyltransferase from the bdelloid rotifer Adineta vaga. J Biol Chem 2023; 299:105017. [PMID: 37414145 PMCID: PMC10406627 DOI: 10.1016/j.jbc.2023.105017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023] Open
Abstract
Much is known about the generation, removal, and roles of 5-methylcytosine (5mC) in eukaryote DNA, and there is a growing body of evidence regarding N6-methyladenine, but very little is known about N4-methylcytosine (4mC) in the DNA of eukaryotes. The gene for the first metazoan DNA methyltransferase generating 4mC (N4CMT) was reported and characterized recently by others, in tiny freshwater invertebrates called bdelloid rotifers. Bdelloid rotifers are ancient, apparently asexual animals, and lack canonical 5mC DNA methyltransferases. Here, we characterize the kinetic properties and structural features of the catalytic domain of the N4CMT protein from the bdelloid rotifer Adineta vaga. We find that N4CMT generates high-level methylation at preferred sites, (a/c)CG(t/c/a), and low-level methylation at disfavored sites, exemplified by ACGG. Like the mammalian de novo 5mC DNA methyltransferase 3A/3B (DNMT3A/3B), N4CMT methylates CpG dinucleotides on both DNA strands, generating hemimethylated intermediates and eventually fully methylated CpG sites, particularly in the context of favored symmetric sites. In addition, like DNMT3A/3B, N4CMT methylates non-CpG sites, mainly CpA/TpG, though at a lower rate. Both N4CMT and DNMT3A/3B even prefer similar CpG-flanking sequences. Structurally, the catalytic domain of N4CMT closely resembles the Caulobacter crescentus cell cycle-regulated DNA methyltransferase. The symmetric methylation of CpG, and similarity to a cell cycle-regulated DNA methyltransferase, together suggest that N4CMT might also carry out DNA synthesis-dependent methylation following DNA replication.
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Affiliation(s)
- Jujun Zhou
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Gundeep Kaur
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Qin Chen
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xuwen Li
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Fabian Mendoza
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Tao Wu
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA.
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
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10
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Sanchez-Martinez S, Ramirez JF, Meese EK, Childs CA, Boothby TC. The tardigrade protein CAHS D interacts with, but does not retain, water in hydrated and desiccated systems. Sci Rep 2023; 13:10449. [PMID: 37369754 DOI: 10.1038/s41598-023-37485-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 06/22/2023] [Indexed: 06/29/2023] Open
Abstract
Tardigrades are a group of microscopic animals renowned for their ability to survive near complete desiccation. A family of proteins, unique to tardigrades, called Cytoplasmic Abundant Heat Soluble (CAHS) proteins are necessary to mediate robust desiccation tolerance in these animals. However, the mechanism(s) by which CAHS proteins help to protect tardigrades during water-loss have not been fully elucidated. Here we use thermogravimetric analysis to empirically test the proposed hypothesis that tardigrade CAHS proteins, due to their propensity to form hydrogels, help to retain water during desiccation. We find that regardless of its gelled state, both in vitro and in vivo, a model CAHS protein (CAHS D) retains no more water than common proteins and control cells in the dry state. However, we find that while CAHS D proteins do not increase the total amount of water retained in a dry system, they interact with the small amount of water that does remain. Our study indicates that desiccation tolerance mediated by CAHS D cannot be simply ascribed to water retention and instead implicates its ability to interact more tightly with residual water as a possible mechanism underlying its protective capacity. These results advance our fundamental understanding of tardigrade desiccation tolerance which could provide potential avenues for new technologies to aid in the storage of dry shelf-stable pharmaceuticals and the generation of stress tolerant crops to ensure food security in the face of global climate change.
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Affiliation(s)
| | - John F Ramirez
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
| | - Emma K Meese
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
| | - Charles A Childs
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
| | - Thomas C Boothby
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA.
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11
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Yoshida Y, Tanaka S. Deciphering the Biological Enigma-Genomic Evolution Underlying Anhydrobiosis in the Phylum Tardigrada and the Chironomid Polypedilum vanderplanki. INSECTS 2022; 13:557. [PMID: 35735894 PMCID: PMC9224920 DOI: 10.3390/insects13060557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/13/2022] [Accepted: 06/17/2022] [Indexed: 02/04/2023]
Abstract
Anhydrobiosis, an ametabolic dehydrated state triggered by water loss, is observed in several invertebrate lineages. Anhydrobiotes revive when rehydrated, and seem not to suffer the ultimately lethal cell damage that results from severe loss of water in other organisms. Here, we review the biochemical and genomic evidence that has revealed the protectant molecules, repair systems, and maintenance pathways associated with anhydrobiosis. We then introduce two lineages in which anhydrobiosis has evolved independently: Tardigrada, where anhydrobiosis characterizes many species within the phylum, and the genus Polypedilum, where anhydrobiosis occurs in only two species. Finally, we discuss the complexity of the evolution of anhydrobiosis within invertebrates based on current knowledge, and propose perspectives to enhance the understanding of anhydrobiosis.
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Affiliation(s)
- Yuki Yoshida
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Sae Tanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Institute for Advanced Biosciences, Keio University, 341-1 Mizukami, Tsuruoka 997-0052, Japan
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12
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Abstract
Tardigrades are ubiquitous meiofauna that are especially renowned for their exceptional extremotolerance to various adverse environments, including pressure, temperature, and even ionizing radiation. This is achieved through a reversible halt of metabolism triggered by desiccation, a phenomenon called anhydrobiosis. Recent establishment of genome resources for two tardigrades, Hypsibius exemplaris and Ramazzottius varieornatus, accelerated research to uncover the molecular mechanisms behind anhydrobiosis, leading to the discovery of many tardigrade-unique proteins. This review focuses on the history, methods, discoveries, and current state and challenges regarding tardigrade genomics, with an emphasis on molecular anhydrobiology. Remaining questions and future perspectives regarding prospective approaches to fully elucidate the molecular machinery of this complex phenomenon are discussed.
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Affiliation(s)
- Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Daishouji, Tsuruoka, Yamagata, Japan; .,Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan.,Graduate School of Media and Governance, Systems Biology Program, Keio University, Fujisawa, Kanagawa, Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan
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13
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Giovannini I, Boothby TC, Cesari M, Goldstein B, Guidetti R, Rebecchi L. Production of reactive oxygen species and involvement of bioprotectants during anhydrobiosis in the tardigrade Paramacrobiotus spatialis. Sci Rep 2022; 12:1938. [PMID: 35121798 PMCID: PMC8816950 DOI: 10.1038/s41598-022-05734-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 12/06/2021] [Indexed: 12/30/2022] Open
Abstract
Water unavailability is an abiotic stress causing unfavourable conditions for life. Nevertheless, some animals evolved anhydrobiosis, a strategy allowing for the reversible organism dehydration and suspension of metabolism as a direct response to habitat desiccation. Anhydrobiotic animals undergo biochemical changes synthesizing bioprotectants to help combat desiccation stresses. One stress is the generation of reactive oxygen species (ROS). In this study, the eutardigrade Paramacrobiotus spatialis was used to investigate the occurrence of ROS associated with the desiccation process. We observed that the production of ROS significantly increases as a function of time spent in anhydrobiosis and represents a direct demonstration of oxidative stress in tardigrades. The degree of involvement of bioprotectants, including those combating ROS, in the P. spatialis was evaluated by perturbing their gene functions using RNA interference and assessing the successful recovery of animals after desiccation/rehydration. Targeting the glutathione peroxidase gene compromised survival during drying and rehydration, providing evidence for the role of the gene in desiccation tolerance. Targeting genes encoding glutathione reductase and catalase indicated that these molecules play roles during rehydration. Our study also confirms the involvement of aquaporins 3 and 10 during rehydration. Therefore, desiccation tolerance depends on the synergistic action of many different molecules working together.
