101
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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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102
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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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103
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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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104
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Shuryak I, Matrosova VY, Gaidamakova EK, Tkavc R, Grichenko O, Klimenkova P, Volpe RP, Daly MJ. Microbial cells can cooperate to resist high-level chronic ionizing radiation. PLoS One 2017; 12:e0189261. [PMID: 29261697 PMCID: PMC5738026 DOI: 10.1371/journal.pone.0189261] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/22/2017] [Indexed: 11/18/2022] Open
Abstract
Understanding chronic ionizing radiation (CIR) effects is of utmost importance to protecting human health and the environment. Diverse bacteria and fungi inhabiting extremely radioactive waste and disaster sites (e.g. Hanford, Chernobyl, Fukushima) represent new targets of CIR research. We show that many microorganisms can grow under intense gamma-CIR dose rates of 13–126 Gy/h, with fungi identified as a particularly CIR-resistant group of eukaryotes: among 145 phylogenetically diverse strains tested, 78 grew under 36 Gy/h. Importantly, we demonstrate that CIR resistance can depend on cell concentration and that certain resistant microbial cells protect their neighbors (not only conspecifics, but even radiosensitive species from a different phylum), from high-level CIR. We apply a mechanistically-motivated mathematical model of CIR effects, based on accumulation/removal kinetics of reactive oxygen species (ROS) and antioxidants, in bacteria (3 Escherichia coli strains and Deinococcus radiodurans) and in fungi (Candida parapsilosis, Kazachstania exigua, Pichia kudriavzevii, Rhodotorula lysinophila, Saccharomyces cerevisiae, and Trichosporon mucoides). We also show that correlations between responses to CIR and acute ionizing radiation (AIR) among studied microorganisms are weak. For example, in D. radiodurans, the best molecular correlate for CIR resistance is the antioxidant enzyme catalase, which is dispensable for AIR resistance; and numerous CIR-resistant fungi are not AIR-resistant. Our experimental findings and quantitative modeling thus demonstrate the importance of investigating CIR responses directly, rather than extrapolating from AIR. Protection of radiosensitive cell-types by radioresistant ones under high-level CIR is a potentially important new tool for bioremediation of radioactive sites and development of CIR-resistant microbiota as radioprotectors.
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Affiliation(s)
- Igor Shuryak
- Center for Radiological Research, Columbia University, New York, NY, United States of America
- * E-mail:
| | - Vera Y. Matrosova
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Elena K. Gaidamakova
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Rok Tkavc
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Olga Grichenko
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Polina Klimenkova
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Robert P. Volpe
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Michael J. Daly
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, United States of America
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105
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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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106
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Avoidance of protein oxidation correlates with the desiccation and radiation resistance of hot and cold desert strains of the cyanobacterium Chroococcidiopsis. Extremophiles 2017; 21:981-991. [DOI: 10.1007/s00792-017-0957-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 08/21/2017] [Indexed: 12/29/2022]
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107
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Matrosova VY, Gaidamakova EK, Makarova KS, Grichenko O, Klimenkova P, Volpe RP, Tkavc R, Ertem G, Conze IH, Brambilla E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Shapiro N, Ivanova N, Kyrpides N, Woyke T, Daligault H, Davenport K, Erkkila T, Goodwin LA, Gu W, Munk C, Teshima H, Xu Y, Chain P, Woolbert M, Gunde-Cimerman N, Wolf YI, Grebenc T, Gostinčar C, Daly MJ. High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460. Stand Genomic Sci 2017; 12:46. [PMID: 28775794 PMCID: PMC5534035 DOI: 10.1186/s40793-017-0258-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/20/2017] [Indexed: 11/24/2022] Open
Abstract
The genetic platforms of Deinococcus species remain the only systems in which massive ionizing radiation (IR)-induced genome damage can be investigated in vivo at exposures commensurate with cellular survival. We report the whole genome sequence of the extremely IR-resistant rod-shaped bacterium Deinococcus ficus KS 0460 and its phenotypic characterization. Deinococcus ficus KS 0460 has been studied since 1987, first under the name Deinobacter grandis, then Deinococcus grandis. The D. ficus KS 0460 genome consists of a 4.019 Mbp sequence (69.7% GC content and 3894 predicted genes) divided into six genome partitions, five of which are confirmed to be circular. Circularity was determined manually by mate pair linkage. Approximately 76% of the predicted proteins contained identifiable Pfam domains and 72% were assigned to COGs. Of all D. ficus KS 0460 proteins, 79% and 70% had homologues in Deinococcus radiodurans ATCC BAA-816 and Deinococcus geothermalis DSM 11300, respectively. The most striking differences between D. ficus KS 0460 and D. radiodurans BAA-816 identified by the comparison of the KEGG pathways were as follows: (i) D. ficus lacks nine enzymes of purine degradation present in D. radiodurans, and (ii) D. ficus contains eight enzymes involved in nitrogen metabolism, including nitrate and nitrite reductases, that D. radiodurans lacks. Moreover, genes previously considered to be important to IR resistance are missing in D. ficus KS 0460, namely, for the Mn-transporter nramp, and proteins DdrF, DdrJ and DdrK, all of which are also missing in Deinococcus deserti. Otherwise, D. ficus KS 0460 exemplifies the Deinococcus lineage.
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Affiliation(s)
- Vera Y. Matrosova
- 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
| | - Elena K. Gaidamakova
- 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
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD USA
| | - Olga Grichenko
- 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
- 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
- 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
| | - Rok Tkavc
- 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
| | - Gözen Ertem
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD USA
| | - Isabel H. Conze
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD USA
- University of Bielefeld, Bielefeld, Germany
| | - Evelyne Brambilla
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Alicia Clum
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Manoj Pillay
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | | | | | | | | | - TBK Reddy
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Chris Daum
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | | | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | | | | | | | | | - Wei Gu
- Los Alamos National Laboratory, Los Alamos, NM USA
| | | | | | - Yan Xu
- Los Alamos National Laboratory, Los Alamos, NM USA
| | | | - Michael Woolbert
- 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
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD USA
| | - Tine Grebenc
- Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Michael J. Daly
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD USA
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108
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DNA damage in protective and adverse inflammatory responses: Friend of foe? Mech Ageing Dev 2017; 165:47-53. [DOI: 10.1016/j.mad.2016.06.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 06/13/2016] [Indexed: 11/17/2022]
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109
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Jung KW, Lim S, Bahn YS. Microbial radiation-resistance mechanisms. J Microbiol 2017; 55:499-507. [PMID: 28664512 DOI: 10.1007/s12275-017-7242-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 06/19/2017] [Indexed: 11/28/2022]
Abstract
Organisms living in extreme environments have evolved a wide range of survival strategies by changing biochemical and physiological features depending on their biological niches. Interestingly, organisms exhibiting high radiation resistance have been discovered in the three domains of life (Bacteria, Archaea, and Eukarya), even though a naturally radiationintensive environment has not been found. To counteract the deleterious effects caused by radiation exposure, radiation- resistant organisms employ a series of defensive systems, such as changes in intracellular cation concentration, excellent DNA repair systems, and efficient enzymatic and non-enzymatic antioxidant systems. Here, we overview past and recent findings about radiation-resistance mechanisms in the three domains of life for potential usage of such radiationresistant microbes in the biotechnology industry.
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Affiliation(s)
- Kwang-Woo Jung
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Sangyong Lim
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea.
| | - Yong-Sun Bahn
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
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110
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Singh VK, Seed TM. A review of radiation countermeasures focusing on injury-specific medicinals and regulatory approval status: part I. Radiation sub-syndromes, animal models and FDA-approved countermeasures. Int J Radiat Biol 2017. [PMID: 28650707 DOI: 10.1080/09553002.2017.1332438] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
PURPOSE The increasing global risk of nuclear and radiological accidents or attacks has driven renewed research interest in developing medical countermeasures to potentially injurious exposures to acute irradiation. Clinical symptoms and signs of a developing acute radiation injury, i.e. the acute radiation syndrome, are grouped into three sub-syndromes named after the dominant organ system affected, namely the hematopoietic, gastrointestinal, and neurovascular systems. The availability of safe and effective countermeasures against the above threats currently represents a significant unmet medical need. This is the first article within a three-part series covering the nature of the radiation sub-syndromes, various animal models for radiation countermeasure development, and the agents currently approved by the United States Food and Drug Administration for countering the medical consequences of several of these prominent radiation exposure-associated syndromes. CONCLUSIONS From the U.S. and global perspectives, biomedical research concerning medical countermeasure development is quite robust, largely due to increased government funding following the 9/11 incidence and subsequent rise of terrorist-associated threats. A wide spectrum of radiation countermeasures for specific types of radiation injuries is currently under investigation. However, only a few radiation countermeasures have been fully approved by regulatory agencies for human use during radiological/nuclear contingencies. Additional research effort, with additional funding, clearly will be needed in order to fill this significant, unmet medical health problem.
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Affiliation(s)
- Vijay K Singh
- a Division of Radioprotection, Department of Pharmacology and Molecular Therapeutics , F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences , Bethesda , MD , USA.,b Armed Forces Radiobiology Research Institute , Uniformed Services University of the Health Sciences , Bethesda , MD , USA
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111
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Gayen M, Gupta P, Morazzani EM, Gaidamakova EK, Knollmann-Ritschel B, Daly MJ, Glass PJ, Maheshwari RK. Deinococcus Mn 2+-peptide complex: A novel approach to alphavirus vaccine development. Vaccine 2017; 35:3672-3681. [PMID: 28576570 DOI: 10.1016/j.vaccine.2017.05.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 04/17/2017] [Accepted: 05/04/2017] [Indexed: 10/19/2022]
Abstract
Over the last ten years, Chikungunya virus (CHIKV), an Old World alphavirus has caused numerous outbreaks in Asian and European countries and the Americas, making it an emerging pathogen of great global health importance. Venezuelan equine encephalitis virus (VEEV), a New World alphavirus, on the other hand, has been developed as a bioweapon in the past due to its ease of preparation, aerosol dispersion and high lethality in aerosolized form. Currently, there are no FDA approved vaccines against these viruses. In this study, we used a novel approach to develop inactivated vaccines for VEEV and CHIKV by applying gamma-radiation together with a synthetic Mn-decapeptide-phosphate complex (MnDpPi), based on manganous-peptide-orthophosphate antioxidants accumulated in the extremely radiation-resistant bacterium Deinococcus radiodurans. Classical gamma-irradiated vaccine development approaches are limited by immunogenicity-loss due to oxidative damage to the surface proteins at the high doses of radiation required for complete virus-inactivation. However, addition of MnDpPi during irradiation process selectively protects proteins, but not the nucleic acids, from the radiation-induced oxidative damage, as required for safe and efficacious vaccine development. Previously, this approach was used to develop a bacterial vaccine. In the present study, we show that this approach can successfully be applied to protecting mice against viral infections. Irradiation of VEEV and CHIKV in the presence of MnDpPi resulted in substantial epitope preservation even at supra-lethal doses of gamma-rays (50,000Gy). Irradiated viruses were found to be completely inactivated and safe in vivo (neonatal mice). Upon immunization, VEEV inactivated in the presence of MnDpPi resulted in drastically improved protective efficacy. Thus, the MnDpPi-based gamma-inactivation approach described here can readily be applied to developing vaccines against any pathogen of interest in a fast and cost-effective manner.
