101
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Zhou C, Dai J, Lu H, Chen Z, Guo M, He Y, Gao K, Ge T, Jin J, Wang L, Tian B, Hua Y, Zhao Y. Succinylome Analysis Reveals the Involvement of Lysine Succinylation in the Extreme Resistance of Deinococcus radiodurans. Proteomics 2019; 19:e1900158. [PMID: 31487437 DOI: 10.1002/pmic.201900158] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/17/2019] [Indexed: 01/18/2023]
Abstract
Increasing evidence shows that the succinylation of lysine residues mainly regulates enzymes involved in the carbon metabolism pathway, in both prokaryotic and eukaryotic cells. Deinococcus radiodurans is one of the most radioresistant organisms on earth and is famous for its robust resistance. A major goal in the current study of protein succinylation is to explore its function in D. radiodurans. High-resolution LC-MS/MS is used for qualitative proteomics to perform a global succinylation analysis of D. radiodurans and 492 succinylation sites in 270 proteins are identified. These proteins are involved in a variety of biological processes and pathways. It is found that the enzymes involved in nucleic acid binding/processing are enriched in D. radiodurans compared with their previously reported levels in other bacteria. The mutagenesis studies confirm that succinylation regulates the enzymatic activities of species-specific proteins PprI and DdrB, which belong to the radiation-desiccation response regulon. Together, these results provide insight into the role of lysine succinylation in the extreme resistance of D. radiodurans.
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Affiliation(s)
- Congli Zhou
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
| | - Jingli Dai
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
| | - Huizhi Lu
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
| | - Zijing Chen
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
| | - Miao Guo
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
| | - Yuan He
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
| | - Kaixuan Gao
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
| | - Tong Ge
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
| | - Jiayu Jin
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
| | - Liangyan Wang
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
| | - Bing Tian
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
| | - Yuejin Hua
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
| | - Ye Zhao
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Zhejiang, 310058, China
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102
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Zhang A, Steen TY. Gut Microbiomics-A Solution to Unloose the Gordian Knot of Biological Effects of Ionizing Radiation. J Hered 2019; 109:212-221. [PMID: 29452420 DOI: 10.1093/jhered/esx059] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 07/05/2017] [Indexed: 12/24/2022] Open
Abstract
The Chernobyl and Fukushima nuclear accidents have called forth a growing body of research on their biological aftermaths. A variety of wild organisms, including primates, birds, fish, insects, and worms are being studied in the affected areas, with emerging morphological, physiological, and genetic aberrations ascribed to ionizing radiation. Despite the effort in surveying Chernobyl and Fukushima wildlife, little is known about the microorganisms associated with these radiation-contaminated animals. The microbiota, especially the gut commensal, plays an important role in shaping the metabolic reservoir and immune system of the host, and is sensitive to a wide array of environmental factors, including ionizing radiation. Humans and limited numbers of laboratory species have been the main subjects of microbiome studies, however, a more practical insight on host-gut microbiota dynamics under environmental impact should be explored in natural habitats. In this analysis, we introduced a working model explaining possible mechanisms of ionizing radiation on the gut microbiota, with an evaluation of the gut microbiota as a potential biomarker for exposure to ionizing radiation.
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Affiliation(s)
- Amy Zhang
- Department of Biological Sciences, Binghamton University, State University of New York, Binghamton, NY
| | - Tomoko Y Steen
- Department of Microbiology and Immunology, School of Medicine, Georgetown University, Washington, DC
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103
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Jin M, Xiao A, Zhu L, Zhang Z, Huang H, Jiang L. The diversity and commonalities of the radiation-resistance mechanisms of Deinococcus and its up-to-date applications. AMB Express 2019; 9:138. [PMID: 31482336 PMCID: PMC6722170 DOI: 10.1186/s13568-019-0862-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 08/23/2019] [Indexed: 01/08/2023] Open
Abstract
Deinococcus is an extremophilic microorganism found in a wide range of habitats, including hot springs, radiation-contaminated areas, Antarctic soils, deserts, etc., and shows some of the highest levels of resistance to ionizing radiation known in nature. The highly efficient radiation-protection mechanisms of Deinococcus depend on a combination of passive and active defense mechanisms, including self-repair of DNA damage (homologous recombination, MMR, ER and ESDSA), efficient cellular damage clearance mechanisms (hydrolysis of damaged proteins, overexpression of repair proteins, etc.), and effective clearance of reactive oxygen species (ROS). Due to these mechanisms, Deinococcus cells are highly resistant to oxidation, radiation and desiccation, which makes them potential chassis cells for wide applications in many fields. This article summarizes the latest research on the radiation-resistance mechanisms of Deinococcus and prospects its biotechnological application potentials.
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104
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Floc'h K, Lacroix F, Servant P, Wong YS, Kleman JP, Bourgeois D, Timmins J. Cell morphology and nucleoid dynamics in dividing Deinococcus radiodurans. Nat Commun 2019; 10:3815. [PMID: 31444361 PMCID: PMC6707255 DOI: 10.1038/s41467-019-11725-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/24/2019] [Indexed: 12/21/2022] Open
Abstract
Our knowledge of bacterial nucleoids originates mostly from studies of rod- or crescent-shaped bacteria. Here we reveal that Deinococcus radiodurans, a relatively large spherical bacterium with a multipartite genome, constitutes a valuable system for the study of the nucleoid in cocci. Using advanced microscopy, we show that D. radiodurans undergoes coordinated morphological changes at both the cellular and nucleoid level as it progresses through its cell cycle. The nucleoid is highly condensed, but also surprisingly dynamic, adopting multiple configurations and presenting an unusual arrangement in which oriC loci are radially distributed around clustered ter sites maintained at the cell centre. Single-particle tracking and fluorescence recovery after photobleaching studies of the histone-like HU protein suggest that its loose binding to DNA may contribute to this remarkable plasticity. These findings demonstrate that nucleoid organization is complex and tightly coupled to cell cycle progression in this organism.
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Affiliation(s)
- Kevin Floc'h
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France
| | | | - Pascale Servant
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Yung-Sing Wong
- Univ. Grenoble Alpes, CNRS, DPM, 38000, Grenoble, France
| | | | | | - Joanna Timmins
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France.
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105
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Lingappa UF, Monteverde DR, Magyar JS, Valentine JS, Fischer WW. How manganese empowered life with dioxygen (and vice versa). Free Radic Biol Med 2019; 140:113-125. [PMID: 30738765 DOI: 10.1016/j.freeradbiomed.2019.01.036] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/25/2019] [Indexed: 01/02/2023]
Abstract
Throughout the history of life on Earth, abiotic components of the environment have shaped the evolution of life, and in turn life has shaped the environment. The element manganese embodies a special aspect of this collaboration; its history is closely entwined with those of photosynthesis and O2-two reigning features that characterize the biosphere today. Manganese chemistry was central to the environmental context and evolutionary innovations that enabled the origin of oxygenic photosynthesis and the ensuing rise of O2. It was also manganese chemistry that provided an early, fortuitous antioxidant system that was instrumental in how life came to cope with oxidative stress and ultimately thrive in an aerobic world. Subsequently, the presence of O2 transformed the biogeochemical dynamics of the manganese cycle, enabling a rich suite of environmental and biological processes involving high-valent manganese and manganese redox cycling. Here, we describe insights from chemistry, biology, and geology, to examine manganese dynamics in the environment, and its unique role in the history of life.
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Affiliation(s)
- Usha F Lingappa
- Div. of Geological & Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA.
| | - Danielle R Monteverde
- Div. of Geological & Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - John S Magyar
- Div. of Geological & Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Joan Selverstone Valentine
- Div. of Geological & Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA; Dept. of Chemistry & Biochemistry, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Woodward W Fischer
- Div. of Geological & Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
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106
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Agapov A, Esyunina D, Kulbachinskiy A. Gre-family factors modulate DNA damage sensing by Deinococcus radiodurans RNA polymerase. RNA Biol 2019; 16:1711-1720. [PMID: 31416390 DOI: 10.1080/15476286.2019.1656027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Deinococcus radiodurans is a highly stress resistant bacterium that encodes universal as well as lineage-specific factors involved in DNA transcription and repair. However, the effects of DNA lesions on RNA synthesis by D. radiodurans RNA polymerase (RNAP) have never been studied. We investigated the ability of this RNAP to transcribe damaged DNA templates and demonstrated that various lesions significantly affect the efficiency and fidelity of RNA synthesis. DNA modifications that disrupt correct base-pairing can strongly inhibit transcription and increase nucleotide misincorporation by D. radiodurans RNAP. The universal transcription factor GreA and Deinococcus-specific factor Gfh1 stimulate RNAP stalling at various DNA lesions, depending on the type of the lesion and the presence of Mn2+ ions, abundant divalent cations in D. radiodurans. Furthermore, Gfh1 stimulates the action of the Mfd translocase, which removes transcription elongation complexes paused at the sites of DNA lesions. Thus, Gre-family factors in D. radiodurans might have evolved to increase the efficiency of DNA damage recognition by the transcription and repair machineries in this bacterium.
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Affiliation(s)
- Aleksei Agapov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
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107
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Huang Y, Shao Y, Zhu Y. Sustained reactive oxygen species generation from percarbamide nanomedicine via a mechanism of X-Ray-initiated free radical chain reactions. J Biomater Appl 2019; 34:728-738. [PMID: 31411100 DOI: 10.1177/0885328219868851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yongping Huang
- 1 Key Laboratory of Inorganic Coating Materials CAS, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai, China.,2 Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Science, Beijing, China
| | - Yiran Shao
- 1 Key Laboratory of Inorganic Coating Materials CAS, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai, China.,2 Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Science, Beijing, China
| | - Yingchun Zhu
- 1 Key Laboratory of Inorganic Coating Materials CAS, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai, China.,2 Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Science, Beijing, China
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108
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Shuryak I, Tkavc R, Matrosova VY, Volpe RP, Grichenko O, Klimenkova P, Conze IH, Balygina IA, Gaidamakova EK, Daly MJ. Chronic gamma radiation resistance in fungi correlates with resistance to chromium and elevated temperatures, but not with resistance to acute irradiation. Sci Rep 2019; 9:11361. [PMID: 31388021 PMCID: PMC6684587 DOI: 10.1038/s41598-019-47007-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/10/2019] [Indexed: 02/07/2023] Open
Abstract
Exposure to chronic ionizing radiation (CIR) from nuclear power plant accidents, acts of terrorism, and space exploration poses serious threats to humans. Fungi are a group of highly radiation-resistant eukaryotes, and an understanding of fungal CIR resistance mechanisms holds the prospect of protecting humans. We compared the abilities of 95 wild-type yeast and dimorphic fungal isolates, representing diverse Ascomycota and Basidiomycota, to resist exposure to five environmentally-relevant stressors: CIR (long-duration growth under 36 Gy/h) and acute (10 kGy/h) ionizing radiation (IR), heavy metals (chromium, mercury), elevated temperature (up to 50 °C), and low pH (2.3). To quantify associations between resistances to CIR and these other stressors, we used correlation analysis, logistic regression with multi-model inference, and customized machine learning. The results suggest that resistance to acute IR in fungi is not strongly correlated with the ability of a given fungal isolate to grow under CIR. Instead, the strongest predictors of CIR resistance in fungi were resistance to chromium (III) and to elevated temperature. These results suggest fundamental differences between the mechanisms of resistance to chronic and acute radiation. Convergent evolution towards radioresistance among genetically distinct groups of organisms is considered here.
