101
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Antiproliferative, antioxidant and binding mechanism analysis of prodigiosin from newly isolated radio-resistant Streptomyces sp. strain WMA-LM31. Mol Biol Rep 2018; 45:1787-1798. [DOI: 10.1007/s11033-018-4324-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 08/20/2018] [Indexed: 10/28/2022]
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102
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Ferrandi A, Castani F, Pitaro M, Tagliaferri S, de la Tour CB, Alduina R, Sommer S, Fasano M, Barbieri P, Mancini M, Bonapace IM. Deinococcus radiodurans' SRA-HNH domain containing protein Shp (Dr1533) is involved in faithful genome inheritance maintenance following DNA damage. Biochim Biophys Acta Gen Subj 2018; 1863:118-129. [PMID: 30308220 DOI: 10.1016/j.bbagen.2018.09.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/18/2018] [Accepted: 09/25/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND Deinococcus radiodurans R1 (DR) survives conditions of extreme desiccation, irradiation and exposure to genotoxic chemicals, due to efficient DNA breaks repair, also through Mn2+ protection of DNA repair enzymes. METHODS Possible annotated domains of the DR1533 locus protein (Shp) were searched by bioinformatic analysis. The gene was cloned and expressed as fusion protein. Band-shift assays of Shp or the SRA and HNH domains were performed on oligonucleotides, genomic DNA from E. coli and DR. shp knock-out mutant was generated by homologous recombination with a kanamycin resistance cassette. RESULTS DR1533 contains an N-terminal SRA domain and a C-terminal HNH motif (SRA-HNH Protein, Shp). Through its SRA domain, Shp binds double-strand oligonucleotides containing 5mC and 5hmC, but also unmethylated and mismatched cytosines in presence of Mn2+. Shp also binds to Escherichia coli dcm+ genomic DNA, and to cytosine unmethylated DR and E. coli dcm- genomic DNAs, but only in presence of Mn2+. Under these binding conditions, Shp displays DNAse activity through its HNH domain. Shp KO enhanced >100 fold the number of spontaneous mutants, whilst the treatment with DNA double strand break inducing agents enhanced up to 3-log the number of survivors. CONCLUSIONS The SRA-HNH containing protein Shp binds to and cuts 5mC DNA, and unmethylated DNA in a Mn2+ dependent manner, and might be involved in faithful genome inheritance maintenance following DNA damage. GENERAL SIGNIFICANCE Our results provide evidence for a potential role of DR Shp protein for genome integrity maintenance, following DNA double strand breaks induced by genotoxic agents.
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Affiliation(s)
- Alex Ferrandi
- Department of Biotechnology and Life Sciences, University of Insubria, Via Manara 7, Busto Arsizio, VA, Italy
| | - Federica Castani
- Department of Biotechnology and Life Sciences, University of Insubria, Via Manara 7, Busto Arsizio, VA, Italy
| | - Mauro Pitaro
- Department of Biotechnology and Life Sciences, University of Insubria, Via Manara 7, Busto Arsizio, VA, Italy
| | - Sara Tagliaferri
- Department of Biotechnology and Life Sciences, University of Insubria, Via Manara 7, Busto Arsizio, VA, Italy
| | - Claire Bouthier de la Tour
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, France and Institut de Génétique et Microbiologie - Université Paris-Sud, Paris, France
| | - Rosa Alduina
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, Palermo, Italy
| | - Suzanne Sommer
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, France and Institut de Génétique et Microbiologie - Université Paris-Sud, Paris, France
| | - Mauro Fasano
- Department of Sciences and High technology, University of Insubria, Via Manara 7, Busto Arsizio, VA, Italy
| | - Paola Barbieri
- Department of Biotechnology and Life Sciences, University of Insubria, Via Manara 7, Busto Arsizio, VA, Italy
| | - Monica Mancini
- Department of Biotechnology and Life Sciences, University of Insubria, Via Manara 7, Busto Arsizio, VA, Italy.
| | - Ian Marc Bonapace
- Department of Biotechnology and Life Sciences, University of Insubria, Via Manara 7, Busto Arsizio, VA, Italy.
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103
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Hieke ASC, Pillai SD. Escherichia coli Cells Exposed to Lethal Doses of Electron Beam Irradiation Retain Their Ability to Propagate Bacteriophages and Are Metabolically Active. Front Microbiol 2018; 9:2138. [PMID: 30250460 PMCID: PMC6139317 DOI: 10.3389/fmicb.2018.02138] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 08/21/2018] [Indexed: 12/14/2022] Open
Abstract
Reports in the literature suggest that bacteria exposed to lethal doses of ionizing radiation, i.e., electron beams, are unable to replicate yet they remain metabolically active. To investigate this phenomenon further, we electron beam irradiated Escherichia coli cells to a lethal dose and measured their membrane integrity, metabolic activity, ATP levels and overall cellular functionality via bacteriophage infection. We also visualized the DNA double-strand breaks in the cells. We used non-irradiated (live) and heat-killed cells as positive and negative controls, respectively. Our results show that the membrane integrity of E. coli cells is maintained and that the cells remain metabolically active up to 9 days post-irradiation when stored at 4°C. The ATP levels in lethally irradiated cells are similar to non-irradiated control cells. We also visualized extensive DNA damage within the cells and confirmed their cellular functionality based on their ability to propagate bacteriophages for up to 9 days post-irradiation. Overall, our findings indicate that lethally irradiated E. coli cells resemble live non-irradiated cells more closely than heat-killed (dead) cells.
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Affiliation(s)
- Anne-Sophie Charlotte Hieke
- National Center for Electron Beam Research (an IAEA Collaborating Centre for Electron Beam Technology), Texas A&M University, College Station, TX, United States.,Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, TX, United States
| | - Suresh D Pillai
- National Center for Electron Beam Research (an IAEA Collaborating Centre for Electron Beam Technology), Texas A&M University, College Station, TX, United States.,Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, TX, United States
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104
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Dubois C, Lecomte C, Ruys SPD, Kuzmic M, Della-Vedova C, Dubourg N, Galas S, Frelon S. Precoce and opposite response of proteasome activity after acute or chronic exposure of C. elegans to γ-radiation. Sci Rep 2018; 8:11349. [PMID: 30054490 PMCID: PMC6063909 DOI: 10.1038/s41598-018-29033-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 07/04/2018] [Indexed: 12/14/2022] Open
Abstract
Species are chronically exposed to ionizing radiation, a natural phenomenon which can be enhanced by human activities. The induced toxicity mechanisms still remain unclear and seem depending on the mode of exposure, i.e. acute and chronic. To better understand these phenomena, studies need to be conducted both at the subcellular and individual levels. Proteins, functional molecules in organisms, are the targets of oxidative damage (especially via their carbonylation (PC)) and are likely to be relevant biomarkers. After exposure of Caenorhabditis elegans to either chronic or acute γ rays we showed that hatching success is impacted after acute but not after chronic irradiation. At the molecular level, the carbonylated protein level in relation with dose was slightly different between acute and chronic exposure whereas the proteolytic activity is drastically modified. Indeed, whereas the 20S proteasome activity is inhibited by acute irradiation from 0.5 Gy, it is activated after chronic irradiation from 1 Gy. As expected, the 20S proteasome activity is mainly modified by irradiation whereas the 26S and 30S activity are less changed. This study provides preliminaries clues to understand the role of protein oxidation and proteolytic activity in the radiation-induced molecular mechanisms after chronic versus acute irradiation in C. elegans.
