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      Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein

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          Abstract

          Tardigrades, also known as water bears, are small aquatic animals. Some tardigrade species tolerate almost complete dehydration and exhibit extraordinary tolerance to various physical extremes in the dehydrated state. Here we determine a high-quality genome sequence of Ramazzottius varieornatus, one of the most stress-tolerant tardigrade species. Precise gene repertoire analyses reveal the presence of a small proportion (1.2% or less) of putative foreign genes, loss of gene pathways that promote stress damage, expansion of gene families related to ameliorating damage, and evolution and high expression of novel tardigrade-unique proteins. Minor changes in the gene expression profiles during dehydration and rehydration suggest constitutive expression of tolerance-related genes. Using human cultured cells, we demonstrate that a tardigrade-unique DNA-associating protein suppresses X-ray-induced DNA damage by ∼40% and improves radiotolerance. These findings indicate the relevance of tardigrade-unique proteins to tolerability and tardigrades could be a bountiful source of new protection genes and mechanisms.

          Abstract

          Tardigrades are resistant to extreme environmental conditions including dehydration, radiation and the vacuum of space. Here the authors present a high-quality genome which displays minimal horizontal gene transfer, and identify the unique tardigrade protein Dsup which suppresses DNA damage.

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          Most cited references48

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          Regulation of mTOR function in response to hypoxia by REDD1 and the TSC1/TSC2 tumor suppressor complex.

          Mammalian target of rapamycin (mTOR) is a central regulator of protein synthesis whose activity is modulated by a variety of signals. Energy depletion and hypoxia result in mTOR inhibition. While energy depletion inhibits mTOR through a process involving the activation of AMP-activated protein kinase (AMPK) by LKB1 and subsequent phosphorylation of TSC2, the mechanism of mTOR inhibition by hypoxia is not known. Here we show that mTOR inhibition by hypoxia requires the TSC1/TSC2 tumor suppressor complex and the hypoxia-inducible gene REDD1/RTP801. Disruption of the TSC1/TSC2 complex through loss of TSC1 or TSC2 blocks the effects of hypoxia on mTOR, as measured by changes in the mTOR targets S6K and 4E-BP1, and results in abnormal accumulation of Hypoxia-inducible factor (HIF). In contrast to energy depletion, mTOR inhibition by hypoxia does not require AMPK or LKB1. Down-regulation of mTOR activity by hypoxia requires de novo mRNA synthesis and correlates with increased expression of the hypoxia-inducible REDD1 gene. Disruption of REDD1 abrogates the hypoxia-induced inhibition of mTOR, and REDD1 overexpression is sufficient to down-regulate S6K phosphorylation in a TSC1/TSC2-dependent manner. Inhibition of mTOR function by hypoxia is likely to be important for tumor suppression as TSC2-deficient cells maintain abnormally high levels of cell proliferation under hypoxia.
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            Evidence for a lack of DNA double-strand break repair in human cells exposed to very low x-ray doses.

            DNA double-strand breaks (DSBs) are generally accepted to be the most biologically significant lesion by which ionizing radiation causes cancer and hereditary disease. However, no information on the induction and processing of DSBs after physiologically relevant radiation doses is available. Many of the methods used to measure DSB repair inadvertently introduce this form of damage as part of the methodology, and hence are limited in their sensitivity. Here we present evidence that foci of gamma-H2AX (a phosphorylated histone), detected by immunofluorescence, are quantitatively the same as DSBs and are capable of quantifying the repair of individual DSBs. This finding allows the investigation of DSB repair after radiation doses as low as 1 mGy, an improvement by several orders of magnitude over current methods. Surprisingly, DSBs induced in cultures of nondividing primary human fibroblasts by very low radiation doses (approximately 1 mGy) remain unrepaired for many days, in strong contrast to efficient DSB repair that is observed at higher doses. However, the level of DSBs in irradiated cultures decreases to that of unirradiated cell cultures if the cells are allowed to proliferate after irradiation, and we present evidence that this effect may be caused by an elimination of the cells carrying unrepaired DSBs. The results presented are in contrast to current models of risk assessment that assume that cellular responses are equally efficient at low and high doses, and provide the opportunity to employ gamma-H2AX foci formation as a direct biomarker for human exposure to low quantities of ionizing radiation.
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              Amino acid signalling upstream of mTOR.

              Mammalian target of rapamycin (mTOR) is a conserved Ser/Thr kinase that is part of mTOR complex 1 (mTORC1), a master regulator that couples amino acid availability to cell growth and autophagy. Multiple cues modulate mTORC1 activity, such as growth factors, stress, energy status and amino acids. Although amino acids are key environmental stimuli, exactly how they are sensed and how they activate mTORC1 is not fully understood. Recently, a model has emerged whereby mTORC1 activation occurs at the lysosome and is mediated through an amino acid sensing cascade involving RAG GTPases, Ragulator and vacuolar H(+)-ATPase (v-ATPase).
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                Author and article information

                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group
                2041-1723
                20 September 2016
                2016
                : 7
                : 12808
                Affiliations
                [1 ]Department of Biological Sciences, Graduate School of Science, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
                [2 ]Graduate School of Environmental Earth Science, Hokkaido University , Kita 8, Nishi 5, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
                [3 ]Institute for Advanced Biosciences, Keio University , Mizukami 246-2, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
                [4 ]Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology , 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
                [5 ]Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo , 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
                [6 ]Genome Biology Laboratory, National Institute of Genetics , 1111 Yata, Mishima, Shizuoka 411-8540, Japan
                [7 ]Comparative Genomics Laboratory, National Institute of Genetics , 1111 Yata, Mishima, Shizuoka 411-8540, Japan
                [8 ]Laboratory of Molecular Radiology, Graduate School of Medicine, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
                [9 ]Phyloinformatics Unit, RIKEN Center for Life Science Technologies , 2-2-3 Minatojima-minami, Chuo-ku, Kobe, Hyogo 650-0047, Japan
                [10 ]Laboratory of Ecological Genetics, Graduate School of Environmental Science, Hokkaido University , Kita 10, Nishi 5, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
                [11 ]The Hakubi Center for Advanced Research and Graduate School of Science, Kyoto University , Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
                [12 ]Laboratory of Extremophiles, Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences , 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
                [13 ]Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo , 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
                [14 ]Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies) , 1111 Yata, Mishima, Shizuoka 411-8540, Japan
                [15 ]Database Center for Life Science , 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan
                Author notes
                [*]

                These authors contributed equally to this work

                Article
                ncomms12808
                10.1038/ncomms12808
                5034306
                27649274
                75546913-7e60-444c-b741-83723f9ff90d
                Copyright © 2016, The Author(s)

                This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/

                History
                : 21 June 2015
                : 03 August 2016
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