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Affiliation(s)
- Igor Shuryak
- Center for Radiological Research, Columbia University Irving Medical Center, New York, NY, USA.
| | - Rok Tkavc
- Department of Pathology, Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, USA
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, USA
| | - Vera Y Matrosova
- Department of Pathology, Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Robert P Volpe
- Department of Pathology, Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Olga Grichenko
- Department of Pathology, Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Polina Klimenkova
- Department of Pathology, Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Isabel H Conze
- Department of Pathology, Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, USA
- Department of Biology, University of Bielefeld, Bielefeld, Germany
| | - Irina A Balygina
- Department of Pathology, Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, USA
- Institute of Medicine and Psychology, Novosibirsk State University, Novosibirsk, Russia
| | - Elena K Gaidamakova
- Department of Pathology, Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Michael J Daly
- Department of Pathology, Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, USA
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109
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Farci D, Guadalupi G, Bierła K, Lobinski R, Piano D. The Role of Iron and Copper on the Oligomerization Dynamics of DR_2577, the Main S-Layer Protein of Deinococcus radiodurans. Front Microbiol 2019; 10:1450. [PMID: 31333601 PMCID: PMC6615493 DOI: 10.3389/fmicb.2019.01450] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/11/2019] [Indexed: 01/04/2023] Open
Abstract
Surface (S)-layers are cryptic structures that coat the external surface of the bacterial cell in many species. The paracrystalline regularity of the S-layer is due to the self-assembling of one or more protein units. The property of self-assembling seems to be mediated by specific topologies of the S-layer proteins as well as the presence of specific ions that provide support in building and stabilizing the bi-dimensional S-layer organization. In the present study, we have investigated the self-assembling mechanism of the main S-layer protein of Deinococcus radiodurans (DR_2577) finding an unusual role played by Fe3+ and Cu2+ in the oligomerization of this protein. These findings may trace a structural and functional metallo-mediated convergence between the role of these metals in the assembling of the S-layer and their well-known roles in protecting against oxidative stress in D. radiodurans.
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Affiliation(s)
- Domenica Farci
- Department of Plant Physiology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland.,Laboratory of Photobiology and Plant Physiology, Department of Life and Environmental Sciences University of Cagliari, Cagliari, Italy
| | - Giulia Guadalupi
- Laboratory of Photobiology and Plant Physiology, Department of Life and Environmental Sciences University of Cagliari, Cagliari, Italy
| | - Katarzyna Bierła
- Laboratory of Analitycal and Bioinorganic Chemistry and Environment, UMR5254 Institute of Analytical and Physical Chemistry for the Environment and Materials (IPREM), Pau, France
| | - Ryszard Lobinski
- Laboratory of Analitycal and Bioinorganic Chemistry and Environment, UMR5254 Institute of Analytical and Physical Chemistry for the Environment and Materials (IPREM), Pau, France
| | - Dario Piano
- Department of Plant Physiology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland.,Laboratory of Photobiology and Plant Physiology, Department of Life and Environmental Sciences University of Cagliari, Cagliari, Italy
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110
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Changes in soil taxonomic and functional diversity resulting from gamma irradiation. Sci Rep 2019; 9:7894. [PMID: 31133738 PMCID: PMC6536540 DOI: 10.1038/s41598-019-44441-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 04/05/2019] [Indexed: 12/30/2022] Open
Abstract
Little is known of the effects of ionizing radiation exposure on soil biota. We exposed soil microcosms to weekly bursts of 60Co gamma radiation over six weeks, at three levels of exposure (0.1 kGy/hr/wk [low], 1 kGy/hr/wk [medium] and 3 kGy/hr/wk [high]). Soil DNA was extracted, and shotgun metagenomes were sequenced and characterised using MG-RAST. We hypothesized that with increasing radiation exposure there would be a decrease in both taxonomic and functional diversity. While bacterial diversity decreased, diversity of fungi and algae unexpectedly increased, perhaps because of release from competition. Despite the decrease in diversity of bacteria and of biota overall, functional gene diversity of algae, bacteria, fungi and total biota increased. Cycles of radiation exposure may increase the range of gene functional strategies viable in soil, a novel ecological example of the effects of stressors or disturbance events promoting some aspects of diversity. Moreover, repeated density-independent population crashes followed by population expansion may allow lottery effects, promoting coexistence. Radiation exposure produced large overall changes in community composition. Our study suggests several potential novel radiation-tolerant groups: in addition to Deinococcus-Thermus, which reached up to 20% relative abundance in the metagenome, the phyla Chloroflexi (bacteria), Chytridiomycota (fungi) and Nanoarcheota (archaea) may be considered as radiation-tolerant.
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111
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Minkoff BB, Bruckbauer ST, Sabat G, Cox MM, Sussman MR. Covalent Modification of Amino Acids and Peptides Induced by Ionizing Radiation from an Electron Beam Linear Accelerator Used in Radiotherapy. Radiat Res 2019; 191:447-459. [PMID: 30849023 PMCID: PMC6506356 DOI: 10.1667/rr15288.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
To identify modifications to amino acids that are directly induced by ionizing radiation, free amino acids and 3-residue peptides were irradiated using a linear accelerator (Linac) radiotherapy device. Mass spectrometry was performed to detail the relative sensitivity to radiation as well as identify covalent, radiation-dependent adducts. The order of reactivity of the 20 common amino acids was generally in agreement with published literature except for His (most reactive of the 20) and Cys (less reactive). Novel and previously identified modifications on the free amino acids were detected. Amino acids were far less reactive when flanked by glycine residues in a tripeptide. Order of reactivity, with GVG most and GEG least, was substantially altered, as were patterns of modification. Radiation reactivity of amino acids is clearly and strongly affected by conversion of the α-amino and α-carboxyl groups to peptide bonds, and the presence of neighboring amino acid residues.
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Affiliation(s)
- Benjamin B. Minkoff
- Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Steven T. Bruckbauer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Grzegorz Sabat
- Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Michael R. Sussman
- Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
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112
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Ott E, Kawaguchi Y, Özgen N, Yamagishi A, Rabbow E, Rettberg P, Weckwerth W, Milojevic T. Proteomic and Metabolomic Profiling of Deinococcus radiodurans Recovering After Exposure to Simulated Low Earth Orbit Vacuum Conditions. Front Microbiol 2019; 10:909. [PMID: 31110498 PMCID: PMC6501615 DOI: 10.3389/fmicb.2019.00909] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/10/2019] [Indexed: 01/26/2023] Open
Abstract
The polyextremophile, gram-positive bacterium Deinococcus radiodurans can withstand harsh conditions of real and simulated outer space environment, e.g., UV and ionizing radiation. A long-term space exposure of D. radiodurans has been performed in Low Earth Orbit (LEO) in frames of the Tanpopo orbital mission aiming to investigate the possibility of interplanetary life transfer. Space vacuum (10-4–10-7 Pa) is a harmful factor, which induces dehydration and affects microbial integrity, severely damaging cellular components: lipids, carbohydrates, proteins, and nucleic acids. However, the molecular strategies by which microorganisms protect their integrity on molecular and cellular levels against vacuum damage are not yet understood. In a simulation experiment, we exposed dried D. radiodurans cells to vacuum (10-4–10-7 Pa), which resembles vacuum pressure present outside the International Space Station in LEO. After 90 days of high vacuum exposure, survival of D. radiodurans cells was 2.5-fold lower compared to control cells. To trigger molecular repair mechanisms, vacuum exposed cells of D. radiodurans were recovered in complex medium for 3 and 6 h. The combined approach of analyzing primary metabolites and proteins revealed important molecular activities during early recovery after vacuum exposure. In total, 1939 proteins covering 63% of D. radiodurans annotated protein sequences were detected. Proteases, tRNA ligases, reactive oxygen species (ROS) scavenging proteins, nucleic acid repair proteins, TCA cycle proteins, and S-layer proteins are highly abundant after vacuum exposure. The overall abundance of amino acids and TCA cycle intermediates is reduced during the recovery phase of D. radiodurans as they are needed as carbon source. Furthermore, vacuum exposure induces an upregulation of Type III histidine kinases, which trigger the expression of S-layer related proteins. Along with the highly abundant transcriptional regulator of FNR/CRP family, specific histidine kinases might be involved in the regulation of vacuum stress response. After repair processes are finished, D. radiodurans switches off the connected repair machinery and focuses on proliferation. Combined comparative analysis of alterations in the proteome and metabolome helps to identify molecular key players in the stress response of D. radiodurans, thus elucidating the mechanisms behind its extraordinary regenerative abilities and enabling this microorganism to withstand vacuum stress.