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Affiliation(s)
- Ilaria Giovannini
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi 213/D, 41125, Modena, Italy.
| | - Thomas C Boothby
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA.,Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michele Cesari
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi 213/D, 41125, Modena, Italy
| | - Bob Goldstein
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Roberto Guidetti
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi 213/D, 41125, Modena, Italy
| | - Lorena Rebecchi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi 213/D, 41125, Modena, Italy
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14
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Yagi-Utsumi M, Aoki K, Watanabe H, Song C, Nishimura S, Satoh T, Yanaka S, Ganser C, Tanaka S, Schnapka V, Goh EW, Furutani Y, Murata K, Uchihashi T, Arakawa K, Kato K. Desiccation-induced fibrous condensation of CAHS protein from an anhydrobiotic tardigrade. Sci Rep 2021; 11:21328. [PMID: 34737320 PMCID: PMC8569203 DOI: 10.1038/s41598-021-00724-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/11/2021] [Indexed: 11/25/2022] Open
Abstract
Anhydrobiosis, one of the most extensively studied forms of cryptobiosis, is induced in certain organisms as a response to desiccation. Anhydrobiotic species has been hypothesized to produce substances that can protect their biological components and/or cell membranes without water. In extremotolerant tardigrades, highly hydrophilic and heat-soluble protein families, cytosolic abundant heat-soluble (CAHS) proteins, have been identified, which are postulated to be integral parts of the tardigrades' response to desiccation. In this study, to elucidate these protein functions, we performed in vitro and in vivo characterizations of the reversible self-assembling property of CAHS1 protein, a major isoform of CAHS proteins from Ramazzottius varieornatus, using a series of spectroscopic and microscopic techniques. We found that CAHS1 proteins homo-oligomerized via the C-terminal α-helical region and formed a hydrogel as their concentration increased. We also demonstrated that the overexpressed CAHS1 proteins formed condensates under desiccation-mimicking conditions. These data strongly suggested that, upon drying, the CAHS1 proteins form oligomers and eventually underwent sol-gel transition in tardigrade cytosols. Thus, it is proposed that the CAHS1 proteins form the cytosolic fibrous condensates, which presumably have variable mechanisms for the desiccation tolerance of tardigrades. These findings provide insights into molecular strategies of organisms to adapt to extreme environments.
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Affiliation(s)
- Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, 465-8603, Japan
| | - Kazuhiro Aoki
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
- National Institute for Basic Biology (NIBB), National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan
| | - Hiroki Watanabe
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Chihong Song
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
- National Institute for Physiological Sciences (NIPS), National Institutes of Natural Sciences, Okazaki, Aichi, 444-8585, Japan
| | - Seiji Nishimura
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, 465-8603, Japan
| | - Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, 465-8603, Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, 465-8603, Japan
| | - Christian Ganser
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Sae Tanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan
| | - Vincent Schnapka
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan
- Ecole Nationale Supérieure de Chimie de Paris, 75005, Paris, France
- Institut de Biologie Structurale, 38044, Grenoble, France
| | - Ean Wai Goh
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan
| | - Yuji Furutani
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, 466-8555, Japan
| | - Kazuyoshi Murata
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
- National Institute for Physiological Sciences (NIPS), National Institutes of Natural Sciences, Okazaki, Aichi, 444-8585, Japan
| | - Takayuki Uchihashi
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
- Department of Physics, Nagoya University, Nagoya, 464-8602, Japan
- Institute for Glyco-Core Research (iGCORE), Nagoya University, Nagoya, 464-8601, Japan
| | - Kazuharu Arakawa
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, 252-0882, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-0882, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan.
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, 465-8603, Japan.
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15
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Chattopadhyay M, Krok E, Orlikowska H, Schwille P, Franquelim HG, Piatkowski L. Hydration Layer of Only a Few Molecules Controls Lipid Mobility in Biomimetic Membranes. J Am Chem Soc 2021; 143:14551-14562. [PMID: 34342967 PMCID: PMC8447254 DOI: 10.1021/jacs.1c04314] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
Self-assembly of
biomembranes results from the intricate interactions
between water and the lipids’ hydrophilic head groups. Therefore,
the lipid–water interplay strongly contributes to modulating
membrane architecture, lipid diffusion, and chemical activity. Here,
we introduce a new method of obtaining dehydrated, phase-separated,
supported lipid bilayers (SLBs) solely by controlling the decrease
of their environment’s relative humidity. This facilitates
the study of the structure and dynamics of SLBs over a wide range
of hydration states. We show that the lipid domain structure of phase-separated
SLBs is largely insensitive to the presence of the hydration layer.
In stark contrast, lipid mobility is drastically affected by dehydration,
showing a 6-fold decrease in lateral diffusion. At the same time,
the diffusion activation energy increases approximately 2-fold for
the dehydrated membrane. The obtained results, correlated with the
hydration structure of a lipid molecule, revealed that about six to
seven water molecules directly hydrating the phosphocholine moiety
play a pivotal role in modulating lipid diffusion. These findings
could provide deeper insights into the fundamental reactions where
local dehydration occurs, for instance during cell–cell fusion,
and help us better understand the survivability of anhydrobiotic organisms.
Finally, the strong dependence of lipid mobility on the number of
hydrating water molecules opens up an application potential for SLBs
as very precise, nanoscale hydration sensors.
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Affiliation(s)
- Madhurima Chattopadhyay
- Faculty of Materials Engineering and Technical Physics, Poznan University of Technology, Piotrowo 3, 60-965 Poznan, Poland
| | - Emilia Krok
- Faculty of Materials Engineering and Technical Physics, Poznan University of Technology, Piotrowo 3, 60-965 Poznan, Poland
| | - Hanna Orlikowska
- Faculty of Materials Engineering and Technical Physics, Poznan University of Technology, Piotrowo 3, 60-965 Poznan, Poland
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Henri G Franquelim
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Lukasz Piatkowski
- Faculty of Materials Engineering and Technical Physics, Poznan University of Technology, Piotrowo 3, 60-965 Poznan, Poland
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16
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Hincha DK, Zuther E, Popova AV. Stabilization of Dry Sucrose Glasses by Four LEA_4 Proteins from Arabidopsis thaliana. Biomolecules 2021; 11:biom11050615. [PMID: 33919135 PMCID: PMC8143093 DOI: 10.3390/biom11050615] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 12/03/2022] Open
Abstract
Cells of many organisms and organs can withstand an (almost) total water loss (anhydrobiosis). Sugars play an essential role in desiccation tolerance due to their glass formation ability during dehydration. In addition, intrinsically disordered LEA proteins contribute to cellular survival under such conditions. One possible mechanism of LEA protein function is the stabilization of sugar glasses. However, little is known about the underlying mechanisms. Here we used FTIR spectroscopy to investigate sucrose (Suc) glass stability dried from water or from two buffer components in the presence of four recombinant LEA and globular reference proteins. Buffer ions influenced the strength of the Suc glass in the order Suc < Suc/Tris < Suc/NaP. LEA proteins strengthened the sugar H-bonded network and the molecular structure in the glassy state. The position of νOH peak and the wavenumber–temperature coefficient (WTCg) provided similar information about the H-bonded network. Protein aggregation of LEA proteins was reduced in the desiccation-induced Suc glassy state. Detailed knowledge about the role of LEA proteins in the stabilization of dry sugar glasses yields information about their role in anhydrobiosis. This may open the possibility to use such proteins in biotechnical applications requiring dry storage of biologicals such as proteins, cells or tissues.
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Affiliation(s)
- Dirk K. Hincha
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany;
| | - Ellen Zuther
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany;
- Correspondence: (E.Z.); (A.V.P.)
| | - Antoaneta V. Popova
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany;
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
- Correspondence: (E.Z.); (A.V.P.)