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Affiliation(s)
- Manoshi Gayen
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA; Henry M. Jackson Foundation, Bethesda, MD 20817, USA
| | - Paridhi Gupta
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA; Henry M. Jackson Foundation, Bethesda, MD 20817, USA.
| | - Elaine M Morazzani
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Elena K Gaidamakova
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA; Henry M. Jackson Foundation, Bethesda, MD 20817, USA
| | | | - Michael J Daly
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.
| | - Pamela J Glass
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Radha K Maheshwari
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
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112
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Frösler J, Panitz C, Wingender J, Flemming HC, Rettberg P. Survival of Deinococcus geothermalis in Biofilms under Desiccation and Simulated Space and Martian Conditions. ASTROBIOLOGY 2017; 17:431-447. [PMID: 28520474 DOI: 10.1089/ast.2015.1431] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Biofilm formation represents a successful survival strategy for bacteria. In biofilms, cells are embedded in a matrix of extracellular polymeric substances (EPS). As they are often more stress-tolerant than single cells, biofilm cells might survive the conditions present in space and on Mars. To investigate this topic, the bacterium Deinococcus geothermalis was chosen as a model organism due to its tolerance toward desiccation and radiation. Biofilms cultivated on membranes and, for comparison, planktonically grown cells deposited on membranes were air-dried and exposed to individual stressors that included prolonged desiccation, extreme temperatures, vacuum, simulated martian atmosphere, and UV irradiation, and they were exposed to combinations of stressors that simulate space (desiccation + vacuum + UV) or martian (desiccation + Mars atmosphere + UV) conditions. The effect of sulfatic Mars regolith simulant on cell viability during stress was investigated separately. The EPS produced by the biofilm cells contained mainly polysaccharides and proteins. To detect viable but nonculturable (VBNC) cells, cultivation-independent viability indicators (membrane integrity, ATP, 16S rRNA) were determined in addition to colony counts. Desiccation for 2 months resulted in a decrease of culturability with minor changes of membrane integrity in biofilm cells and major loss of membrane integrity in planktonic bacteria. Temperatures between -25°C and +60°C, vacuum, and Mars atmosphere affected neither culturability nor membrane integrity in both phenotypes. Monochromatic (254 nm; ≥1 kJ m-2) and polychromatic (200-400 nm; >5.5 MJ m-2 for planktonic cells and >270 MJ m-2 for biofilms) UV irradiation significantly reduced the culturability of D. geothermalis but did not affect cultivation-independent viability markers, indicating the induction of a VBNC state in UV-irradiated cells. In conclusion, a substantial proportion of the D. geothermalis population remained viable under all stress conditions tested, and in most cases the biofilm form proved advantageous for surviving space and Mars-like conditions. Key Words: Biofilms-Desiccation-UV radiation-Mars-Lithopanspermia. Astrobiology 17, 431-447.
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Affiliation(s)
- Jan Frösler
- 1 Biofilm Centre, University of Duisburg-Essen , Essen, Germany
| | - Corinna Panitz
- 2 Uniklinik/RWTH Aachen, Institute of Pharmacology and Toxicology , Aachen, Germany
| | - Jost Wingender
- 1 Biofilm Centre, University of Duisburg-Essen , Essen, Germany
| | | | - Petra Rettberg
- 3 DLR (Deutsches Zentrum für Luft- und Raumfahrt e.V.), Institute of Aerospace Medicine , Radiation Biology Department, Research Group Astrobiology, Cologne, Germany
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113
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Blanchard L, Guérin P, Roche D, Cruveiller S, Pignol D, Vallenet D, Armengaud J, de Groot A. Conservation and diversity of the IrrE/DdrO-controlled radiation response in radiation-resistant Deinococcus bacteria. Microbiologyopen 2017; 6. [PMID: 28397370 PMCID: PMC5552922 DOI: 10.1002/mbo3.477] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/22/2017] [Accepted: 02/28/2017] [Indexed: 12/26/2022] Open
Abstract
The extreme radiation resistance of Deinococcus bacteria requires the radiation‐stimulated cleavage of protein DdrO by a specific metalloprotease called IrrE. DdrO is the repressor of a predicted radiation/desiccation response (RDR) regulon, composed of radiation‐induced genes having a conserved DNA motif (RDRM) in their promoter regions. Here, we showed that addition of zinc ions to purified apo‐IrrE, and short exposure of Deinococcus cells to zinc ions, resulted in cleavage of DdrO in vitro and in vivo, respectively. Binding of IrrE to RDRM‐containing DNA or interaction of IrrE with DNA‐bound DdrO was not observed. The data are in line with IrrE being a zinc peptidase, and indicate that increased zinc availability, caused by oxidative stress, triggers the in vivo cleavage of DdrO unbound to DNA. Transcriptomics and proteomics of Deinococcus deserti confirmed the IrrE‐dependent regulation of predicted RDR regulon genes and also revealed additional members of this regulon. Comparative analysis showed that the RDR regulon is largely well conserved in Deinococcus species, but also showed diversity in the regulon composition. Notably, several RDR genes with an important role in radiation resistance in Deinococcus radiodurans, for example pprA, are not conserved in some other radiation‐resistant Deinococcus species.
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Affiliation(s)
- Laurence Blanchard
- Lab Bioenerget Cellulaire, CEA, DRF, BIAM, Saint-Paul-lez-Durance, France.,CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance, France.,Aix-Marseille Université, Saint-Paul-lez-Durance, France
| | - Philippe Guérin
- Laboratory "Innovative technologies for Detection and Diagnostic", CEA-Marcoule, DRF/IBITEC-S/SPI/Li2D, Bagnols-sur-Cèze, France
| | - David Roche
- CEA, DRF, Institut de Génomique, LABGeM, Evry, France.,UMR-CNRS 8030 Génomique Métabolique, CEA Institut de Génomique - Genoscope, Evry, France
| | - Stéphane Cruveiller
- CEA, DRF, Institut de Génomique, LABGeM, Evry, France.,UMR-CNRS 8030 Génomique Métabolique, CEA Institut de Génomique - Genoscope, Evry, France
| | - David Pignol
- Lab Bioenerget Cellulaire, CEA, DRF, BIAM, Saint-Paul-lez-Durance, France.,CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance, France.,Aix-Marseille Université, Saint-Paul-lez-Durance, France
| | - David Vallenet
- CEA, DRF, Institut de Génomique, LABGeM, Evry, France.,UMR-CNRS 8030 Génomique Métabolique, CEA Institut de Génomique - Genoscope, Evry, France
| | - Jean Armengaud
- Laboratory "Innovative technologies for Detection and Diagnostic", CEA-Marcoule, DRF/IBITEC-S/SPI/Li2D, Bagnols-sur-Cèze, France
| | - Arjan de Groot
- Lab Bioenerget Cellulaire, CEA, DRF, BIAM, Saint-Paul-lez-Durance, France.,CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance, France.,Aix-Marseille Université, Saint-Paul-lez-Durance, France
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114
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Elevated Rate of Genome Rearrangements in Radiation-Resistant Bacteria. Genetics 2017; 205:1677-1689. [PMID: 28188144 PMCID: PMC5378121 DOI: 10.1534/genetics.116.196154] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/30/2017] [Indexed: 01/27/2023] Open
Abstract
A number of bacterial, archaeal, and eukaryotic species are known for their resistance to ionizing radiation. One of the challenges these species face is a potent environmental source of DNA double-strand breaks, potential drivers of genome structure evolution. Efficient and accurate DNA double-strand break repair systems have been demonstrated in several unrelated radiation-resistant species and are putative adaptations to the DNA damaging environment. Such adaptations are expected to compensate for the genome-destabilizing effect of environmental DNA damage and may be expected to result in a more conserved gene order in radiation-resistant species. However, here we show that rates of genome rearrangements, measured as loss of gene order conservation with time, are higher in radiation-resistant species in multiple, phylogenetically independent groups of bacteria. Comparison of indicators of selection for genome organization between radiation-resistant and phylogenetically matched, nonresistant species argues against tolerance to disruption of genome structure as a strategy for radiation resistance. Interestingly, an important mechanism affecting genome rearrangements in prokaryotes, the symmetrical inversions around the origin of DNA replication, shapes genome structure of both radiation-resistant and nonresistant species. In conclusion, the opposing effects of environmental DNA damage and DNA repair result in elevated rates of genome rearrangements in radiation-resistant bacteria.