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Affiliation(s)
- Cécile Dubois
- IRSN/PSE-ENV/SRTE - Laboratoire d'ecotoxicologie des radionucléides - BP3, 13115, St Paul lez Durance Cedex, France
| | - Catherine Lecomte
- IRSN/PSE-ENV/SRTE - Laboratoire d'ecotoxicologie des radionucléides - BP3, 13115, St Paul lez Durance Cedex, France
| | - Sébastien Pyr Dit Ruys
- IRSN/PSE-ENV/SRTE - Laboratoire d'ecotoxicologie des radionucléides - BP3, 13115, St Paul lez Durance Cedex, France
| | - Mira Kuzmic
- IRSN/PSE-ENV/SRTE - Laboratoire d'ecotoxicologie des radionucléides - BP3, 13115, St Paul lez Durance Cedex, France
| | | | - Nicolas Dubourg
- IRSN/PSE-ENV/SRTE - Laboratoire d'ecotoxicologie des radionucléides - BP3, 13115, St Paul lez Durance Cedex, France
| | - Simon Galas
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | - Sandrine Frelon
- IRSN/PSE-ENV/SRTE - Laboratoire d'ecotoxicologie des radionucléides - BP3, 13115, St Paul lez Durance Cedex, France.
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105
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Aanderud ZT, Saurey S, Ball BA, Wall DH, Barrett JE, Muscarella ME, Griffin NA, Virginia RA, Barberán A, Adams BJ. Stoichiometric Shifts in Soil C:N:P Promote Bacterial Taxa Dominance, Maintain Biodiversity, and Deconstruct Community Assemblages. Front Microbiol 2018; 9:1401. [PMID: 30018601 PMCID: PMC6037766 DOI: 10.3389/fmicb.2018.01401] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/07/2018] [Indexed: 11/13/2022] Open
Abstract
Imbalances in C:N:P supply ratios may cause bacterial resource limitations and constrain biogeochemical processes, but the importance of shifts in soil stoichiometry are complicated by the nearly limitless interactions between an immensely rich species pool and a multiple chemical resource forms. To more clearly identify the impact of soil C:N:P on bacteria, we evaluated the cumulative effects of single and coupled long-term nutrient additions (i.e., C as mannitol, N as equal concentrations NH4+ and NO3-, and P as Na3PO4) and water on communities in an Antarctic polar desert, Taylor Valley. Untreated soils possessed relatively low bacterial diversity, simplified organic C sources due to the absence of plants, limited inorganic N, and excess soil P potentially attenuating links between C:N:P. After 6 years of adding resources, an alleviation of C and N colimitation allowed one rare Micrococcaceae, an Arthrobacter species, to dominate, comprising 47% of the total community abundance and elevating soil respiration by 136% relative to untreated soils. The addition of N alone reduced C:N ratios, elevated bacterial richness and diversity, and allowed rare taxa relying on ammonium and nitrite for metabolism to become more abundant [e.g., nitrite oxidizing Nitrospira species (Nitrosomonadaceae), denitrifiers utilizing nitrite (Gemmatimonadaceae) and members of Rhodobacteraceae with a high affinity for ammonium]. Based on community co-occurrence networks, lower C:P ratios in soils following P and CP additions created more diffuse and less connected communities by disrupting 73% of species interactions and selecting for taxa potentially exploiting abundant P. Unlike amended nutrients, water additions alone elicited no lasting impact on communities. Our results suggest that as soils become nutrient rich a wide array of outcomes are possible from species dominance and the deconstruction of species interconnectedness to the maintenance of biodiversity.
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Affiliation(s)
- Zachary T. Aanderud
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, United States
| | - Sabrina Saurey
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, United States
| | - Becky A. Ball
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ, United States
| | - Diana H. Wall
- Department of Biology, School of Global Environmental Sustainability, Colorado State University, Fort Collins, CO, United States
| | - John E. Barrett
- Department of Biological Sciences, Virginia Polytechnic Institute, Blacksburg, VA, United States
| | - Mario E. Muscarella
- Department of Plant Biology, University of Illinois Urbana-Champaign, Champaign, IL, United States
| | - Natasha A. Griffin
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, United States
| | - Ross A. Virginia
- Environmental Studies Program, Dartmouth College, Hanover, NH, United States
| | - Albert Barberán
- Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Byron J. Adams
- Evolutionary Ecology Laboratories, and Monte L. Bean Museum, Department of Biology, Brigham Young University, Provo, UT, United States
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106
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Novel Sequence Features of DNA Repair Genes/Proteins from Deinococcus Species Implicated in Protection from Oxidatively Generated Damage. Genes (Basel) 2018. [PMID: 29518000 PMCID: PMC5867870 DOI: 10.3390/genes9030149] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Deinococcus species display a high degree of resistance to radiation and desiccation due to their ability to protect critical proteome from oxidatively generated damage; however, the underlying mechanisms are not understood. Comparative analysis of DNA repair proteins reported here has identified 22 conserved signature indels (CSIs) in the proteins UvrA1, UvrC, UvrD, UvsE, MutY, MutM, Nth, RecA, RecD, RecG, RecQ, RecR, RuvC, RadA, PolA, DnaE, LigA, GyrA and GyrB, that are uniquely shared by all/most Deinococcus homologs. Of these CSIs, a 30 amino acid surface-exposed insert in the Deinococcus UvrA1, which distinguishes it from all other UvrA homologs, is of much interest. The uvrA1 gene in Deinococcus also exhibits specific genetic linkage (predicted operonic arrangement) to genes for three other proteins including a novel Deinococcus-specific transmembrane protein (designated dCSP-1) and the proteins DsbA and DsbB, playing central roles in protein disulfide bond formation by oxidation-reduction of CXXC (C represents cysteine, X any other amino acid) motifs. The CXXC motifs provide important targets for oxidation damage and they are present in many DNA repair proteins including five in UvrA, which are part of Zinc-finger elements. A conserved insert specific for Deinococcus is also present in the DsbA protein. Additionally, the uvsE gene in Deinococcus also shows specific linkage to the gene for a membrane-associated protein. To account for these novel observations, a model is proposed where specific interaction of the Deinococcus UvrA1 protein with membrane-bound dCSP-1 enables the UvrA1 to receive electrons from DsbA-DsbB oxido-reductase machinery to ameliorate oxidation damage in the UvrA1 protein.