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Affiliation(s)
- Emanuel Ott
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Yuko Kawaguchi
- Planetary Exploration Research Center (PERC), Chiba Institute of Technology (CIT), Chiba, Japan
| | - Natalie Özgen
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Akihiko Yamagishi
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta, Yokohama, Japan
| | - Elke Rabbow
- Department of Radiation Biology, Institute of Aerospace Medicine, German Aerospace Center, Cologne, Germany
| | - Petra Rettberg
- Department of Radiation Biology, Institute of Aerospace Medicine, German Aerospace Center, Cologne, Germany
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.,Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Tetyana Milojevic
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
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113
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Liu Y, Zhang H, Han J, Jiang S, Geng X, Xue D, Chen Y, Zhang C, Zhou Z, Zhang W, Chen M, Lin M, Wang J. Functional assessment of hydrophilic domains of late embryogenesis abundant proteins from distant organisms. Microb Biotechnol 2019; 12:752-762. [PMID: 31012266 PMCID: PMC6559209 DOI: 10.1111/1751-7915.13416] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 04/06/2019] [Indexed: 01/03/2023] Open
Abstract
Late embryogenesis abundant (LEA) proteins play a protective role during desiccation and oxidation stresses. LEA3 proteins are a major group characterized by a hydrophilic domain (HD) with a highly conserved repeating 11-amino acid motif. We compared four different HD orthologs from distant organisms: (i) DrHD from the extremophilic bacterium Deinococcus radiodurans; (ii) CeHD from the nematode Caenorhabditis elegans; (iii) YlHD from the yeast Yarrowia lipolytica; and (iv) BnHD from the plant Brassica napus. Circular dichroism spectroscopy showed that all four HDs were intrinsically disordered in phosphate buffer and then folded into α-helical structures with the addition of glycerol or trifluoroethanol. Heterologous HD expression conferred enhanced desiccation and oxidation tolerance to Escherichia coli. These four HDs protected the enzymatic activities of lactate dehydrogenase (LDH) by preventing its aggregation under desiccation stress. The HDs also interacted with LDH, which was intensified by the addition of hydrogen peroxide (H2 O2 ), suggesting a protective role in a chaperone-like manner. Based on these results, the HDs of LEA3 proteins show promise as protectants for desiccation and oxidation stresses, especially DrHD, which is a potential ideal stress-response element that can be applied in synthetic biology due to its extraordinary protection and stress resistance ability.
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Affiliation(s)
- Yingying Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Heng Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiahui Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shijie Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621000, China
| | - Xiuxiu Geng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621000, China
| | - Dong Xue
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yun Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhengfu Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ming Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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114
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Burger A, Lichtscheidl I. Strontium in the environment: Review about reactions of plants towards stable and radioactive strontium isotopes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 653:1458-1512. [PMID: 30759584 DOI: 10.1016/j.scitotenv.2018.10.312] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/22/2018] [Accepted: 10/23/2018] [Indexed: 06/09/2023]
Abstract
Radiostrontium is released to the environment from routine and accidental discharge and acts on living organisms either from external sources or after absorption. When incorporated by plants, it enters the food chain and causes primary threat to human health and the environment. Understanding the mechanisms of plants for strontium uptake and retention is therefore essential for decision making concerning agriculture: are uptake rates low enough so that plants can serve as food? Or is radiostrontium accumulated so that plants should not be eaten but could be probably used for extracting strontium from water and soil in hot spots of pollution? The review presents a summary of studies about the origin of stable and radioactive strontium in the environment and effects coming from both internal and external exposure of plants. Mobility and availability of strontium to plant roots in soil are controlled by external factors such as chemical composition of the soil and pH, temperature and agricultural soil cultivation as well as soil biological networks built by microbial communities. Plant surfaces may receive input of strontium from deposition induced by atmospheric pollution or by acquisition from water through the whole immersed surface. Cells have entry mechanisms for strontium such as plasma membrane transporters for calcium and potassium. Part of absorbed strontium can be lost via processes discussed in this review. We give examples on strontium transfer factors for 149 plants to estimate plant absorption capacity for strontium from soil, water and air. Uptake efficiency of terrestrial and aquatic plants is deciding about their remediation potential to either remove radiostrontium by accumulation and rhizofiltration or to retain it in roots or aerial parts. Data of strontium content in soils after fallout and edible plants from long-term monitoring support the evaluation of the potential hazards posed by strontium input to the food chain.
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Affiliation(s)
- Anna Burger
- University of Vienna, Core Facility Cell Imaging and Ultrastructure Research, Althanstrasse 14, A-1090 Vienna, Austria.
| | - Irene Lichtscheidl
- University of Vienna, Core Facility Cell Imaging and Ultrastructure Research, Althanstrasse 14, A-1090 Vienna, Austria
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115
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Ii KM, Kono N, Paulino-Lima IG, Tomita M, Rothschild LJ, Arakawa K. Complete Genome Sequence of Arthrobacter sp. Strain MN05-02, a UV-Resistant Bacterium from a Manganese Deposit in the Sonoran Desert. J Genomics 2019; 7:18-25. [PMID: 30820258 PMCID: PMC6389495 DOI: 10.7150/jgen.32194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 01/08/2019] [Indexed: 12/26/2022] Open
Abstract
Arthrobacter sp. strain MN05-02 is a UV-resistant bacterium isolated from a manganese deposit in the Sonoran Desert, Arizona, USA. The LD10 of this strain is 123 Jm-2, which is twice that of Escherichia coli, and therefore can be a useful resource for comparative study of UV resistance and the role of manganese on this phenotype. Its complete genome is comprised of a chromosome of 3,488,433 bp and a plasmid of 154,991 bp. The chromosome contains 3,430 putative genes, including 3,366 protein coding genes, 52 tRNA and 12 rRNA genes. Carotenoid biosynthesis operon structure coded within the genome mirrors the characteristic orange-red pigment this bacterium produces, which presumably partly contribute to its UV resistance.
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Affiliation(s)
- Konosuke Mark Ii
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan.,Faculty of Environment and Information Studies, Keio University, Yamagata, 997-0052, Japan
| | - Nobuaki Kono
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan.,Graduate School of Media and Governance, Keio University, Yamagata, 997-0052, Japan
| | - Ivan Glaucio Paulino-Lima
- Blue Marble Space Institute of Science at NASA Ames Research Center, Mountain View, CA, USA, 94035-0001
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan.,Faculty of Environment and Information Studies, Keio University, Yamagata, 997-0052, Japan.,Graduate School of Media and Governance, Keio University, Yamagata, 997-0052, Japan
| | | | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan.,Faculty of Environment and Information Studies, Keio University, Yamagata, 997-0052, Japan.,Graduate School of Media and Governance, Keio University, Yamagata, 997-0052, Japan
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116
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Wadhawan S, Gautam S. Rescue of Escherichia coli cells from UV-induced death and filamentation by caspase-3 inhibitor. Int Microbiol 2019; 22:369-376. [DOI: 10.1007/s10123-019-00060-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 01/03/2019] [Accepted: 01/20/2019] [Indexed: 12/25/2022]
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117
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Shuryak I. Review of microbial resistance to chronic ionizing radiation exposure under environmental conditions. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2019; 196:50-63. [PMID: 30388428 DOI: 10.1016/j.jenvrad.2018.10.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 10/21/2018] [Indexed: 06/08/2023]
Abstract
Ionizing radiation (IR) produces multiple types of damage to nucleic acids, proteins and other crucial cellular components. Nevertheless, various microorganisms from phylogenetically distant taxa (bacteria, archaea, fungi) can resist IR levels many orders of magnitude above natural background. This intriguing phenomenon of radioresistance probably arose independently many times throughout evolution as a byproduct of selective pressures from other stresses (e.g. desiccation, UV radiation, chemical oxidants). Most of the literature on microbial radioresistance is based on acute γ-irradiation experiments performed in the laboratory, typically involving pure cultures grown under near-optimal conditions. There is much less information about the upper limits of radioresistance in the field, such as in radioactively-contaminated areas, where several radiation types (e.g. α and β, as well as γ) and other stressors (e.g. non-optimal temperature and nutrient levels, toxic chemicals, interspecific competition) act over multiple generations. Here we discuss several examples of radioresistant microbes isolated from extremely radioactive locations (e.g. Chernobyl and Mayak nuclear plant sites) and estimate the radiation dose rates they were able to tolerate. Some of these organisms (e.g. the fungus Cladosporium cladosporioides, the cyanobacterium Geitlerinema amphibium) are widely-distributed and colonize a variety of habitats. These examples suggest that resistance to chronic IR and chemical contamination is not limited to rare specialized strains from extreme environments, but can occur among common microbial taxa, perhaps due to overlap between mechanisms of resistance to IR and other stressors.
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Affiliation(s)
- Igor Shuryak
- Center for Radiological Research, Columbia University, 630 West 168(th) street, VC-11-234/5, New York, NY, 10032, USA.
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118
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Devigne A, Meyer L, de la Tour CB, Eugénie N, Sommer S, Servant P. The absence of the RecN protein suppresses the cellular defects of Deinococcus radiodurans irradiated cells devoid of the PprA protein by limiting recombinational repair of DNA lesions. DNA Repair (Amst) 2019; 73:144-154. [DOI: 10.1016/j.dnarep.2018.11.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 11/26/2018] [Accepted: 11/26/2018] [Indexed: 11/30/2022]
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119
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Cho C, Lee GW, Hong SH, Kaur S, Jung KW, Jung JH, Lim S, Chung BY, Lee SS. Novel functions of peroxiredoxin Q from Deinococcus radiodurans R1 as a peroxidase and a molecular chaperone. FEBS Lett 2018; 593:219-229. [PMID: 30488429 PMCID: PMC6590489 DOI: 10.1002/1873-3468.13302] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 12/02/2022]
Abstract
Deinococcus radiodurans R1 is extremely resistant to ionizing radiation and oxidative stress. In this study, we characterized DR0846, a candidate peroxiredoxin in D. radiodurans. DR0846 is a peroxiredoxin Q containing two conserved cysteine residues. DR0846 exists mainly in monomeric form with an intramolecular disulfide bond between the two cysteine residues. We found that DR0846 functions as a molecular chaperone as well as a peroxidase. A mutational analysis indicates that the two cysteine residues are essential for enzymatic activity. A double‐deletion mutant lacking DR0846 and catalase DR1998 exhibits decreased oxidative and heat shock stress tolerance with respect to the single mutants or the wild‐type cells. These results suggest that DR0846 contributes to resistance against oxidative and heat stresses in D. radiodurans.
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Affiliation(s)
- Chuloh Cho
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | | | - Sung H Hong
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - Shubhpreet Kaur
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - Kwang-Woo Jung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - Jong-Hyun Jung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea.,Department of Radiation Biotechnology and Applied Radioisotope, Korea University of Science and Technology, Daejeon, Korea
| | - Sangyong Lim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea.,Department of Radiation Biotechnology and Applied Radioisotope, Korea University of Science and Technology, Daejeon, Korea
| | - Byung Yeoup Chung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - Seung Sik Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea.,Department of Radiation Biotechnology and Applied Radioisotope, Korea University of Science and Technology, Daejeon, Korea
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120
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Zhang Y, Liu GJ. Effects of cesium accumulation on chlorophyll content and fluorescence of Brassica juncea L. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2018; 195:26-32. [PMID: 30241014 DOI: 10.1016/j.jenvrad.2018.09.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 08/23/2018] [Accepted: 09/10/2018] [Indexed: 06/08/2023]
Abstract
The aim of our study was to investigate the toxicological mechanism of cesium on Indian mustard (Brassica juncea L.). The impact of cesium toxicity to plants was evaluated using phytophysiology and genetic methods. In this study, Brassica juncea was grown on Cs-contaminated Hoagland's nutrient solution, and chlorophyll content, chlorophyll fluorescence, and Cs bioaccumulation were measured. Transcriptome data was used to perform an in-depth analysis of the molecular mechanisms underlying the effects of Cs accumulation. The results showed that Cs accumulated up to 3586.70 mg kg-1 in B. juncea treated with 100 mg L-1 Cs. The chlorophyll content and several chlorophyll fluorescence parameters (Fv/F0, Fv/Fm, ΦPS II, qP, and NPQ) significantly decreased under Cs exposure. The starting process of PSII was also inhibited under higher Cs conditions. These results indicate that excessive Cs can damage PS II in leaves, decreasing photochemical activity and the energy conversion rate. Further analysis revealed that Cs interfered with the expression of chloroplastic metabolic genes (25 up and 36 down) and inhibited the expression of PsaB, psbC, PetF, LHCA1, and LHCB5. The results indicate that stable Cs leads to abnormal expression of genes related to photosynthesis pathway, blocking the electron transport process from plastoquinone-QA to plastoquinone-QB, resulting in abnormal photosynthesis, which leads to abnormal growth of B. juncea.