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115
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Ranawat P, Rawat S. Stress response physiology of thermophiles. Arch Microbiol 2017; 199:391-414. [DOI: 10.1007/s00203-016-1331-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 12/07/2016] [Accepted: 12/16/2016] [Indexed: 10/20/2022]
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116
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Crosas E, Castellvi A, Crespo I, Fulla D, Gil-Ortiz F, Fuertes G, Kamma-Lorger CS, Malfois M, Aranda MAG, Juanhuix J. Uridine as a new scavenger for synchrotron-based structural biology techniques. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:53-62. [PMID: 28009546 DOI: 10.1107/s1600577516018452] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/17/2016] [Indexed: 06/06/2023]
Abstract
Macromolecular crystallography (MX) and small-angle X-ray scattering (SAXS) studies on proteins at synchrotron light sources are commonly limited by the structural damage produced by the intense X-ray beam. Several effects, such as aggregation in protein solutions and global and site-specific damage in crystals, reduce the data quality or even introduce artefacts that can result in a biologically misguiding structure. One strategy to reduce these negative effects is the inclusion of an additive in the buffer solution to act as a free radical scavenger. Here the properties of uridine as a scavenger for both SAXS and MX experiments on lysozyme at room temperature are examined. In MX experiments, upon addition of uridine at 1 M, the critical dose D1/2 is increased by a factor of ∼1.7, a value similar to that obtained in the presence of the most commonly used scavengers such as ascorbate and sodium nitrate. Other figures of merit to assess radiation damage show a similar trend. In SAXS experiments, the scavenging effect of 40 mM uridine is similar to that of 5% v/v glycerol, and greater than 2 mM DTT and 1 mM ascorbic acid. In all cases, the protective effect of uridine is proportional to its concentration.
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Affiliation(s)
- Eva Crosas
- ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | - Albert Castellvi
- ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | - Isidro Crespo
- ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | - Daniel Fulla
- ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | - Fernando Gil-Ortiz
- ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | | | | | - Marc Malfois
- ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | - Miguel A G Aranda
- ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | - Jordi Juanhuix
- ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
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117
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Hussain S, Dutta A, Sarkar A, Singh A, Gupta ML, Biswas S. Proteomic analysis of irradiated lung tissue of mice using gel-based proteomic approach. Int J Radiat Biol 2016; 93:373-380. [PMID: 28000521 DOI: 10.1080/09553002.2016.1266058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
PURPOSE Exposure to radiation causes severe alterations of protein expression level inside the cell, thus it may influence the biological events and stress response. In the present investigation, we have demonstrated the effect of radiation on mice lung tissues. MATERIALS AND METHODS Two-dimensional gel electrophoresis (2-DE) coupled with MALDI-TOF/TOF was used to check the expression changes in lung proteome profile of strain 'A' female mice after exposure to lethal doses of gamma irradiation at different time periods (24 and 48 h). Identified proteins were analysed for their altered expression and were further validated by Western blotting and enzyme-linked immunosorbent assay (ELISA). RESULTS Nine significant differentially expressed proteins were identified from irradiated lungs tissues. The expression level of zinc finger protein was found to be up regulated at 24 h irradiation in comparison to 48 h irradiation. CONCLUSIONS Zinc finger protein may be considered as a radiation responsive protein. Alteration in its expression pattern may primarily affect binding specificity of the protein that can further result in the interference in transcriptional control of multiple stress responsive genes.
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Affiliation(s)
- Shabir Hussain
- a Department of Genomics & Molecular Medicine , CSIR - Institute of Genomics & Integrative Biology (IGIB), Delhi University Campus , Delhi , India
| | - Ajaswrata Dutta
- b Division of Radioprotective Drug Development Research , Institute of Nuclear Medicine and Allied Sciences , Delhi , India
| | - Ashish Sarkar
- a Department of Genomics & Molecular Medicine , CSIR - Institute of Genomics & Integrative Biology (IGIB), Delhi University Campus , Delhi , India
| | - Abhinav Singh
- b Division of Radioprotective Drug Development Research , Institute of Nuclear Medicine and Allied Sciences , Delhi , India
| | - Manju Lata Gupta
- b Division of Radioprotective Drug Development Research , Institute of Nuclear Medicine and Allied Sciences , Delhi , India
| | - Sagarika Biswas
- a Department of Genomics & Molecular Medicine , CSIR - Institute of Genomics & Integrative Biology (IGIB), Delhi University Campus , Delhi , India
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118
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Lasch P, Grunow R, Antonation K, Weller SA, Jacob D. Inactivation techniques for MALDI-TOF MS analysis of highly pathogenic bacteria – A critical review. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.04.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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119
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Jeon SH, Kang MS, Joo ES, Kim EB, Lim S, Jeong SW, Jung HY, Srinivasan S, Kim MK. Deinococcus persicinus sp. nov., a radiation-resistant bacterium from soil. Int J Syst Evol Microbiol 2016; 66:5077-5082. [DOI: 10.1099/ijsem.0.001473] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Seon Hwa Jeon
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 139-774, Republic of Korea
| | - Myung-Suk Kang
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 404-107, Republic of Korea
| | - Eun Sun Joo
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 139-774, Republic of Korea
| | - Eun Bit Kim
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 139-774, Republic of Korea
| | - Sangyong Lim
- Radiation Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup 580-185, Republic of Korea
| | - Sun-wook Jeong
- Radiation Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup 580-185, Republic of Korea
| | - Hee-Young Jung
- College of Agricultural and Life Sciences, Kyungpook National University, Daegu 702-701, Republic of Korea
- Institute of Plant Medicine, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Sathiyaraj Srinivasan
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 139-774, Republic of Korea
| | - Myung Kyum Kim
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 139-774, Republic of Korea
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120
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Unraveling Fungal Radiation Resistance Regulatory Networks through the Genome-Wide Transcriptome and Genetic Analyses of Cryptococcus neoformans. mBio 2016; 7:mBio.01483-16. [PMID: 27899501 PMCID: PMC5137497 DOI: 10.1128/mbio.01483-16] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The basidiomycetous fungus Cryptococcus neoformans has been known to be highly radiation resistant and has been found in fatal radioactive environments such as the damaged nuclear reactor at Chernobyl. To elucidate the mechanisms underlying the radiation resistance phenotype of C. neoformans, we identified genes affected by gamma radiation through genome-wide transcriptome analysis and characterized their functions. We found that genes involved in DNA damage repair systems were upregulated in response to gamma radiation. Particularly, deletion of recombinase RAD51 and two DNA-dependent ATPase genes, RAD54 and RDH54, increased cellular susceptibility to both gamma radiation and DNA-damaging agents. A variety of oxidative stress response genes were also upregulated. Among them, sulfiredoxin contributed to gamma radiation resistance in a peroxiredoxin/thioredoxin-independent manner. Furthermore, we found that genes involved in molecular chaperone expression, ubiquitination systems, and autophagy were induced, whereas genes involved in the biosynthesis of proteins and fatty acids/sterols were downregulated. Most importantly, we discovered a number of novel C. neoformans genes, the expression of which was modulated by gamma radiation exposure, and their deletion rendered cells susceptible to gamma radiation exposure, as well as DNA damage insults. Among these genes, we found that a unique transcription factor containing the basic leucine zipper domain, named Bdr1, served as a regulator of the gamma radiation resistance of C. neoformans by controlling expression of DNA repair genes, and its expression was regulated by the evolutionarily conserved DNA damage response protein kinase Rad53. Taken together, the current transcriptome and functional analyses contribute to the understanding of the unique molecular mechanism of the radiation-resistant fungus C. neoformans. Although there are no natural environments under intense radiation, some living organisms have been found to show high radiation resistance. Organisms harboring the ability of radiation resistance have unique regulatory networks to overcome this stress. Cryptococcus neoformans is one of the radiation-resistant fungi and is found in highly radioactive environments. However, it remains elusive how radiation-resistant eukaryotic microorganisms work differentially from radiation-sensitive ones. Here, we performed transcriptome analysis of C. neoformans to explore gene expression profiles after gamma radiation exposure and functionally characterized some of identified radiation resistance genes. Notably, we identified a novel regulator of radiation resistance, named Bdr1 (a bZIP TF for DNA damage response 1), which is a transcription factor (TF) that is not closely homologous to any known TF and is transcriptionally controlled by the Rad53 kinase. Therefore, our work could shed light on understanding not only the radiation response but also the radiation resistance mechanism of C. neoformans.
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121
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Lampe N, Biron DG, Brown JMC, Incerti S, Marin P, Maigne L, Sarramia D, Seznec H, Breton V. Simulating the Impact of the Natural Radiation Background on Bacterial Systems: Implications for Very Low Radiation Biological Experiments. PLoS One 2016; 11:e0166364. [PMID: 27851794 PMCID: PMC5112919 DOI: 10.1371/journal.pone.0166364] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 10/27/2016] [Indexed: 11/19/2022] Open
Abstract
At very low radiation dose rates, the effects of energy depositions in cells by ionizing radiation is best understood stochastically, as ionizing particles deposit energy along tracks separated by distances often much larger than the size of cells. We present a thorough analysis of the stochastic impact of the natural radiative background on cells, focusing our attention on E. coli grown as part of a long term evolution experiment in both underground and surface laboratories. The chance per day that a particle track interacts with a cell in the surface laboratory was found to be 6 × 10-5 day-1, 100 times less than the expected daily mutation rate for E. coli under our experimental conditions. In order for the chance cells are hit to approach the mutation rate, a gamma background dose rate of 20 μGy hr-1 is predicted to be required.
