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Górecki I, Kołodziejczyk A, Harasymczuk M, Młynarczyk G, Szymanek-Majchrzak K. The Impact of Harsh Stratospheric Conditions on Survival and Antibiotic Resistance Profile of Non-Spore Forming Multidrug Resistant Human Pathogenic Bacteria Causing Hospital-Associated Infections. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:2787. [PMID: 36833485 PMCID: PMC9956888 DOI: 10.3390/ijerph20042787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Bacteria are constantly being lifted to the stratosphere due to air movements caused by weather phenomena, volcanic eruptions, or human activity. In the upper parts of the atmosphere, they are exposed to extremely harsh and mutagenic conditions such as UV and space radiation or ozone. Most bacteria cannot withstand that stress, but for a fraction of them, it can act as a trigger for selective pressure and rapid evolution. We assessed the impact of stratospheric conditions on the survival and antibiotic resistance profile of common non-spore-forming human pathogenic bacteria, both sensitive and extremely dangerous multidrug-resistant variants, with plasmid-mediated mechanisms of resistance. Pseudomonas aeruginosa did not survive the exposure. In the case of strains that were recovered alive, the survival was extremely low: From 0.00001% of Klebsiella pneumoniae carrying the ndm-1 gene and methicillin-resistant Staphylococcus aureus mecA-positive with reduced susceptibility to vancomycin (MRSA/VISA), to a maximum of 0.001% of K. pneumoniae sensitive to all common antibiotics and S. aureus sensitive to vancomycin (MRSA/VSSA). We noticed a tendency towards increased antibiotic susceptibility after the stratospheric flight. Antimicrobial resistance is a current real, global, and increasing problem, and our results can inform current understandings of antibiotic resistance mechanisms and development in bacteria.
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Affiliation(s)
- Ignacy Górecki
- Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego, Str. 5, 02-004 Warsaw, Poland
| | - Agata Kołodziejczyk
- Analog Astronaut Training Center, Morelowa Str. 1F/4, 30-222 Cracow, Poland
- Space Technology Centre, AGH University of Technology, Czarnowiejska Str. 36, 30-054 Cracow, Poland
| | - Matt Harasymczuk
- Analog Astronaut Training Center, Morelowa Str. 1F/4, 30-222 Cracow, Poland
| | - Grażyna Młynarczyk
- Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego, Str. 5, 02-004 Warsaw, Poland
| | - Ksenia Szymanek-Majchrzak
- Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego, Str. 5, 02-004 Warsaw, Poland
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2
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Akter A, Lyons O, Mehra V, Isenman H, Abbate V. Radiometal chelators for infection diagnostics. FRONTIERS IN NUCLEAR MEDICINE (LAUSANNE, SWITZERLAND) 2023; 2:1058388. [PMID: 37388440 PMCID: PMC7614707 DOI: 10.3389/fnume.2022.1058388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Infection of native tissues or implanted devices is common, but clinical diagnosis is frequently difficult and currently available noninvasive tests perform poorly. Immunocompromised individuals (for example transplant recipients, or those with cancer) are at increased risk. No imaging test in clinical use can specifically identify infection, or accurately differentiate bacterial from fungal infections. Commonly used [18F]fluorodeoxyglucose (18FDG) positron emission computed tomography (PET/CT) is sensitive for infection, but limited by poor specificity because increased glucose uptake may also indicate inflammation or malignancy. Furthermore, this tracer provides no indication of the type of infective agent (bacterial, fungal, or parasitic). Imaging tools that directly and specifically target microbial pathogens are highly desirable to improve noninvasive infection diagnosis and localization. A growing field of research is exploring the utility of radiometals and their chelators (siderophores), which are small molecules that bind radiometals and form a stable complex allowing sequestration by microbes. This radiometal-chelator complex can be directed to a specific microbial target in vivo, facilitating anatomical localization by PET or single photon emission computed tomography. Additionally, bifunctional chelators can further conjugate therapeutic molecules (e.g., peptides, antibiotics, antibodies) while still bound to desired radiometals, combining specific imaging with highly targeted antimicrobial therapy. These novel therapeutics may prove a useful complement to the armamentarium in the global fight against antimicrobial resistance. This review will highlight current state of infection imaging diagnostics and their limitations, strategies to develop infection-specific diagnostics, recent advances in radiometal-based chelators for microbial infection imaging, challenges, and future directions to improve targeted diagnostics and/or therapeutics.
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Affiliation(s)
- Asma Akter
- Department of Analytical, Environmental and Forensic Sciences, King’s College London, London, United Kingdom
| | - Oliver Lyons
- Vascular Endovascular and Transplant Surgery, Christchurch Public Hospital, Christchurch, New Zealand
- Department of Surgery, University of Otago, Christchurch, New Zealand
| | - Varun Mehra
- Department of Hematology, King’s College Hospital NHS Foundation Trust, London, United Kingdom
| | - Heather Isenman
- Department of Infectious Diseases, General Medicine, Christchurch Hospital, Christchurch, New Zealand
| | - Vincenzo Abbate
- Department of Analytical, Environmental and Forensic Sciences, King’s College London, London, United Kingdom
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3
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Wu JH, McGenity TJ, Rettberg P, Simões MF, Li WJ, Antunes A. The archaeal class Halobacteria and astrobiology: Knowledge gaps and research opportunities. Front Microbiol 2022; 13:1023625. [PMID: 36312929 PMCID: PMC9608585 DOI: 10.3389/fmicb.2022.1023625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 09/07/2022] [Indexed: 09/19/2023] Open
Abstract
Water bodies on Mars and the icy moons of the outer solar system are now recognized as likely being associated with high levels of salt. Therefore, the study of high salinity environments and their inhabitants has become increasingly relevant for Astrobiology. Members of the archaeal class Halobacteria are the most successful microbial group living in hypersaline conditions and are recognized as key model organisms for exposure experiments. Despite this, data for the class is uneven across taxa and widely dispersed across the literature, which has made it difficult to properly assess the potential for species of Halobacteria to survive under the polyextreme conditions found beyond Earth. Here we provide an overview of published data on astrobiology-linked exposure experiments performed with members of the Halobacteria, identifying clear knowledge gaps and research opportunities.