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17
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Hesgrove C, Boothby TC. The biology of tardigrade disordered proteins in extreme stress tolerance. Cell Commun Signal 2020; 18:178. [PMID: 33148259 PMCID: PMC7640644 DOI: 10.1186/s12964-020-00670-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/29/2020] [Indexed: 02/06/2023] Open
Abstract
Abstract Disordered proteins have long been known to help mediate tolerance to different abiotic stresses including freezing, osmotic stress, high temperatures, and desiccation in a diverse set of organisms. Recently, three novel families of intrinsically disordered proteins were identified in tardigrades, microscopic animals capable of surviving a battery of environmental extremes. These three families include the Cytoplasmic-, Secreted-, and Mitochondrial- Abundant Heat Soluble (CAHS, SAHS, and MAHS) proteins, which are collectively termed Tardigrade Disordered Proteins (TDPs). At the level of sequence conservation TDPs are unique to tardigrades, and beyond their high degree of disorder the CAHS, SAHS, and MAHS families do not resemble one another. All three families are either highly expressed constitutively, or significantly enriched in response to desiccation. In vivo, ex vivo, and in vitro experiments indicate functional roles for members of each TDP family in mitigating cellular perturbations induced by various abiotic stresses. What is currently lacking is a comprehensive and holistic understanding of the fundamental mechanisms by which TDPs function, and the properties of TDPs that allow them to function via those mechanisms. A quantitative and systematic approach is needed to identify precisely what cellular damage TDPs work to prevent, what sequence features are important for these functions, and how those sequence features contribute to the underlying mechanisms of protection. Such an approach will inform us not only about these fascinating proteins, but will also provide insights into how the sequence of a disordered protein can dictate its functional, structural, and dynamic properties. Video Abstract
Graphical abstract ![]()
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Affiliation(s)
- Cherie Hesgrove
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
| | - Thomas C Boothby
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA.
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18
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Hibshman JD, Clegg JS, Goldstein B. Mechanisms of Desiccation Tolerance: Themes and Variations in Brine Shrimp, Roundworms, and Tardigrades. Front Physiol 2020; 11:592016. [PMID: 33192606 PMCID: PMC7649794 DOI: 10.3389/fphys.2020.592016] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/25/2020] [Indexed: 01/05/2023] Open
Abstract
Water is critical for the survival of most cells and organisms. Remarkably, a small number of multicellular animals are able to survive nearly complete drying. The phenomenon of anhydrobiosis, or life without water, has been of interest to researchers for over 300 years. In this review we discuss advances in our understanding of protectants and mechanisms of desiccation tolerance that have emerged from research in three anhydrobiotic invertebrates: brine shrimp (Artemia), roundworms (nematodes), and tardigrades (water bears). Discovery of molecular protectants that allow each of these three animals to survive drying diversifies our understanding of desiccation tolerance, and convergent themes suggest mechanisms that may offer a general model for engineering desiccation tolerance in other contexts.
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Affiliation(s)
- Jonathan D. Hibshman
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - James S. Clegg
- Bodega Marine Laboratory, University of California, Davis, Davis, CA, United States
| | - Bob Goldstein
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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19
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Common Functions of Disordered Proteins across Evolutionary Distant Organisms. Int J Mol Sci 2020; 21:ijms21062105. [PMID: 32204351 PMCID: PMC7139818 DOI: 10.3390/ijms21062105] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 12/14/2022] Open
Abstract
Intrinsically disordered proteins and regions typically lack a well-defined structure and thus fall outside the scope of the classic sequence–structure–function relationship. Hence, classic sequence- or structure-based bioinformatic approaches are often not well suited to identify homology or predict the function of unknown intrinsically disordered proteins. Here, we give selected examples of intrinsic disorder in plant proteins and present how protein function is shared, altered or distinct in evolutionary distant organisms. Furthermore, we explore how examining the specific role of disorder across different phyla can provide a better understanding of the common features that protein disorder contributes to the respective biological mechanism.
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20
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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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21
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Ultrastructural analysis of the dehydrated tardigrade Hypsibius exemplaris unveils an anhydrobiotic-specific architecture. Sci Rep 2020; 10:4324. [PMID: 32152342 PMCID: PMC7062702 DOI: 10.1038/s41598-020-61165-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 02/18/2020] [Indexed: 01/06/2023] Open
Abstract
Tardigrades can cope with adverse environmental conditions by turning into anhydrobiotes with a characteristic tun shape. Tun formation is an essential morphological adaptation for tardigrade entry into the anhydrobiotic state. The tun cell structure and ultrastructure have rarely been explored in tardigrades in general and never in Hypsibius exemplaris. We used transmission electron microscopy to compare cellular organization and ultrastructures between hydrated and anhydrobiotic H. exemplaris. Despite a globally similar cell organelle structure and a number of cells not significantly different between hydrated and desiccated tardigrades, reductions in the sizes of both cells and mitochondria were detected in dehydrated animals. Moreover, in anhydrobiotes, secretory active cells with a dense endoplasmic reticulum network were observed. Interestingly, these anhydrobiote-specific cells are in a close relationship with a specific extracellular structure surrounding each cell. It is possible that this rampart-like extracellular structure resulted from the accumulation of anhydrobiotic-specific material to protect the cells. Interestingly, after five hours of rehydration, the number of secretory cells decreased, and the specific extracellular structure began to disappear. Twenty-four hours after the beginning of rehydration, the cellular structure and ultrastructure were comparable to those observed in hydrated tardigrades.
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García-Roger EM, Lubzens E, Fontaneto D, Serra M. Facing Adversity: Dormant Embryos in Rotifers. THE BIOLOGICAL BULLETIN 2019; 237:119-144. [PMID: 31714860 DOI: 10.1086/705701] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
An in-depth look at the basic aspects of dormancy in cyclic parthenogenetic organisms is now possible thanks to research efforts conducted over the past two decades with rotifer dormant embryos. In this review, we assemble and compose the current knowledge on four central themes: (1) distribution of dormancy in animals, with an overview on the phylogenetic distribution of embryo dormancy in metazoans, and (2) physiological and cellular processes involved in dormancy, with a strong emphasis on the dormant embryos of cyclically parthenogenetic monogonont rotifers; and discussions of (3) the selective pressures and (4) the evolutionary and population implications of dormancy in these animals. Dormancy in metazoans is a widespread phenomenon with taxon-specific features, and rotifers are among the animals in which dormancy is an intrinsic feature of their life cycle. Our review shows that embryo dormancy in rotifers shares common functional pathways with other taxa at the molecular and cellular level, despite the independent evolution of dormancy across phyla. These pathways include the arrest of similar metabolic routes and the usage of common metabolites for the stabilization of cellular structures and to confer stress resistance. We conclude that specific features of recurrent harsh environmental conditions are a powerful selective pressure for the fine-tuning of dormancy patterns in rotifers. We hypothesize that similar mechanisms at the organism level will lead to similar adaptive consequences at the population level across taxa, among which the formation of egg banks, the coexistence of species, and the possibility of differentiation among populations and local adaptation stand out. Our review shows how studies of rotifers have contributed to improved knowledge of all of these aspects.