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Affiliation(s)
- Yu Zhang
- The School of Public Affairs, University of Science and Technology of China, Hefei, Anhui, 23023, China
| | - Gui-Jian Liu
- The School of Public Affairs, University of Science and Technology of China, Hefei, Anhui, 23023, China.
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121
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Peana M, Chasapis CT, Simula G, Medici S, Zoroddu MA. A Model for Manganese interaction with Deinococcus radiodurans proteome network involved in ROS response and defense. J Trace Elem Med Biol 2018; 50:465-473. [PMID: 29449107 DOI: 10.1016/j.jtemb.2018.02.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/17/2018] [Accepted: 02/01/2018] [Indexed: 01/28/2023]
Abstract
A complex network of regulatory proteins takes part in the mechanism underlying the radioresistance of Deinoccocus radiodurans bacterium (DR). The interaction of Mn(II) ions with DR-proteins and peptides seems to be responsible for proteins protection from oxidative damage induced by Reactive Oxygen Species during irradiation. In the present work we describe a combined approach of bioinformatic strategies based on structural data and annotation to predict the Mn(II)-binding proteins encoded by the genome of DR and, in parallel, the same predictions for other bacteria were performed; the comparison revealed that, in most of the cases, the content of Mn(II)-binding proteins is significantly higher in radioresistant than in radiosensitive bacteria. Moreover, we report the in silico protein-protein interaction network of the putative Mn(II)-proteins, remodeled in order to enhance the knowledge about the impact of Mn-binding proteins in DR ability to protect also DNA from various damaging agents such as ionizing radiation, UV radiation and oxidative stress.
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Affiliation(s)
- M Peana
- Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy.
| | - C T Chasapis
- Institute of Chemical Engineering Sciences (ICE-HT), Foundation for Research and Technology, Hellas (FORTH), 26504, Patras, Greece.
| | - G Simula
- Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy
| | - S Medici
- Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy
| | - M A Zoroddu
- Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy
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122
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Shuryak I. Modeling species richness and abundance of phytoplankton and zooplankton in radioactively contaminated water bodies. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2018; 192:14-25. [PMID: 29883873 DOI: 10.1016/j.jenvrad.2018.05.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 04/04/2018] [Accepted: 05/22/2018] [Indexed: 06/08/2023]
Abstract
Water bodies polluted by the Mayak nuclear plant in Russia provide valuable information on multi-generation effects of radioactive contamination on freshwater organisms. For example, lake Karachay was probably the most radioactive lake in the world: its water contained ∼2 × 107 Bq/L of radionuclides and estimated dose rates to plankton exceeded 5 Gy/h. We performed quantitative modeling of radiation effects on phytoplankton and zooplankton species richness and abundance in Mayak-contaminated water bodies. Due to collinearity between radioactive contamination, water body size and salinity, we combined these variables into one (called HabitatFactors). We employed a customized machine learning approach, where synthetic noise variables acted as benchmarks of predictor performance. HabitatFactors was the only predictor that outperformed noise variables and, therefore, we used it for parametric modeling of plankton responses. Best-fit model predictions suggested 50% species richness reduction at HabitatFactors values corresponding to dose rates of 104-105 μGy/h for phytoplankton, and 103-104 μGy/h for zooplankton. Under conditions similar to those in lake Karachay, best-fit models predicted 81-98% species richness reductions for various taxa (Cyanobacteria, Bacillariophyta, Chlorophyta, Rotifera, Cladocera and Copepoda), ∼20-300-fold abundance reduction for total zooplankton, but no abundance reduction for phytoplankton. Rotifera was the only taxon whose fractional abundance increased with contamination level, reaching 100% in lake Karachay, but Rotifera species richness declined with contamination level, as in other taxa. Under severe radioactive and chemical contamination, one species of Cyanobacteria (Geitlerinema amphibium) dominated phytoplankton, and rotifers from the genus Brachionus dominated zooplankton. The modeling approaches proposed here are applicable to other radioecological data sets. The results provide quantitative information and easily interpretable model parameter estimates for the shapes and magnitudes of freshwater plankton responses to a wide range of radioactive contamination levels.
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Affiliation(s)
- Igor Shuryak
- Center for Radiological Research, Columbia University, New York, NY, United States.
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123
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Ferrandi A, Castani F, Pitaro M, Tagliaferri S, de la Tour CB, Alduina R, Sommer S, Fasano M, Barbieri P, Mancini M, Bonapace IM. Deinococcus radiodurans' SRA-HNH domain containing protein Shp (Dr1533) is involved in faithful genome inheritance maintenance following DNA damage. Biochim Biophys Acta Gen Subj 2018; 1863:118-129. [PMID: 30308220 DOI: 10.1016/j.bbagen.2018.09.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/18/2018] [Accepted: 09/25/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND Deinococcus radiodurans R1 (DR) survives conditions of extreme desiccation, irradiation and exposure to genotoxic chemicals, due to efficient DNA breaks repair, also through Mn2+ protection of DNA repair enzymes. METHODS Possible annotated domains of the DR1533 locus protein (Shp) were searched by bioinformatic analysis. The gene was cloned and expressed as fusion protein. Band-shift assays of Shp or the SRA and HNH domains were performed on oligonucleotides, genomic DNA from E. coli and DR. shp knock-out mutant was generated by homologous recombination with a kanamycin resistance cassette. RESULTS DR1533 contains an N-terminal SRA domain and a C-terminal HNH motif (SRA-HNH Protein, Shp). Through its SRA domain, Shp binds double-strand oligonucleotides containing 5mC and 5hmC, but also unmethylated and mismatched cytosines in presence of Mn2+. Shp also binds to Escherichia coli dcm+ genomic DNA, and to cytosine unmethylated DR and E. coli dcm- genomic DNAs, but only in presence of Mn2+. Under these binding conditions, Shp displays DNAse activity through its HNH domain. Shp KO enhanced >100 fold the number of spontaneous mutants, whilst the treatment with DNA double strand break inducing agents enhanced up to 3-log the number of survivors. CONCLUSIONS The SRA-HNH containing protein Shp binds to and cuts 5mC DNA, and unmethylated DNA in a Mn2+ dependent manner, and might be involved in faithful genome inheritance maintenance following DNA damage. GENERAL SIGNIFICANCE Our results provide evidence for a potential role of DR Shp protein for genome integrity maintenance, following DNA double strand breaks induced by genotoxic agents.
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Affiliation(s)
- Alex Ferrandi
- Department of Biotechnology and Life Sciences, University of Insubria, Via Manara 7, Busto Arsizio, VA, Italy
| | - Federica Castani
- Department of Biotechnology and Life Sciences, University of Insubria, Via Manara 7, Busto Arsizio, VA, Italy
| | - Mauro Pitaro
- Department of Biotechnology and Life Sciences, University of Insubria, Via Manara 7, Busto Arsizio, VA, Italy
| | - Sara Tagliaferri
- Department of Biotechnology and Life Sciences, University of Insubria, Via Manara 7, Busto Arsizio, VA, Italy
| | - Claire Bouthier de la Tour
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, France and Institut de Génétique et Microbiologie - Université Paris-Sud, Paris, France
| | - Rosa Alduina
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, Palermo, Italy
| | - Suzanne Sommer
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, France and Institut de Génétique et Microbiologie - Université Paris-Sud, Paris, France
| | - Mauro Fasano
- Department of Sciences and High technology, University of Insubria, Via Manara 7, Busto Arsizio, VA, Italy
| | - Paola Barbieri
- Department of Biotechnology and Life Sciences, University of Insubria, Via Manara 7, Busto Arsizio, VA, Italy
| | - Monica Mancini
- Department of Biotechnology and Life Sciences, University of Insubria, Via Manara 7, Busto Arsizio, VA, Italy.
| | - Ian Marc Bonapace
- Department of Biotechnology and Life Sciences, University of Insubria, Via Manara 7, Busto Arsizio, VA, Italy.
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124
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Maurya GK, Misra HS. Plasmids for making multiple knockouts in a radioresistant bacterium Deinococcus radiodurans. Plasmid 2018; 100:6-13. [PMID: 30261215 DOI: 10.1016/j.plasmid.2018.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 08/28/2018] [Accepted: 09/07/2018] [Indexed: 11/26/2022]
Abstract
The gene knockouts are mostly created using homologous recombination-based replacement of target gene(s) with the expressing cassette of selection marker gene(s). Here, we constructed a series of plasmids bearing the expressing cassettes of genes encoding different antibiotics markers like nptII (KanR), aadA (SpecR), cat (CmR) and aac(3) (GenR). D. radiodurans is a radioresistant Gram positive bacterium that does not support the independent maintenance of colE1 origin-based plasmids. Using these constructs, the disruption mutants of both single and multiple genes involved in segregation of secondary genome elements have been generated in this bacterium. Unlike single mutants, the double and triple mutants showed growth retardation under normal growth conditions and the synergistic effects with Topoisomerase II inhibitor on the growth of this bacterium. Thus, these plasmids could be useful in creating multiple deletions/disruptions in bacteria that do not support independent maintenance of colE1 origin-based plasmid.
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Affiliation(s)
- Ganesh K Maurya
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Mumbai 400094, India
| | - Hari S Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Mumbai 400094, India.