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Affiliation(s)
- Jia-Hui Wu
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Taipa, Macau SAR, China
- China National Space Administration (CNSA), Macau Center for Space Exploration and Science, Taipa, Macau SAR, China
| | - Terry J. McGenity
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Petra Rettberg
- German Aerospace Center (DLR), Institute of Aerospace Medicine, Köln, Germany
| | - Marta F. Simões
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Taipa, Macau SAR, China
- China National Space Administration (CNSA), Macau Center for Space Exploration and Science, Taipa, Macau SAR, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - André Antunes
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Taipa, Macau SAR, China
- China National Space Administration (CNSA), Macau Center for Space Exploration and Science, Taipa, Macau SAR, China
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Martínez GM, Pire C, Martínez-Espinosa RM. Hypersaline environments as natural sources of microbes with potential applications in biotechnology: the case of solar evaporation systems to produce salt in Alicante County (Spain). CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100136. [PMID: 35909606 PMCID: PMC9325878 DOI: 10.1016/j.crmicr.2022.100136] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 04/14/2022] [Accepted: 04/24/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Guillermo Martínez Martínez
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, Alicante, E-03080 Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, Alicante, E-03080 Spain
| | - Carmen Pire
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, Alicante, E-03080 Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, Alicante, E-03080 Spain
| | - Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, Alicante, E-03080 Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, Alicante, E-03080 Spain
- Corresponding author.
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Moretti R, Lampazzi E, Damiani C, Fabbri G, Lombardi G, Pioli C, Desiderio A, Serrao A, Calvitti M. Increased biting rate and decreased Wolbachia density in irradiated Aedes mosquitoes. Parasit Vectors 2022; 15:67. [PMID: 35209944 PMCID: PMC8867665 DOI: 10.1186/s13071-022-05188-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/01/2022] [Indexed: 11/21/2022] Open
Abstract
Background Releasing considerable numbers of radiation-sterilized males is a promising strategy to suppress mosquito vectors. However, releases may also include small percentages of biting females, which translate to non-negligible numbers when releases are large. Currently, the effects of irradiation on host-seeking and host-biting behaviors have not been exhaustively investigated. Information is also lacking regarding the effects of sterilizing treatment on the endosymbiotic bacterium Wolbachia, which is known to affect the vector competence of infected mosquitos. Methods To ascertain the effects of irradiation on females, the pupae of two Aedes albopictus strains, differing in their natural or artificial Wolbachia infection type, and Aedes aegypti—which is not infected by Wolbachia—were treated with various doses of X-rays and monitored for key fitness parameters and biting behavior over a period of 2 weeks. The effect of radiation on Wolbachia was investigated by quantitative polymerase chain reaction (qPCR) and fluorescence in situ hybridization (FISH) analysis. Results Partial Aedes albopictus female sterility was achieved at 28 Gy, but the number of weekly bites more than doubled compared to that of the controls. Radiation doses of 35 and 45 Gy completely inhibited progeny production but did not significantly affect the survival or flight ability of Ae. albopictus females and caused a tripling of the number of bites per female per week (compared to untreated controls). These results were also confirmed in Ae. aegypti after treatment at 50 Gy. Wolbachia density decreased significantly in 45-Gy-irradiated females, with the greatest decreases in the early irradiation group (26 ± 2-h-old pupae). Wolbachia density also decreased as adults aged. This trend was confirmed in ovaries but not in extra-ovarian tissues. FISH analysis showed a strongly reduced Wolbachia-specific fluorescence in the ovaries of 13 ± 1-day-old females. Conclusions These results suggest that, under sterile insect technique (SIT) programs, the vector capacity of a target population could increase with the frequency of the irradiated females co-released with the sterile males due to an increased biting rate. In the context of successful suppression, the related safety issues are expected to be generally negligible, but they should be conservatively evaluated when large-scale programs relying on imperfect sexing and high overflooding release ratios are run for long periods in areas endemic for arboviral diseases. Also, the effects of irradiation on the vector competence deserve further investigation. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05188-9.
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Affiliation(s)
- Riccardo Moretti
- Biotechnology and Agroindustry Division, ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development), Casaccia Research Center, Rome, Italy.