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107
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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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108
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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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109
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McMillan LJ, Hwang S, Farah RE, Koh J, Chen S, Maupin-Furlow JA. Multiplex quantitative SILAC for analysis of archaeal proteomes: a case study of oxidative stress responses. Environ Microbiol 2017; 20:385-401. [PMID: 29194950 DOI: 10.1111/1462-2920.14014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 11/27/2017] [Accepted: 11/28/2017] [Indexed: 01/08/2023]
Abstract
Stable isotope labelling of amino acids in cell culture (SILAC) is a quantitative proteomic method that can illuminate new pathways used by cells to adapt to different lifestyles and niches. Archaea, while thriving in extreme environments and accounting for ∼20%-40% of the Earth's biomass, have not been analyzed with the full potential of SILAC. Here, we report SILAC for quantitative comparison of archaeal proteomes, using Haloferax volcanii as a model. A double auxotroph was generated that allowed for complete incorporation of 13 C/15 N-lysine and 13 C-arginine such that each peptide derived from trypsin digestion was labelled. This strain was found amenable to multiplex SILAC by case study of responses to oxidative stress by hypochlorite. A total of 2565 proteins was identified by LC-MS/MS analysis (q-value ≤ 0.01) that accounted for 64% of the theoretical proteome. Of these, 176 proteins were altered at least 1.5-fold (p-value < 0.05) in abundance during hypochlorite stress. Many of the differential proteins were of unknown function. Those of known function included transcription factor homologs related to oxidative stress by 3D-homology modelling and orthologous group comparisons. Thus, SILAC is found to be an ideal method for quantitative proteomics of archaea that holds promise to unravel gene function.
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Affiliation(s)
- Lana J McMillan
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.,Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Sungmin Hwang
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Rawan E Farah
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Jin Koh
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
| | - Sixue Chen
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA.,Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA.,Department of Biology, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.,Genetics Institute, University of Florida, Gainesville, FL 32611, USA
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110
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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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111
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Ott E, Kawaguchi Y, Kölbl D, Chaturvedi P, Nakagawa K, Yamagishi A, Weckwerth W, Milojevic T. Proteometabolomic response of Deinococcus radiodurans exposed to UVC and vacuum conditions: Initial studies prior to the Tanpopo space mission. PLoS One 2017; 12:e0189381. [PMID: 29244852 PMCID: PMC5731708 DOI: 10.1371/journal.pone.0189381] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/24/2017] [Indexed: 11/18/2022] Open
Abstract
The multiple extremes resistant bacterium Deinococcus radiodurans is able to withstand harsh conditions of simulated outer space environment. The Tanpopo orbital mission performs a long-term space exposure of D. radiodurans aiming to investigate the possibility of interplanetary transfer of life. The revealing of molecular machinery responsible for survivability of D. radiodurans in the outer space environment can improve our understanding of underlying stress response mechanisms. In this paper, we have evaluated the molecular response of D. radiodurans after the exposure to space-related conditions of UVC irradiation and vacuum. Notably, scanning electron microscopy investigations showed that neither morphology nor cellular integrity of irradiated cells was affected, while integrated proteomic and metabolomic analysis revealed numerous molecular alterations in metabolic and stress response pathways. Several molecular key mechanisms of D. radiodurans, including the tricarboxylic acid cycle, the DNA damage response systems, ROS scavenging systems and transcriptional regulators responded in order to cope with the stressful situation caused by UVC irradiation under vacuum conditions. These results reveal the effectiveness of the integrative proteometabolomic approach as a tool in molecular analysis of microbial stress response caused by space-related factors.
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Affiliation(s)
- Emanuel Ott
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Yuko Kawaguchi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Denise Kölbl
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Palak Chaturvedi
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Kazumichi Nakagawa
- Graduate School of Human Development and Environment, Kobe University, Kobe, Japan
| | - Akihiko Yamagishi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
- * E-mail: (TM); (WW)
| | - Tetyana Milojevic
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
- * E-mail: (TM); (WW)
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112
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Dani P, Ujaoney AK, Apte SK, Basu B. Regulation of potassium dependent ATPase (kdp) operon of Deinococcus radiodurans. PLoS One 2017; 12:e0188998. [PMID: 29206865 PMCID: PMC5716572 DOI: 10.1371/journal.pone.0188998] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/16/2017] [Indexed: 11/19/2022] Open
Abstract
The genome of D. radiodurans harbors genes for structural and regulatory proteins of Kdp ATPase, in an operon pattern, on Mega plasmid 1. Organization of its two-component regulatory genes is unique. Here we demonstrate that both, the structural as well as regulatory components of the kdp operon of D. radiodurans are expressed quickly as the cells experience potassium limitation but are not expressed upon increase in osmolarity. The cognate DNA binding response regulator (RR) effects the expression of kdp operon during potassium deficiency through specific interaction with the kdp promoter. Deletion of the gene encoding RR protein renders the mutant D. radiodurans (ΔRR) unable to express kdp operon under potassium limitation. The ΔRR D. radiodurans displays no growth defect when grown on rich media or when exposed to oxidative or heat stress but shows reduced growth following gamma irradiation. The study elucidates the functional and regulatory aspects of the novel kdp operon of this extremophile, for the first time.