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Kamilari M, Jørgensen A, Schiøtt M, Møbjerg N. Comparative transcriptomics suggest unique molecular adaptations within tardigrade lineages. BMC Genomics 2019; 20:607. [PMID: 31340759 PMCID: PMC6652013 DOI: 10.1186/s12864-019-5912-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 06/17/2019] [Indexed: 12/19/2022] Open
Abstract
Background Tardigrades are renowned for their ability to enter cryptobiosis (latent life) and endure extreme stress, including desiccation and freezing. Increased focus is on revealing molecular mechanisms underlying this tolerance. Here, we provide the first transcriptomes from the heterotardigrade Echiniscoides cf. sigismundi and the eutardigrade Richtersius cf. coronifer, and compare these with data from other tardigrades and six eukaryote models. Investigating 107 genes/gene families, our study provides a thorough analysis of tardigrade gene content with focus on stress tolerance. Results E. cf. sigismundi, a strong cryptobiont, apparently lacks expression of a number of stress related genes. Most conspicuous is the lack of transcripts from genes involved in classical Non-Homologous End Joining. Our analyses suggest that post-cryptobiotic survival in tardigrades could rely on high fidelity transcription-coupled DNA repair. Tardigrades seem to lack many peroxins, but they all have a comprehensive number of genes encoding proteins involved in antioxidant defense. The “tardigrade unique proteins” (CAHS, SAHS, MAHS, RvLEAM), seem to be missing in the heterotardigrade lineage, revealing that cryptobiosis in general cannot be attributed solely to these proteins. Our investigation further reveals a unique and highly expressed cold shock domain. We hypothesize that the cold shock protein acts as a RNA-chaperone involved in regulation of translation following freezing. Conclusions Our results show common gene family contractions and expansions within stress related gene pathways in tardigrades, but also indicate that evolutionary lineages have a high degree of divergence. Different taxa and lineages may exhibit unique physiological adaptations towards stress conditions involving possible unknown functional homologues and/or novel physiological and biochemical mechanisms. To further substantiate the current results genome assemblies coupled with transcriptome data and experimental investigations are needed from tardigrades belonging to different evolutionary lineages. Electronic supplementary material The online version of this article (10.1186/s12864-019-5912-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maria Kamilari
- Section for Cell Biology and Physiology, Department of Biology, August Krogh Building, University of Copenhagen, Universitetsparken 13, Copenhagen, Denmark
| | - Aslak Jørgensen
- Section for Cell Biology and Physiology, Department of Biology, August Krogh Building, University of Copenhagen, Universitetsparken 13, Copenhagen, Denmark
| | - Morten Schiøtt
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen, Denmark
| | - Nadja Møbjerg
- Section for Cell Biology and Physiology, Department of Biology, August Krogh Building, University of Copenhagen, Universitetsparken 13, Copenhagen, Denmark.
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Abstract
Climate change has accentuated the importance of understanding how organisms respond to stresses imposed by changes to their environment, like water availability. Unusual organisms, called anhydrobiotes, can survive loss of almost all intracellular water. Desiccation tolerance of anhydrobiotes provides an unusual window to study the stresses and stress response imposed by water loss. Because of the myriad of stresses that could be induced by water loss, desiccation tolerance seemed likely to require many established stress effectors. The sugar trehalose and hydrophilins (small intrinsically disordered proteins) had also been proposed as stress effectors against desiccation because they were found in nearly all anhydrobiotes, and could mitigate desiccation-induced damage to model proteins and membranes in vitro. Here, we summarize in vivo studies of desiccation tolerance in worms, yeast, and tardigrades. These studies demonstrate the remarkable potency of trehalose and a subset of hydrophilins as the major stress effectors of desiccation tolerance. They act, at least in part, by limiting in vivo protein aggregation and loss of membrane integrity. The apparent specialization of individual hydrophilins for desiccation tolerance suggests that other hydrophilins may have distinct roles in mitigating additional cellular stresses, thereby defining a potentially new functionally diverse set of stress effectors.
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Affiliation(s)
- Douglas Koshland
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Hugo Tapia
- Biology Program, California State University-Channel Islands, Camarillo, CA 93012
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25
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Metabolomics reveals novel insight on dormancy of aquatic invertebrate encysted embryos. Sci Rep 2019; 9:8878. [PMID: 31222034 PMCID: PMC6586685 DOI: 10.1038/s41598-019-45061-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 05/28/2019] [Indexed: 11/08/2022] Open
Abstract
Numerous aquatic invertebrates survive harsh environments by displaying dormancy as encysted embryos. This study aimed at determining whether metabolomics could provide molecular insight to explain the "dormancy syndrome" by highlighting functional pathways and metabolites, hence offering a novel comprehensive molecular view of dormancy. We compared the metabolome of morphologically distinct dormant encysted embryos (resting eggs) and non-dormant embryos (amictic eggs) of a rotifer (Brachionus plicatilis). Metabolome profiling revealed ~5,000 features, 1,079 of which were annotated. Most of the features were represented at significantly higher levels in non-dormant than dormant embryos. A large number of features was assigned to putative functional pathways indicating novel differences between dormant and non-dormant states. These include features associated with glycolysis, the TCA and urea cycles, amino acid, purine and pyrimidine metabolism. Interestingly, ATP, nucleobases, cyclic nucleotides, thymidine and uracil, were not detected in dormant resting eggs, suggesting an impairment of response to environmental and internal cues, cessation of DNA synthesis, transcription and plausibly translation in the dormant embryos. The levels of trehalose or its analogues, with a role in survival under desiccation conditions, were higher in resting eggs. In conclusion, the current study highlights metabolomics as a major analytical tool to functionally compare dormancy across species.
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Kaczmarek Ł, Roszkowska M, Fontaneto D, Jezierska M, Pietrzak B, Wieczorek R, Poprawa I, Kosicki JZ, Karachitos A, Kmita H. Staying young and fit? Ontogenetic and phylogenetic consequences of animal anhydrobiosis. J Zool (1987) 2019. [DOI: 10.1111/jzo.12677] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Ł. Kaczmarek
- Department of Animal Taxonomy and Ecology Faculty of Biology Adam Mickiewicz University in Poznan Poznań Poland
| | - M. Roszkowska
- Department of Animal Taxonomy and Ecology Faculty of Biology Adam Mickiewicz University in Poznan Poznań Poland
- Department of Bioenergetics Institute of Molecular Biology and Biotechnology Faculty of Biology Adam Mickiewicz University in Poznan Poznań Poland
| | - D. Fontaneto
- National Research Council Water Research Institute (CNR‐IRSA) Verbania Italy
| | - M. Jezierska
- Department of Animal Histology and Embryology University of Silesia in Katowice Katowice Poland
| | - B. Pietrzak
- Department of Hydrobiology Faculty of Biology Biological and Chemical Research Centre University of Warsaw Warszawa Poland
| | - R. Wieczorek
- Faculty of Chemistry University of Warsaw Warsaw Poland
| | - I. Poprawa
- Department of Animal Histology and Embryology University of Silesia in Katowice Katowice Poland
| | - J. Z. Kosicki
- Department of Avian Biology and Ecology Faculty of Biology Adam Mickiewicz University Poznan Poznań Poland
| | - A. Karachitos
- Department of Bioenergetics Institute of Molecular Biology and Biotechnology Faculty of Biology Adam Mickiewicz University in Poznan Poznań Poland
| | - H. Kmita
- Department of Bioenergetics Institute of Molecular Biology and Biotechnology Faculty of Biology Adam Mickiewicz University in Poznan Poznań Poland
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27
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Hecox-Lea BJ, Mark Welch DB. Evolutionary diversity and novelty of DNA repair genes in asexual Bdelloid rotifers. BMC Evol Biol 2018; 18:177. [PMID: 30486781 PMCID: PMC6264785 DOI: 10.1186/s12862-018-1288-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 11/02/2018] [Indexed: 11/26/2022] Open
Abstract
Background Bdelloid rotifers are the oldest, most diverse and successful animal taxon for which males, hermaphrodites, and traditional meiosis are unknown. Their degenerate tetraploid genome, with 2–4 copies of most loci, includes thousands of genes acquired from all domains of life by horizontal transfer. Many bdelloid species thrive in ephemerally aquatic habitats by surviving desiccation at any life stage with no loss of fecundity or lifespan. Their unique genomic diversity and the intense selective pressure of desiccation provide an exceptional opportunity to study the evolution of diversity and novelty in genes involved in DNA repair. Results We used genomic data and RNA-Seq of the desiccation process in the bdelloid Adineta vaga to characterize DNA damage reversal, translesion synthesis, and the major DNA repair pathways: base, nucleotide, and alternate excision repair, mismatch repair (MMR), and double strand break repair by homologous recombination (HR) and classical non-homologous end joining (NHEJ). We identify multiple horizontally transferred DNA damage response genes otherwise unknown in animals (AlkD, Fpg, LigK UVDE), and the presence of genes often considered vertebrate specific, particularly in the NHEJ complex and X family polymerases. While 75–100% of genes involved in MMR and HR are present in 0–2 copies, genes involved in NHEJ, which are present in only a single copy in nearly all other animals, are retained in 3–8 copies. We present structural predictions and expression evidence of neo- or sub-functionalization of multiple copy genes involved in NHEJ and other repair processes. Conclusion The horizontally-acquired genes and duplicated genes in BER and NHEJ suggest resilience to oxidative damage is conferred in part by increased DNA damage recognition and efficient end repair capabilities. The pattern of gene loss and retention in MMR and HR may facilitate recombination and gene conversion between divergent sequences, thus providing at least some of the benefits of sex. The unique retention and divergence of duplicates genes in NHEJ may be facilitated by the lack of efficient selection in the absence of meiotic recombination and independent assortment, and may contribute to the evolutionary success of bdelloids. Electronic supplementary material The online version of this article (10.1186/s12862-018-1288-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bette J Hecox-Lea
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA.,Department of Biology, Northeastern University, Boston, MA, USA
| | - David B Mark Welch
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA.
