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Shatilovich A, Gade VR, Pippel M, Hoffmeyer TT, Tchesunov AV, Stevens L, Winkler S, Hughes GM, Traikov S, Hiller M, Rivkina E, Schiffer PH, Myers EW, Kurzchalia TV. A novel nematode species from the Siberian permafrost shares adaptive mechanisms for cryptobiotic survival with C. elegans dauer larva. PLoS Genet 2023; 19:e1010798. [PMID: 37498820 PMCID: PMC10374039 DOI: 10.1371/journal.pgen.1010798] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/24/2023] [Indexed: 07/29/2023] Open
Abstract
Some organisms in nature have developed the ability to enter a state of suspended metabolism called cryptobiosis when environmental conditions are unfavorable. This state-transition requires execution of a combination of genetic and biochemical pathways that enable the organism to survive for prolonged periods. Recently, nematode individuals have been reanimated from Siberian permafrost after remaining in cryptobiosis. Preliminary analysis indicates that these nematodes belong to the genera Panagrolaimus and Plectus. Here, we present precise radiocarbon dating indicating that the Panagrolaimus individuals have remained in cryptobiosis since the late Pleistocene (~46,000 years). Phylogenetic inference based on our genome assembly and a detailed morphological analysis demonstrate that they belong to an undescribed species, which we named Panagrolaimus kolymaensis. Comparative genome analysis revealed that the molecular toolkit for cryptobiosis in P. kolymaensis and in C. elegans is partly orthologous. We show that biochemical mechanisms employed by these two species to survive desiccation and freezing under laboratory conditions are similar. Our experimental evidence also reveals that C. elegans dauer larvae can remain viable for longer periods in suspended animation than previously reported. Altogether, our findings demonstrate that nematodes evolved mechanisms potentially allowing them to suspend life over geological time scales.
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Affiliation(s)
- Anastasia Shatilovich
- Institute of Physicochemical and Biological Problems in Soil Science RAS, Pushchino, Russia
- Zoological Institute RAS, St. Petersburg, Russia
| | - Vamshidhar R. Gade
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
| | | | | | - Alexei V. Tchesunov
- Department of Invertebrate Zoology, Lomonosov Moscow State University, Moscow, Russia
| | - Lewis Stevens
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Sylke Winkler
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
- DRESDEN concept Genome Center, Dresden, Germany
| | - Graham M. Hughes
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin, Ireland
| | - Sofia Traikov
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | - Michael Hiller
- Center for Systems Biology, Dresden, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Society for Nature Research & Goethe University, Frankfurt am Main, Germany
| | - Elizaveta Rivkina
- Institute of Physicochemical and Biological Problems in Soil Science RAS, Pushchino, Russia
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2
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Deciphering the mechanism of anhydrobiosis in the entomopathogenic nematode Heterorhabditis indica through comparative transcriptomics. PLoS One 2022; 17:e0275342. [PMID: 36301967 PMCID: PMC9612587 DOI: 10.1371/journal.pone.0275342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 09/14/2022] [Indexed: 11/07/2022] Open
Abstract
The entomopathogenic nematode, Heterorhabditis indica, is a popular biocontrol agent of high commercial significance. It possesses tremendous genetic architecture to survive desiccation stress by undergoing anhydrobiosis to increase its lifespan-an attribute exploited in the formulation technology. The comparative transcriptome of unstressed and anhydrobiotic H. indica revealed several previously concealed metabolic events crucial for adapting towards the moisture stress. During the induction of anhydrobiosis in the infective juveniles (IJ), 1584 transcripts were upregulated and 340 downregulated. As a strategy towards anhydrobiotic survival, the IJ showed activation of several genes critical to antioxidant defense, detoxification pathways, signal transduction, unfolded protein response and molecular chaperones and ubiquitin-proteasome system. Differential expression of several genes involved in gluconeogenesis - β-oxidation of fatty acids, glyoxylate pathway; glyceroneogenesis; fatty acid biosynthesis; amino-acid metabolism - shikimate pathway, sachharopine pathway, kyneurine pathway, lysine biosynthesis; one-carbon metabolism-polyamine pathway, transsulfuration pathway, folate cycle, methionine cycle, nucleotide biosynthesis; mevalonate pathway; and glyceraldehyde-3-phosphate dehydrogenase were also observed. We report the role of shikimate pathway, sachharopine pathway and glyceroneogenesis in anhydrobiotes, and seven classes of repeat proteins, specifically in H. indica for the first time. These results provide insights into anhydrobiotic survival strategies which can be utilized to strengthen the development of novel formulations with enhanced and sustained shelf-life.