| | - Elena Lampazzi
- Biotechnology and Agroindustry Division, ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development), Casaccia Research Center, Rome, Italy
| | - Claudia Damiani
- School of Biosciences and Medical Veterinary, University of Camerino, Camerino, MC, Italy.,Biovecblok S.r.L, Camerino, MC, Italy
| | - Giulia Fabbri
- Biotechnology and Agroindustry Division, ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development), Casaccia Research Center, Rome, Italy.,School of Biosciences and Medical Veterinary, University of Camerino, Camerino, MC, Italy
| | - Giulia Lombardi
- Biotechnology and Agroindustry Division, ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development), Casaccia Research Center, Rome, Italy.,School of Biosciences and Medical Veterinary, University of Camerino, Camerino, MC, Italy
| | - Claudio Pioli
- Laboratory of Biomedical Technologies, ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development), Casaccia Research Center, Rome, Italy
| | - Angiola Desiderio
- Biotechnology and Agroindustry Division, ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development), Casaccia Research Center, Rome, Italy
| | - Aurelio Serrao
- School of Biosciences and Medical Veterinary, University of Camerino, Camerino, MC, Italy.,Biovecblok S.r.L, Camerino, MC, Italy
| | - Maurizio Calvitti
- Biotechnology and Agroindustry Division, ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development), Casaccia Research Center, Rome, Italy
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Eugénie N, Zivanovic Y, Lelandais G, Coste G, Bouthier de la Tour C, Bentchikou E, Servant P, Confalonieri F. Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium Deinococcus radiodurans by Integrative Genomic Analyses. Cells 2021; 10:cells10102536. [PMID: 34685516 PMCID: PMC8533742 DOI: 10.3390/cells10102536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 12/02/2022] Open
Abstract
Numerous genes are overexpressed in the radioresistant bacterium Deinococcus radiodurans after exposure to radiation or prolonged desiccation. It was shown that the DdrO and IrrE proteins play a major role in regulating the expression of approximately twenty genes. The transcriptional repressor DdrO blocks the expression of these genes under normal growth conditions. After exposure to genotoxic agents, the IrrE metalloprotease cleaves DdrO and relieves gene repression. At present, many questions remain, such as the number of genes regulated by DdrO. Here, we present the first ChIP-seq analysis performed at the genome level in Deinococcus species coupled with RNA-seq, which was achieved in the presence or not of DdrO. We also resequenced our laboratory stock strain of D. radiodurans R1 ATCC 13939 to obtain an accurate reference for read alignments and gene expression quantifications. We highlighted genes that are directly under the control of this transcriptional repressor and showed that the DdrO regulon in D. radiodurans includes numerous other genes than those previously described, including DNA and RNA metabolism proteins. These results thus pave the way to better understand the radioresistance pathways encoded by this bacterium and to compare the stress-induced responses mediated by this pair of proteins in diverse bacteria.
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7
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Kumari N, Raghavan SC. G-quadruplex DNA structures and their relevance in radioprotection. Biochim Biophys Acta Gen Subj 2021; 1865:129857. [PMID: 33508382 DOI: 10.1016/j.bbagen.2021.129857] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND DNA, the genetic material of most of the organisms, is the crucial element of life. Integrity of DNA needs to be maintained for transmission of genetic material from one generation to another. All organisms are constantly challenged by the environmental conditions which can lead to the induction of DNA damage. Ionizing radiation (IR) has been known to induce DNA damage and IR sensitivity varies among different organisms. The causes for differential radiosensitivity among various organisms have not been studied in great detail. SCOPE OF REVIEW We discuss DNA secondary structure formation, GC content of the genome, role of G-quadruplex formation, and its relationship with radiosensitivity of the genome. MAJOR CONCLUSION In Deinococcus radiodurans, the bacterium that exhibits maximum radio resistance, multiple G-quadruplex forming motifs are reported. In human cells, G-quadruplex formation led to differential radiosensitivity. In this article, we have discussed, the role of secondary DNA structure formation like G-quadruplex in shielding the genome from radiation and its implications in understanding evolution of radio protective effect of an organism. We also discuss role of GC content and its correlation with radio resistance. GENERAL SIGNIFICANCE This review provides an insight into the role of G-quadruplexes in providing differential radiosensitivity at different site of the genome and in different organisms. It further discusses the possibility of higher GC content contributing towards reduced radiosensitivity in different organisms, evolution of radiosensitivity, and regulation of multiple cellular processes.
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Affiliation(s)
- Nitu Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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8
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Effects of Heavy Ion Particle Irradiation on Spore Germination of Bacillus spp. from Extremely Hot and Cold Environments. Life (Basel) 2020; 10:life10110264. [PMID: 33143156 PMCID: PMC7693761 DOI: 10.3390/life10110264] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 10/27/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
Extremophiles are optimal models in experimentally addressing questions about the effects of cosmic radiation on biological systems. The resistance to high charge energy (HZE) particles, and helium (He) ions and iron (Fe) ions (LET at 2.2 and 200 keV/µm, respectively, until 1000 Gy), of spores from two thermophiles, Bacillushorneckiae SBP3 and Bacilluslicheniformis T14, and two psychrotolerants, Bacillus sp. A34 and A43, was investigated. Spores survived He irradiation better, whereas they were more sensitive to Fe irradiation (until 500 Gy), with spores from thermophiles being more resistant to irradiations than psychrotolerants. The survived spores showed different germination kinetics, depending on the type/dose of irradiation and the germinant used. After exposure to He 1000 Gy, D-glucose increased the lag time of thermophilic spores and induced germination of psychrotolerants, whereas L-alanine and L-valine increased the germination efficiency, except alanine for A43. FTIR spectra showed important modifications to the structural components of spores after Fe irradiation at 250 Gy, which could explain the block in spore germination, whereas minor changes were observed after He radiation that could be related to the increased permeability of the inner membranes and alterations of receptor complex structures. Our results give new insights on HZE resistance of extremophiles that are useful in different contexts, including astrobiology.
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Merino N, Aronson HS, Bojanova DP, Feyhl-Buska J, Wong ML, Zhang S, Giovannelli D. Living at the Extremes: Extremophiles and the Limits of Life in a Planetary Context. Front Microbiol 2019; 10:780. [PMID: 31037068 PMCID: PMC6476344 DOI: 10.3389/fmicb.2019.00780] [Citation(s) in RCA: 198] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/27/2019] [Indexed: 01/21/2023] Open
Abstract
Prokaryotic life has dominated most of the evolutionary history of our planet, evolving to occupy virtually all available environmental niches. Extremophiles, especially those thriving under multiple extremes, represent a key area of research for multiple disciplines, spanning from the study of adaptations to harsh conditions, to the biogeochemical cycling of elements. Extremophile research also has implications for origin of life studies and the search for life on other planetary and celestial bodies. In this article, we will review the current state of knowledge for the biospace in which life operates on Earth and will discuss it in a planetary context, highlighting knowledge gaps and areas of opportunity.