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Affiliation(s)
- Pratiksha Dani
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Aman Kumar Ujaoney
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - Shree Kumar Apte
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - Bhakti Basu
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
- * E-mail:
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113
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Fields C, Levin M. Multiscale memory and bioelectric error correction in the cytoplasm-cytoskeleton-membrane system. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2017; 10. [DOI: 10.1002/wsbm.1410] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/19/2017] [Accepted: 10/04/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Chris Fields
- 21 Rue des Lavandiéres, 11160 Caunes Minervois; France
| | - Michael Levin
- Allen Discovery Center at Tufts University; Medford MA USA
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114
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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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115
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Mishra K, Alsbeih G. Appraisal of biochemical classes of radioprotectors: evidence, current status and guidelines for future development. 3 Biotech 2017; 7:292. [PMID: 28868219 DOI: 10.1007/s13205-017-0925-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 08/21/2017] [Indexed: 12/13/2022] Open
Abstract
The search for efficient radioprotective agents to protect from radiation-induced toxicity, due to planned or accidental radiation exposure, is still ongoing worldwide. Despite decades of research and development of widely different biochemical classes of natural and derivative compounds, a safe and effective radioprotector is largely unmet. In this comprehensive review, we evaluated the evidence for the radioprotective performance of classical thiols, vitamins, minerals, dietary antioxidants, phytochemicals, botanical and bacterial preparations, DNA-binding agents, cytokines, and chelators including adaptogens. Where radioprotection was demonstrated, the compounds have shown moderate dose modifying factors ranging from 1.1 to 2.7. To date, only few compounds found way to clinic with limited margin of dose prescription due to side effects. Most of these compounds (amifostine, filgratism, pegfilgrastim, sargramostim, palifermin, recombinant salmonella flagellin, Prussian blue, potassium iodide) act primarily via scavenging of free radicals, modulation of oxidative stress, signal transduction, cell proliferation or enhance radionuclide elimination. However, the gain in radioprotection remains hampered with low margin of tolerance. Future development of more effective radioprotectors requires an appropriate nontoxic compound, a model system and biomarkers of radiation exposure. These are important to test the effectiveness of radioprotection on physiological tissues during radiotherapy and field application in cases of nuclear eventualities.
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Affiliation(s)
- Krishnanand Mishra
- Radiation Biology Section, Biomedical Physics Department, King Faisal Specialist Hospital and Research Centre (KFSH&RC), Riyadh, Saudi Arabia
| | - Ghazi Alsbeih
- Radiation Biology Section, Biomedical Physics Department, King Faisal Specialist Hospital and Research Centre (KFSH&RC), Riyadh, Saudi Arabia
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116
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Jones DL, Baxter BK. DNA Repair and Photoprotection: Mechanisms of Overcoming Environmental Ultraviolet Radiation Exposure in Halophilic Archaea. Front Microbiol 2017; 8:1882. [PMID: 29033920 PMCID: PMC5626843 DOI: 10.3389/fmicb.2017.01882] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/14/2017] [Indexed: 12/31/2022] Open
Abstract
Halophilic archaea push the limits of life at several extremes. In particular, they are noted for their biochemical strategies in dealing with osmotic stress, low water activity and cycles of desiccation in their hypersaline environments. Another feature common to their habitats is intense ultraviolet (UV) radiation, which is a challenge that microorganisms must overcome. The consequences of high UV exposure include DNA lesions arising directly from bond rearrangement of adjacent bipyrimidines, or indirectly from oxidative damage, which may ultimately result in mutation and cell death. As such, these microorganisms have evolved a number of strategies to navigate the threat of DNA damage, which we differentiate into two categories: DNA repair and photoprotection. Photoprotection encompasses damage avoidance strategies that serve as a "first line of defense," and in halophilic archaea include pigmentation by carotenoids, mechanisms of oxidative damage avoidance, polyploidy, and genomic signatures that make DNA less susceptible to photodamage. Photolesions that do arise are addressed by a number of DNA repair mechanisms that halophilic archaea efficiently utilize, which include photoreactivation, nucleotide excision repair, base excision repair, and homologous recombination. This review seeks to place DNA damage, repair, and photoprotection in the context of halophilic archaea and the solar radiation of their hypersaline environments. We also provide new insight into the breadth of strategies and how they may work together to produce remarkable UV-resistance for these microorganisms.
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Affiliation(s)
| | - Bonnie K. Baxter
- Department of Biology, Great Salt Lake Institute, Westminster College, Salt Lake City, UT, United States
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117
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Bak EN, Larsen MG, Moeller R, Nissen SB, Jensen LR, Nørnberg P, Jensen SJK, Finster K. Silicates Eroded under Simulated Martian Conditions Effectively Kill Bacteria-A Challenge for Life on Mars. Front Microbiol 2017; 8:1709. [PMID: 28955310 PMCID: PMC5601068 DOI: 10.3389/fmicb.2017.01709] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 08/23/2017] [Indexed: 11/17/2022] Open
Abstract
The habitability of Mars is determined by the physical and chemical environment. The effect of low water availability, temperature, low atmospheric pressure and strong UV radiation has been extensively studied in relation to the survival of microorganisms. In addition to these stress factors, it was recently found that silicates exposed to simulated saltation in a Mars-like atmosphere can lead to a production of reactive oxygen species. Here, we have investigated the stress effect induced by quartz and basalt abraded in Mars-like atmospheres by examining the survivability of the three microbial model organisms Pseudomonas putida, Bacillus subtilis, and Deinococcus radiodurans upon exposure to the abraded silicates. We found that abraded basalt that had not been in contact with oxygen after abrasion killed more than 99% of the vegetative cells while endospores were largely unaffected. Exposure of the basalt samples to oxygen after abrasion led to a significant reduction in the stress effect. Abraded quartz was generally less toxic than abraded basalt. We suggest that the stress effect of abraded silicates may be caused by a production of reactive oxygen species and enhanced by transition metal ions in the basalt leading to hydroxyl radicals through Fenton-like reactions. The low survivability of the usually highly resistant D. radiodurans indicates that the effect of abraded silicates, as is ubiquitous on the Martian surface, would limit the habitability of Mars as well as the risk of forward contamination. Furthermore, the reactivity of abraded silicates could have implications for future manned missions, although the lower effect of abraded silicates exposed to oxygen suggests that the effects would be reduced in human habitats.