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Affiliation(s)
- Nathanael Lampe
- Clermont Université, Université Blaise Pascal, CNRS/IN2P3, Laboratoire de Physique Corpusculaire, BP 10448, F-63000 Clermont-Ferrand, France
| | - David G. Biron
- Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes Génome et Environnement, UMR CNRS 6023, BP 10448, F-63000 Clermont-Ferrand, France
| | - Jeremy M. C. Brown
- School of Mathematics and Physics, Queen’s University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Sébastien Incerti
- Université de Bordeaux, CENBG, UMR 5797, F-33170 Gradignan, France
- CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France
| | - Pierre Marin
- Clermont Université, Université Blaise Pascal, CNRS/IN2P3, Laboratoire de Physique Corpusculaire, BP 10448, F-63000 Clermont-Ferrand, France
| | - Lydia Maigne
- Clermont Université, Université Blaise Pascal, CNRS/IN2P3, Laboratoire de Physique Corpusculaire, BP 10448, F-63000 Clermont-Ferrand, France
| | - David Sarramia
- Clermont Université, Université Blaise Pascal, CNRS/IN2P3, Laboratoire de Physique Corpusculaire, BP 10448, F-63000 Clermont-Ferrand, France
| | - Hervé Seznec
- Université de Bordeaux, CENBG, UMR 5797, F-33170 Gradignan, France
- CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France
| | - Vincent Breton
- Clermont Université, Université Blaise Pascal, CNRS/IN2P3, Laboratoire de Physique Corpusculaire, BP 10448, F-63000 Clermont-Ferrand, France
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Rivasseau C, Farhi E, Compagnon E, de Gouvion Saint Cyr D, van Lis R, Falconet D, Kuntz M, Atteia A, Couté A. Coccomyxa actinabiotis sp. nov. (Trebouxiophyceae, Chlorophyta), a new green microalga living in the spent fuel cooling pool of a nuclear reactor. JOURNAL OF PHYCOLOGY 2016; 52:689-703. [PMID: 27470701 DOI: 10.1111/jpy.12442] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 05/04/2016] [Indexed: 06/06/2023]
Abstract
Life can thrive in extreme environments where inhospitable conditions prevail. Organisms which resist, for example, acidity, pressure, low or high temperature, have been found in harsh environments. Most of them are bacteria and archaea. The bacterium Deinococcus radiodurans is considered to be a champion among all living organisms, surviving extreme ionizing radiation levels. We have discovered a new extremophile eukaryotic organism that possesses a resistance to ionizing radiations similar to that of D. radiodurans. This microorganism, an autotrophic freshwater green microalga, lives in a peculiar environment, namely the cooling pool of a nuclear reactor containing spent nuclear fuels, where it is continuously submitted to nutritive, metallic, and radiative stress. We investigated its morphology and its ultrastructure by light, fluorescence and electron microscopy as well as its biochemical properties. Its resistance to UV and gamma radiation was assessed. When submitted to different dose rates of the order of some tens of mGy · h-1 to several thousands of Gy · h-1 , the microalga revealed to be able to survive intense gamma-rays irradiation, up to 2,000 times the dose lethal to human. The nuclear genome region spanning the genes for small subunit ribosomal RNA-Internal Transcribed Spacer (ITS) 1-5.8S rRNA-ITS2-28S rRNA (beginning) was sequenced (4,065 bp). The phylogenetic position of the microalga was inferred from the 18S rRNA gene. All the revealed characteristics make the alga a new species of the genus Coccomyxa in the class Trebouxiophyceae, which we name Coccomyxa actinabiotis sp. nov.
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Affiliation(s)
- Corinne Rivasseau
- Commissariat à l'Energie Atomique et aux Energies Alternatives, LPCV, CNRS, CEA, INRA, Univ. Grenoble-Alpes, BIG, F-38000, Grenoble, France
| | | | - Estelle Compagnon
- Institut Laue-Langevin, F-38009, Grenoble, France
- CEA, LPCV, CNRS, INRA, Univ. Grenoble-Alpes, F-38000, Grenoble, France
| | - Diane de Gouvion Saint Cyr
- Institut Laue-Langevin, F-38009, Grenoble, France
- CEA, LPCV, CNRS, INRA, Univ. Grenoble-Alpes, F-38000, Grenoble, France
| | - Robert van Lis
- CNRS, BIP, Univ. Aix-Marseille, F-13402, Marseille, France
| | - Denis Falconet
- CNRS, LPCV, CEA, INRA, Univ. Grenoble-Alpes, F-38000, Grenoble, France
| | - Marcel Kuntz
- CNRS, LPCV, CEA, INRA, Univ. Grenoble-Alpes, F-38000, Grenoble, France
| | - Ariane Atteia
- CNRS, Laboratoire de Bioénergétique et Ingénierie de Protéines, Univ. Aix-Marseille, F-13402, Marseille, France
| | - Alain Couté
- Muséum National d'Histoire Naturelle, UMR7245, F-75005, Paris, France
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123
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Lampe N, Marin P, Castor J, Warot G, Incerti S, Maigne L, Sarramia D, Breton V. Background study of absorbed dose in biological experiments at the Modane Underground Laboratory. EPJ WEB OF CONFERENCES 2016. [DOI: 10.1051/epjconf/201612400006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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124
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Paulino-Lima IG, Fujishima K, Navarrete JU, Galante D, Rodrigues F, Azua-Bustos A, Rothschild LJ. Extremely high UV-C radiation resistant microorganisms from desert environments with different manganese concentrations. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 163:327-36. [PMID: 27614243 DOI: 10.1016/j.jphotobiol.2016.08.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 08/10/2016] [Indexed: 12/25/2022]
Abstract
Desiccation resistance and a high intracellular Mn/Fe ratio contribute to ionizing radiation resistance of Deinococcus radiodurans. We hypothesized that this was a general phenomenon and thus developed a strategy to search for highly radiation-resistant organisms based on their natural environment. While desiccation is a typical feature of deserts, the correlation between radiation resistance and the intracellular Mn/Fe ratio of indigenous microorganisms or the Mn/Fe ratio of the environment, has not yet been described. UV-C radiation is highly damaging to biomolecules including DNA. It was used in this study as a selective tool because of its relevance to early life on earth, high altitude aerobiology and the search for life beyond Earth. Surface soil samples were collected from the Sonoran Desert, Arizona (USA), from the Atacama Desert in Chile and from a manganese mine in northern Argentina. Microbial isolates were selected after exposure to UV-C irradiation and growth. The isolates comprised 28 genera grouped within six phyla, which we ranked according to their resistance to UV-C irradiation. Survival curves were performed for the most resistant isolates and correlated with their intracellular Mn/Fe ratio, which was determined by ICP-MS. Five percent of the isolates were highly resistant, including one more resistant than D. radiodurans, a bacterium generally considered the most radiation-resistant organism, thus used as a model for radiation resistance studies. No correlation was observed between the occurrence of resistant microorganisms and the Mn/Fe ratio in the soil samples. However, all resistant isolates showed an intracellular Mn/Fe ratio much higher than the sensitive isolates. Our findings could represent a new front in efforts to harness mechanisms of UV-C radiation resistance from extreme environments.
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Affiliation(s)
| | - Kosuke Fujishima
- University Affiliated Research Center, NASA Ames Research Center, Moffett Field, CA, 94035-0001, USA
| | - Jesica Urbina Navarrete
- University Affiliated Research Center, NASA Ames Research Center, Moffett Field, CA, 94035-0001, USA
| | - Douglas Galante
- Brazilian Synchrotron Light Laboratory, Campinas, 13083-970, Brazil
| | - Fabio Rodrigues
- Institute of Chemistry, University of São Paulo, 05508-000, Brazil
| | - Armando Azua-Bustos
- Centro de Investigación Biomédica, UniversidadAutónoma de Chile, Santiago, 8910060, Chile
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Gupta P, Gayen M, Smith JT, Gaidamakova EK, Matrosova VY, Grichenko O, Knollmann-Ritschel B, Daly MJ, Kiang JG, Maheshwari RK. MDP: A Deinococcus Mn2+-Decapeptide Complex Protects Mice from Ionizing Radiation. PLoS One 2016; 11:e0160575. [PMID: 27500529 PMCID: PMC4976947 DOI: 10.1371/journal.pone.0160575] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/21/2016] [Indexed: 11/24/2022] Open
Abstract
The radioprotective capacity of a rationally-designed Mn2+-decapeptide complex (MDP), based on Mn antioxidants in the bacterium Deinococcus radiodurans, was investigated in a mouse model of radiation injury. MDP was previously reported to be extraordinarily radioprotective of proteins in the setting of vaccine development. The peptide-component (DEHGTAVMLK) of MDP applied here was selected from a group of synthetic peptides screened in vitro for their ability to protect cultured human cells and purified enzymes from extreme damage caused by ionizing radiation (IR). We show that the peptides accumulated in Jurkat T-cells and protected them from 100 Gy. MDP preserved the activity of T4 DNA ligase exposed to 60,000 Gy. In vivo, MDP was nontoxic and protected B6D2F1/J (female) mice from acute radiation syndrome. All irradiated mice treated with MDP survived exposure to 9.5 Gy (LD70/30) in comparison to the untreated mice, which displayed 63% lethality after 30 days. Our results show that MDP provides early protection of white blood cells, and attenuates IR-induced damage to bone marrow and hematopoietic stem cells via G-CSF and GM-CSF modulation. Moreover, MDP mediated the immunomodulation of several cytokine concentrations in serum including G-CSF, GM-CSF, IL-3 and IL-10 during early recovery. Our results present the necessary prelude for future efforts towards clinical application of MDP as a promising IR countermeasure. Further investigation of MDP as a pre-exposure prophylactic and post-exposure therapeutic in radiotherapy and radiation emergencies is warranted.