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Affiliation(s)
- Nancy Merino
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Lab, Livermore, CA, United States
| | - Heidi S Aronson
- Department of Biology, University of Southern California, Los Angeles, CA, United States
| | - Diana P Bojanova
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Jayme Feyhl-Buska
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Michael L Wong
- Department of Astronomy - Astrobiology Program, University of Washington, Seattle, WA, United States.,NASA Astrobiology Institute's Virtual Planetary Laboratory, University of Washington, Seattle, WA, United States
| | - Shu Zhang
- Section of Infection and Immunity, Herman Ostrow School of Dentistry of USC, University of Southern California, Los Angeles, CA, United States
| | - Donato Giovannelli
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Department of Biology, University of Naples "Federico II", Naples, Italy.,Department of Marine and Coastal Science, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States.,Institute for Biological Resources and Marine Biotechnology, National Research Council of Italy, Ancona, Italy
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10
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DdrI, a cAMP Receptor Protein Family Member, Acts as a Major Regulator for Adaptation of Deinococcus radiodurans to Various Stresses. J Bacteriol 2018; 200:JB.00129-18. [PMID: 29686138 DOI: 10.1128/jb.00129-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 04/16/2018] [Indexed: 12/11/2022] Open
Abstract
The DNA damage response ddrI gene encodes a transcription regulator belonging to the cAMP receptor protein (CRP) family. Cells devoid of the DdrI protein exhibit a pleiotropic phenotype, including growth defects and sensitivity to DNA-damaging agents and to oxidative stress. Here, we show that the absence of the DdrI protein also confers sensitivity to heat shock treatment, and several genes involved in heat shock response were shown to be upregulated in a DdrI-dependent manner. Interestingly, expression of the Escherichia coli CRP partially compensates for the absence of the DdrI protein. Microscopic observations of ΔddrI mutant cells revealed an increased proportion of two-tetrad and anucleated cells in the population compared to the wild-type strain, indicating that DdrI is crucial for the completion of cell division and/or chromosome segregation. We show that DdrI is also involved in the megaplasmid MP1 stability and in efficient plasmid transformation by facilitating the maintenance of the incoming plasmid in the cell. The in silico prediction of putative DdrI binding sites in the D. radiodurans genome suggests that hundreds of genes, belonging to several functional groups, may be regulated by DdrI. In addition, the DdrI protein absolutely requires cAMP for in vitro binding to specific target sequences, and it acts as a dimer. All these data underline the major role of DdrI in D. radiodurans physiology under normal and stress conditions by regulating, both directly and indirectly, a cohort of genes involved in various cellular processes, including central metabolism and specific responses to diverse harmful environments.IMPORTANCEDeinococcus radiodurans has been extensively studied to elucidate the molecular mechanisms responsible for its exceptional ability to withstand lethal effects of various DNA-damaging agents. A complex network, including efficient DNA repair, protein protection against oxidation, and diverse metabolic pathways, plays a crucial role for its radioresistance. The regulatory networks orchestrating these various pathways are still missing. Our data provide new insights into the crucial contribution of the transcription factor DdrI for the D. radiodurans ability to withstand harmful conditions, including UV radiation, mitomycin C treatment, heat shock, and oxidative stress. Finally, we highlight that DdrI is also required for accurate cell division, for maintenance of plasmid replicons, and for central metabolism processes responsible for the overall cell physiology.
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Beblo-Vranesevic K, Bohmeier M, Perras AK, Schwendner P, Rabbow E, Moissl-Eichinger C, Cockell CS, Vannier P, Marteinsson VT, Monaghan EP, Ehrenfreund P, Garcia-Descalzo L, Gómez F, Malki M, Amils R, Gaboyer F, Westall F, Cabezas P, Walter N, Rettberg P. Lack of correlation of desiccation and radiation tolerance in microorganisms from diverse extreme environments tested under anoxic conditions. FEMS Microbiol Lett 2018; 365:4883205. [PMID: 29474542 PMCID: PMC5939664 DOI: 10.1093/femsle/fny044] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/19/2018] [Indexed: 12/21/2022] Open
Abstract
Four facultative anaerobic and two obligate anaerobic bacteria were isolated from extreme environments (deep subsurface halite mine, sulfidic anoxic spring, mineral-rich river) in the frame MASE (Mars Analogues for Space Exploration) project. The isolates were investigated under anoxic conditions for their survivability after desiccation up to 6 months and their tolerance to ionizing radiation up to 3000 Gy. The results indicated that tolerances to both stresses are strain-specific features. Yersinia intermedia MASE-LG-1 showed a high desiccation tolerance but its radiation tolerance was very low. The most radiation-tolerant strains were Buttiauxella sp. MASE-IM-9 and Halanaerobium sp. MASE-BB-1. In both cases, cultivable cells were detectable after an exposure to 3 kGy of ionizing radiation, but cells only survived desiccation for 90 and 30 days, respectively. Although a correlation between desiccation and ionizing radiation resistance has been hypothesized for some aerobic microorganisms, our data showed that there was no correlation between tolerance to desiccation and ionizing radiation, suggesting that the physiological basis of both forms of tolerances is not necessarily linked. In addition, these results indicated that facultative and obligate anaerobic organisms living in extreme environments possess varied species-specific tolerances to extremes.