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28
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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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Furuki T, Sakurai M. Physicochemical Aspects of the Biological Functions of Trehalose and Group 3 LEA Proteins as Desiccation Protectants. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1081:271-286. [PMID: 30288715 DOI: 10.1007/978-981-13-1244-1_15] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In this review, we first focus on the mechanism by which the larva of the sleeping chironomid, Polypedilum vanderplanki, survives an extremely dehydrated state and describe how trehalose and probably late embryogenesis abundant (LEA) proteins work as desiccation protectants. Second, we summarize the solid-state and solution properties of trehalose and discuss why trehalose works better than other disaccharides as a desiccation protectant. Third, we describe the structure and function of two model peptides based on group 3 LEA proteins after a short introduction of native LEA proteins themselves. Finally, we present our conclusions and a perspective on the application of trehalose and LEA model peptides to the long-term storage of biological materials.
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Affiliation(s)
- Takao Furuki
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, Japan
| | - Minoru Sakurai
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, Japan.
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30
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Seybold AC, Wharton DA, Thorne MAS, Marshall CJ. Investigating trehalose synthesis genes after cold acclimation in the Antarctic nematode Panagrolaimus sp. DAW1. Biol Open 2017; 6:1953-1959. [PMID: 29175859 PMCID: PMC5769639 DOI: 10.1242/bio.023341] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Panagrolaimus sp. DAW1 is a freeze-tolerant Antarctic nematode which survives extensive intracellular ice formation. The molecular mechanisms of this extreme adaptation are still poorly understood. We recently showed that desiccation-enhanced RNA interference (RNAi) soaking can be used in conjunction with quantitative polymerase chain reaction (qPCR) to screen for phenotypes associated with reduced expression of candidate genes in Panagrolaimus sp. DAW1. Here, we present the use of this approach to investigate the role of trehalose synthesis genes in this remarkable organism. Previous studies have shown that acclimating Panagrolaimus sp. DAW1 at 5°C before freezing or desiccation substantially enhances survival. In this study, the expression of tps-2 and other genes associated with trehalose metabolism, as well as lea-1, hsp-70 and gpx-1, in cold-acclimated and non-acclimated nematodes was analyzed using qPCR. Pd-tps-2 and Pd-lea-1 were significantly upregulated after cold acclimation, indicating an inducible expression in the cold adaptation of Panagrolaimus sp. DAW1. The role of trehalose synthesis genes in Panagrolaimus sp. DAW1 was further investigated by RNAi. Compared to the controls, Pd-tps-2a(RNAi)-treated and cold-acclimated nematodes showed a significant decrease in mRNA, but no change in trehalose content or freezing survival. The involvement of two other trehalose synthesis genes (tps-2b and gob-1) was also investigated. These findings provide the first functional genomic investigation of trehalose synthesis genes in the non-model organism Panagrolaimus sp. DAW1. The presence of several trehalose synthesis genes with different RNAi sensitivities suggests the existence of multiple backup systems in Panagrolaimus sp. DAW1, underlining the importance of this sugar in preparation for freezing. Summary: Functional genomics was used to investigate trehalose synthesis genes after cold acclimation in Panagrolaimus sp. DAW1, an Antarctic nematode with the ability to survive intracellular freezing.
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Affiliation(s)
- Anna C Seybold
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| | - David A Wharton
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Michael A S Thorne
- British Antarctic Survey, Natural Environment Research Council, Cambridge, CB3 0ET, United Kingdom
| | - Craig J Marshall
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand .,Genetics Otago, University of Otago, Dunedin 9054, New Zealand
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31
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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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32
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Boothby TC, Pielak GJ. Intrinsically Disordered Proteins and Desiccation Tolerance: Elucidating Functional and Mechanistic Underpinnings of Anhydrobiosis. Bioessays 2017; 39. [DOI: 10.1002/bies.201700119] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/08/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Thomas C. Boothby
- Department of ChemistryUniversity of North Carolina at Chapel HillChapel HillNC27599USA
| | - Gary J. Pielak
- Department of ChemistryUniversity of North Carolina at Chapel HillChapel HillNC27599USA
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Boothby TC, Tapia H, Brozena AH, Piszkiewicz S, Smith AE, Giovannini I, Rebecchi L, Pielak GJ, Koshland D, Goldstein B. Tardigrades Use Intrinsically Disordered Proteins to Survive Desiccation. Mol Cell 2017; 65:975-984.e5. [PMID: 28306513 DOI: 10.1016/j.molcel.2017.02.018] [Citation(s) in RCA: 216] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 12/14/2016] [Accepted: 02/16/2017] [Indexed: 11/19/2022]
Abstract
Tardigrades are microscopic animals that survive a remarkable array of stresses, including desiccation. How tardigrades survive desiccation has remained a mystery for more than 250 years. Trehalose, a disaccharide essential for several organisms to survive drying, is detected at low levels or not at all in some tardigrade species, indicating that tardigrades possess potentially novel mechanisms for surviving desiccation. Here we show that tardigrade-specific intrinsically disordered proteins (TDPs) are essential for desiccation tolerance. TDP genes are constitutively expressed at high levels or induced during desiccation in multiple tardigrade species. TDPs are required for tardigrade desiccation tolerance, and these genes are sufficient to increase desiccation tolerance when expressed in heterologous systems. TDPs form non-crystalline amorphous solids (vitrify) upon desiccation, and this vitrified state mirrors their protective capabilities. Our study identifies TDPs as functional mediators of tardigrade desiccation tolerance, expanding our knowledge of the roles and diversity of disordered proteins involved in stress tolerance.