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3
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Deciphering the Biological Enigma-Genomic Evolution Underlying Anhydrobiosis in the Phylum Tardigrada and the Chironomid Polypedilum vanderplanki. INSECTS 2022; 13:insects13060557. [PMID: 35735894 PMCID: PMC9224920 DOI: 10.3390/insects13060557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/13/2022] [Accepted: 06/17/2022] [Indexed: 02/04/2023]
Abstract
Anhydrobiosis, an ametabolic dehydrated state triggered by water loss, is observed in several invertebrate lineages. Anhydrobiotes revive when rehydrated, and seem not to suffer the ultimately lethal cell damage that results from severe loss of water in other organisms. Here, we review the biochemical and genomic evidence that has revealed the protectant molecules, repair systems, and maintenance pathways associated with anhydrobiosis. We then introduce two lineages in which anhydrobiosis has evolved independently: Tardigrada, where anhydrobiosis characterizes many species within the phylum, and the genus Polypedilum, where anhydrobiosis occurs in only two species. Finally, we discuss the complexity of the evolution of anhydrobiosis within invertebrates based on current knowledge, and propose perspectives to enhance the understanding of anhydrobiosis.
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4
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Soil Nematodes as the Silent Sufferers of Climate-Induced Toxicity: Analysing the Outcomes of Their Interactions with Climatic Stress Factors on Land Cover and Agricultural Production. Appl Biochem Biotechnol 2022; 195:2519-2586. [PMID: 35593954 DOI: 10.1007/s12010-022-03965-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/10/2022] [Indexed: 11/02/2022]
Abstract
Unsustainable anthropogenic activities over the last few decades have resulted in alterations of the global climate. It can be perceived through changes in the rainfall patterns and rise in mean annual temperatures. Climatic stress factors exert their effects on soil health mainly by modifying the soil microenvironments where the soil fauna reside. Among the members of soil fauna, the soil nematodes have been found to be sensitive to these stress factors primarily because of their low tolerance limits. Additionally, because of their higher and diverse trophic positions in the soil food web they can integrate the effects of many stress factors acting together. This is important because under natural conditions the climatic stress factors do not exert their effect individually. Rather, they interact amongst themselves and other abiotic stress factors in the soil to generate their impacts. Some of these interactions may be synergistic while others may be antagonistic. As such, it becomes very difficult to assess their impacts on soil health by simply analysing the physicochemical properties of soil. This makes soil nematodes outstanding candidates for studying the effects of climatic stress factors on soil biology. The knowledge obtained therefrom can be used to design sustainable agricultural practices because most of the conventional techniques aim at short-term benefits with complete disregard of soil biology. This can partly ensure food security in the coming decades for the expanding population. Moreover, understanding soil biology can help to preserve landscapes that have developed over long periods of climatic stability and belowground soil biota interactions.
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5
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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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6
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Wan X, Saito JA, Hou S, Geib SM, Yuryev A, Higa LM, Womersley CZ, Alam M. The Aphelenchus avenae genome highlights evolutionary adaptation to desiccation. Commun Biol 2021; 4:1232. [PMID: 34711923 PMCID: PMC8553787 DOI: 10.1038/s42003-021-02778-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 10/09/2021] [Indexed: 02/08/2023] Open
Abstract
Some organisms can withstand complete body water loss (losing up to 99% of body water) and stay in ametabolic state for decades until rehydration, which is known as anhydrobiosis. Few multicellular eukaryotes on their adult stage can withstand life without water. We still have an incomplete understanding of the mechanism for metazoan survival of anhydrobiosis. Here we report the 255-Mb genome of Aphelenchus avenae, which can endure relative zero humidity for years. Gene duplications arose genome-wide and contributed to the expansion and diversification of 763 kinases, which represents the second largest metazoan kinome to date. Transcriptome analyses of ametabolic state of A. avenae indicate the elevation of ATP level for global recycling of macromolecules and enhancement of autophagy in the early stage of anhydrobiosis. We catalogue 74 species-specific intrinsically disordered proteins, which may facilitate A. avenae to survive through desiccation stress. Our findings refine a molecular basis evolving for survival in extreme water loss and open the way for discovering new anti-desiccation strategies. Wan et al. report the genome and transcriptome of the Aphelenchus avenae nematode that can withstand long-term extreme desiccation. This study compares gene features to eight other nematode species and identifies intrinsically disordered proteins and changes in gene expression that contribute toward anhydrobiosis adaptation.