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Affiliation(s)
- Ebbe N Bak
- Department of Bioscience, Aarhus UniversityAarhus, Denmark
| | | | - Ralf Moeller
- Space Microbiology Research Group, Institute of Aerospace Medicine, German Aerospace Center (DLR)Cologne, Germany
| | - Silas B Nissen
- Department of Bioscience, Aarhus UniversityAarhus, Denmark
| | - Lasse R Jensen
- Department of Bioscience, Aarhus UniversityAarhus, Denmark
| | - Per Nørnberg
- Department of Bioscience, Aarhus UniversityAarhus, Denmark
| | | | - Kai Finster
- Department of Bioscience, Aarhus UniversityAarhus, Denmark.,Stellar Astrophysics Center, Department of Physics and Astronomy, Aarhus UniversityAarhus, Denmark
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118
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Chen A, Contreras LM, Keitz BK. Imposed Environmental Stresses Facilitate Cell-Free Nanoparticle Formation by Deinococcus radiodurans. Appl Environ Microbiol 2017; 83:e00798-17. [PMID: 28687649 PMCID: PMC5583488 DOI: 10.1128/aem.00798-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/22/2017] [Indexed: 12/11/2022] Open
Abstract
The biological synthesis of metal nanoparticles has been examined in a wide range of organisms, due to increased interest in green synthesis and environmental remediation applications involving heavy metal ion contamination. Deinococcus radiodurans is particularly attractive for environmental remediation involving metal reduction, due to its high levels of resistance to radiation and other environmental stresses. However, few studies have thoroughly examined the relationships between environmental stresses and the resulting effects on nanoparticle biosynthesis. In this work, we demonstrate cell-free nanoparticle production and study the effects of metal stressor concentrations and identity, temperature, pH, and oxygenation on the production of extracellular silver nanoparticles by D. radiodurans R1. We also report the synthesis of bimetallic silver and gold nanoparticles following the addition of a metal stressor (silver or gold), highlighting how production of these particles is enabled through the application of environmental stresses. Additionally, we found that both the morphology and size of monometallic and bimetallic nanoparticles were dependent on the environmental stresses imposed on the cells. The nanoparticles produced by D. radiodurans exhibited antimicrobial activity comparable to that of pure silver nanoparticles and displayed catalytic activity comparable to that of pure gold nanoparticles. Overall, we demonstrate that biosynthesized nanoparticle properties can be partially controlled through the tuning of applied environmental stresses, and we provide insight into how their application may affect nanoparticle production in D. radiodurans during bioremediation.IMPORTANCE Biosynthetic production of nanoparticles has recently gained prominence as a solution to rising concerns regarding increased bacterial resistance to antibiotics and a desire for environmentally friendly methods of bioremediation and chemical synthesis. To date, a range of organisms have been utilized for nanoparticle formation. The extremophile D. radiodurans, which can withstand significant environmental stresses and therefore is more robust for metal reduction applications, has yet to be exploited for this purpose. Thus, this work improves our understanding of the impact of environmental stresses on biogenic nanoparticle morphology and composition during metal reduction processes in this organism. This work also contributes to enhancing the controlled synthesis of nanoparticles with specific attributes and functions using biological systems.
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Affiliation(s)
- Angela Chen
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Benjamin K Keitz
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
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119
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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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120
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G9a coordinates with the RPA complex to promote DNA damage repair and cell survival. Proc Natl Acad Sci U S A 2017; 114:E6054-E6063. [PMID: 28698370 DOI: 10.1073/pnas.1700694114] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Histone methyltransferase G9a has critical roles in promoting cancer-cell growth and gene suppression, but whether it is also associated with the DNA damage response is rarely studied. Here, we report that loss of G9a impairs DNA damage repair and enhances the sensitivity of cancer cells to radiation and chemotherapeutics. In response to DNA double-strand breaks (DSBs), G9a is phosphorylated at serine 211 by casein kinase 2 (CK2) and recruited to chromatin. The chromatin-enriched G9a can then directly interact with replication protein A (RPA) and promote loading of the RPA and Rad51 recombinase to DSBs. This mechanism facilitates homologous recombination (HR) and cell survival. We confirmed the interaction between RPA and G9a to be critical for RPA foci formation and HR upon DNA damage. Collectively, our findings demonstrate a regulatory pathway based on CK2-G9a-RPA that permits HR in cancer cells and provide further rationale for the use of G9a inhibitors as a cancer therapeutic.
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121
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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: 26] [Impact Index Per Article: 3.7] [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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122
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Ujaoney AK, Padwal MK, Basu B. Proteome dynamics during post-desiccation recovery reveal convergence of desiccation and gamma radiation stress response pathways in Deinococcus radiodurans. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017. [PMID: 28645711 DOI: 10.1016/j.bbapap.2017.06.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Deinococcus radiodurans is inherently resistant to both ionizing radiation and desiccation. Fifteen months of desiccation was found to be the LD50 dose for D. radiodurans. Desiccated cells of D. radiodurans entered 6h of growth arrest during post-desiccation recovery (PDR). Proteome dynamics during PDR were mapped by resolving cellular proteins by 2-dimensional gel electrophoresis coupled with mass spectrometry. At least 41 proteins, represented by 51 spots on proteome profiles, were differentially expressed throughout PDR. High upregulation in expression was observed for DNA repair proteins involved in single strand annealing (DdrA and DdrB), nucleotide excision repair (UvrA and UvrB), homologous recombination (RecA) and other vital proteins that contribute to DNA replication, recombination and repair (Ssb, GyrA and GyrB). Expression of CRP/FNR family transcriptional regulator (Crp) remained high throughout PDR. Other pathways such as cellular detoxification, protein homeostasis and metabolism displayed both, moderately induced and repressed proteins. Functional relevance of proteomic modulations to surviving desiccation stress is discussed in detail. Comparison of our data with the published literature revealed convergence of radiation and desiccation stress responses of D. radiodurans. This is the first report that substantiates the hypothesis that the radiation stress resistance of D. radiodurans is incidental to its desiccation stress resistance.
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Affiliation(s)
- Aman Kumar Ujaoney
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Mahesh Kumar Padwal
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Bhakti Basu
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India.
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123
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Villa JK, Amador P, Janovsky J, Bhuyan A, Saldanha R, Lamkin TJ, Contreras LM. A Genome-Wide Search for Ionizing-Radiation-Responsive Elements in Deinococcus radiodurans Reveals a Regulatory Role for the DNA Gyrase Subunit A Gene's 5' Untranslated Region in the Radiation and Desiccation Response. Appl Environ Microbiol 2017; 83:e00039-17. [PMID: 28411225 PMCID: PMC5452802 DOI: 10.1128/aem.00039-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/07/2017] [Indexed: 12/19/2022] Open
Abstract
Tight regulation of gene expression is important for the survival of Deinococcus radiodurans, a model bacterium of extreme stress resistance. Few studies have examined the use of regulatory RNAs as a possible contributing mechanism to ionizing radiation (IR) resistance, despite their proffered efficient and dynamic gene expression regulation under IR stress. This work presents a transcriptome-based approach for the identification of stress-responsive regulatory 5' untranslated region (5'-UTR) elements in D. radiodurans R1 that can be broadly applied to other bacteria. Using this platform and an in vivo fluorescence screen, we uncovered the presence of a radiation-responsive regulatory motif in the 5' UTR of the DNA gyrase subunit A gene. Additional screens under H2O2-induced oxidative stress revealed the specificity of the response of this element to IR stress. Further examination of the sequence revealed a regulatory motif of the radiation and desiccation response (RDR) in the 5' UTR that is necessary for the recovery of D. radiodurans from high doses of IR. Furthermore, we suggest that it is the preservation of predicted RNA structure, in addition to DNA sequence consensus of the motif, that permits this important regulatory ability.IMPORTANCEDeinococcus radiodurans is an extremely stress-resistant bacterium capable of tolerating up to 3,000 times more ionizing radiation than human cells. As an integral part of the stress response mechanism of this organism, we suspect that it maintains stringent control of gene expression. However, understanding of its regulatory pathways remains incomplete to date. Untranslated RNA elements have been demonstrated to play crucial roles in gene regulation throughout bacteria. In this work, we focus on searching for and characterizing responsive RNA elements under radiation stress and propose that multiple levels of gene regulation work simultaneously to enable this organism to efficiently recover from exposure to ionizing radiation. The model we propose serves as a generic template to investigate similar mechanisms of gene regulation under stress that have likely evolved in other bacterial species.