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125
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Guttman A, Szilasi S, Donczo B, Szarka M. Authors' Reply to the Commentary in the journal of Electrophoresis regarding "The effect of simulated space radiation on the N-glycosylation of human immunoglobulin G1" by J.J. Bevelacqua and S.M.J. Mortazavi. Electrophoresis 2018; 39:2851-2853. [PMID: 30101988 DOI: 10.1002/elps.201800321] [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: 07/26/2018] [Accepted: 07/27/2018] [Indexed: 11/06/2022]
Abstract
By reading the commentary of Bevelacqua and Mortazavi regarding our recently published paper titled as "The effect of simulated space radiation on the N-glycosylation of human immunoglobulin G1"[1], we are afraid that some of the important messaging aspects of our paper might not have been articulated adequately to be fully understandable for a wider audience, i.e., not separation scientists. First, we should clarify that complete space radiation description was not the goal of this paper. In this short communication we only intended to show the effect of simulated space radiation on the conserved N-glycosylation of IgG1 molecules with the goal to understand if they could be utilized as disease biomarkers during longer space missions, similar to that as they are currently used here on Earth, e.g. for autoimmune disease or aging markers. Therefore, no discussion was given about any biological effects either as our study only investigated the qualitative effects of proton irradiation on the N-linked carbohydrate decomposition of IgG type 1 molecules with the intent of suggesting them to be used as biomarkers during deep space travel. Radioadaptation was never an issue in our study for the reasons mentioned above.
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Affiliation(s)
- Andras Guttman
- Horvath Csaba Laboratory of Bioseparation Sciences, Research Centre for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Translational Glycomics Research Group, Research Institute for Biomolecular and Chemical Engineering, University of Pannonia, Veszprem, Hungary
| | - Szabolcs Szilasi
- Institute for Nuclear Research, Hungarian Academy of Sciences, Debrecen, Hungary
| | - Boglarka Donczo
- Horvath Csaba Laboratory of Bioseparation Sciences, Research Centre for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Mate Szarka
- Horvath Csaba Laboratory of Bioseparation Sciences, Research Centre for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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Dai S, Jin Y, Li T, Weng Y, Xu X, Zhang G, Li J, Pang R, Tian B, Hua Y. DR1440 is a potential iron efflux protein involved in maintenance of iron homeostasis and resistance of Deinococcus radiodurans to oxidative stress. PLoS One 2018; 13:e0202287. [PMID: 30106993 PMCID: PMC6091924 DOI: 10.1371/journal.pone.0202287] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 07/31/2018] [Indexed: 01/18/2023] Open
Abstract
Iron acquisition by bacteria is well studied, but iron export from bacteria is less understood. Herein, we identified dr1440 with a P-type ATPase motif as a potential exporter of iron from Deinococcus radiodurans, a bacterium known for its extreme resistance to radiation and oxidants. The DR1440 was located in cell membrane as demonstrated by fluorescence labelling analysis. Mutation of dr1440 resulted in cellular accumulation of iron ions, and expression level of dr1440 was up-regulated significantly under iron ion or hydrogen peroxide stress in the wild-type strain, implicating DR1440 as a potential iron efflux protein. The dr1440 mutant displayed higher sensitivity to iron ions and oxidative stresses including hydrogen peroxide, hypochlorous acid, and gamma-ray irradiation compared with the wild-type strain. The high amount of iron in the mutant strain resulted in severe protein carbonylation, suggesting that DR1440 might contribute to intracellular protein protection against reactive oxygen species (ROS) generated from ferrous ion-mediated Fenton-reaction. Mutations of S297A and C299A led to intracellular accumulation of iron, indicating that S297 and C299 might be important functional residues of DR1440. Thus, DR1440 is a potential iron efflux protein involved in iron homeostasis and oxidative stress-resistance of D. radiodurans.
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Affiliation(s)
- Shang Dai
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Ye Jin
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Tao Li
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Yulan Weng
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Xiaolin Xu
- Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi, Xinjiang, China
| | - Genlin Zhang
- Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi, Xinjiang, China
| | - Jiulong Li
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Renjiang Pang
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Bing Tian
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
- * E-mail:
| | - Yuejin Hua
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
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127
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Singh H. Desiccation and radiation stress tolerance in cyanobacteria. J Basic Microbiol 2018; 58:813-826. [PMID: 30080267 DOI: 10.1002/jobm.201800216] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/29/2018] [Accepted: 07/16/2018] [Indexed: 11/10/2022]
Abstract
Cyanobacteria are among the oldest living organisms on this planet, existing since more than 3 billion years. They are ideal organisms for investigating biological processes such as photosynthesis, respiration, circadian rhythm, photoregulation of gene expression, developmental gene rearrangements, and specialized cell differentiation. They are nearly ubiquitous in distribution, have colonized a wide range of ecosystems including soil, air, dry rock, and aquatic systems, and even occupy extreme niches that are inaccessible to other organisms. Such wide ecological distribution reflects their capacity to acclimate to extreme environments. They show great adaptive abilities and have survived various adverse physiological growth conditions like desiccation, high temperatures, extreme pH, cold, osmosis, salt, light, nitrogen, and high salinity. Their ancient origin and surviving through numerous stresses during evolution indicates their remarkable capabilities to survive and prevail under different environmental and man-made stresses. It has been hypothesized that similar and overlap stress response mechanisms help them to survive different stresses. It has been stated that responses against stresses like radiation has been accidental-exhibited because of similar response against desiccation stress, which has prevailed more during evolution. These overlaps and similarities in stress responses have been instrumental in making these organisms a large class of biological entities today. Present review discuss about stress tolerance in cyanobacteria against two extreme stresses - desiccation and gamma radiation. It also discuss the commonality and underlying molecular mechanisms in these two stress responses.
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Affiliation(s)
- Harinder Singh
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS (Deemed-to-be) University, Vile Parle (W), Mumbai, India
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128
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Levels and fluxes in enzymatic antioxidants following gamma irradiation are inadequate to confer radiation resistance in Drosophila melanogaster. Mol Biol Rep 2018; 45:1175-1186. [DOI: 10.1007/s11033-018-4270-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 07/16/2018] [Indexed: 10/28/2022]
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130
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Complete genome sequence of Nibribacter radioresistens DG15C, a radiation resistant bacterium. Mol Cell Toxicol 2018. [DOI: 10.1007/s13273-018-0035-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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131
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Szarka M, Szilasi S, Donczo B, Sarkozy D, Rajta I, Guttman A. The effect of simulated space radiation on the
N
‐glycosylation of human immunoglobulin G1. Electrophoresis 2018; 39:2872-2876. [DOI: 10.1002/elps.201800151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 05/11/2018] [Accepted: 05/11/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Mate Szarka
- Horváth Csaba Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of MedicineUniversity of Debrecen Debrecen Hungary
| | - Szabolcs Szilasi
- Institute for Nuclear ResearchHungarian Academy of Sciences Debrecen Hungary
| | - Boglarka Donczo
- Horváth Csaba Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of MedicineUniversity of Debrecen Debrecen Hungary
| | - Daniel Sarkozy
- Horváth Csaba Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of MedicineUniversity of Debrecen Debrecen Hungary
| | - Istvan Rajta
- Institute for Nuclear ResearchHungarian Academy of Sciences Debrecen Hungary
| | - Andras Guttman
- Horváth Csaba Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of MedicineUniversity of Debrecen Debrecen Hungary
- Translational Glycomics Research Group, Research Institute for Biomolecular and Chemical EngineeringUniversity of Pannonia Veszprem Hungary
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132
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Pacelli C, Bryan RA, Onofri S, Selbmann L, Zucconi L, Shuryak I, Dadachova E. The effect of protracted X-ray exposure on cell survival and metabolic activity of fast and slow growing fungi capable of melanogenesis. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:255-263. [PMID: 29473314 DOI: 10.1111/1758-2229.12632] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 02/14/2018] [Accepted: 02/16/2018] [Indexed: 06/08/2023]
Abstract
The aim of this study was to analyse how protracted exposure to X-rays delivered at low dose rates of 0.0032-0.052 kGy h-1 affects the survival and metabolic activity of two microfungi capable of melanogenesis: fast-growing Cryptococcus neoformans (CN) and slow-growing Cryomyces antarcticus (CA). Melanized CN and CA cells survived the protracted exposure better than non-melanized ones, which was consistent with previous reports on the radioprotective role of melanin in these fungi after high dose rate exposures. The survival data were described by the linear quadratic dose response model. The XTT metabolic profiles were practically identical for melanized CN and CA with activity dose-dependent increasing: no changes in the activity of the non-melanized CN and CA were recorded by this assay. In contrast, the MTT assay, which measures the intracellular energy-related processes, recorded an increase in activity of non-melanized CN and CA cells, but not in their melanized counterparts. This could reflect intensive repair processes initiated by the non-melanized cells post exposure. This study suggests that differences in radiation responses between melanized and non-melanized fungal cells occur over a wide range of radiation dose rates.
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Affiliation(s)
- Claudia Pacelli
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
- Department of Radiology, Albert Einstein College of Medicine, Bronx, New York, NY, USA
| | - Ruth A Bryan
- Department of Radiology, Albert Einstein College of Medicine, Bronx, New York, NY, USA
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Igor Shuryak
- Center for Radiological Research, Columbia University, New York, NY, USA
| | - Ekaterina Dadachova
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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133
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Senatore G, Mastroleo F, Leys N, Mauriello G. Effect of microgravity & space radiation on microbes. Future Microbiol 2018; 13:831-847. [PMID: 29745771 DOI: 10.2217/fmb-2017-0251] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
One of the new challenges facing humanity is to reach increasingly further distant space targets. It is therefore of upmost importance to understand the behavior of microorganisms that will unavoidably reach the space environment together with the human body and equipment. Indeed, microorganisms could activate their stress defense mechanisms, modifying properties related to human pathogenesis. The host-microbe interactions, in fact, could be substantially affected under spaceflight conditions and the study of microorganisms' growth and activity is necessary for predicting these behaviors and assessing precautionary measures during spaceflight. This review gives an overview of the effects of microgravity and space radiation on microorganisms both in real and simulated conditions.