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Affiliation(s)
- Xuehua Wan
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, HI, USA. .,TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China.
| | - Jennifer A Saito
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, HI, USA
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, HI, USA
| | - Scott M Geib
- Tropical Crop and Commodity Protection Research Unit, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI, USA
| | - Anton Yuryev
- Elsevier Life Sciences Solutions, Rockville, MD, USA
| | - Lynne M Higa
- School of Life Sciences, University of Hawaii, Honolulu, HI, USA
| | | | - Maqsudul Alam
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, HI, USA
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7
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Weng L. Technologies and Applications Toward Preservation of Cells in a Dry State for Therapies. Biopreserv Biobank 2021; 19:332-341. [PMID: 33493407 DOI: 10.1089/bio.2020.0130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Cell-based therapeutics promise to transform the treatment of a wide range of diseases, many of which, up to this point, are incurable. During the past decade, an increasing number of cell therapies have been approved by government regulatory agencies in the United States, Europe, and Japan. Thousands of clinical trials based on live cell therapies are now taking place around the world. But most of these live cell therapies face temporal and/or spatial distances between manufacture and administration, posing a risk of degradation in potency. Cryopreservation has become the predominant biobanking approach to maintain the product's safety and efficacy during transportation and storage. However, the necessity of cryogenic shipment and storage could limit patient access to these emerging therapies and increase the costs of logistics. In the (bio)pharmaceutical industries, freeze-drying and desiccation are established preservation procedures for manufacturing small molecule drugs, liposomes, and monoclonal antibodies. Over the past two decades, there has been a growing body of research exploring the freeze-drying or drying of mammalian cells, with varying degrees of success. This article provides an overview of the technologies that were adopted or developed in these pioneering studies, paving the road toward the preservation of cell-based therapeutics in a dry state for biomanufacturing.
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Affiliation(s)
- Lindong Weng
- Sana Biotechnology, Inc., South San Francisco, California, USA
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8
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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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9
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Kijak H, Ratajczak E. What Do We Know About the Genetic Basis of Seed Desiccation Tolerance and Longevity? Int J Mol Sci 2020; 21:E3612. [PMID: 32443842 PMCID: PMC7279459 DOI: 10.3390/ijms21103612] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 01/02/2023] Open
Abstract
Long-term seed storage is important for protecting both economic interests and biodiversity. The extraordinary properties of seeds allow us to store them in the right conditions for years. However, not all types of seeds are resilient, and some do not tolerate extreme desiccation or low temperature. Seeds can be divided into three categories: (1) orthodox seeds, which tolerate water losses of up to 7% of their water content and can be stored at low temperature; (2) recalcitrant seeds, which require a humidity of 27%; and (3) intermediate seeds, which lose their viability relatively quickly compared to orthodox seeds. In this article, we discuss the genetic bases for desiccation tolerance and longevity in seeds and the differences in gene expression profiles between the mentioned types of seeds.