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Affiliation(s)
- Jordan K Villa
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA
| | - Paul Amador
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA
| | - Justin Janovsky
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA
| | - Arijit Bhuyan
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas,USA
| | | | - Thomas J Lamkin
- Air Force Research Laboratory/XPRA Wright-Patterson AFB, Ohio, USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas,USA
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124
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Hashimoto T, Kunieda T. DNA Protection Protein, a Novel Mechanism of Radiation Tolerance: Lessons from Tardigrades. Life (Basel) 2017; 7:life7020026. [PMID: 28617314 PMCID: PMC5492148 DOI: 10.3390/life7020026] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 06/08/2017] [Accepted: 06/12/2017] [Indexed: 01/19/2023] Open
Abstract
Genomic DNA stores all genetic information and is indispensable for maintenance of normal cellular activity and propagation. Radiation causes severe DNA lesions, including double-strand breaks, and leads to genome instability and even lethality. Regardless of the toxicity of radiation, some organisms exhibit extraordinary tolerance against radiation. These organisms are supposed to possess special mechanisms to mitigate radiation-induced DNA damages. Extensive study using radiotolerant bacteria suggested that effective protection of proteins and enhanced DNA repair system play important roles in tolerability against high-dose radiation. Recent studies using an extremotolerant animal, the tardigrade, provides new evidence that a tardigrade-unique DNA-associating protein, termed Dsup, suppresses the occurrence of DNA breaks by radiation in human-cultured cells. In this review, we provide a brief summary of the current knowledge on extremely radiotolerant animals, and present novel insights from the tardigrade research, which expand our understanding on molecular mechanism of exceptional radio-tolerability.
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Affiliation(s)
- Takuma Hashimoto
- Laboratory for Radiation Biology, School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan.
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Takekazu Kunieda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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125
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Anaganti N, Basu B, Mukhopadhyaya R, Apte SK. Proximity of Radiation Desiccation Response Motif to the core promoter is essential for basal repression as well as gamma radiation-induced gyrB gene expression in Deinococcus radiodurans. Gene 2017; 615:8-17. [DOI: 10.1016/j.gene.2017.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/14/2017] [Accepted: 03/01/2017] [Indexed: 11/28/2022]
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126
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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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127
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Han W, Zhou C, Cheng J, Pan M, Hua Y, Zhao Y. Characterization and role of a 2',3'-cyclic phosphodiesterase from Deinococcus radiodurans. Biotechnol Lett 2017; 39:1211-1217. [PMID: 28497175 DOI: 10.1007/s10529-017-2349-7] [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] [Received: 03/02/2017] [Accepted: 05/04/2017] [Indexed: 12/17/2022]
Abstract
OBJECTIVES A 2',3'-cyclic phosphodiesterase gene (drCPDase) has been characterized from Deinococcus radiodurans and is involved in the robust resistance of this organism. RESULTS Cells lacking 2',3'-cyclic phosphodiesterase gene (drCPDase) showed modest growth defects and displayed increased sensitivities to high doses of various DNA-damaging agents including ionizing radiation, mitomycin C, UV and H2O2. The transcriptional level of drCPDase increased after H2O2 treatment. Additional nucleotide monophosphate partially recovered the phenotype of drCPDase knockout cells. Complementation of E. coli with drCPDase resulted in enhanced H2O2 resistance. CONCLUSIONS The 2',3'-cyclic phosphodiesterase (drCPDase) contributes to the extreme resistance of D. radiodurans and is presumably involved in damaged nucleotide detoxification.
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Affiliation(s)
- Wanchun Han
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Congli Zhou
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Jiahui Cheng
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Mingzhe Pan
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Yuejin Hua
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Ye Zhao
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China.
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128
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A tamB homolog is involved in maintenance of cell envelope integrity and stress resistance of Deinococcus radiodurans. Sci Rep 2017; 7:45929. [PMID: 28383523 PMCID: PMC5382914 DOI: 10.1038/srep45929] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/06/2017] [Indexed: 12/21/2022] Open
Abstract
The translocation and assembly module (TAM) in bacteria consists of TamA and TamB that form a complex to control the transport and secretion of outer membrane proteins. Herein, we demonstrated that the DR_1462-DR_1461-DR_1460 gene loci on chromosome 1 of Deinococcus radiodurans, which lacks tamA homologs, is a tamB homolog (DR_146T) with two tamB motifs and a DUF490 motif. Mutation of DR_146T resulted in cell envelope peeling and a decrease in resistance to shear stress and osmotic pressure, as well as an increase in oxidative stress resistance, consistent with the phenotype of a surface layer (S-layer) protein SlpA (DR_2577) mutant, demonstrating the involvement of DR_146T in maintenance of cell envelope integrity. The 123 kDa SlpA was absent and only its fragments were present in the cell envelope of DR_146T mutant, suggesting that DR_146T might be involved in maintenance of the S-layer. A mutant lacking the DUF490 motif displayed only a slight alteration in phenotype compared with the wild type, suggesting DUF490 is less important than tamB motif for the function of DR_146T. These findings enhance our understanding of the properties of the multilayered envelope in extremophilic D. radiodurans, as well as the diversity and functions of TAMs in bacteria.