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Affiliation(s)
- Kristina Beblo-Vranesevic
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), Linder Hoehe, 51147 Cologne, Germany
| | - Maria Bohmeier
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), Linder Hoehe, 51147 Cologne, Germany
| | - Alexandra K Perras
- Department of Internal Medicine, Medical University of Graz, Auerbruggerplatz 15, 8010 Graz, Austria
- Department of Microbiology and Archaea, University of Regensburg, Universitätsstr. 31, 93053 Regensburg, Germany
| | - Petra Schwendner
- UK Center for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, EH9 3FD, Edinburgh, UK
| | - Elke Rabbow
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), Linder Hoehe, 51147 Cologne, Germany
| | - Christine Moissl-Eichinger
- Department of Internal Medicine, Medical University of Graz, Auerbruggerplatz 15, 8010 Graz, Austria
- BioTechMed Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Charles S Cockell
- UK Center for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, EH9 3FD, Edinburgh, UK
| | | | - Viggo T Marteinsson
- MATISProkaria, Vinlandsleid 12, 113 Reykjavík, Iceland
- Faculty of Food Science and Nutrition, University of Iceland, Vatnsmýrarvegur 16, 101 Reykjavík, Iceland
| | - Euan P Monaghan
- Leiden Observatory, Universiteit Leiden, Niels Bohrweg 2, 2333 Leiden, Netherland
| | - Pascale Ehrenfreund
- Leiden Observatory, Universiteit Leiden, Niels Bohrweg 2, 2333 Leiden, Netherland
- Space Policy Institute, George Washington University, 1957 E Street, 20052 Washington DC, USA
| | - Laura Garcia-Descalzo
- Instituto Nacional de Técnica Aeroespacial-Centro de Astrobiología (INTA-CAB), Torrejón de Ardoz, 28850 Madrid, Spain
| | - Felipe Gómez
- Instituto Nacional de Técnica Aeroespacial-Centro de Astrobiología (INTA-CAB), Torrejón de Ardoz, 28850 Madrid, Spain
| | - Moustafa Malki
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid (UAM), Calle Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Ricardo Amils
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid (UAM), Calle Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Frédéric Gaboyer
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique (CNRS), Rue Charles Sadron, 45071 Orléans, France
| | - Frances Westall
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique (CNRS), Rue Charles Sadron, 45071 Orléans, France
| | - Patricia Cabezas
- European Science Foundation (ESF), Quai Lezay-Marnésia, 67080 Strasbourg, France
| | - Nicolas Walter
- European Science Foundation (ESF), Quai Lezay-Marnésia, 67080 Strasbourg, France
| | - Petra Rettberg
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), Linder Hoehe, 51147 Cologne, Germany
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12
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Li S, Porcel E, Remita H, Marco S, Réfrégiers M, Dutertre M, Confalonieri F, Lacombe S. Platinum nanoparticles: an exquisite tool to overcome radioresistance. Cancer Nanotechnol 2017; 8:4. [PMID: 28757899 PMCID: PMC5506239 DOI: 10.1186/s12645-017-0028-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 07/03/2017] [Indexed: 12/13/2022] Open
Abstract
Backgroud Small metallic nanoparticles are proposed as potential nanodrugs to optimize the performances of radiotherapy. This strategy, based on the enrichment of tumours with nanoparticles to amplify radiation effects in the tumour, aims at increasing the cytopathic effect in tumours while healthy tissue is preserved, an important challenge in radiotherapy. Another major cause of radiotherapy failure is the radioresistance of certain cancers. Surprisingly, the use of nanoparticles to overcome radioresistance has not, to the best of our knowledge, been extensively investigated. The mechanisms of radioresistance have been extensively studied using Deinococcus radiodurans, the most radioresistant organism ever reported, as a model. Methods In this work, we investigated the impact of ultra-small platinum nanoparticles (1.7 nm) on this organism, including uptake, toxicity, and effects on radiation responses. Results We showed that the nanoparticles penetrate D. radiodurans cells, despite the 150 nm cell wall thickness with a minimal inhibition concentration on the order of 4.8 mg L−1. We also found that the nanoparticles amplify gamma ray radiation effects by >40%. Conclusions Finally, this study demonstrates the capacity of metallic nanoparticles to amplify radiation in radioresistant organisms, thus opening the perspective to use nanoparticles not only to improve tumour targeting but also to overcome radioresistance. Electronic supplementary material The online version of this article (doi:10.1186/s12645-017-0028-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sha Li
- CNRS, UMR 8214, Institut des Sciences Moléculaires d'Orsay, Université Paris Sud, 91405 Orsay Cedex, France
| | - Erika Porcel
- CNRS, UMR 8214, Institut des Sciences Moléculaires d'Orsay, Université Paris Sud, 91405 Orsay Cedex, France
| | - Hynd Remita
- CNRS, UMR 8000, Laboratoire de Chimie Physique, Université Paris-Sud, 91405 Orsay Cedex, France
| | - Sergio Marco
- Institut Curie/INSERM U759, Campus Universitaire d'Orsay, 91405 Orsay Cedex, France
| | | | - Murielle Dutertre
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Univ. Paris-Sud, Université Paris Saclay, 91405 Orsay, France
| | - Fabrice Confalonieri
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Univ. Paris-Sud, Université Paris Saclay, 91405 Orsay, France
| | - Sandrine Lacombe
- CNRS, UMR 8214, Institut des Sciences Moléculaires d'Orsay, Université Paris Sud, 91405 Orsay Cedex, France
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13
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Ranawat P, Rawat S. Radiation resistance in thermophiles: mechanisms and applications. World J Microbiol Biotechnol 2017; 33:112. [DOI: 10.1007/s11274-017-2279-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 04/26/2017] [Indexed: 12/28/2022]
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14