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Affiliation(s)
- Hanna Kijak
- Institute of Dendrology, Polish Academy of Sciences, 62-035 Kórnik, Poland;
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10
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Schiffer PH, Danchin EGJ, Burnell AM, Creevey CJ, Wong S, Dix I, O'Mahony G, Culleton BA, Rancurel C, Stier G, Martínez-Salazar EA, Marconi A, Trivedi U, Kroiher M, Thorne MAS, Schierenberg E, Wiehe T, Blaxter M. Signatures of the Evolution of Parthenogenesis and Cryptobiosis in the Genomes of Panagrolaimid Nematodes. iScience 2019; 21:587-602. [PMID: 31759330 PMCID: PMC6889759 DOI: 10.1016/j.isci.2019.10.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 07/17/2019] [Accepted: 10/21/2019] [Indexed: 12/12/2022] Open
Abstract
Most animal species reproduce sexually and fully parthenogenetic lineages are usually short lived in evolution. Still, parthenogenesis may be advantageous as it avoids the cost of sex and permits colonization by single individuals. Panagrolaimid nematodes have colonized environments ranging from arid deserts to Arctic and Antarctic biomes. Many are obligatory meiotic parthenogens, and most have cryptobiotic abilities, being able to survive repeated cycles of complete desiccation and freezing. To identify systems that may contribute to these striking abilities, we sequenced and compared the genomes and transcriptomes of parthenogenetic and outcrossing panagrolaimid species, including cryptobionts and non-cryptobionts. The parthenogens are triploids, most likely originating through hybridization. Adaptation to cryptobiosis shaped the genomes of panagrolaimid nematodes and is associated with the expansion of gene families and signatures of selection on genes involved in cryptobiosis. All panagrolaimids have acquired genes through horizontal gene transfer, some of which are likely to contribute to cryptobiosis.
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Affiliation(s)
- Philipp H Schiffer
- CLOE, Department for Biosciences, University College London, London, UK; Zoologisches Institut, Universität zu Köln, 50674 Köln, Germany; Institut für Genetik, Universität zu Köln, 50674 Köln, Germany.
| | | | - Ann M Burnell
- Maynooth University Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
| | | | - Simon Wong
- Irish Centre for High-End Computing, Tower Building, Trinity Technology & Enterprise Campus, Grand Canal Quay, Dublin D02 HP83, Ireland
| | - Ilona Dix
- Maynooth University Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
| | - Georgina O'Mahony
- Maynooth University Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
| | - Bridget A Culleton
- Maynooth University Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland; Megazyme, Bray Business Park, Bray, Co. Wicklow A98 YV29, Ireland
| | | | - Gary Stier
- Zoologisches Institut, Universität zu Köln, 50674 Köln, Germany
| | - Elizabeth A Martínez-Salazar
- Unidad Académica de Ciencias Biológicas, Laboratorio de Colecciones Biológicas y Sistemática Molecular, Universidad Autónoma de Zacatecas, Zacatecas, México
| | - Aleksandra Marconi
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Urmi Trivedi
- Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Michael Kroiher
- Zoologisches Institut, Universität zu Köln, 50674 Köln, Germany
| | - Michael A S Thorne
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | | | - Thomas Wiehe
- Institut für Genetik, Universität zu Köln, 50674 Köln, Germany
| | - Mark Blaxter
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3FL, UK; Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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11
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Vasanthan T, Nederveen JP, Stone J. Quantum-like decreased embryogenesis time with increased cold exposure time. Sci Rep 2019; 9:1229. [PMID: 30718526 PMCID: PMC6362279 DOI: 10.1038/s41598-018-35396-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 06/13/2018] [Indexed: 11/10/2022] Open
Abstract
Three theoretical models have been proposed to explain lifespan extension resulting from exposure to extreme conditions in microscopic animals: individuals become completely dormant and stop aging, continue to age or age but at a diminished rate. Here we show that the earliest life history stages, embryonic cell divisions, in the tardigrade species Hypsibius dujardini are retarded when eggs are reared at 0 °C. Compared to control specimens reared at 22 °C, juveniles that hatched from eggs exposed to 0 °C for 4 days and returned to 22 °C experienced a three-day lag, indicating that their biological age was less than their chronological age. As cold exposure duration increased (days = 10, 20, 40), incubation period at 22 °C decreased incrementally (days = 3, 2, 1), suggesting that tardigrades involve a threshold-determined, quantum-like, energetic-based system for controlling embryogenesis.
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Affiliation(s)
- Tarushika Vasanthan
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada.,Origins Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4M1, Canada
| | - Joshua P Nederveen
- Department of Kinesiology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Jonathon Stone
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada. .,Origins Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4M1, Canada.