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Affiliation(s)
- Thomas C Boothby
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Hugo Tapia
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Alexandra H Brozena
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Samantha Piszkiewicz
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Austin E Smith
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ilaria Giovannini
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Lorena Rebecchi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Gary J Pielak
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Doug Koshland
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Bob Goldstein
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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34
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Chen Q, Li D, Wang F, Zhang R, Ling Y. Trehalose metabolism genes of Aphelenchoides besseyi (Nematoda: Aphelenchoididae) in hypertonic osmotic pressure survival. Biol Open 2017; 6:664-672. [PMID: 28396490 PMCID: PMC5450318 DOI: 10.1242/bio.023267] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Some organisms can survive extreme desiccation caused by hypertonic osmotic pressure by entering a state of suspended animation known as osmobiosis. The free-living mycophagous nematode Aphelenchoides besseyi can be induced to enter osmobiosis by soaking in osmolytes. It is assumed that sugars (in particular trehalose) are instrumental for survival under environmental stress. In A. besseyi, two putative trehalose-6-phosphate synthase genes (TPS) encoding enzymes catalyzing trehalose synthesis, and a putative trehalase gene (TRE) encoding enzymes that catalyze hydrolysis of trehalose were identified and then characterized based on their transcriptome. RT-qPCR analyses showed that each of these genes is expressed as mRNA when A. besseyi is entering in, during and recovering from osmobiosis, but only for certain periods. The changes of TRE activity were consistent with the transcript level changes of the TRE gene, and the trehalose level declined at certain periods when the nematodes were in, as well as recovering from, osmobiosis; this suggested that the hydrolysis of threhalose is essential. The feeding method of RNA interference (RNAi) was used to temporarily knock down the expression of each of the TPS and TRE genes. No obviously different phenotype was observed from any of the genes silenced individually or simultaneously, but the survival under hypertonic osmotic pressure reduced significantly and the recovery was delayed. These results indicated that trehalose metabolism genes should play a role in osmobiosis regulation and function within a restricted time frame. Summary: Trehalose metabolism genes should play a role in osmobiosis regulation and also function within a restricted time frame. Silence of any of these genes will cut down the nematode survival under hypertonic osmotic condition.
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Affiliation(s)
- Qiaoli Chen
- College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Danlei Li
- College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Feng Wang
- College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Ruizhi Zhang
- College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Yaming Ling
- College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China
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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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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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Banerjee A, Poddar S, Manna S, Saha SK. Mutualistic association of rotifer Philodina roseola with the branchiuran fish ectoparasite Argulus bengalensis at its embryonic stage. Biol Lett 2016; 12:20151043. [PMID: 27009886 DOI: 10.1098/rsbl.2015.1043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/28/2016] [Indexed: 11/12/2022] Open
Abstract
Several rotifers including Philodina spp. are well known to make commensal and parasitic associations with different animals. The present investigation was carried out to decipher the relationship of Philodina roseola with a piscine ectoparasite Argulus bengalensis in its embryonic stage. Mechanical removal of the symbiont P. roseola from the argulid egg strips resulted in the complete (100%) failure in hatching. Several P. roseola individuals were found to feed on the solidified jelly coat of the eggs enabling the larvae to emerge under both laboratory and field conditions. Under the laboratory condition, the experimental removal of P. roseola did not affect the embryonic development, but it rendered the jelly coat intact; therefore, the larvae were unable to make hatching furrow and subsequently died. The results of our experiments thus prove this service-resource relationship to be a mutualism. Although the association is facultative for P. roseola, it is obligatory for Argulus spp. An act of intervention in this relationship thus offers a promising control of argulosis.
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Affiliation(s)
- Anirban Banerjee
- Fish Biology Research Unit, Department of Zoology, Visva-Bharati, Santiniketan 731235, India
| | - Soumabrota Poddar
- Fish Biology Research Unit, Department of Zoology, Visva-Bharati, Santiniketan 731235, India
| | - Subha Manna
- Department of Zoology, Jhargram Raj College, Jhargram 721507, India
| | - Samar Kumar Saha
- Fish Biology Research Unit, Department of Zoology, Visva-Bharati, Santiniketan 731235, India
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Kondo K, Kubo T, Kunieda T. Suggested Involvement of PP1/PP2A Activity and De Novo Gene Expression in Anhydrobiotic Survival in a Tardigrade, Hypsibius dujardini, by Chemical Genetic Approach. PLoS One 2015; 10:e0144803. [PMID: 26690982 PMCID: PMC4686906 DOI: 10.1371/journal.pone.0144803] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 11/24/2015] [Indexed: 12/19/2022] Open
Abstract
Upon desiccation, some tardigrades enter an ametabolic dehydrated state called anhydrobiosis and can survive a desiccated environment in this state. For successful transition to anhydrobiosis, some anhydrobiotic tardigrades require pre-incubation under high humidity conditions, a process called preconditioning, prior to exposure to severe desiccation. Although tardigrades are thought to prepare for transition to anhydrobiosis during preconditioning, the molecular mechanisms governing such processes remain unknown. In this study, we used chemical genetic approaches to elucidate the regulatory mechanisms of anhydrobiosis in the anhydrobiotic tardigrade, Hypsibius dujardini. We first demonstrated that inhibition of transcription or translation drastically impaired anhydrobiotic survival, suggesting that de novo gene expression is required for successful transition to anhydrobiosis in this tardigrade. We then screened 81 chemicals and identified 5 chemicals that significantly impaired anhydrobiotic survival after severe desiccation, in contrast to little or no effect on survival after high humidity exposure only. In particular, cantharidic acid, a selective inhibitor of protein phosphatase (PP) 1 and PP2A, exhibited the most profound inhibitory effects. Another PP1/PP2A inhibitor, okadaic acid, also significantly and specifically impaired anhydrobiotic survival, suggesting that PP1/PP2A activity plays an important role for anhydrobiosis in this species. This is, to our knowledge, the first report of the required activities of signaling molecules for desiccation tolerance in tardigrades. The identified inhibitory chemicals could provide novel clues to elucidate the regulatory mechanisms underlying anhydrobiosis in tardigrades.
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Affiliation(s)
- Koyuki Kondo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113–0033, Japan
| | - Takeo Kubo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113–0033, Japan
| | - Takekazu Kunieda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113–0033, Japan
- * E-mail:
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Bailey TL, Wang M, Solocinski J, Nathan BP, Chakraborty N, Menze MA. Protective effects of osmolytes in cryopreserving adherent neuroblastoma (Neuro-2a) cells. Cryobiology 2015; 71:472-80. [PMID: 26408850 DOI: 10.1016/j.cryobiol.2015.08.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 08/12/2015] [Accepted: 08/26/2015] [Indexed: 12/13/2022]
Abstract
A simple method to cryopreserve adherent monolayers of neuronal cells is currently not available, but the development of this technique could facilitate numerous applications in the field of biomedical engineering, cell line development, and drug screening. However, complex tissues of some exceptional animals survive freezing in nature. These animals are known to accumulate several small molecular weight solutes prior to freezing. Following a similar strategy, we investigated the effects of osmolytes such as trehalose, proline, and sucrose as additives to the traditional cryoprotectant dimethyl sulfoxide (Me2SO) in modulating the cryopreservation outcome of mouse neuroblastoma (Neuro-2a) cells. Neuro-2a cells adhered to cell culture plates were incubated for 24 h at varying concentrations of trehalose, proline, sucrose and combinations of these compounds. Cells were cryopreserved for 24 h and cell viability post-freezing and thawing was quantified by trypan blue exclusion assay. On average, only 13.5% of adherent cells survived freezing in the presence of 10% Me2SO alone (control). Pre-incubation of cells with medium containing both trehalose and proline severely decreased cell proliferation, but increased cell recovery to about 53% of control. Furthermore, characterization using Raman microspectroscopy revealed that the addition of both trehalose and proline to 10% Me2SO substantially increased the size, and altered the nature, of ice crystals formed during freezing. Our results suggest that pre-incubation of Neuro-2a cells with trehalose and proline in combination provides cell protection along with alterations of ice structure in order to increase cell survival post-freezing.
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Affiliation(s)
- Trisha L Bailey
- Department of Biological Sciences, Eastern Illinois University, Charleston, IL 61920, USA
| | - Mian Wang
- Department of Mechanical Engineering, University of Michigan, Dearborn, MI 48128, USA
| | - Jason Solocinski
- Department of Mechanical Engineering, University of Michigan, Dearborn, MI 48128, USA
| | - Britto P Nathan
- Department of Biological Sciences, Eastern Illinois University, Charleston, IL 61920, USA
| | - Nilay Chakraborty
- Department of Mechanical Engineering, University of Michigan, Dearborn, MI 48128, USA
| | - Michael A Menze
- Department of Biological Sciences, Eastern Illinois University, Charleston, IL 61920, USA.