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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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15
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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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16
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Barbier E, Lagorce A, Hachemi A, Dutertre M, Gorlas A, Morand L, Saint-Pierre C, Ravanat JL, Douki T, Armengaud J, Gasparutto D, Confalonieri F, Breton J. Oxidative DNA Damage and Repair in the Radioresistant Archaeon Thermococcus gammatolerans. Chem Res Toxicol 2016; 29:1796-1809. [PMID: 27676238 DOI: 10.1021/acs.chemrestox.6b00128] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The hyperthermophilic archaeon Thermococcus gammatolerans can resist huge doses of γ-irradiation, up to 5.0 kGy, without loss of viability. The potential to withstand such harsh conditions is probably due to complementary passive and active mechanisms, including repair of damaged chromosomes. In this work, we documented the formation and repair of oxidative DNA lesions in T. gammatolerans. The basal level of the oxidized nucleoside, 8-oxo-2'-deoxyguanosine (8-oxo-dGuo), was established at 9.2 (± 0.9) 8-oxo-dGuo per 106 nucleosides, a higher level than those usually measured in eukaryotic cells or bacteria. A significant increase in oxidative damage, i.e., up to 24.2 (± 8.0) 8-oxo-dGuo/106 nucleosides, was measured for T. gammatolerans exposed to a 5.0 kGy dose of γ-rays. Surprisingly, the yield of radiation-induced modifications was lower than those previously observed for human cells exposed to doses corresponding to a few grays. One hour after irradiation, 8-oxo-dGuo levels were significantly reduced, indicating an efficient repair. Two putative base excision repair (BER) enzymes, TGAM_1277 and TGAM_1653, were demonstrated both by proteomics and transcriptomics to be present in the cells without exposure to ionizing radiation. Their transcripts were moderately upregulated after gamma irradiation. After heterologous production and purification of these enzymes, biochemical assays based on electrophoresis and MALDI-TOF (matrix-assisted laser desorption ionization-time of flight) mass spectrometry indicated that both have a β-elimination cleavage activity. TGAM_1653 repairs 8-oxo-dGuo, whereas TGAM_1277 is also able to remove lesions affecting pyrimidines (1-[2-deoxy-β-d-erythro-pentofuranosyl]-5-hydroxyhydantoin (5-OH-dHyd) and 1-[2-deoxy-β-d-erythro-pentofuranosyl]-5-hydroxy-5-methylhydantoin (5-OH-5-Me-dHyd)). This work showed that in normal growth conditions or in the presence of a strong oxidative stress, T. gammatolerans has the potential to rapidly reduce the extent of DNA oxidation, with at least these two BER enzymes as bodyguards with distinct substrate ranges.
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Affiliation(s)
- Ewa Barbier
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Arnaud Lagorce
- University of Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France.,University of Perpignan, IHPE - UMR 5244 CNRS/IFREMER/Univ. Montpellier, Montpellier, F-34095, France
| | - Amine Hachemi
- University of Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Murielle Dutertre
- University of Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Aurore Gorlas
- University of Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Lucie Morand
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Christine Saint-Pierre
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Jean-Luc Ravanat
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Thierry Douki
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Jean Armengaud
- CEA, DSV-Li2D, Laboratory "Innovative Technologies for Detection and Diagnostics", BP 17171, Bagnols-sur-Cèze, F-30207, France
| | - Didier Gasparutto
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Fabrice Confalonieri
- University of Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Jean Breton
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
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17
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Nault L, Bouchab L, Dupré-Crochet S, Nüße O, Erard M. Environmental Effects on Reactive Oxygen Species Detection-Learning from the Phagosome. Antioxid Redox Signal 2016; 25:564-76. [PMID: 27225344 DOI: 10.1089/ars.2016.6747] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
SIGNIFICANCE Reactive oxygen species (ROS) fulfill numerous roles in biology ranging from signal transduction to the induction of cell death. To advance our understanding of these sometimes contradictory roles, quantitative, specific, and sensitive ROS measurements are required. RECENT ADVANCES Several organic or genetically encoded probes were successfully developed for ROS detection. CRITICAL ISSUES In some cases, ROS production occurs in a harsh environment such as low pH or high concentration of proteases. However, the ROS sensor may be sensitive to such environmental conditions and therefore becomes inaccurate. While the sensitivity of many ROS sensors to pH is known, many other environmental conditions remain unexplored. This article illustrates the interference between ROS sensors and their environment using the phagosome as an example. In the phagosome, pH changes, high concentration of ROS, and the presence of many proteases generate a hostile and rapidly changing environment. FUTURE DIRECTIONS Difficulties due to cell movement and continuous formation of new phagosomes can be reduced by ratio measurements, if appropriate dyes are identified. For detection in live cells and subcellular locations, fluorescent proteins (FPs) offer several advantages and are used to create biosensors for ROS. Some FPs are directly sensitive to certain ROS as shown here. Although this may compromise their use in an environment with high levels of ROS, it can also be exploited for ROS measurement directly with the FPs themselves. For all types of ROS detection, we suggest a set of basic guidelines for testing the environmental sensitivity of an ROS sensor. Antioxid. Redox Signal. 25, 564-576.