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12
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Kitazume H, Dayi M, Tanaka R, Kikuchi T. Assessment of the behaviour and survival of nematodes under low oxygen concentrations. PLoS One 2018; 13:e0197122. [PMID: 29758056 PMCID: PMC5951539 DOI: 10.1371/journal.pone.0197122] [Citation(s) in RCA: 11] [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: 07/12/2017] [Accepted: 04/26/2018] [Indexed: 11/18/2022] Open
Abstract
Oxygen is required for the completion of almost all known metazoan lifecycles, but many metazoans harbour abilities to withstand varying degrees and periods of hypoxia. Caenorhabditis elegans, one of the most popular model organism is extensively used as a model for the study of hypoxia and anoxia biology and it has been found that this nematode is capable of tolerance to varying degrees of hypoxia. Considering the extremely high diversity of nematodes, the effects of low oxygen concentration and mechanisms of adaptation to oxygen depletion differ among species. In this study, we used a simple assay to examine anoxia tolerance in four nematode species, including three free-living and one plant parasitic nematode. We found that the plant parasitic nematode Bursaphelenchus xylophilus can survive more than 14 days under anoxic conditions. Comparisons of behaviour during anoxia induction and the repertoire of oxygen sensation genes among the tested species suggested the existence of different oxygen sensation systems between B. xylophilus and C. elegans, which quickly introduce suspended animation in response to oxygen depletion to survive long-term anoxia.
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Affiliation(s)
- Hiromi Kitazume
- Division of Parasitology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Mehmet Dayi
- Faculty of Forestry, Duzce University, Konuralp Campus, Duzce, Turkey
| | - Ryusei Tanaka
- Division of Parasitology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Taisei Kikuchi
- Division of Parasitology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
- * E-mail:
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13
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Involvement of Heat Shock Proteins in Invertebrate Anhydrobiosis. HEAT SHOCK PROTEINS AND STRESS 2018. [DOI: 10.1007/978-3-319-90725-3_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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14
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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: 6] [Impact Index Per Article: 0.9] [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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15
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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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16
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17
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Yaari M, Doron-Faigenboim A, Koltai H, Salame L, Glazer I. Transcriptome analysis of stress tolerance in entomopathogenic nematodes of the genus Steinernema. Int J Parasitol 2015; 46:83-95. [PMID: 26598027 DOI: 10.1016/j.ijpara.2015.08.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Revised: 08/13/2015] [Accepted: 08/14/2015] [Indexed: 11/16/2022]
Abstract
Entomopathogenic nematodes of the genus Steinernema are effective biological control agents. The infective stage of these parasites can withstand environmental stresses such as desiccation and heat, but the molecular and physiological mechanisms involved in this tolerance are poorly understood. We used 454 pyrosequencing to analyse transcriptome expression in Steinernema spp. that differ in their tolerance to stress. We compared these species, following heat and desiccation treatments, with their non-stressed counterparts. More than 98% of the transcripts found matched homologous sequences in the UniRef90 database, mostly nematode genes (85%). Among those, 60.8% aligned to the vertebrate parasites including Ascaris suum, Loa loa, and Brugia malayi, 23.3% aligned to bacteriovores, mostly from the genus Caenorhabditis, and 1% aligned to EPNs. Analysing gene expression patterns of the stress response showed a large fraction of down-regulated genes in the desiccation-tolerant nematode Steinernema riobrave, whereas a larger fraction of the genes in the susceptible Steinernema feltiae Carmiel and Gvulot strains were up-regulated. We further compared metabolic pathways and the expression of specific stress-related genes. In the more tolerant nematode, more genes were down-regulated whereas in the less tolerant strains, more genes were up-regulated. This phenomenon warrants further exploration of the mechanism governing induction of the down-regulation process. The present study revealed many genes and metabolic cycles that are differentially expressed in the stressed nematodes. Some of those are well known in other nematodes or anhydrobiotic organisms, but several are new and should be further investigated for their involvement in desiccation and heat tolerance. Our data establish a foundation for further exploration of stress tolerance in entomopathogenic nematodes and, in the long term, for improving their ability to withstand suboptimal environmental conditions.