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Against All Odds: Trehalose-6-Phosphate Synthase and Trehalase Genes in the Bdelloid Rotifer Adineta vaga Were Acquired by Horizontal Gene Transfer and Are Upregulated during Desiccation. PLoS One 2015; 10:e0131313. [PMID: 26161530 PMCID: PMC4498783 DOI: 10.1371/journal.pone.0131313] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/31/2015] [Indexed: 01/15/2023] Open
Abstract
The disaccharide sugar trehalose is essential for desiccation resistance in most metazoans that survive dryness; however, neither trehalose nor the enzymes involved in its metabolism have ever been detected in bdelloid rotifers despite their extreme resistance to desiccation. Here we screened the genome of the bdelloid rotifer Adineta vaga for genes involved in trehalose metabolism. We discovered a total of four putative trehalose-6-phosphate synthase (TPS) and seven putative trehalase (TRE) gene copies in the genome of this ameiotic organism; however, no trehalose-6-phosphate phosphatase (TPP) gene or domain was detected. The four TPS copies of A. vaga appear more closely related to plant and fungi proteins, as well as to some protists, whereas the seven TRE copies fall in bacterial clades. Therefore, A. vaga likely acquired its trehalose biosynthesis and hydrolysis genes by horizontal gene transfers. Nearly all residues important for substrate binding in the predicted TPS domains are highly conserved, supporting the hypothesis that several copies of the genes might be functional. Besides, RNAseq library screening showed that trehalase genes were highly expressed compared to TPS genes, explaining probably why trehalose had not been detected in previous studies of bdelloids. A strong overexpression of their TPS genes was observed when bdelloids enter desiccation, suggesting a possible signaling role of trehalose-6-phosphate or trehalose in this process.
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Szydlowski L, Boschetti C, Crisp A, Barbosa E, Tunnacliffe A. Multiple horizontally acquired genes from fungal and prokaryotic donors encode cellulolytic enzymes in the bdelloid rotifer Adineta ricciae. Gene 2015; 566:125-37. [DOI: 10.1016/j.gene.2015.04.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 04/01/2015] [Accepted: 04/03/2015] [Indexed: 10/23/2022]
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Popova AV, Rausch S, Hundertmark M, Gibon Y, Hincha DK. The intrinsically disordered protein LEA7 from Arabidopsis thaliana protects the isolated enzyme lactate dehydrogenase and enzymes in a soluble leaf proteome during freezing and drying. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1517-25. [PMID: 25988244 DOI: 10.1016/j.bbapap.2015.05.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 04/24/2015] [Accepted: 05/10/2015] [Indexed: 10/23/2022]
Abstract
The accumulation of Late Embryogenesis Abundant (LEA) proteins in plants is associated with tolerance against stresses such as freezing and desiccation. Two main functions have been attributed to LEA proteins: membrane stabilization and enzyme protection. We have hypothesized previously that LEA7 from Arabidopsis thaliana may stabilize membranes because it interacts with liposomes in the dry state. Here we show that LEA7, contrary to this expectation, did not stabilize liposomes during drying and rehydration. Instead, it partially preserved the activity of the enzyme lactate dehydrogenase (LDH) during drying and freezing. Fourier-transform infrared (FTIR) spectroscopy showed no evidence of aggregation of LDH in the dry or rehydrated state under conditions that lead to complete loss of activity. To approximate the complex influence of intracellular conditions on the protective effects of a LEA protein in a convenient in-vitro assay, we measured the activity of two Arabidopsis enzymes (glucose-6-P dehydrogenase and ADP-glucose pyrophosphorylase) in total soluble leaf protein extract (Arabidopsis soluble proteome, ASP) after drying and rehydration or freezing and thawing. LEA7 partially preserved the activity of both enzymes under these conditions, suggesting its role as an enzyme protectant in vivo. Further FTIR analyses indicated the partial reversibility of protein aggregation in the dry ASP during rehydration. Similarly, aggregation in the dry ASP was strongly reduced by LEA7. In addition, mixtures of LEA7 with sucrose or verbascose reduced aggregation more than the single additives, presumably through the effects of the protein on the H-bonding network of the sugar glasses.
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Affiliation(s)
- Antoaneta V Popova
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Saskia Rausch
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Michaela Hundertmark
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Yves Gibon
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Dirk K Hincha
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany.
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Increasing intracellular trehalose is sufficient to confer desiccation tolerance to Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2015; 112:6122-7. [PMID: 25918381 DOI: 10.1073/pnas.1506415112] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Diverse organisms capable of surviving desiccation, termed anhydrobiotes, include species from bacteria, yeast, plants, and invertebrates. However, most organisms are sensitive to desiccation, likely due to an assortment of different stresses such as protein misfolding and aggregation, hyperosmotic stress, membrane fracturing, and changes in cell volume and shape leading to an overcrowded cytoplasm and metabolic arrest. The exact stress(es) that cause lethality in desiccation-sensitive organisms and how the lethal stresses are mitigated in desiccation-tolerant organisms remain poorly understood. The presence of trehalose in anhydrobiotes has been strongly correlated with desiccation tolerance. In the yeast Saccharomyces cerevisiae, trehalose is essential for survival after long-term desiccation. Here, we establish that the elevation of intracellular trehalose in dividing yeast by its import from the media converts yeast from extreme desiccation sensitivity to a high level of desiccation tolerance. This trehalose-induced tolerance is independent of utilization of trehalose as an energy source, de novo synthesis of other stress effectors, or the metabolic effects of trehalose biosynthetic intermediates, indicating that a chemical property of trehalose is directly responsible for desiccation tolerance. Finally, we demonstrate that elevated intracellular maltose can also make dividing yeast tolerant to short-term desiccation, indicating that other disaccharides have stress effector activity. However, trehalose is much more effective than maltose at conferring tolerance to long-term desiccation. The effectiveness and sufficiency of trehalose as an antagonizer of desiccation-induced damage in yeast emphasizes its potential to confer desiccation tolerance to otherwise sensitive organisms.
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Hespeels B, Knapen M, Hanot-Mambres D, Heuskin AC, Pineux F, LUCAS S, Koszul R, Van Doninck K. Gateway to genetic exchange? DNA double-strand breaks in the bdelloid rotifer Adineta vaga submitted to desiccation. J Evol Biol 2015; 27:1334-45. [PMID: 25105197 DOI: 10.1111/jeb.12326] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The bdelloid rotifer lineage Adineta vaga inhabits temporary habitats subjected to frequent episodes of drought. The recently published draft sequence of the genome of A. vaga revealed a peculiar genomic structure incompatible with meiosis and suggesting that DNA damage induced by desiccation may have reshaped the genomic structure of these organisms. However, the causative link between DNA damage and desiccation has never been proven to date in rotifers. To test for the hypothesis that desiccation induces DNA double-strand breaks (DSBs), we developed a protocol allowing a high survival rate of desiccated A. vaga. Using pulsed-field gel electrophoresis to monitor genomic integrity, we followed the occurrence of DSBs in dried bdelloids and observed an accumulation of these breaks with time spent in dehydrated state. These DSBs are gradually repaired upon rehydration. Even when the genome was entirely shattered into small DNA fragments by proton radiation, A. vaga individuals were able to efficiently recover from desiccation and repair a large amount of DSBs. Interestingly, when investigating the influence of UV-A and UV-B exposure on the genomic integrity of desiccated bdelloids, we observed that these natural radiations also caused important DNA DSBs, suggesting that the genome is not protected during the desiccated stage but that the repair mechanisms are extremely efficient in these intriguing organisms.