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Affiliation(s)
- Giuliana Senatore
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Naples, Italy
| | - Felice Mastroleo
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), 2400 Mol, Belgium
| | - Natalie Leys
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), 2400 Mol, Belgium
| | - Gianluigi Mauriello
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Naples, Italy
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134
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Adam-Guillermin C, Hertal-Aas T, Oughton D, Blanchard L, Alonzo F, Armant O, Horemans N. Radiosensitivity and transgenerational effects in non-human species. Ann ICRP 2018; 47:327-341. [PMID: 29745724 DOI: 10.1177/0146645318756844] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The ALLIANCE working group on effects of ionising radiation on wildlife brings together European researchers to work on the topics of radiosensitivity and transgenerational effects in non-human biota. Differences in radiation sensitivity across species and phyla are poorly understood, but have important implications for understanding the overall effects of radiation and for radiation protection; for example, sensitive species may require special attention in monitoring and radiation protection, and differences in sensitivity between species also lead to overall effects at higher levels (community, ecosystem), since interactions between species can be altered. Hence, understanding the mechanisms of interspecies radiation sensitivity differences may help to clarify mechanisms underpinning intraspecies variation. Differences in sensitivity may only be revealed when organisms are exposed to ionising radiation over several generations. This issue of potential long-term or hereditary effects for both humans and wildlife exposed to low doses of ionising radiation is a major concern. Animal and plant studies suggest that gamma irradiation can lead to observable effects in the F1 generation that are not attributable to inheritance of a rare stable DNA mutation. Several studies have provided evidence of an increase in genomic instability detected in germ or somatic cells of F1 organisms from exposed F0 organisms. This can lead to induced radiosensitivity, and can result in phenotypic effects or lead to reproductive effects and teratogenesis. In particular, studies have been conducted to understand the possible role of epigenetic modifications, such as DNA methylation, histone modifications, or expression of non-coding RNAs in radiosensitivity, as well as in adaptation effects. As such, research using biological models in which the relative contribution of genetic and epigenetic processes can be elucidated is highly valuable.
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Affiliation(s)
- C Adam-Guillermin
- a Institut de Radioprotection et de Sûreté Nucléaire, PSE-ENV/SRTE/LECO, Cadarache, Saint Paul Lez Durance, France
| | | | - D Oughton
- b Norwegian University of Life Sciences, Norway
| | - L Blanchard
- c Commissariat à l'énergie atomique et aux énergies alternatives, France.,d Centre national de la recherche scientifique, France.,e Aix-Marseille Université, France
| | - F Alonzo
- a Institut de Radioprotection et de Sûreté Nucléaire, PSE-ENV/SRTE/LECO, Cadarache, Saint Paul Lez Durance, France
| | - O Armant
- a Institut de Radioprotection et de Sûreté Nucléaire, PSE-ENV/SRTE/LECO, Cadarache, Saint Paul Lez Durance, France
| | - N Horemans
- f Belgian Nuclear Research Centre, Belgium
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135
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Feliciello I, Zahradka D, Zahradka K, Ivanković S, Puc N, Đermić D. RecF, UvrD, RecX and RecN proteins suppress DNA degradation at DNA double-strand breaks in Escherichia coli. Biochimie 2018; 148:116-126. [DOI: 10.1016/j.biochi.2018.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/13/2018] [Indexed: 01/15/2023]
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136
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Paithankar JG, Raghu SV, Patil RK. Concomitant changes in radiation resistance and trehalose levels during life stages of Drosophila melanogaster suggest radio-protective function of trehalose. Int J Radiat Biol 2018; 94:576-589. [PMID: 29613812 DOI: 10.1080/09553002.2018.1460499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
PURPOSE During development, various life stages of Drosophila melanogaster (D. melanogaster) show different levels of resistance to gamma irradiation, with the early pupal stage being the most radiation sensitive. This provides us an opportunity to explore the biochemical basis of such variations. The present study was carried out to understand the mechanisms underlying radiation resistance during life stages of D. melanogaster. MATERIALS AND METHODS Homogenates from all the life stages of D. melanogaster were prepared at stipulated age. These homogenates were used for the determination of (1) enzymatic antioxidants: superoxide dismutase (SOD), catalase, D. melanogaster glutathione peroxidase (DmGPx), and glutathione S-transferase (GST); (2) reducing non-enzymatic antioxidants: total antioxidant capacity (TAC), reduced glutathione (GSH) and non-reducing non-enzymatic antioxidant trehalose; and (3) levels of protein carbonyl (PC) content. Age-dependent changes in radiation resistance and associated biochemical changes were also studied in young (2 d) and old (20 and 30 d) flies. RESULTS TAC and GSH were found high in the early pupal stage, whereas catalase and DmGPx were found to increase in the early pupal stage. The non-feeding third instar (NFTI) larvae were found to have high levels of SOD and GST, besides NFTI larvae showed high levels of trehalose. A remarkable decrease was observed in radiation resistance and trehalose levels during the early pupal stage. The PC level was the highest during early pupal stage and was the lowest in NFTI larvae. Older flies showed high level of PC compared with young flies. CONCLUSION In vitro increments in trehalose concentration correspond to reduced formation of PCs, suggesting a protective role of trehalose against free radicals. A strong correlation between levels of trehalose and PC formation suggests amelioration of proteome damage due to ionizing radiation (IR). Stages with high trehalose levels showed protected proteome and high radiation resistance, suggesting a significant role for this disaccharide in radiation resistance.
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Affiliation(s)
| | | | - Rajashekhar K Patil
- a Department of Applied Zoology , Mangalore University , Mangalore , Karnataka , India.,b Centre for Radioisotopes and Radiation Technology (CARRT) , Mangalore University , Mangalore , Karnataka , India
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137
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Burger A, Lichtscheidl I. Stable and radioactive cesium: A review about distribution in the environment, uptake and translocation in plants, plant reactions and plants' potential for bioremediation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 618:1459-1485. [PMID: 29122347 DOI: 10.1016/j.scitotenv.2017.09.298] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 09/26/2017] [Accepted: 09/27/2017] [Indexed: 05/23/2023]
Abstract
Radiocesium in water, soil, and air represents a severe threat to human health and the environment. It either acts directly on living organisms from external sources, or it becomes incorporated through the food chain, or both. Plants are at the base of the food chain; it is therefore essential to understand the mechanisms of plants for cesium retention and uptake. In this review we summarize investigations about sources of stable and radioactive cesium in the environment and harmful effects caused by internal and external exposure of plants to radiocesium. Uptake of cesium into cells occurs through molecular mechanisms such as potassium and calcium transporters in the plasma membrane. In soil, bioavailability of cesium depends on the chemical composition of the soil and physical factors such as pH, temperature and tilling as well as on environmental factors such as soil microorganisms. Uptake of cesium occurs also from air through interception and absorption on leaves and from water through the whole submerged surface. We reviewed information about reducing cesium in the vegetation by loss processes, and we extracted transfer factors from the available literature and give an overview over the uptake capacities of 72 plants for cesium from the substratum to the biomass. Plants with high uptake potential could be used to remediate soil and water from radiocesium by accumulation and rhizofiltration. Inside plants, cesium distributes fast between the different plant organs and cells, but cesium in soil is extremely stable and remains for decades in the rhizosphere. Monitoring of contaminated soil therefore has to continue for many decades, and edible plants grown on such soil must continuously be monitored.
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Affiliation(s)
- Anna Burger
- University of Vienna, Core Facility Cell Imaging and Ultrastructure Research, Althanstrasse 14, A-1090 Vienna, Austria.
| | - Irene Lichtscheidl
- University of Vienna, Core Facility Cell Imaging and Ultrastructure Research, Althanstrasse 14, A-1090 Vienna, Austria
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138
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Novel Sequence Features of DNA Repair Genes/Proteins from Deinococcus Species Implicated in Protection from Oxidatively Generated Damage. Genes (Basel) 2018. [PMID: 29518000 PMCID: PMC5867870 DOI: 10.3390/genes9030149] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Deinococcus species display a high degree of resistance to radiation and desiccation due to their ability to protect critical proteome from oxidatively generated damage; however, the underlying mechanisms are not understood. Comparative analysis of DNA repair proteins reported here has identified 22 conserved signature indels (CSIs) in the proteins UvrA1, UvrC, UvrD, UvsE, MutY, MutM, Nth, RecA, RecD, RecG, RecQ, RecR, RuvC, RadA, PolA, DnaE, LigA, GyrA and GyrB, that are uniquely shared by all/most Deinococcus homologs. Of these CSIs, a 30 amino acid surface-exposed insert in the Deinococcus UvrA1, which distinguishes it from all other UvrA homologs, is of much interest. The uvrA1 gene in Deinococcus also exhibits specific genetic linkage (predicted operonic arrangement) to genes for three other proteins including a novel Deinococcus-specific transmembrane protein (designated dCSP-1) and the proteins DsbA and DsbB, playing central roles in protein disulfide bond formation by oxidation-reduction of CXXC (C represents cysteine, X any other amino acid) motifs. The CXXC motifs provide important targets for oxidation damage and they are present in many DNA repair proteins including five in UvrA, which are part of Zinc-finger elements. A conserved insert specific for Deinococcus is also present in the DsbA protein. Additionally, the uvsE gene in Deinococcus also shows specific linkage to the gene for a membrane-associated protein. To account for these novel observations, a model is proposed where specific interaction of the Deinococcus UvrA1 protein with membrane-bound dCSP-1 enables the UvrA1 to receive electrons from DsbA-DsbB oxido-reductase machinery to ameliorate oxidation damage in the UvrA1 protein.
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139
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Gostinčar C, Gunde-Cimerman N. Overview of Oxidative Stress Response Genes in Selected Halophilic Fungi. Genes (Basel) 2018; 9:E143. [PMID: 29509668 PMCID: PMC5867864 DOI: 10.3390/genes9030143] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/22/2018] [Accepted: 02/27/2018] [Indexed: 11/17/2022] Open
Abstract
Exposure of microorganisms to stress, including to high concentrations of salt, can lead to increased production of reactive oxygen species in the cell. To limit the resulting damage, cells have evolved a variety of antioxidant defenses. The role of these defenses in halotolerance has been proposed before. Whole genome sequencing for some of the most halotolerant and halophilic fungal species has enabled us to investigate the possible links between oxidative and salt stress tolerance on the genomic level. We identified genes involved in oxidative stress response in the halophilic basidiomycete Wallemia ichthyophaga, and halotolerant ascomycetous black yeasts Hortaea werneckii and Aureobasidium pullulans, and compared them to genes from 16 other fungi, both asco- and basidiomycetes. According to our results, W. ichthyophaga can survive salinities detrimental to most other organisms with only a moderate number of oxidative stress response genes. In other investigated species, however, the maximum tolerated salinity correlated with the number of genes encoding three major enzymes of the cellular oxidative stress response: superoxide dismutases, catalases, and peroxiredoxins. This observation supports the hypothetical link between the antioxidant capacity of cells and their halotolerance.
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Affiliation(s)
- Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.