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Affiliation(s)
- Mor Yaari
- Department of Entomology and Nematology, Agricultural Research Organization, The Volcani Center, P.O. Box 6, Bet Dagan 50250, Israel
| | - Adi Doron-Faigenboim
- Department of Ornamental Horticulture, Agricultural Research Organization, Israel
| | - Hinanit Koltai
- Department of Ornamental Horticulture, Agricultural Research Organization, Israel
| | - Liora Salame
- Department of Entomology and Nematology, Agricultural Research Organization, The Volcani Center, P.O. Box 6, Bet Dagan 50250, Israel
| | - Itamar Glazer
- Department of Entomology and Nematology, Agricultural Research Organization, The Volcani Center, P.O. Box 6, Bet Dagan 50250, Israel.
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18
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Anderson D, Ferreras E, Trindade M, Cowan D. A novel bacterial Water Hypersensitivity-like protein shows in vivo protection against cold and freeze damage. FEMS Microbiol Lett 2015; 362:fnv110. [PMID: 26187747 DOI: 10.1093/femsle/fnv110] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2015] [Indexed: 11/13/2022] Open
Abstract
Metagenomic library screening, by functional or sequence analysis, has become an established method for the identification of novel genes and gene products, including genetic elements implicated in microbial stress response and adaptation. We have identified, using a sequence-based approach, a fosmid clone from an Antarctic desert soil metagenome library containing a novel gene which codes for a protein homologous to a Water Hypersensitivity domain (WHy). The WHy domain is typically found as a component of specific LEA (Late Embryogenesis Abundant) proteins, particularly the LEA-14 (LEA-8) variants, which occur widely in plants, nematodes, bacteria and archaea and which are typically induced by exposure to stress conditions. The novel WHy-like protein (165 amino acid, 18.6 kDa) exhibits a largely invariant NPN motif at the N-terminus and has high sequence identity to genes identified in Pseudomonas genomes. Expression of this protein in Escherichia coli significantly protected the recombinant host against cold and freeze stress.
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Affiliation(s)
- Dominique Anderson
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Bellville 7535, Cape Town, South Africa
| | - Eloy Ferreras
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Hatfield 0028, Pretoria, South Africa
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Bellville 7535, Cape Town, South Africa
| | - Don Cowan
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Bellville 7535, Cape Town, South Africa Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Hatfield 0028, Pretoria, South Africa
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19
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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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20
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Yang Y, Ma Y, Chen X, Guo X, Yan B, Du A. Screening and analysis of Hc-ubq and Hc-gst related to desiccation survival of infective Haemonchus contortus larvae. Vet Parasitol 2015; 210:179-85. [DOI: 10.1016/j.vetpar.2015.03.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 03/18/2015] [Accepted: 03/22/2015] [Indexed: 01/18/2023]
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21
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Culleton BA, Lall P, Kinsella GK, Doyle S, McCaffrey J, Fitzpatrick DA, Burnell AM. A role for the Parkinson's disease protein DJ-1 as a chaperone and antioxidant in the anhydrobiotic nematode Panagrolaimus superbus. Cell Stress Chaperones 2015; 20:121-37. [PMID: 25318690 PMCID: PMC4255249 DOI: 10.1007/s12192-014-0531-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/16/2014] [Accepted: 07/28/2014] [Indexed: 01/23/2023] Open
Abstract
Mutations in the human DJ-1/PARK7 gene are associated with familial Parkinson's disease. DJ-1 belongs to a large, functionally diverse family with homologues in all biological kingdoms. Several activities have been demonstrated for DJ-1: an antioxidant protein, a redox-regulated molecular chaperone and a modulator of multiple cellular signalling pathways. The majority of functional studies have focussed on human DJ-1 (hDJ-1), but studies on DJ-1 homologues in Drosophila melanogaster, Caenorhabditis elegans, Dugesia japonica and Escherichia coli also provide evidence of a role for DJ-1 as an antioxidant. Here, we show that dehydration is a potent inducer of a dj-1 gene in the anhydrobiotic nematode Panagrolaimus superbus. Our secondary structure and homology modelling analyses shows that recombinant DJ-1 protein from P. superbus (PsuDJ-1.1) is a well-folded protein, which is similar in structure to the hDJ-1. PsuDJ-1.1 is a heat stable protein; with T1/2 unfolding transition values of 76 and 70 °C obtained from both circular dichroism (CD) and Fourier transform infrared spectroscopy (FTIR) measurements respectively. We found that PsuDJ-1.1 is an efficient antioxidant that also functions as a 'holdase' molecular chaperone that can maintain its chaperone function in a reducing environment. In addition to its chaperone activity, PsuDJ-1.1 may also be an important non-enzymatic antioxidant, capable of providing protection to P. superbus from oxidative damage when the nematodes are in a desiccated, anhydrobiotic state.