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Affiliation(s)
- Paridhi Gupta
- Department of Pathology, Uniformed Services University of the Health Sciences (USUHS), School of Medicine, Bethesda, Maryland, United States of America
- * E-mail: (PG); (MJD)
| | - Manoshi Gayen
- Department of Pathology, Uniformed Services University of the Health Sciences (USUHS), School of Medicine, Bethesda, Maryland, United States of America
- Biological Sciences Group, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Joan T. Smith
- Radiation Combined Injury Program, Armed Forces Radiobiology Research Institute (AFRRI), Bethesda, Maryland, United States of America
| | - Elena K. Gaidamakova
- Department of Pathology, Uniformed Services University of the Health Sciences (USUHS), School of Medicine, Bethesda, Maryland, United States of America
| | - Vera Y. Matrosova
- Department of Pathology, Uniformed Services University of the Health Sciences (USUHS), School of Medicine, Bethesda, Maryland, United States of America
| | - Olga Grichenko
- Department of Pathology, Uniformed Services University of the Health Sciences (USUHS), School of Medicine, Bethesda, Maryland, United States of America
| | - Barbara Knollmann-Ritschel
- Department of Pathology, Uniformed Services University of the Health Sciences (USUHS), School of Medicine, Bethesda, Maryland, United States of America
| | - Michael J. Daly
- Department of Pathology, Uniformed Services University of the Health Sciences (USUHS), School of Medicine, Bethesda, Maryland, United States of America
- * E-mail: (PG); (MJD)
| | - Juliann G. Kiang
- Radiation Combined Injury Program, Armed Forces Radiobiology Research Institute (AFRRI), Bethesda, Maryland, United States of America
| | - Radha K. Maheshwari
- Department of Pathology, Uniformed Services University of the Health Sciences (USUHS), School of Medicine, Bethesda, Maryland, United States of America
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126
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Lee JJ, Lee YH, Park SJ, Lim S, Jeong SW, Lee SY, Cho YJ, Kim MK, Jung HY. Deinococcus seoulensis sp. nov., a bacterium isolated from sediment at Han River in Seoul, Republic of Korea. J Microbiol 2016; 54:537-42. [PMID: 27480633 DOI: 10.1007/s12275-016-6253-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 07/12/2016] [Accepted: 07/12/2016] [Indexed: 12/11/2022]
Abstract
Strain 16F1E(T) was isolated from a 3-kGy-irradiated sediment sample collected at Han River in Seoul, Republic of Korea. Cells of this strain were observed to be Gram-positive, pililike structure, and short rod shape, and colonies were red in color. The strain showed the highest degree of 16S rRNA gene sequence similarity to Deinococcus aquaticus PB314(T) (98.8%), Deinococcus depolymerans TDMA-24(T) (98.1%), Deinococcus caeni Ho-08(T) (98.0%), and Deinococcus grandis DSM 3963(T) (97.0%). 16S rRNA gene sequence analysis identified this strain as a member of the genus Deinococcus (Family: Deinococcaceae). The genomic DNA G+C content of strain 16F1ET was 66.9 mol%. The low levels of DNA-DNA hybridization (< 56.2%) with the species mentioned above identified strain 16F1E(T) as a novel Deinococcus species. Its oxidase and catalase activities as well as the production of acid from glucose were positive. Growth of the strain was observed at 10-37°C (optimum: 20-30°C) and pH 4-10 (optimum: pH 7-8). The cells tolerated less than 5% NaCl and had low resistance to gamma radiation (D10 < 4 kGy). Strain 16F1ET possessed the following chemotaxonomic characteristics: C16:0, C15:1 ω6c, and C16:1 ω7c as the major fatty acids; phosphoglycolipid as the predominant polar lipid; and menaquinone-8 as the predominant respiratory isoprenoid quinone. Based on the polyphasic evidence, as well as the phylogenetic, genotypic, phenotypic, and chemotaxonomic characterization results, strain 16F1E(T) (=KCTC 33793(T) =JCM 31404(T)) is proposed to represent the type strain of a novel species, Deinococcus seoulensis sp. nov.
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Affiliation(s)
- Jae-Jin Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Yeon-Hee Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Su-Jin Park
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Sangyong Lim
- Radiation Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Sun-Wook Jeong
- Radiation Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Seung-Yeol Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Young-Je Cho
- School of Food Science and Biotechnology/Food and Bio-Industry Research Institute, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Myung Kyum Kim
- Department of Bio and Environmental Technology, Seoul Women's University, Seoul, 01797, Republic of Korea
| | - Hee-Young Jung
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea. .,Institute of Plant Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea.
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127
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128
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Protection against Radiotherapy-Induced Toxicity. Antioxidants (Basel) 2016; 5:antiox5030022. [PMID: 27399787 PMCID: PMC5039571 DOI: 10.3390/antiox5030022] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 06/27/2016] [Accepted: 06/28/2016] [Indexed: 01/18/2023] Open
Abstract
Radiation therapy is a highly utilized therapy in the treatment of malignancies with up to 60% of cancer patients receiving radiation therapy as a part of their treatment regimen. Radiation therapy does, however, cause a wide range of adverse effects that can be severe and cause permanent damage to the patient. In an attempt to minimize these effects, a small number of compounds have been identified and are in use clinically for the prevention and treatment of radiation associated toxicities. Furthermore, there are a number of emerging therapies being developed for use as agents that protect against radiation-induced toxicities. The aim of this review was to evaluate and summarise the evidence that exists for both the known radioprotectant agents and the agents that show promise as future radioprotectant agents.
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129
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Rajpurohit YS, Bihani SC, Waldor MK, Misra HS. Phosphorylation of Deinococcus radiodurans RecA Regulates Its Activity and May Contribute to Radioresistance. J Biol Chem 2016; 291:16672-85. [PMID: 27255712 DOI: 10.1074/jbc.m116.736389] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Indexed: 11/06/2022] Open
Abstract
Deinococcus radiodurans has a remarkable capacity to survive exposure to extreme levels of radiation that cause hundreds of DNA double strand breaks (DSBs). DSB repair in this bacterium depends on its recombinase A protein (DrRecA). DrRecA plays a pivotal role in both extended synthesis-dependent strand annealing and slow crossover events of DSB repair during the organism's recovery from DNA damage. The mechanisms that control DrRecA activity during the D. radiodurans response to γ radiation exposure are unknown. Here, we show that DrRecA undergoes phosphorylation at Tyr-77 and Thr-318 by a DNA damage-responsive serine threonine/tyrosine protein kinase (RqkA). Phosphorylation modifies the activity of DrRecA in several ways, including increasing its affinity for dsDNA and its preference for dATP over ATP. Strand exchange reactions catalyzed by phosphorylated versus unphosphorylated DrRecA also differ. In silico analysis of DrRecA structure support the idea that phosphorylation can modulate crucial functions of this protein. Collectively, our findings suggest that phosphorylation of DrRecA enables the recombinase to selectively use abundant dsDNA substrate present during post-irradiation recovery for efficient DSB repair, thereby promoting the extraordinary radioresistance of D. radiodurans.
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Affiliation(s)
| | - Subhash C Bihani
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai-400085, India and
| | - Matthew K Waldor
- the Division of Infectious Diseases and Howard Hughes Medical Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
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130
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Oh TJ, Han SR, Ahn DH, Park H, Kim AY. Complete genome sequence of Hymenobacter sp. strain PAMC26554, an ionizing radiation-resistant bacterium isolated from an Antarctic lichen. J Biotechnol 2016; 227:19-20. [DOI: 10.1016/j.jbiotec.2016.04.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 04/06/2016] [Indexed: 11/16/2022]
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131
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Grieshop K, Stångberg J, Martinossi-Allibert I, Arnqvist G, Berger D. Strong sexual selection in males against a mutation load that reduces offspring production in seed beetles. J Evol Biol 2016; 29:1201-10. [DOI: 10.1111/jeb.12862] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/08/2016] [Accepted: 03/09/2016] [Indexed: 01/15/2023]
Affiliation(s)
- K. Grieshop
- Department of Ecology and Genetics; Animal Ecology; Uppsala University; Uppsala Sweden
| | - J. Stångberg
- Department of Ecology and Genetics; Animal Ecology; Uppsala University; Uppsala Sweden
| | | | - G. Arnqvist
- Department of Ecology and Genetics; Animal Ecology; Uppsala University; Uppsala Sweden
| | - D. Berger
- Department of Ecology and Genetics; Animal Ecology; Uppsala University; Uppsala Sweden
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132
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Kim MK, Kang MS, Lee DH, Joo ES, Kim EB, Jeon SH, Jung HY, Srinivasan S. Complete genome sequence of Deinococcus actinosclerus BM2(T), a bacterium with Gamma-radiation resistance isolated from soil in South Korea. J Biotechnol 2016; 224:53-4. [PMID: 26953742 DOI: 10.1016/j.jbiotec.2016.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 03/02/2016] [Indexed: 10/22/2022]
Abstract
A Gram-positive, short-rod shaped and non-motile bacterium Deinococcus actinosclerus BM2(T), resistant to gamma and UV radiation, was isolated from a soil sample collected in South Korea. Strain BM2(T) showed high resistance to gamma radiation with D10 value of 9 kGy. The complete genome of D. actinosclerus BM2(T) consists of a single chromosome (3,264,334bp). The genome features showed the presence of intracellular proteases that help to eliminate radiation-induced ROS during recovery from ionizing radiation damage.
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Affiliation(s)
- Myung Kyum Kim
- Department of Bio & Environmental Technology, College of Natural Sciences, Seoul Women's University, Seoul 139-774, Republic of Korea
| | - Myung Suk Kang
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 404-170, Republic of Korea
| | - Do Hee Lee
- Department of Bio & Environmental Technology, College of Natural Sciences, Seoul Women's University, Seoul 139-774, Republic of Korea
| | - Eun Sun Joo
- Department of Bio & Environmental Technology, College of Natural Sciences, Seoul Women's University, Seoul 139-774, Republic of Korea
| | - Eun Bit Kim
- Department of Bio & Environmental Technology, College of Natural Sciences, Seoul Women's University, Seoul 139-774, Republic of Korea
| | - Seon Hwa Jeon
- Department of Bio & Environmental Technology, College of Natural Sciences, Seoul Women's University, Seoul 139-774, Republic of Korea
| | - Hee-Young Jung
- College of Agricultural and Life Sciences, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Sathiyaraj Srinivasan
- Department of Bio & Environmental Technology, College of Natural Sciences, Seoul Women's University, Seoul 139-774, Republic of Korea.
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133
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Li Y, Wang Z, Liu X, Tang J, Peng B, Wei Y. X-ray Irradiated Vaccine Confers protection against Pneumonia caused by Pseudomonas aeruginosa. Sci Rep 2016; 6:18823. [PMID: 26879055 PMCID: PMC4754647 DOI: 10.1038/srep18823] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 11/24/2015] [Indexed: 02/05/2023] Open
Abstract
Pseudomonas aeruginosa is a gram-negative bacterium and one of the leading causes of nosocomial infection worldwide, however, no effective vaccine is currently available in the market. Here, we demonstrate that inactivation of the bacteria by X-ray irradiation inhibits its replication capability but retained antigenic expression functionally thus allowing its use as a potential vaccine. Mice immunized by this vaccine were challenged by the parental strain, the O-antigen-homologous strain PAO-1 (O2/O5) and heterologous strain PAO-6 (O6) in an acute pneumonia model. We further measured the protective effect of the vaccine, as well as host innate and cellular immunity responses. We found immunized mice could protect against both strains. Notably, the antiserum only had significant protective role against similar bacteria, while adoptive transfer of lymphocytes significantly controlled the spread of the virulent heterologous serogroup PAO-6 infection, and the protective role could be reversed by CD4 rather than CD8 antibody. We further revealed that vaccinated mice could rapidly recruit neutrophils to the airways early after intranasal challenge by PAO-6, and the irradiated vaccine was proved to be protective by the generated CD4(+) IL-17(+) Th17 cells. In conclusion, the generation of inactivated but metabolically active microbes is a promising strategy for safely vaccinating against Pseudomonas aeruginosa.