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129
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Lebre PH, De Maayer P, Cowan DA. Xerotolerant bacteria: surviving through a dry spell. Nat Rev Microbiol 2017; 15:285-296. [DOI: 10.1038/nrmicro.2017.16] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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130
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Extremely high intracellular concentration of glucose-6-phosphate and NAD(H) in Deinococcus radiodurans. Extremophiles 2017; 21:399-407. [PMID: 28083699 DOI: 10.1007/s00792-016-0913-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 12/27/2016] [Indexed: 10/20/2022]
Abstract
Deinococcus radiodurans is highly resistant to ionizing radiation and UV radiation, and oxidative stress caused by such radiations. NADP(H) seems to be important for this resistance (Slade and Radman, Microbiol Mol Biol Rev 75:133-191; Slade, Radman, Microbiol Mol Biol Rev 75:133-191, 2011), but the mechanism underlying the generation of NADP(H) or NAD(H) in D. radiodurans has not fully been addressed. Intracellular concentrations of NAD+, NADH, NADP+, and NADPH in D. radiodurans are also not determined yet. We found that cell extracts of D. radiodurans catalyzed reduction of NAD(P)+ in vitro, indicating that D. radiodurans cells contain both enzymes and a high concentration of substrates for this activity. The enzyme and the substrate were attributed to glucose-6-phosphate dehydrogenase and glucose-6-phosphate of which intracellular concentration was extremely high. Unexpectedly, the intracellular concentration of NAD(H) was also much greater than that of NADP(H), suggesting some significant roles of NADH. These unusual features of this bacterium would shed light on a new aspect of physiology of this bacterium.
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131
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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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132
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Li J, Li Q, Ma X, Tian B, Li T, Yu J, Dai S, Weng Y, Hua Y. Biosynthesis of gold nanoparticles by the extreme bacterium Deinococcus radiodurans and an evaluation of their antibacterial properties. Int J Nanomedicine 2016; 11:5931-5944. [PMID: 27877039 PMCID: PMC5108609 DOI: 10.2147/ijn.s119618] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Deinococcus radiodurans is an extreme bacterium known for its high resistance to stresses including radiation and oxidants. The ability of D. radiodurans to reduce Au(III) and biosynthesize gold nanoparticles (AuNPs) was investigated in aqueous solution by ultraviolet and visible (UV/Vis) absorption spectroscopy, electron microscopy, X-ray diffraction (XRD), dynamic light scattering (DLS), Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS). D. radiodurans efficiently synthesized AuNPs from 1 mM Au(III) solution in 8 h. The AuNPs were of spherical, triangular and irregular shapes with an average size of 43.75 nm and a polydispersity index of 0.23 as measured by DLS. AuNPs were distributed in the cell envelope, across the cytosol and in the extracellular space. XRD analysis confirmed the crystallite nature of the AuNPs from the cell supernatant. Data from the FTIR and XPS showed that upon binding to proteins or compounds through interactions with carboxyl, amine, phospho and hydroxyl groups, Au(III) may be reduced to Au(I), and further reduced to Au(0) with the capping groups to stabilize the AuNPs. Biosynthesis of AuNPs was optimized with respect to the initial concentration of gold salt, bacterial growth period, solution pH and temperature. The purified AuNPs exhibited significant antibacterial activity against both Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) bacteria by damaging their cytoplasmic membrane. Therefore, the extreme bacterium D. radiodurans can be used as a novel bacterial candidate for efficient biosynthesis of AuNPs, which exhibited potential in biomedical application as an antibacterial agent.
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Affiliation(s)
- Jiulong Li
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University
| | - Qinghao Li
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University
| | - Xiaoqiong Ma
- Central Laboratory, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Bing Tian
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University
| | - Tao Li
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University
| | - Jiangliu Yu
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University
| | - Shang Dai
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University
| | - Yulan Weng
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University
| | - Yuejin Hua
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University
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133
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Peana M, Medici S, Pangburn HA, Lamkin TJ, Ostrowska M, Gumienna-Kontecka E, Zoroddu MA. Manganese binding to antioxidant peptides involved in extreme radiation resistance in Deinococcus radiodurans. J Inorg Biochem 2016; 164:49-58. [DOI: 10.1016/j.jinorgbio.2016.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/23/2016] [Accepted: 08/25/2016] [Indexed: 12/13/2022]
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134
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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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135
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Agapov AA, Kulbachinskiy AV. Mechanisms of Stress Resistance and Gene Regulation in the Radioresistant Bacterium Deinococcus radiodurans. BIOCHEMISTRY (MOSCOW) 2016; 80:1201-16. [PMID: 26567564 DOI: 10.1134/s0006297915100016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The bacterium Deinococcus radiodurans reveals extraordinary resistance to ionizing radiation, oxidative stress, desiccation, and other damaging conditions. In this review, we consider the main molecular mechanisms underlying such resistance, including the action of specific DNA repair and antioxidation systems, and transcription regulation during the anti-stress response.
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Affiliation(s)
- A A Agapov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
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136
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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: 18] [Impact Index Per Article: 2.3] [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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138
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Regulation of transcriptional pausing through the secondary channel of RNA polymerase. Proc Natl Acad Sci U S A 2016; 113:8699-704. [PMID: 27432968 DOI: 10.1073/pnas.1603531113] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Transcriptional pausing has emerged as an essential mechanism of genetic regulation in both bacteria and eukaryotes, where it serves to coordinate transcription with other cellular processes and to activate or halt gene expression rapidly in response to external stimuli. Deinococcus radiodurans, a highly radioresistant and stress-resistant bacterium, encodes three members of the Gre family of transcription factors: GreA and two Gre factor homologs, Gfh1 and Gfh2. Whereas GreA is a universal bacterial factor that stimulates RNA cleavage by RNA polymerase (RNAP), the functions of lineage-specific Gfh proteins remain unknown. Here, we demonstrate that these proteins, which bind within the RNAP secondary channel, strongly enhance site-specific transcriptional pausing and intrinsic termination. Uniquely, the pause-stimulatory activity of Gfh proteins depends on the nature of divalent ions (Mg(2+) or Mn(2+)) present in the reaction and is also modulated by the nascent RNA structure and the trigger loop in the RNAP active site. Our data reveal remarkable plasticity of the RNAP active site in response to various regulatory stimuli and highlight functional diversity of transcription factors that bind inside the secondary channel of RNAP.