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Affiliation(s)
- Laurent Nault
- Laboratoire de Chimie Physique, Université Paris-Sud, CNRS UMR 8000, Université Paris Saclay , Orsay, France
| | - Leïla Bouchab
- Laboratoire de Chimie Physique, Université Paris-Sud, CNRS UMR 8000, Université Paris Saclay , Orsay, France
| | - Sophie Dupré-Crochet
- Laboratoire de Chimie Physique, Université Paris-Sud, CNRS UMR 8000, Université Paris Saclay , Orsay, France
| | - Oliver Nüße
- Laboratoire de Chimie Physique, Université Paris-Sud, CNRS UMR 8000, Université Paris Saclay , Orsay, France
| | - Marie Erard
- Laboratoire de Chimie Physique, Université Paris-Sud, CNRS UMR 8000, Université Paris Saclay , Orsay, France
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18
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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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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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20
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Passot FM, Nguyen HH, Dard-Dascot C, Thermes C, Servant P, Espéli O, Sommer S. Nucleoid organization in the radioresistant bacteriumDeinococcus radiodurans. Mol Microbiol 2015; 97:759-74. [DOI: 10.1111/mmi.13064] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Fanny Marie Passot
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS; Université Paris Sud; Bâtiment 409 Orsay 91405 France
| | - Hong Ha Nguyen
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS; Université Paris Sud; Bâtiment 409 Orsay 91405 France
| | - Cloelia Dard-Dascot
- Plateforme Intégrée IMAGIF - CNRS; Avenue de la Terrasse; Gif sur Yvette 91198 France
| | - Claude Thermes
- Plateforme Intégrée IMAGIF - CNRS; Avenue de la Terrasse; Gif sur Yvette 91198 France
| | - Pascale Servant
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS; Université Paris Sud; Bâtiment 409 Orsay 91405 France
| | - Olivier Espéli
- Center for Interdisciplinary Research In Biology (CIRB); Collège de France; CNRS UMR 7241, INSERM U1050, 11 place Marcelin Berthelot Paris 75005 France
| | - Suzanne Sommer
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS; Université Paris Sud; Bâtiment 409 Orsay 91405 France
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21
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Ludanyi M, Blanchard L, Dulermo R, Brandelet G, Bellanger L, Pignol D, Lemaire D, de Groot A. Radiation response in Deinococcus deserti: IrrE is a metalloprotease that cleaves repressor protein DdrO. Mol Microbiol 2014; 94:434-49. [PMID: 25170972 DOI: 10.1111/mmi.12774] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2014] [Indexed: 11/28/2022]
Abstract
Deinococcus bacteria are famous for their extreme radiation tolerance. The IrrE protein was shown to be essential for radiation tolerance and, in an unelucidated manner, for induction of a number of genes in response to radiation, including recA and other DNA repair genes. Earlier studies indicated that IrrE could be a zinc peptidase, but proteolytic activity was not demonstrated. Here, using several in vivo and in vitro experiments, IrrE from Deinococcus deserti was found to interact with DdrO, a predicted regulator encoded by a radiation-induced gene that is, like irrE, highly conserved in Deinococcus. Moreover, IrrE was found to cleave DdrO in vitro and when the proteins were coexpressed in Escherichia coli. This cleavage was not observed in the presence of metal chelator EDTA or when IrrE contains a mutation in the conserved active-site motif of metallopeptidases. In D. deserti, IrrE-dependent cleavage of DdrO was observed after exposure to radiation. Furthermore, DdrO-dependent repression of the promoter of a radiation-induced gene was shown. These results demonstrate that IrrE is a metalloprotease and we propose that IrrE-mediated cleavage inactivates repressor protein DdrO, leading to transcriptional induction of various genes required for repair and survival after exposure of Deinococcus to radiation.
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Affiliation(s)
- Monika Ludanyi
- CEA, DSV, IBEB, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, F-13108, France; CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance, F-13108, France; Aix-Marseille Université, Saint-Paul-lez-Durance, F-13108, France
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22
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Egas C, Barroso C, Froufe HJC, Pacheco J, Albuquerque L, da Costa MS. Complete genome sequence of the Radiation-Resistant bacterium Rubrobacter radiotolerans RSPS-4. Stand Genomic Sci 2014; 9:1062-75. [PMID: 25197483 PMCID: PMC4148983 DOI: 10.4056/sigs.5661021] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rubrobacter radiotolerans strain RSPS-4 is a slightly thermophilic member of the phylum “Actinobacteria” isolated from a hot spring in São Pedro do Sul, Portugal. This aerobic and halotolerant bacterium is also extremely resistant to gamma and UV radiation, which are the main reasons for the interest in sequencing its genome. Here, we present the complete genome sequence of strain RSPS-4 as well as its assembly and annotation. We also compare the gene sequence of this organism with that of the type strain of the species R. radiotolerans isolated from a hot spring in Japan. The genome of strain RSPS-4 comprises one circular chromosome of 2,875,491 bp with a G+C content of 66.91%, and 3 circular plasmids of 190,889 bp, 149,806 bp and 51,047 bp, harboring 3,214 predicted protein coding genes, 46 tRNA genes and a single rRNA operon.
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Affiliation(s)
- C Egas
- Next Generation Sequencing Unit, Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
| | - C Barroso
- Next Generation Sequencing Unit, Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
| | - H J C Froufe
- Next Generation Sequencing Unit, Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
| | - J Pacheco
- Next Generation Sequencing Unit, Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
| | - L Albuquerque
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - M S da Costa
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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23
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de la Tour CB, Passot FM, Toueille M, Mirabella B, Guérin P, Blanchard L, Servant P, de Groot A, Sommer S, Armengaud J. Comparative proteomics reveals key proteins recruited at the nucleoid of Deinococcus after irradiation-induced DNA damage. Proteomics 2013; 13:3457-69. [PMID: 24307635 DOI: 10.1002/pmic.201300249] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 10/19/2013] [Accepted: 10/23/2013] [Indexed: 11/09/2022]
Abstract
The nucleoids of radiation-resistant Deinococcus species show a high degree of compaction maintained after ionizing irradiation. We identified proteins recruited after irradiation in nucleoids of Deinococcus radiodurans and Deinococcus deserti by means of comparative proteomics. Proteins in nucleoid-enriched fractions from unirradiated and irradiated Deinococcus were identified and semiquantified by shotgun proteomics. The ssDNA-binding protein SSB, DNA gyrase subunits GyrA and GyrB, DNA topoisomerase I, RecA recombinase, UvrA excinuclease, RecQ helicase, DdrA, DdrB, and DdrD proteins were found in significantly higher amounts in irradiated nucleoids of both Deinococcus species. We observed, by immunofluorescence microscopy, the subcellular localization of these proteins in D. radiodurans, showing for the first time the recruitment of the DdrD protein into the D. radiodurans nucleoid. We specifically followed the kinetics of recruitment of RecA, DdrA, and DdrD to the nucleoid after irradiation. Remarkably, RecA proteins formed irregular filament-like structures 1 h after irradiation, before being redistributed throughout the cells by 3 h post-irradiation. Comparable dynamics of DdrD localization were observed, suggesting a possible functional interaction between RecA and DdrD. Several proteins involved in nucleotide synthesis were also seen in higher quantities in the nucleoids of irradiated cells, indicative of the existence of a mechanism for orchestrating the presence of proteins involved in DNA metabolism in nucleoids in response to massive DNA damage. All MS data have been deposited in the ProteomeXchange with identifier PXD00196 (http://proteomecentral.proteomexchange.org/dataset/PXD000196).