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Affiliation(s)
- Yanyan Li
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,State Key Labortary of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Cheng Du, China
| | - Zhenling Wang
- State Key Labortary of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Cheng Du, China
| | - Xiaoxiao Liu
- State Key Labortary of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Cheng Du, China
| | - Jianying Tang
- State Key Labortary of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Cheng Du, China
| | - Bin Peng
- State Key Labortary of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Cheng Du, China.,Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Yuquan Wei
- State Key Labortary of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Cheng Du, China
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134
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Sun Joo E, Jin Lee J, Kang MS, Lim S, Jeong SW, Bit Kim E, Hwa Jeon S, Srinivasan S, Kyum Kim M. Deinococcus actinosclerus sp. nov., a novel bacterium isolated from soil of a rocky hillside. Int J Syst Evol Microbiol 2016; 66:1003-1008. [DOI: 10.1099/ijsem.0.000825] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Eun Sun Joo
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul 139-774, Korea
| | - Jae Jin Lee
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul 139-774, Korea
| | - Myung-Suk Kang
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 404-107, Republic of Korea
| | - Sangyong Lim
- Radiation Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup 580-185, Republic of Korea
| | - Sun-wook Jeong
- Radiation Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup 580-185, Republic of Korea
| | - Eun Bit Kim
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul 139-774, Korea
| | - Seon Hwa Jeon
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul 139-774, Korea
| | - Sathiyaraj Srinivasan
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul 139-774, Korea
| | - Myung Kyum Kim
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul 139-774, Korea
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135
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Hymenobacter rubidus sp. nov., bacterium isolated from a soil. Antonie van Leeuwenhoek 2016; 109:457-66. [DOI: 10.1007/s10482-016-0652-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 01/13/2016] [Indexed: 01/28/2023]
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136
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PprA Protein Is Involved in Chromosome Segregation via Its Physical and Functional Interaction with DNA Gyrase in Irradiated Deinococcus radiodurans Bacteria. mSphere 2016; 1:mSphere00036-15. [PMID: 27303692 PMCID: PMC4863600 DOI: 10.1128/msphere.00036-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 12/09/2015] [Indexed: 11/30/2022] Open
Abstract
D. radiodurans is one of the most radiation-resistant organisms known. This bacterium is able to cope with high levels of DNA lesions generated by exposure to extreme doses of ionizing radiation and to reconstruct a functional genome from hundreds of radiation-induced chromosomal fragments. Here, we identified partners of PprA, a radiation-induced Deinococcus-specific protein, previously shown to be required for radioresistance. Our study leads to three main findings: (i) PprA interacts with DNA gyrase after irradiation, (ii) treatment of cells with novobiocin results in defects in chromosome segregation that are aggravated by the absence of PprA, and (iii) PprA stimulates the decatenation activity of DNA gyrase. Our results extend the knowledge of how D. radiodurans cells survive exposure to extreme doses of gamma irradiation and point out the link between DNA repair, chromosome segregation, and DNA gyrase activities in the radioresistant D. radiodurans bacterium. PprA, a radiation-induced Deinococcus-specific protein, was previously shown to be required for cell survival and accurate chromosome segregation after exposure to ionizing radiation. Here, we used an in vivo approach to determine, by shotgun proteomics, putative PprA partners coimmunoprecipitating with PprA when cells were exposed to gamma rays. Among them, we found the two subunits of DNA gyrase and, thus, chose to focus our work on characterizing the activities of the deinococcal DNA gyrase in the presence or absence of PprA. Loss of PprA rendered cells hypersensitive to novobiocin, an inhibitor of the B subunit of DNA gyrase. We showed that treatment of bacteria with novobiocin resulted in induction of the radiation desiccation response (RDR) regulon and in defects in chromosome segregation that were aggravated by the absence of PprA. In vitro, the deinococcal DNA gyrase, like other bacterial DNA gyrases, possesses DNA negative supercoiling and decatenation activities. These two activities are inhibited in vitro by novobiocin and nalidixic acid, whereas PprA specifically stimulates the decatenation activity of DNA gyrase. Together, these results suggest that PprA plays a major role in chromosome decatenation via its interaction with the deinococcal DNA gyrase when D. radiodurans cells are recovering from exposure to ionizing radiation. IMPORTANCED. radiodurans is one of the most radiation-resistant organisms known. This bacterium is able to cope with high levels of DNA lesions generated by exposure to extreme doses of ionizing radiation and to reconstruct a functional genome from hundreds of radiation-induced chromosomal fragments. Here, we identified partners of PprA, a radiation-induced Deinococcus-specific protein, previously shown to be required for radioresistance. Our study leads to three main findings: (i) PprA interacts with DNA gyrase after irradiation, (ii) treatment of cells with novobiocin results in defects in chromosome segregation that are aggravated by the absence of PprA, and (iii) PprA stimulates the decatenation activity of DNA gyrase. Our results extend the knowledge of how D. radiodurans cells survive exposure to extreme doses of gamma irradiation and point out the link between DNA repair, chromosome segregation, and DNA gyrase activities in the radioresistant D. radiodurans bacterium.
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137
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Kim MK, Joo ES, Lee SY, Lee DS, Srinivasan S, Jung HY. Complete genome sequence of Hymenobacter sp. DG25B, a novel bacterium with gamma-radiation resistance isolated from soil in South Korea. J Biotechnol 2016; 217:98-9. [DOI: 10.1016/j.jbiotec.2015.11.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 11/20/2015] [Indexed: 10/22/2022]
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138
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Aridhi S, Sghaier H, Zoghlami M, Maddouri M, Nguifo EM. Prediction of Ionizing Radiation Resistance in Bacteria Using a Multiple Instance Learning Model. J Comput Biol 2016; 23:10-20. [DOI: 10.1089/cmb.2015.0134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Sabeur Aridhi
- Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes (LIMOS)–Université Blaise Pascal (UBP), Clermont Ferrand, France
- Centre National de Recherche Scientifique (CNRS), UMR 6158, LIMOS, Aubière, France
- University of Tunis El Manar, Faculty of Sciences of Tunis, LIPAH, Tunis, Tunisia
| | - Haïtham Sghaier
- National Center for Nuclear Sciences and Technology (CNSTN), Sidi Thabet Technopark, Ariana, Tunisia
- Laboratory BVBGR, ISBST, University of Manouba, La Manouba, Tunisia
| | - Manel Zoghlami
- Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes (LIMOS)–Université Blaise Pascal (UBP), Clermont Ferrand, France
- Centre National de Recherche Scientifique (CNRS), UMR 6158, LIMOS, Aubière, France
- University of Tunis El Manar, Faculty of Sciences of Tunis, LIPAH, Tunis, Tunisia
| | - Mondher Maddouri
- University of Tunis El Manar, Faculty of Sciences of Tunis, LIPAH, Tunis, Tunisia
- Taibah University, Medinah, Saudi Arabia
| | - Engelbert Mephu Nguifo
- Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes (LIMOS)–Université Blaise Pascal (UBP), Clermont Ferrand, France
- Centre National de Recherche Scientifique (CNRS), UMR 6158, LIMOS, Aubière, France
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139
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Jeong SW, Jung JH, Kim MK, Seo HS, Lim HM, Lim S. The three catalases in Deinococcus radiodurans: Only two show catalase activity. Biochem Biophys Res Commun 2015; 469:443-8. [PMID: 26692481 DOI: 10.1016/j.bbrc.2015.12.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 12/03/2015] [Indexed: 01/31/2023]
Abstract
Deinococcus radiodurans, which is extremely resistant to ionizing radiation and oxidative stress, is known to have three catalases (DR1998, DRA0146, and DRA0259). In this study, to investigate the role of each catalase, we constructed catalase mutants (Δdr1998, ΔdrA0146, and ΔdrA0259) of D. radiodurans. Of the three mutants, Δdr1998 exhibited the greatest decrease in hydrogen peroxide (H2O2) resistance and the highest increase in intracellular reactive oxygen species (ROS) levels following H2O2 treatments, whereas ΔdrA0146 showed no change in its H2O2 resistance or ROS level. Catalase activity was not attenuated in ΔdrA0146, and none of the three bands detected in an in-gel catalase activity assay disappeared in ΔdrA0146. The purified His-tagged recombinant DRA0146 did not show catalase activity. In addition, the phylogenetic analysis of the deinococcal catalases revealed that the DR1998-type catalase is common in the genus Deinococcus, but the DRA0146-type catalase was found in only 4 of 23 Deinococcus species. Taken together, these results indicate that DR1998 plays a critical role in the anti-oxidative system of D. radiodurans by detoxifying H2O2, but DRA0146 does not have catalase activity and is not involved in the resistance to H2O2 stress.
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Affiliation(s)
- Sun-Wook Jeong
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 580-185, Republic of Korea; Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, 305-764, Republic of Korea
| | - Jong-Hyun Jung
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 580-185, Republic of Korea
| | - Min-Kyu Kim
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 580-185, Republic of Korea
| | - Ho Seong Seo
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 580-185, Republic of Korea
| | - Heon-Man Lim
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, 305-764, Republic of Korea
| | - Sangyong Lim
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 580-185, Republic of Korea.