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140
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Beblo-Vranesevic K, Bohmeier M, Perras AK, Schwendner P, Rabbow E, Moissl-Eichinger C, Cockell CS, Vannier P, Marteinsson VT, Monaghan EP, Ehrenfreund P, Garcia-Descalzo L, Gómez F, Malki M, Amils R, Gaboyer F, Westall F, Cabezas P, Walter N, Rettberg P. Lack of correlation of desiccation and radiation tolerance in microorganisms from diverse extreme environments tested under anoxic conditions. FEMS Microbiol Lett 2018; 365:4883205. [PMID: 29474542 PMCID: PMC5939664 DOI: 10.1093/femsle/fny044] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/19/2018] [Indexed: 12/21/2022] Open
Abstract
Four facultative anaerobic and two obligate anaerobic bacteria were isolated from extreme environments (deep subsurface halite mine, sulfidic anoxic spring, mineral-rich river) in the frame MASE (Mars Analogues for Space Exploration) project. The isolates were investigated under anoxic conditions for their survivability after desiccation up to 6 months and their tolerance to ionizing radiation up to 3000 Gy. The results indicated that tolerances to both stresses are strain-specific features. Yersinia intermedia MASE-LG-1 showed a high desiccation tolerance but its radiation tolerance was very low. The most radiation-tolerant strains were Buttiauxella sp. MASE-IM-9 and Halanaerobium sp. MASE-BB-1. In both cases, cultivable cells were detectable after an exposure to 3 kGy of ionizing radiation, but cells only survived desiccation for 90 and 30 days, respectively. Although a correlation between desiccation and ionizing radiation resistance has been hypothesized for some aerobic microorganisms, our data showed that there was no correlation between tolerance to desiccation and ionizing radiation, suggesting that the physiological basis of both forms of tolerances is not necessarily linked. In addition, these results indicated that facultative and obligate anaerobic organisms living in extreme environments possess varied species-specific tolerances to extremes.
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Affiliation(s)
- Kristina Beblo-Vranesevic
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), Linder Hoehe, 51147 Cologne, Germany
| | - Maria Bohmeier
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), Linder Hoehe, 51147 Cologne, Germany
| | - Alexandra K Perras
- Department of Internal Medicine, Medical University of Graz, Auerbruggerplatz 15, 8010 Graz, Austria
- Department of Microbiology and Archaea, University of Regensburg, Universitätsstr. 31, 93053 Regensburg, Germany
| | - Petra Schwendner
- UK Center for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, EH9 3FD, Edinburgh, UK
| | - Elke Rabbow
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), Linder Hoehe, 51147 Cologne, Germany
| | - Christine Moissl-Eichinger
- Department of Internal Medicine, Medical University of Graz, Auerbruggerplatz 15, 8010 Graz, Austria
- BioTechMed Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Charles S Cockell
- UK Center for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, EH9 3FD, Edinburgh, UK
| | | | - Viggo T Marteinsson
- MATISProkaria, Vinlandsleid 12, 113 Reykjavík, Iceland
- Faculty of Food Science and Nutrition, University of Iceland, Vatnsmýrarvegur 16, 101 Reykjavík, Iceland
| | - Euan P Monaghan
- Leiden Observatory, Universiteit Leiden, Niels Bohrweg 2, 2333 Leiden, Netherland
| | - Pascale Ehrenfreund
- Leiden Observatory, Universiteit Leiden, Niels Bohrweg 2, 2333 Leiden, Netherland
- Space Policy Institute, George Washington University, 1957 E Street, 20052 Washington DC, USA
| | - Laura Garcia-Descalzo
- Instituto Nacional de Técnica Aeroespacial-Centro de Astrobiología (INTA-CAB), Torrejón de Ardoz, 28850 Madrid, Spain
| | - Felipe Gómez
- Instituto Nacional de Técnica Aeroespacial-Centro de Astrobiología (INTA-CAB), Torrejón de Ardoz, 28850 Madrid, Spain
| | - Moustafa Malki
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid (UAM), Calle Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Ricardo Amils
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid (UAM), Calle Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Frédéric Gaboyer
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique (CNRS), Rue Charles Sadron, 45071 Orléans, France
| | - Frances Westall
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique (CNRS), Rue Charles Sadron, 45071 Orléans, France
| | - Patricia Cabezas
- European Science Foundation (ESF), Quai Lezay-Marnésia, 67080 Strasbourg, France
| | - Nicolas Walter
- European Science Foundation (ESF), Quai Lezay-Marnésia, 67080 Strasbourg, France
| | - Petra Rettberg
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), Linder Hoehe, 51147 Cologne, Germany
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141
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Jiang L, Chen Z, Liu L, Wang M, Liu Y, Yu Z. Effect of chlorine dioxide on decontamination of fresh‐cut coriander and identification of bacterial species in fresh‐cutting process. J FOOD PROCESS PRES 2018. [DOI: 10.1111/jfpp.13465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Li Jiang
- College of Food Science and Technology, Nanjing Agricultural UniversityNanjing 210095 PR China
| | - Zhouyao Chen
- College of Food Science and Technology, Nanjing Agricultural UniversityNanjing 210095 PR China
| | - Lu Liu
- College of Food Science and Technology, Nanjing Agricultural UniversityNanjing 210095 PR China
| | - Mian Wang
- College of Food Science and Technology, Nanjing Agricultural UniversityNanjing 210095 PR China
| | - Yanyi Liu
- College of Food Science and Technology, Nanjing Agricultural UniversityNanjing 210095 PR China
| | - Zhifang Yu
- College of Food Science and Technology, Nanjing Agricultural UniversityNanjing 210095 PR China
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142
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Tkavc R, Matrosova VY, Grichenko OE, Gostinčar C, Volpe RP, Klimenkova P, Gaidamakova EK, Zhou CE, Stewart BJ, Lyman MG, Malfatti SA, Rubinfeld B, Courtot M, Singh J, Dalgard CL, Hamilton T, Frey KG, Gunde-Cimerman N, Dugan L, Daly MJ. Prospects for Fungal Bioremediation of Acidic Radioactive Waste Sites: Characterization and Genome Sequence of Rhodotorula taiwanensis MD1149. Front Microbiol 2018; 8:2528. [PMID: 29375494 PMCID: PMC5766836 DOI: 10.3389/fmicb.2017.02528] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/05/2017] [Indexed: 02/03/2023] Open
Abstract
Highly concentrated radionuclide waste produced during the Cold War era is stored at US Department of Energy (DOE) production sites. This radioactive waste was often highly acidic and mixed with heavy metals, and has been leaking into the environment since the 1950s. Because of the danger and expense of cleanup of such radioactive sites by physicochemical processes, in situ bioremediation methods are being developed for cleanup of contaminated ground and groundwater. To date, the most developed microbial treatment proposed for high-level radioactive sites employs the radiation-resistant bacterium Deinococcus radiodurans. However, the use of Deinococcus spp. and other bacteria is limited by their sensitivity to low pH. We report the characterization of 27 diverse environmental yeasts for their resistance to ionizing radiation (chronic and acute), heavy metals, pH minima, temperature maxima and optima, and their ability to form biofilms. Remarkably, many yeasts are extremely resistant to ionizing radiation and heavy metals. They also excrete carboxylic acids and are exceptionally tolerant to low pH. A special focus is placed on Rhodotorula taiwanensis MD1149, which was the most resistant to acid and gamma radiation. MD1149 is capable of growing under 66 Gy/h at pH 2.3 and in the presence of high concentrations of mercury and chromium compounds, and forming biofilms under high-level chronic radiation and low pH. We present the whole genome sequence and annotation of R. taiwanensis strain MD1149, with a comparison to other Rhodotorula species. This survey elevates yeasts to the frontier of biology's most radiation-resistant representatives, presenting a strong rationale for a role of fungi in bioremediation of acidic radioactive waste sites.
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Affiliation(s)
- Rok Tkavc
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Vera Y Matrosova
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Olga E Grichenko
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Robert P Volpe
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Polina Klimenkova
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Elena K Gaidamakova
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Carol E Zhou
- Lawrence Livermore National Laboratory, Computing Applications and Research Department, Livermore, CA, United States
| | - Benjamin J Stewart
- Biosciences and Biotechnology Division, Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Mathew G Lyman
- Biosciences and Biotechnology Division, Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Stephanie A Malfatti
- Biosciences and Biotechnology Division, Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Bonnee Rubinfeld
- Biosciences and Biotechnology Division, Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Melanie Courtot
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | - Jatinder Singh
- Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Clifton L Dalgard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,The American Genome Center, Bethesda, MD, United States
| | - Theron Hamilton
- Biological Defense Research Directorate, Naval Medical Research Center, Fredrick, MD, United States
| | - Kenneth G Frey
- Biological Defense Research Directorate, Naval Medical Research Center, Fredrick, MD, United States
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Lawrence Dugan
- Biosciences and Biotechnology Division, Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Michael J Daly
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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143
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Doble PA, Miklos GLG. Distributions of manganese in diverse human cancers provide insights into tumour radioresistance. Metallomics 2018; 10:1191-1210. [DOI: 10.1039/c8mt00110c] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We show that measuring manganese levels in tumours of cancer patients is predictive for their radiation treatment.
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Affiliation(s)
- Philip A. Doble
- Elemental Bio-imaging Facility
- University of Technology Sydney
- Broadway
- Australia
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144
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Complete genome sequence of Spirosoma pulveris JSH 5-14T, a bacterium isolated from a dust sample. Mol Cell Toxicol 2017. [DOI: 10.1007/s13273-017-0041-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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145
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Ott E, Kawaguchi Y, Kölbl D, Chaturvedi P, Nakagawa K, Yamagishi A, Weckwerth W, Milojevic T. Proteometabolomic response of Deinococcus radiodurans exposed to UVC and vacuum conditions: Initial studies prior to the Tanpopo space mission. PLoS One 2017; 12:e0189381. [PMID: 29244852 PMCID: PMC5731708 DOI: 10.1371/journal.pone.0189381] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/24/2017] [Indexed: 11/18/2022] Open
Abstract
The multiple extremes resistant bacterium Deinococcus radiodurans is able to withstand harsh conditions of simulated outer space environment. The Tanpopo orbital mission performs a long-term space exposure of D. radiodurans aiming to investigate the possibility of interplanetary transfer of life. The revealing of molecular machinery responsible for survivability of D. radiodurans in the outer space environment can improve our understanding of underlying stress response mechanisms. In this paper, we have evaluated the molecular response of D. radiodurans after the exposure to space-related conditions of UVC irradiation and vacuum. Notably, scanning electron microscopy investigations showed that neither morphology nor cellular integrity of irradiated cells was affected, while integrated proteomic and metabolomic analysis revealed numerous molecular alterations in metabolic and stress response pathways. Several molecular key mechanisms of D. radiodurans, including the tricarboxylic acid cycle, the DNA damage response systems, ROS scavenging systems and transcriptional regulators responded in order to cope with the stressful situation caused by UVC irradiation under vacuum conditions. These results reveal the effectiveness of the integrative proteometabolomic approach as a tool in molecular analysis of microbial stress response caused by space-related factors.