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Archaeal DNA polymerase D but not DNA polymerase B is required for genome replication in Thermococcus kodakarensis. J Bacteriol 2013; 195:2322-8. [PMID: 23504010 DOI: 10.1128/jb.02037-12] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Three evolutionarily distinct families of replicative DNA polymerases, designated polymerase B (Pol B), Pol C, and Pol D, have been identified. Members of the Pol B family are present in all three domains of life, whereas Pol C exists only in Bacteria and Pol D exists only in Archaea. Pol B enzymes replicate eukaryotic chromosomal DNA, and as members of the Pol B family are present in all Archaea, it has been assumed that Pol B enzymes also replicate archaeal genomes. Here we report the construction of Thermococcus kodakarensis strains with mutations that delete or inactivate key functions of Pol B. T. kodakarensis strains lacking Pol B had no detectable loss in viability and no growth defects or changes in spontaneous mutation frequency but had increased sensitivity to UV irradiation. In contrast, we were unable to introduce mutations that inactivated either of the genes encoding the two subunits of Pol D. The results reported establish that Pol D is sufficient for viability and genome replication in T. kodakarensis and argue that Pol D rather than Pol B is likely the replicative DNA polymerase in this archaeon. The majority of Archaea contain Pol D, and, as discussed, if Pol D is the predominant replicative polymerase in Archaea, this profoundly impacts hypotheses for the origin(s), evolution, and distribution of the different DNA replication enzymes and systems now employed in the three domains of life.
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Im S, Song D, Joe M, Kim D, Park DH, Lim S. Comparative survival analysis of 12 histidine kinase mutants of Deinococcus radiodurans after exposure to DNA-damaging agents. Bioprocess Biosyst Eng 2013; 36:781-9. [PMID: 23355081 DOI: 10.1007/s00449-013-0904-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Accepted: 01/15/2013] [Indexed: 11/25/2022]
Abstract
Bacteria are able to adapt to changes in the environment using two-component signal transduction systems (TCSs) composed of a histidine kinase (HK) and a response regulator (RR). Deinococcus radiodurans, one of the most resistant organisms to ionizing radiation, has 20 putative HKs and 25 putative RRs. In this study, we constructed 12 D. radiodurans mutant strains lacking a gene encoding a HK and surveyed their resistance to γ-radiation, UV-B radiation (302 nm), mitomycin C (MMC), and H(2)O(2). Five (dr0860 (-), dr1174 (-), dr1556 (-), dr2244 (-), and dr2419 (-)) of the 12 mutant strains showed at least a one-log cycle reduction in γ-radiation resistance. The mutations (1) dr1174, dr1227, and dr2244 and (2) dr0860, dr2416, and dr2419 caused decreases in resistance to UV radiation and MMC, respectively. Only the dr2416 and dr2419 mutant strains showed higher sensitivity to H(2)O(2) than the wild-type. Reductions in the resistance to γ-radiation and H(2)O(2), but not to UV and MMC, were observed in the absence of DR2415, which seems to be a cognate RR of DR2416. This result suggests that DR2415/DR2416 (DrtR/S: DNA damage response TCS) may be another TCS responsible for the extreme resistance of D. radiodurans to DNA-damaging agents.
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Affiliation(s)
- Seonghun Im
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 580-185, Republic of Korea
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Role of Mn2+ and compatible solutes in the radiation resistance of thermophilic bacteria and archaea. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2012; 2012:845756. [PMID: 23209374 PMCID: PMC3505630 DOI: 10.1155/2012/845756] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 09/18/2012] [Accepted: 10/13/2012] [Indexed: 01/28/2023]
Abstract
Radiation-resistant bacteria have garnered a great deal of attention from scientists seeking to expose the mechanisms underlying their incredible survival abilities. Recent analyses showed that the resistance to ionizing radiation (IR) in the archaeon Halobacterium salinarum is dependent upon Mn-antioxidant complexes responsible for the scavenging of reactive oxygen species (ROS) generated by radiation. Here we examined the role of the compatible solutes trehalose, mannosylglycerate, and di-myo-inositol phosphate in the radiation resistance of aerobic and anaerobic thermophiles. We found that the IR resistance of the thermophilic bacteria Rubrobacter xylanophilus and Rubrobacter radiotolerans was highly correlated to the accumulation of high intracellular concentration of trehalose in association with Mn, supporting the model of Mn2+-dependent ROS scavenging in the aerobes. In contrast, the hyperthermophilic archaea Thermococcus gammatolerans and Pyrococcus furiosus did not contain significant amounts of intracellular Mn, and we found no significant antioxidant activity from mannosylglycerate and di-myo-inositol phosphate in vitro. We therefore propose that the low levels of IR-generated ROS under anaerobic conditions combined with highly constitutively expressed detoxification systems in these anaerobes are key to their radiation resistance and circumvent the need for the accumulation of Mn-antioxidant complexes in the cell.
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