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140
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Hansler A, Chen Q, Ma Y, Gross SS. Untargeted metabolite profiling reveals that nitric oxide bioynthesis is an endogenous modulator of carotenoid biosynthesis in Deinococcus radiodurans and is required for extreme ionizing radiation resistance. Arch Biochem Biophys 2015; 589:38-52. [PMID: 26550929 DOI: 10.1016/j.abb.2015.10.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/12/2015] [Accepted: 10/12/2015] [Indexed: 10/22/2022]
Abstract
Deinococcus radiodurans (Drad) is the most radioresistant organism known. Although mechanisms that underlie the extreme radioresistance of Drad are incompletely defined, resistance to UV irradiation-induced killing was found to be greatly attenuated in an NO synthase (NOS) knockout strain of Drad (Δnos). We now show that endogenous NO production is also critical for protection of Drad against γ-irradiation (3000 Gy), a result of accelerated growth recovery, not protection against killing. NO-donor treatment rescued radiosensitization in Δnos Drad but did not influence radiosensitivity in wild type Drad. To discover molecular mechanisms by which endogenous NO confers radioresistance, metabolite profiling studies were performed. Untargeted LC-MS-based metabolite profiling in Drad quantified relative abundances of 1425 molecules and levels of 294 of these were altered by >5-fold (p < 0.01). Unexpectedly, these studies identified a dramatic perturbation in carotenoid biosynthetic intermediates in Δnos Drad, including a reciprocal switch in the pathway end-products from deoxydeinoxanthin to deinoxanthin. NO supplementation rescued these nos deletion-associated changes in carotenoid biosynthesis, and fully-restored radioresistance to wildtype levels. Because carotenoids were shown to be important contributors to radioprotection in Drad, our findings suggest that endogenously-produced NO serves to maintain a spectrum of carotenoids critical for Drad's ability to withstand radiation insult.
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Affiliation(s)
- Alex Hansler
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA
| | - Qiuying Chen
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA
| | - Yuliang Ma
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA
| | - Steven S Gross
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA.
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141
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Interactions between Biliverdin, Oxidative Damage, and Spleen Morphology after Simulated Aggressive Encounters in Veiled Chameleons. PLoS One 2015; 10:e0138007. [PMID: 26368930 PMCID: PMC4569575 DOI: 10.1371/journal.pone.0138007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 08/24/2015] [Indexed: 12/02/2022] Open
Abstract
Stressors frequently increase oxidative damage–unless organisms simultaneously mount effective antioxidant responses. One putative mitigative mechanism is the use of biliverdin, an antioxidant produced in the spleen during erythrocyte degradation. We hypothesized that both wild and captive-bred male veiled chameleons (Chamaeleo calyptratus), which are highly aggressive to conspecifics, would respond to agonistic displays with increased levels of oxidative damage, but that increased levels of biliverdin would limit this increase. We found that even just visual exposure to a potential combatant resulted in decreased body mass during the subsequent 48-hour period, but that hematocrit, biliverdin concentration in the bile, relative spleen size, and oxidative damage in plasma, liver, and spleen were unaffected. Contrary to our predictions, we found that individuals with smaller spleens exhibited greater decreases in hematocrit and higher bile biliverdin concentrations, suggesting a revision to the idea of spleen-dependent erythrocyte processing. Interestingly, individuals with larger spleens had reduced oxidative damage in both the liver and spleen, demonstrating the spleen’s importance in modulating oxidative damage. We also uncovered differences in spleen size and oxidative damage between wild and captive-bred chameleons, highlighting environmentally dependent differences in oxidative physiology. Lastly, we found no relationship between oxidative damage and biliverdin concentration, calling into question biliverdin’s antioxidant role in this species.
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142
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Pulschen AA, Rodrigues F, Duarte RTD, Araujo GG, Santiago IF, Paulino-Lima IG, Rosa CA, Kato MJ, Pellizari VH, Galante D. UV-resistant yeasts isolated from a high-altitude volcanic area on the Atacama Desert as eukaryotic models for astrobiology. Microbiologyopen 2015; 4:574-88. [PMID: 26147800 PMCID: PMC4554453 DOI: 10.1002/mbo3.262] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 03/18/2015] [Accepted: 03/27/2015] [Indexed: 11/17/2022] Open
Abstract
The Sairecabur volcano (5971 m), in the Atacama Desert, is a high-altitude extreme environment with high daily temperature variations, acidic soils, intense UV radiation, and low availability of water. Four different species of yeasts were isolated from this region using oligotrophic media, identified and characterized for their tolerance to extreme conditions. rRNA sequencing revealed high identity (>98%) to Cryptococcus friedmannii, Exophiala sp., Holtermanniella watticus, and Rhodosporidium toruloides. To our knowledge, this is the first report of these yeasts in the Atacama Desert. All isolates showed high resistance to UV-C, UV-B and environmental-UV radiation, capacity to grow at moderate saline media (0.75–2.25 mol/L NaCl) and at moderate to cold temperatures, being C. friedmannii and H. watticus able to grow in temperatures down to −6.5°C. The presence of pigments, analyzed by Raman spectroscopy, correlated with UV resistance in some cases, but there is evidence that, on the natural environment, other molecular mechanisms may be as important as pigmentation, which has implications for the search of spectroscopic biosignatures on planetary surfaces. Due to the extreme tolerances of the isolated yeasts, these organisms represent interesting eukaryotic models for astrobiological purposes.
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Affiliation(s)
- André A Pulschen
- Chemistry Institute, Universidade de São Paulo, São Paulo, Brazil
| | - Fabio Rodrigues
- Chemistry Institute, Universidade de São Paulo, São Paulo, Brazil
| | - Rubens T D Duarte
- Microbiology, Immunology and Parasitology Department, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Gabriel G Araujo
- Interunities Graduate Program in Biotechnology, Universidade de São Paulo, São Paulo, Brazil.,Brazilian Synchrotron Light Laboratory, Campinas, Brazil
| | - Iara F Santiago
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ivan G Paulino-Lima
- NASA Postdoctoral Program Fellow at NASA Ames Research Center, Moffett Field, California
| | - Carlos A Rosa
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Massuo J Kato
- Chemistry Institute, Universidade de São Paulo, São Paulo, Brazil
| | | | - Douglas Galante
- Interunities Graduate Program in Biotechnology, Universidade de São Paulo, São Paulo, Brazil.,Brazilian Synchrotron Light Laboratory, Campinas, Brazil
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143
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Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes. ISME JOURNAL 2015; 10:21-9. [PMID: 26125681 DOI: 10.1038/ismej.2015.108] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 05/04/2015] [Accepted: 05/09/2015] [Indexed: 01/27/2023]
Abstract
The Geodermatophilaceae are unique model systems to study the ability to thrive on or within stones and their proteogenomes (referring to the whole protein arsenal encoded by the genome) could provide important insight into their adaptation mechanisms. Here we report the detailed comparative genome analysis of Blastococcus saxobsidens (Bs), Modestobacter marinus (Mm) and Geodermatophilus obscurus (Go) isolated respectively from the interior and the surface of calcarenite stones and from desert sandy soils. The genome-scale analysis of Bs, Mm and Go illustrates how adaptation to these niches can be achieved through various strategies including 'molecular tinkering/opportunism' as shown by the high proportion of lost, duplicated or horizontally transferred genes and ORFans. Using high-throughput discovery proteomics, the three proteomes under unstressed conditions were analyzed, highlighting the most abundant biomarkers and the main protein factors. Proteomic data corroborated previously demonstrated stone-related ecological distribution. For instance, these data showed starvation-inducible, biofilm-related and DNA-protection proteins as signatures of the microbes associated with the interior, surface and outside of stones, respectively.
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144
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Recent progress in understanding the molecular mechanisms of radioresistance in Deinococcus bacteria. Extremophiles 2015; 19:707-19. [DOI: 10.1007/s00792-015-0759-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 05/17/2015] [Indexed: 12/17/2022]
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145
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Kurth D, Belfiore C, Gorriti MF, Cortez N, Farias ME, Albarracín VH. Genomic and proteomic evidences unravel the UV-resistome of the poly-extremophile Acinetobacter sp. Ver3. Front Microbiol 2015; 6:328. [PMID: 25954258 PMCID: PMC4406064 DOI: 10.3389/fmicb.2015.00328] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 04/01/2015] [Indexed: 12/20/2022] Open
Abstract
Ultraviolet radiation can damage biomolecules, with detrimental or even lethal effects for life. Even though lower wavelengths are filtered by the ozone layer, a significant amount of harmful UV-B and UV-A radiation reach Earth's surface, particularly in high altitude environments. high-altitude Andean lakes (HAALs) are a group of disperse shallow lakes and salterns, located at the Dry Central Andes region in South America at altitudes above 3,000 m. As it is considered one of the highest UV-exposed environments, HAAL microbes constitute model systems to study UV-resistance mechanisms in environmental bacteria at various complexity levels. Herein, we present the genome sequence of Acinetobacter sp. Ver3, a gammaproteobacterium isolated from Lake Verde (4,400 m), together with further experimental evidence supporting the phenomenological observations regarding this bacterium ability to cope with increased UV-induced DNA damage. Comparison with the genomes of other Acinetobacter strains highlighted a number of unique genes, such as a novel cryptochrome. Proteomic profiling of UV-exposed cells identified up-regulated proteins such as a specific cytoplasmic catalase, a putative regulator, and proteins associated to amino acid and protein synthesis. Down-regulated proteins were related to several energy-generating pathways such as glycolysis, beta-oxidation of fatty acids, and electronic respiratory chain. To the best of our knowledge, this is the first report on a genome from a polyextremophilic Acinetobacter strain. From the genomic and proteomic data, an "UV-resistome" was defined, encompassing the genes that would support the outstanding UV-resistance of this strain.