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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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Boswell LC, Menze MA, Hand SC. Group 3 late embryogenesis abundant proteins from embryos of Artemia franciscana: structural properties and protective abilities during desiccation. Physiol Biochem Zool 2014; 87:640-51. [PMID: 25244376 DOI: 10.1086/676936] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Group 3 late embryogenesis abundant (LEA) proteins are highly hydrophilic, and their expression is associated with desiccation tolerance in both plants and animals. Here we show that two LEA proteins from embryos of Artemia franciscana, AfrLEA2 and AfrLEA3m, are intrinsically disordered in solution but upon desiccation gain secondary structure, as measured by circular dichroism. Trifluoroethanol and sodium dodecyl sulfate are both shown to induce α-helical structure in AfrLEA2 and AfrLEA3m. Bioinformatic predictions of secondary-structure content for both proteins correspond most closely to conformations measured in the dry state. Because some LEA proteins afford protection to desiccation-sensitive proteins during drying and subsequent rehydration, we tested for this capacity in AfrLEA2 and AfrLEA3m. The protective capacities vary, depending on the target enzyme. For the cytoplasmic enzyme lactate dehydrogenase, neither AfrLEA2 nor AfrLEA3m, with or without trehalose present, was able to afford protection better than that provided by bovine serum albumin (BSA) under the same conditions. However, for another cytoplasmic enzyme, phosphofructokinase, both AfrLEA2 and AfrLEA3m in the presence of trehalose were able to afford protection far greater than that provided by BSA with trehalose. Finally, for the mitochondrial enzyme citrate synthase, 400-μg/mL AfrLEA3m without trehalose provided significantly more protection than the same concentration of either AfrLEA2 or BSA.
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Affiliation(s)
- Leaf C Boswell
- Division of Cellular, Developmental, and Integrative Biology, Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803; 2Department of Biological Sciences, Eastern Illinois University, Charleston, Illinois 61920
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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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Ito C, Goto SG, Numata H. Desiccation and heat tolerance of eggs of the Asian tadpole shrimp, Triops granarius. Zoolog Sci 2013; 30:760-6. [PMID: 24004083 DOI: 10.2108/zsj.30.760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Triops granarius (Lucas) is a freshwater crustacean that is distributed from South Africa to the Eurasian continent. This species lives in temporary water pools and is exposed to desiccation and extreme temperatures after the water dries up in its habitat. To withstand this severe environment, Triops eggs enter anhydrobiosis when dehydrated. To clarify the physiological characteristics of T. granarius anhydrobiosis, we examined hatching rates after rehydration of eggs that were dehydrated at several humidity levels for 10 or 100 days. Lower humidity produced higher hatching rates when dehydration was continued for 100 days. These results suggest that drying at low humidity is required for long-term anhydrobiosis of T. granarius eggs. The eggs survived desiccation when dehydrated at the blastula, gastrula, and early organogenesis stages. The most dehydration-tolerant stage was early organogenesis. Non-dehydrated eggs hatched after temperature treatments of up to 50°C for 1 h, but did not hatch after exposure to 60°C for 1 h in air and under water. Similar results were obtained for dehydrated eggs exposed to high temperatures under water. In contrast, dehydrated eggs hatched after 1 h at 80°C in air but did not after 1 h at 90°C in air. Our results show that Triops eggs exhibit tolerance for desiccation and high temperature in a dried state, once they have entered anhydrobiosis.
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Affiliation(s)
- Chihiro Ito
- 1 Graduate School of Science, Osaka City University, Osaka 558-8585, Japan
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Tripathi R, Boschetti C, McGee B, Tunnacliffe A. Trafficking of bdelloid rotifer late embryogenesis abundant proteins. ACTA ACUST UNITED AC 2012; 215:2786-94. [PMID: 22837450 DOI: 10.1242/jeb.071647] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The bdelloid rotifer Adineta ricciae is an asexual microinvertebrate that can survive desiccation by entering an ametabolic state known as anhydrobiosis. Two late embryogenesis abundant (LEA) proteins, ArLEA1A and ArLEA1B, have been hypothesized to contribute to desiccation tolerance in these organisms, since in vitro assays suggest that ArLEA1A and ArLEA1B stabilize desiccation-sensitive proteins and membranes, respectively. To examine their functions in vivo, it is important to analyse the cellular distribution of the bdelloid LEA proteins. Bioinformatics predicted their translocation into the endoplasmic reticulum (ER) via an N-terminal ER translocation signal and persistence in the same compartment via a variant C-terminal retention signal sequence ATEL. We assessed the localization of LEA proteins in bdelloids and in a mammalian cell model. The function of the N-terminal sequence of ArLEA1A and ArLEA1B in mediating ER translocation was verified, but our data showed that, unlike classical ER-retention signals, ATEL allows progression from the ER to the Golgi and limited secretion of the proteins into the extracellular medium. These results suggest that the N-terminal ER translocation signal and C-terminal ATEL sequence act together to regulate the distribution of rotifer LEA proteins within intracellular vesicular compartments, as well as the extracellular space. We speculate that this mechanism allows a small number of LEA proteins to offer protection to a large number of desiccation-sensitive molecules and structures both inside and outside cells in the bdelloid rotifer.
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Affiliation(s)
- Rashmi Tripathi
- Cell and Organism Engineering Laboratory, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB2 3RA, UK
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Boschetti C, Carr A, Crisp A, Eyres I, Wang-Koh Y, Lubzens E, Barraclough TG, Micklem G, Tunnacliffe A. Biochemical diversification through foreign gene expression in bdelloid rotifers. PLoS Genet 2012; 8:e1003035. [PMID: 23166508 PMCID: PMC3499245 DOI: 10.1371/journal.pgen.1003035] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 08/29/2012] [Indexed: 11/19/2022] Open
Abstract
Bdelloid rotifers are microinvertebrates with unique characteristics: they have survived tens of millions of years without sexual reproduction; they withstand extreme desiccation by undergoing anhydrobiosis; and they tolerate very high levels of ionizing radiation. Recent evidence suggests that subtelomeric regions of the bdelloid genome contain sequences originating from other organisms by horizontal gene transfer (HGT), of which some are known to be transcribed. However, the extent to which foreign gene expression plays a role in bdelloid physiology is unknown. We address this in the first large scale analysis of the transcriptome of the bdelloid Adineta ricciae: cDNA libraries from hydrated and desiccated bdelloids were subjected to massively parallel sequencing and assembled transcripts compared against the UniProtKB database by blastx to identify their putative products. Of ~29,000 matched transcripts, ~10% were inferred from blastx matches to be horizontally acquired, mainly from eubacteria but also from fungi, protists, and algae. After allowing for possible sources of error, the rate of HGT is at least 8%-9%, a level significantly higher than other invertebrates. We verified their foreign nature by phylogenetic analysis and by demonstrating linkage of foreign genes with metazoan genes in the bdelloid genome. Approximately 80% of horizontally acquired genes expressed in bdelloids code for enzymes, and these represent 39% of enzymes in identified pathways. Many enzymes encoded by foreign genes enhance biochemistry in bdelloids compared to other metazoans, for example, by potentiating toxin degradation or generation of antioxidants and key metabolites. They also supplement, and occasionally potentially replace, existing metazoan functions. Bdelloid rotifers therefore express horizontally acquired genes on a scale unprecedented in animals, and foreign genes make a profound contribution to their metabolism. This represents a potential mechanism for ancient asexuals to adapt rapidly to changing environments and thereby persist over long evolutionary time periods in the absence of sex.
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Affiliation(s)
- Chiara Boschetti
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Adrian Carr
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Cambridge Systems Biology Centre, Cambridge, United Kingdom
| | - Alastair Crisp
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Isobel Eyres
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Yuan Wang-Koh
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Esther Lubzens
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
- National Institute of Oceanography, Haifa, Israel
| | | | - Gos Micklem
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Cambridge Systems Biology Centre, Cambridge, United Kingdom
- * E-mail: (G Micklem); (A Tunnacliffe)
| | - Alan Tunnacliffe
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (G Micklem); (A Tunnacliffe)
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