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Affiliation(s)
- Emanuel Ott
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Yuko Kawaguchi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Denise Kölbl
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Palak Chaturvedi
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Kazumichi Nakagawa
- Graduate School of Human Development and Environment, Kobe University, Kobe, Japan
| | - Akihiko Yamagishi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
- * E-mail: (TM); (WW)
| | - Tetyana Milojevic
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
- * E-mail: (TM); (WW)
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146
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Wen L, Yue L, Shi Y, Ren L, Chen T, Li N, Zhang S, Yang W, Yang Z. Deinococcus radiodurans pprI expression enhances the radioresistance of eukaryotes. Oncotarget 2017; 7:15339-55. [PMID: 26992215 PMCID: PMC4941245 DOI: 10.18632/oncotarget.8137] [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] [Received: 08/06/2015] [Accepted: 03/04/2016] [Indexed: 12/12/2022] Open
Abstract
PprI accelerates radiation-induced DNA damage repair via regulating the expression of DNA repair genes and enhances antioxidative enzyme activity in Deinococcus radiodurans after radiation. The main aim of our study was to determine whether the expression of pprI gene could fulfil its DNA repair function in eukaryotes and enhance the radioresistance of eukaryotic organism or not. In this study, we constructed pEGFP-c1-pprI eukaryotic expression vector and established a human lung epithelial cell line BEAS-2B with stable integration of pprI gene. We found that pprIexpression enhanced radioresistance of BEAS-2B cells, decreased γ-H2AX foci formation and apoptosis in irradiated BEAS-2B cells and alleviated radiation induced G2/M arrest of BEAS-2B cells. Moreover, we transferred pEGFP-c1-pprI vector into muscle of BALB/c mice by in vivo electroporation and studied the protective effect of prokaryotic pprI gene in irradiated mice. We found that pprI expression alleviated acute radiation induced hematopoietic system, lung, small intestine and testis damage and increased survival rate of irradiated mice via regulating Rad51 expression in different organs. These findings suggest that prokaryotic pprI gene expression in mammalian cells could enhance radioresistance in vitro and in vivo.
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Affiliation(s)
- Ling Wen
- Department of Radiation Toxicology, School of Radiological Medicine and Protection, Medical College of Soochow University, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, Jiangsu, China
| | - Ling Yue
- Department of Radiation Toxicology, School of Radiological Medicine and Protection, Medical College of Soochow University, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, Jiangsu, China
| | - Yi Shi
- Department of Radiation Toxicology, School of Radiological Medicine and Protection, Medical College of Soochow University, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, Jiangsu, China
| | - Lili Ren
- Department of Radiation Toxicology, School of Radiological Medicine and Protection, Medical College of Soochow University, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, Jiangsu, China
| | - Tingting Chen
- Department of Radiation Toxicology, School of Radiological Medicine and Protection, Medical College of Soochow University, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, Jiangsu, China
| | - Na Li
- Department of Radiation Toxicology, School of Radiological Medicine and Protection, Medical College of Soochow University, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, Jiangsu, China
| | - Shuyu Zhang
- Department of Radiation Genetics, School of Radiological Medicine and Protection, Medical College of Soochow University, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, Jiangsu, China
| | - Wei Yang
- Department of Radiobiology, School of Radiological Medicine and Protection, Medical College of Soochow University, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, Jiangsu, China
| | - Zhanshan Yang
- Department of Radiation Toxicology, School of Radiological Medicine and Protection, Medical College of Soochow University, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, Jiangsu, China
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147
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Wang Y, Wang M, Dong K, Ye H. Engineering Mammalian Designer Cells for the Treatment of Metabolic Diseases. Biotechnol J 2017; 13:e1700160. [PMID: 29144600 DOI: 10.1002/biot.201700160] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 11/03/2017] [Indexed: 12/22/2022]
Abstract
Synthetic biology applies engineering principles to biological systems and has significantly advanced the design of synthetic gene circuits that can reprogram cell activities to perform new functions. The ability to engineer mammalian designer cells with robust therapeutic behaviors has brought new opportunities for treating metabolic diseases. In this review, the authors highlight the most recent advances in the development of synthetic designer cells uploaded with open- or closed-loop gene circuits for the treatment of metabolic disorders including diabetes, hypertension, hyperuricemia, and obesity, and discuss the current technologies and future perspectives in applying these designer cells for clinical applications. In the future, more and more rationally designed cells will be constructed and revolutionized to treat a number of metabolic disorders in an intelligent manner.
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Affiliation(s)
- Yidan Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Meiyan Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Kaili Dong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Haifeng Ye
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
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148
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Across the tree of life, radiation resistance is governed by antioxidant Mn 2+, gauged by paramagnetic resonance. Proc Natl Acad Sci U S A 2017; 114:E9253-E9260. [PMID: 29042516 PMCID: PMC5676931 DOI: 10.1073/pnas.1713608114] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Despite concerted functional genomic efforts to understand the complex phenotype of ionizing radiation (IR) resistance, a genome sequence cannot predict whether a cell is IR-resistant or not. Instead, we report that absorption-display electron paramagnetic resonance (EPR) spectroscopy of nonirradiated cells is highly diagnostic of IR survival and repair efficiency of DNA double-strand breaks (DSBs) caused by exposure to gamma radiation across archaea, bacteria, and eukaryotes, including fungi and human cells. IR-resistant cells, which are efficient at DSB repair, contain a high cellular content of manganous ions (Mn2+) in high-symmetry (H) antioxidant complexes with small metabolites (e.g., orthophosphate, peptides), which exhibit narrow EPR signals (small zero-field splitting). In contrast, Mn2+ ions in IR-sensitive cells, which are inefficient at DSB repair, exist largely as low-symmetry (L) complexes with substantially broadened spectra seen with enzymes and strongly chelating ligands. The fraction of cellular Mn2+ present as H-complexes (H-Mn2+), as measured by EPR of live, nonirradiated Mn-replete cells, is now the strongest known gauge of biological IR resistance between and within organisms representing all three domains of life: Antioxidant H-Mn2+ complexes, not antioxidant enzymes (e.g., Mn superoxide dismutase), govern IR survival. As the pool of intracellular metabolites needed to form H-Mn2+ complexes depends on the nutritional status of the cell, we conclude that IR resistance is predominantly a metabolic phenomenon. In a cross-kingdom analysis, the vast differences in taxonomic classification, genome size, and radioresistance between cell types studied here support that IR resistance is not controlled by the repertoire of DNA repair and antioxidant enzymes.
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149
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Schmier BJ, Chen X, Wolin S, Shuman S. Deletion of the rnl gene encoding a nick-sealing RNA ligase sensitizes Deinococcus radiodurans to ionizing radiation. Nucleic Acids Res 2017; 45:3812-3821. [PMID: 28126918 PMCID: PMC5397189 DOI: 10.1093/nar/gkx038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 01/23/2017] [Indexed: 11/14/2022] Open
Abstract
Deinococcus radiodurans RNA ligase (DraRnl) seals 3΄-OH/5΄-PO4 nicks in duplex nucleic acids in which the 3΄-OH nick terminus consists of two or more ribonucleotides. DraRnl exemplifies a widely distributed Rnl5 family of nick-sealing RNA ligases, the physiological functions of which are uncharted. Here we show via gene knockout that whereas DraRnl is inessential for growth of D. radiodurans, its absence sensitizes the bacterium to killing by ionizing radiation (IR). DraRnl protein is present in exponentially growing and stationary phase cells, but is depleted during the early stages of recovery from 10 kGy of IR and subsequently replenished during the late phase of post-IR genome reassembly. Absence of DraRnl elicts a delay in reconstitution of the 10 kGy IR-shattered D. radiodurans replicons that correlates with the timing of DraRnl replenishment in wild-type cells. Complementation with a catalytically dead mutant highlights that nick sealing activity is important for the radioprotective function of DraRnl. Our findings suggest a scenario in which DraRnl acts at genomic nicks resulting from gap-filling by a ribonucleotide-incorporating repair polymerase.
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Affiliation(s)
- Brad J Schmier
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Xinguo Chen
- Cell Biology Department, Yale School of Medicine, New Haven, CT 06536, USA
| | - Sandra Wolin
- Cell Biology Department, Yale School of Medicine, New Haven, CT 06536, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
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150
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Đermić E, Zahradka D, Vujaklija D, Ivanković S, Đermić D. 3'-Terminated Overhangs Regulate DNA Double-Strand Break Processing in Escherichia coli. G3 (BETHESDA, MD.) 2017; 7:3091-3102. [PMID: 28710290 PMCID: PMC5592934 DOI: 10.1534/g3.117.043521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/11/2017] [Indexed: 01/18/2023]
Abstract
Double-strand breaks (DSBs) are lethal DNA lesions, which are repaired by homologous recombination in Escherichia coli To study DSB processing in vivo, we induced DSBs into the E. coli chromosome by γ-irradiation and measured chromosomal degradation. We show that the DNA degradation is regulated by RecA protein concentration and its rate of association with single-stranded DNA (ssDNA). RecA decreased DNA degradation in wild-type, recB, and recD strains, indicating that it is a general phenomenon in E. coli On the other hand, DNA degradation was greatly reduced and unaffected by RecA in the recB1080 mutant (which produces long overhangs) and in a strain devoid of four exonucleases that degrade a 3' tail (ssExos). 3'-5' ssExos deficiency is epistatic to RecA deficiency concerning DNA degradation, suggesting that bound RecA is shielding the 3' tail from degradation by 3'-5' ssExos. Since 3' tail preservation is common to all these situations, we infer that RecA polymerization constitutes a subset of mechanisms for preserving the integrity of 3' tails emanating from DSBs, along with 3' tail's massive length, or prevention of their degradation by inactivation of 3'-5' ssExos. Thus, we conclude that 3' overhangs are crucial in controlling the extent of DSB processing in E. coli This study suggests a regulatory mechanism for DSB processing in E. coli, wherein 3' tails impose a negative feedback loop on DSB processing reactions, specifically on helicase reloading onto dsDNA ends.
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Affiliation(s)
- Edyta Đermić
- Department of Plant Pathology, Faculty of Agriculture, University of Zagreb, 10000, Croatia
| | - Davor Zahradka
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Dušica Vujaklija
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Siniša Ivanković
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Damir Đermić
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia
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