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Affiliation(s)
- Daniel Kurth
- Laboratorio de Investigaciones Microbiologicas Lagunas Andinas, Centro Científico Tecnológico, Planta Piloto de Procesos Industriales Microbiológicos - Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán Argentina
| | - Carolina Belfiore
- Laboratorio de Investigaciones Microbiologicas Lagunas Andinas, Centro Científico Tecnológico, Planta Piloto de Procesos Industriales Microbiológicos - Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán Argentina
| | - Marta F Gorriti
- Laboratorio de Investigaciones Microbiologicas Lagunas Andinas, Centro Científico Tecnológico, Planta Piloto de Procesos Industriales Microbiológicos - Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán Argentina
| | - Néstor Cortez
- Centro Científico Tecnológico, IBR - CONICET, Universidad Nacional de Rosario Rosario, Argentina
| | - María E Farias
- Laboratorio de Investigaciones Microbiologicas Lagunas Andinas, Centro Científico Tecnológico, Planta Piloto de Procesos Industriales Microbiológicos - Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán Argentina
| | - Virginia H Albarracín
- Laboratorio de Investigaciones Microbiologicas Lagunas Andinas, Centro Científico Tecnológico, Planta Piloto de Procesos Industriales Microbiológicos - Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán Argentina ; Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, San Miguel de Tucumán Argentina
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146
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Dulermo R, Onodera T, Coste G, Passot F, Dutertre M, Porteron M, Confalonieri F, Sommer S, Pasternak C. Identification of new genes contributing to the extreme radioresistance of Deinococcus radiodurans using a Tn5-based transposon mutant library. PLoS One 2015; 10:e0124358. [PMID: 25884619 PMCID: PMC4401554 DOI: 10.1371/journal.pone.0124358] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/02/2015] [Indexed: 01/19/2023] Open
Abstract
Here, we have developed an extremely efficient in vivo Tn5-based mutagenesis procedure to construct a Deinococcus radiodurans insertion mutant library subsequently screened for sensitivity to genotoxic agents such as γ and UV radiations or mitomycin C. The genes inactivated in radiosensitive mutants belong to various functional categories, including DNA repair functions, stress responses, signal transduction, membrane transport, several metabolic pathways, and genes of unknown function. Interestingly, preliminary characterization of previously undescribed radiosensitive mutants suggests the contribution of cyclic di-AMP signaling in the recovery of D. radiodurans cells from genotoxic stresses, probably by modulating several pathways involved in the overall cell response. Our analyses also point out a new transcriptional regulator belonging to the GntR family, encoded by DR0265, and a predicted RNase belonging to the newly described Y family, both contributing to the extreme radioresistance of D. radiodurans. Altogether, this work has revealed new cell responses involved either directly or indirectly in repair of various cell damage and confirmed that D. radiodurans extreme radiation resistance is determined by a multiplicity of pathways acting as a complex network.
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Affiliation(s)
- Rémi Dulermo
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Takefumi Onodera
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Geneviève Coste
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Fanny Passot
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Murielle Dutertre
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Martine Porteron
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Fabrice Confalonieri
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Suzanne Sommer
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Cécile Pasternak
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
- * E-mail:
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147
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Shuryak I, Bryan RA, Broitman J, Marino SA, Morgenstern A, Apostolidis C, Dadachova E. Effects of radiation type and delivery mode on a radioresistant eukaryote Cryptococcus neoformans. Nucl Med Biol 2015; 42:515-23. [PMID: 25800676 DOI: 10.1016/j.nucmedbio.2015.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 02/24/2015] [Accepted: 02/26/2015] [Indexed: 01/22/2023]
Abstract
INTRODUCTION Most research on radioresistant fungi, particularly on human pathogens such as Cryptococcus neoformans, involves sparsely-ionizing radiation. Consequently, fungal responses to densely-ionizing radiation, which can be harnessed to treat life-threatening fungal infections, remain incompletely understood. METHODS We addressed this issue by quantifying and comparing the effects of densely-ionizing α-particles (delivered either by external beam or by (213)Bi-labeled monoclonal antibodies), and sparsely-ionizing (137)Cs γ-rays, on Cryptococcus neoformans. RESULTS The best-fit linear-quadratic parameters for clonogenic survival were the following: α = 0.24 × 10(-2) Gy(-1) for γ-rays and 1.07 × 10(-2) Gy(-1) for external-beam α-particles, and β = 1.44 × 10(-5) Gy(-2) for both radiation types. Fungal cell killing by radiolabeled antibodies was consistent with predictions based on the α-particle dose to the cell nucleus and the linear-quadratic parameters for external-beam α-particles. The estimated RBE (for α-particles vs. γ-rays) at low doses was 4.47 for the initial portion of the α-particle track, and 7.66 for the Bragg peak. Non-radiological antibody effects accounted for up to 23% of cell death. CONCLUSIONS These results quantify the degree of C. neoformans resistance to densely-ionizing radiations, and show how this resistance can be overcome with fungus-specific radiolabeled antibodies.
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Affiliation(s)
- Igor Shuryak
- Center for Radiological Research, Columbia University Medical Center, New York, New York
| | - Ruth A Bryan
- Department of Radiology, Albert Einstein College of Medicine, Bronx, New York
| | - Jack Broitman
- Department of Radiology, Albert Einstein College of Medicine, Bronx, New York
| | - Stephen A Marino
- Radiological Research Accelerator Facility, Nevis Laboratories, Irvington, New York
| | - Alfred Morgenstern
- European Commission, Joint Research Centre, Institute for Transuranium Elements, Karlsruhe, Germany
| | - Christos Apostolidis
- European Commission, Joint Research Centre, Institute for Transuranium Elements, Karlsruhe, Germany
| | - Ekaterina Dadachova
- Department of Radiology, Albert Einstein College of Medicine, Bronx, New York; Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York.
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148
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Folgosa F, Camacho I, Penas D, Guilherme M, Fróis J, Ribeiro PA, Tavares P, Pereira AS. UV radiation effects on a DNA repair enzyme: conversion of a [4Fe-4S](2+) cluster into a [2Fe-2S] (2+). RADIATION AND ENVIRONMENTAL BIOPHYSICS 2015; 54:111-121. [PMID: 25249071 DOI: 10.1007/s00411-014-0569-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 09/17/2014] [Indexed: 06/03/2023]
Abstract
Organisms are often exposed to different types of ionizing radiation that, directly or not, will promote damage to DNA molecules and/or other cellular structures. Because of that, organisms developed a wide range of response mechanisms to deal with these threats. Endonuclease III is one of the enzymes responsible to detect and repair oxidized pyrimidine base lesions. However, the effect of radiation on the structure/function of these enzymes is not clear yet. Here, we demonstrate the effect of UV-C radiation on E. coli endonuclease III through several techniques, namely UV-visible, fluorescence and Mössbauer spectroscopies, as well as SDS-PAGE and electrophoretic mobility shift assay. We demonstrate that irradiation with a UV-C source has dramatic consequences on the absorption, fluorescence, structure and functionality of the protein, affecting its [4Fe-4S] cluster and its DNA-binding ability, which results in its inactivation. An UV-C radiation-induced conversion of the [4Fe-4S](2+) into a [2Fe-2S](2+) was observed for the first time and proven by Mössbauer and UV-visible analysis. This work also shows that the DNA-binding capability of endonuclease III is highly dependent of the nuclearity of the endogenous iron-sulfur cluster. Thus, from our point of view, in a cellular context, these results strengthen the argument that cellular sensitivity to radiation can also be due to loss of radiation-induced damage repair ability.
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Affiliation(s)
- Filipe Folgosa
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
- CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Inês Camacho
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Daniela Penas
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Márcia Guilherme
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - João Fróis
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Paulo A Ribeiro
- CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Pedro Tavares
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Alice S Pereira
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.
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149
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Tsai CH, Liao R, Chou B, Contreras LM. Transcriptional analysis of Deinococcus radiodurans reveals novel small RNAs that are differentially expressed under ionizing radiation. Appl Environ Microbiol 2015; 81:1754-64. [PMID: 25548054 PMCID: PMC4325154 DOI: 10.1128/aem.03709-14] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 12/19/2014] [Indexed: 02/08/2023] Open
Abstract
Small noncoding RNAs (sRNAs) are posttranscriptional regulators that have been identified in multiple species and shown to play essential roles in responsive mechanisms to environmental stresses. The natural ability of specific bacteria to resist high levels of radiation has been of high interest to mechanistic studies of DNA repair and biomolecular protection. Deinococcus radiodurans is a model extremophile for radiation studies that can survive doses of ionizing radiation of >12,000 Gy, 3,000 times higher than for most vertebrates. Few studies have investigated posttranscriptional regulatory mechanisms of this organism that could be relevant in its general gene regulatory patterns. In this study, we identified 199 potential sRNA candidates in D. radiodurans by whole-transcriptome deep sequencing analysis and confirmed the expression of 41 sRNAs by Northern blotting and reverse transcriptase PCR (RT-PCR). A total of 8 confirmed sRNAs showed differential expression during recovery after acute ionizing radiation (15 kGy). We have also found and confirmed 7 sRNAs in Deinococcus geothermalis, a closely related radioresistant species. The identification of several novel sRNAs in Deinococcus bacteria raises important questions about the evolution and nature of global gene regulation in radioresistance.
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Affiliation(s)
- Chen-Hsun Tsai
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Rick Liao
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Brendan Chou
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas, USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
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150
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Appukuttan D, Seo HS, Jeong S, Im S, Joe M, Song D, Choi J, Lim S. Expression and mutational analysis of DinB-like protein DR0053 in Deinococcus radiodurans. PLoS One 2015; 10:e0118275. [PMID: 25706748 PMCID: PMC4338110 DOI: 10.1371/journal.pone.0118275] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 01/12/2015] [Indexed: 11/19/2022] Open
Abstract
In order to understand the mechanism governing radiation resistance in Deinococcus radiodurans, current efforts are aimed at identifying potential candidates from a large repertoire of unique Deinococcal genes and protein families. DR0053 belongs to the DinB/YfiT protein family, which is an over-represented protein family in D. radiodurans. We observed that dr0053 transcript levels were highly induced in response to gamma radiation (γ-radiation) and mitomycin C (MMC) exposure depending on PprI, RecA and the DrtR/S two-component signal transduction system. Protein profiles demonstrated that DR0053 is a highly induced protein in cultures exposed to 10 kGy γ-radiation. We were able to determine the transcriptional start site of dr0053, which was induced upon irradiation, and to assign the 133-bp promoter region of dr0053 as essential for radiation responsiveness through primer extension and promoter deletion analyses. A dr0053 mutant strain displayed sensitivity to γ-radiation and MMC exposure, but not hydrogen peroxide, suggesting that DR0053 helps cells recover from DNA damage. Bioinformatic analyses revealed that DR0053 is similar to the Bacillus subtilis protein YjoA, which is a substrate of bacterial protein-tyrosine kinases. Taken together, the DNA damage-inducible (din) gene dr0053 may be regulated at the transcriptional and post-translational levels.
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Affiliation(s)
- Deepti Appukuttan
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Ho Seong Seo
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Sunwook Jeong
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Sunghun Im
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Minho Joe
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Dusup Song
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Jungjoon Choi
- Department of Agricultural Biotechnology, Center for Agricultural Biomaterials, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Sangyong Lim
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
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