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Affiliation(s)
- Bridget A. Culleton
- />Department of Biology, National University of Ireland Maynooth, Maynooth, Co Kildare Ireland
- />Megazyme International Ireland, Bray Business Park, Bray, Co Wicklow Ireland
| | - Patrick Lall
- />Department of Chemistry, National University of Ireland Maynooth, Maynooth, Co Kildare Ireland
| | - Gemma K. Kinsella
- />Department of Biology, National University of Ireland Maynooth, Maynooth, Co Kildare Ireland
| | - Sean Doyle
- />Department of Biology, National University of Ireland Maynooth, Maynooth, Co Kildare Ireland
| | - John McCaffrey
- />Department of Chemistry, National University of Ireland Maynooth, Maynooth, Co Kildare Ireland
| | - David A. Fitzpatrick
- />Department of Biology, National University of Ireland Maynooth, Maynooth, Co Kildare Ireland
| | - Ann M. Burnell
- />Department of Biology, National University of Ireland Maynooth, Maynooth, Co Kildare Ireland
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22
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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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23
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Thorne MAS, Kagoshima H, Clark MS, Marshall CJ, Wharton DA. Molecular analysis of the cold tolerant Antarctic nematode, Panagrolaimus davidi. PLoS One 2014; 9:e104526. [PMID: 25098249 PMCID: PMC4123951 DOI: 10.1371/journal.pone.0104526] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 07/11/2014] [Indexed: 01/25/2023] Open
Abstract
Isolated and established in culture from the Antarctic in 1988, the nematode Panagrolaimus davidi has proven to be an ideal model for the study of adaptation to the cold. Not only is it the best-documented example of an organism surviving intracellular freezing but it is also able to undergo cryoprotective dehydration. As part of an ongoing effort to develop a molecular understanding of this remarkable organism, we have assembled both a transcriptome and a set of genomic scaffolds. We provide an overview of the transcriptome and a survey of genes involved in temperature stress. We also explore, in silico, the possibility that P. davidi will be susceptible to an environmental RNAi response, important for further functional studies.
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Affiliation(s)
- Michael A. S. Thorne
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
- * E-mail:
| | - Hiroshi Kagoshima
- Transdisciplinary Research Integration Center, Research Organization of Information and Systems, Tokyo, Japan
- National Institute of Genetics, Mishima, Japan
| | - Melody S. Clark
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| | - Craig J. Marshall
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - David A. Wharton
- Department of Zoology, University of Otago, Dunedin, New Zealand
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Bauters L, Haegeman A, Kyndt T, Gheysen G. Analysis of the transcriptome of Hirschmanniella oryzae to explore potential survival strategies and host-nematode interactions. MOLECULAR PLANT PATHOLOGY 2014; 15:352-63. [PMID: 24279397 PMCID: PMC6638887 DOI: 10.1111/mpp.12098] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The rice root nematode Hirschmanniella oryzae is the most abundant plant-parasitic nematode in flooded rice fields and is distributed world-wide. Although it is economically less important than sedentary nematodes, it can cause severe yield reductions and economic losses in specific environmental conditions. No transcriptome data for this genus were available until now. We have performed 454 sequencing on a mixed life stages population to gain an insight into nematode-plant interactions and nematode survival strategies. The results of two assembly strategies were combined to reduce the redundancy of the data, generating a final dataset of 21 360 contigs. The data were screened for putative plant cell wall-modifying proteins, which facilitate nematode migration through host roots. A β-mannanase, previously not reported in nematodes, was detected in the dataset. The data were screened for putative effector proteins that may alter the host defence mechanism. Two enzymes, chorismate mutase and isochorismatase, thought to be involved in the salicyclic acid pathway, were identified. Experimental treatments of H. oryzae with artificial seawater showed that late embryogenesis abundant (LEA) proteins and SXP/RAL-2 are induced, suggesting that these proteins are involved in the process of anhydrobiosis. The newly generated data can highlight potential differences between sedentary and migratory nematodes, and will be useful in the further study of host-nematode interactions and the developmental biology of this nematode.
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Affiliation(s)
- Lander Bauters
- Department of Molecular Biotechnology, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
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25
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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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26
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Erkut C, Vasilj A, Boland S, Habermann B, Shevchenko A, Kurzchalia TV. Molecular strategies of the Caenorhabditis elegans dauer larva to survive extreme desiccation. PLoS One 2013; 8:e82473. [PMID: 24324795 PMCID: PMC3853187 DOI: 10.1371/journal.pone.0082473] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 11/02/2013] [Indexed: 11/19/2022] Open
Abstract
Massive water loss is a serious challenge for terrestrial animals, which usually has fatal consequences. However, some organisms have developed means to survive this stress by entering an ametabolic state called anhydrobiosis. The molecular and cellular mechanisms underlying this phenomenon are poorly understood. We recently showed that Caenorhabditis elegans dauer larva, an arrested stage specialized for survival in adverse conditions, is resistant to severe desiccation. However, this requires a preconditioning step at a mild desiccative environment to prepare the organism for harsher desiccation conditions. A systems approach was used to identify factors that are activated during this preconditioning. Using microarray analysis, proteomics, and bioinformatics, genes, proteins, and biochemical pathways that are upregulated during this process were identified. These pathways were validated via reverse genetics by testing the desiccation tolerances of mutants. These data show that the desiccation response is activated by hygrosensation (sensing the desiccative environment) via head neurons. This leads to elimination of reactive oxygen species and xenobiotics, expression of heat shock and intrinsically disordered proteins, polyamine utilization, and induction of fatty acid desaturation pathway. Remarkably, this response is specific and involves a small number of functional pathways, which represent the generic toolkit for anhydrobiosis in plants and animals.
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Affiliation(s)
- Cihan Erkut
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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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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28
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Banton MC, Tunnacliffe A. MAPK phosphorylation is implicated in the adaptation to desiccation stress in nematodes. J Exp Biol 2012; 215:4288-98. [DOI: 10.1242/jeb.074799] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Summary
Some nematodes can survive almost complete desiccation by entering an ametabolic state called anhydrobiosis requiring the accumulation of protective molecules such as trehalose and LEA proteins. However, it is not known how anhydrobiotic organisms sense and regulate the response to water loss. Mitogen-activated protein kinases (MAPKs) are highly conserved signalling proteins that regulate adaptation to various stresses. Here, we first compared the anhydrobiotic potential of three nematode species, Caenorhabditis elegans (Maupas, 1900), Aphelenchus avenae (Bastian, 1865) and Panagrolaimus superbus (Fuchs, 1930), and then determined the phosphorylation status of the MAPKs p38, JNK and ERK during desiccation and rehydration. C. elegans was unable to undergo anhydrobiosis even after an initial phase of slow drying (preconditioning), while A. avenae did survive desiccation after preconditioning. In contrast, P. superbus withstood desiccation under rapid drying conditions, although survival rates improved with preconditioning. These results characterise C. elegans as desiccation sensitive, A. avenae as a slow desiccation strategist anhydrobiote, and P. superbus as a fast desiccation strategist anhydrobiote. Both C. elegans and A. avenae showed increased MAPK phosphorylation during drying, consistent with an attempt to mount protection systems against desiccation stress. In P. superbus, however, MAPK phosphorylation was apparent prior to water loss and then decreased on dehydration, suggesting that signal transduction pathways are constitutively active in this nematode. Inhibition of p38 and JNK in P. superbus decreased its desiccation tolerance. This is consistent with the designation of P. superbus as a fast desiccation strategist and its high level of preparedness for anhydrobiosis in the hydrated state. These findings show that MAPKs play an important role in the survival of organisms during anhydrobiosis.
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