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139
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Timmins J, Moe E. A Decade of Biochemical and Structural Studies of the DNA Repair Machinery of Deinococcus radiodurans: Major Findings, Functional and Mechanistic Insight and Challenges. Comput Struct Biotechnol J 2016; 14:168-176. [PMID: 27924191 PMCID: PMC5128194 DOI: 10.1016/j.csbj.2016.04.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/02/2016] [Accepted: 04/07/2016] [Indexed: 10/27/2022] Open
Affiliation(s)
- Joanna Timmins
- Université Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Elin Moe
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT the Arctic University of Norway, N-9037 Tromsø, Norway
- Instituto de Tecnologia Quimica e Biologica (ITQB), Universidade Nova de Lisboa, Av da Republica (EAN), 2780-157 Oeiras, Portugal
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140
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Wang L, Hu J, Liu M, Yang S, Zhao Y, Cheng K, Xu G, Li M, Tian B, Hua Y. Proteomic insights into the functional basis for the response regulator DrRRA of Deinococcus radiodurans. Int J Radiat Biol 2016; 92:273-80. [PMID: 26948123 DOI: 10.3109/09553002.2016.1150618] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Purpose To investigate the function basis of the recently discovered response regulator, drRRA (DNA damage response regulator A) in Deinococcus radiodurans, we compared the proteomic profile of the radiation-sensitive drRRA mutant with that of wild-type strain under both non-stress and gamma radiation treatment. Materials and methods Total proteins of D. radiodurans cells were subjected to two-dimension electrophoresis. Protein spots in 2-Dimension gels were silver stained and scanned. Spots that changed significantly in expression levels were selected for mass spectrometry analysis. Seven genes encoding representative proteins were knocked out for stress resistance analysis. Results A total of 52 proteins displayed significant expression level changes at least 1.5-fold in the mutant relative to wild-type strain under non-stress conditions, with 31 repressed and 21 induced proteins, which might affect the cell response of D. radiodurans to gamma radiation. The proteins were distributed into functional groups including stress response, metabolism, and function unknown. Disruptions of several altered proteins including DRA0259 (Catalase E) and DR1538 (Osmotically inducible protein C), reduced the antioxidant activity of D. radiodurans. Conclusion Combined with our previous result of transcriptional profile, we further confirmed that inactivation of DrRRA affects the expression of various stress response systems.
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Affiliation(s)
- Liangyan Wang
- a Key Laboratory of Chinese Ministry of Agriculture and Zhejiang Province for Nuclear Agricultural Sciences , Institute of Nuclear Agricultural Sciences, Zhejiang University , Hangzhou , Zhejiang , China
| | - Jing Hu
- a Key Laboratory of Chinese Ministry of Agriculture and Zhejiang Province for Nuclear Agricultural Sciences , Institute of Nuclear Agricultural Sciences, Zhejiang University , Hangzhou , Zhejiang , China
| | - Mengjia Liu
- a Key Laboratory of Chinese Ministry of Agriculture and Zhejiang Province for Nuclear Agricultural Sciences , Institute of Nuclear Agricultural Sciences, Zhejiang University , Hangzhou , Zhejiang , China
| | - Su Yang
- a Key Laboratory of Chinese Ministry of Agriculture and Zhejiang Province for Nuclear Agricultural Sciences , Institute of Nuclear Agricultural Sciences, Zhejiang University , Hangzhou , Zhejiang , China
| | - Ye Zhao
- a Key Laboratory of Chinese Ministry of Agriculture and Zhejiang Province for Nuclear Agricultural Sciences , Institute of Nuclear Agricultural Sciences, Zhejiang University , Hangzhou , Zhejiang , China
| | - Kaiying Cheng
- a Key Laboratory of Chinese Ministry of Agriculture and Zhejiang Province for Nuclear Agricultural Sciences , Institute of Nuclear Agricultural Sciences, Zhejiang University , Hangzhou , Zhejiang , China
| | - Guangzhi Xu
- a Key Laboratory of Chinese Ministry of Agriculture and Zhejiang Province for Nuclear Agricultural Sciences , Institute of Nuclear Agricultural Sciences, Zhejiang University , Hangzhou , Zhejiang , China ;,b Institute of Agriculture and Food Science, Zhejiang Agriculture and Forest University , Lin'an , Zhejiang , China
| | - Mingfeng Li
- a Key Laboratory of Chinese Ministry of Agriculture and Zhejiang Province for Nuclear Agricultural Sciences , Institute of Nuclear Agricultural Sciences, Zhejiang University , Hangzhou , Zhejiang , China ;,c Dongying Environmental Protection Agency , Dongying , Shandong , China
| | - Bing Tian
- a Key Laboratory of Chinese Ministry of Agriculture and Zhejiang Province for Nuclear Agricultural Sciences , Institute of Nuclear Agricultural Sciences, Zhejiang University , Hangzhou , Zhejiang , China
| | - Yuejin Hua
- a Key Laboratory of Chinese Ministry of Agriculture and Zhejiang Province for Nuclear Agricultural Sciences , Institute of Nuclear Agricultural Sciences, Zhejiang University , Hangzhou , Zhejiang , China
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DNA Gyrase of Deinococcus radiodurans is characterized as Type II bacterial topoisomerase and its activity is differentially regulated by PprA in vitro. Extremophiles 2016; 20:195-205. [DOI: 10.1007/s00792-016-0814-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 01/20/2016] [Indexed: 11/26/2022]
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142
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Topoisomerase IB of Deinococcus radiodurans resolves guanine quadruplex DNA structures in vitro. J Biosci 2015; 40:833-43. [DOI: 10.1007/s12038-015-9571-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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143
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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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144
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Clanton R, Saucier D, Ford J, Akabani G. Microbial influences on hormesis, oncogenesis, and therapy: A review of the literature. ENVIRONMENTAL RESEARCH 2015; 142:239-256. [PMID: 26183884 DOI: 10.1016/j.envres.2015.06.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/11/2015] [Accepted: 06/23/2015] [Indexed: 06/04/2023]
Abstract
Utilization of environmental stimuli for growth is the main factor contributing to the evolution of prokaryotes and eukaryotes, independently and mutualistically. Epigenetics describes an organism's ability to vary expression of certain genes based on their environmental stimuli. The diverse degree of dose-dependent responses based on their variances in expressed genetic profiles makes it difficult to ascertain whether hormesis or oncogenesis has or is occurring. In the medical field this is shown where survival curves used in determining radiotherapeutic doses have substantial uncertainties, some as large as 50% (Barendsen, 1990). Many in-vitro radiobiological studies have been limited by not taking into consideration the innate presence of microbes in biological systems, which have either grown symbiotically or pathogenically. Present in-vitro studies neglect to take into consideration the varied responses that commensal and opportunistic pathogens will have when exposed to the same stimuli and how such responses could act as stimuli for their macro/microenvironment. As a result many theories such as radiation carcinogenesis explain microscopic events but fail to describe macroscopic events (Cohen, 1995). As such, this review shows how microorganisms have the ability to perturb risks of cancer and enhance hormesis after irradiation. It will also look at bacterial significance in the microenvironment of the tumor before and during treatment. In addition, bacterial systemic communication after irradiation and the host's immune responses to infection could explain many of the phenomena associated with bystander effects. Therefore, the present literature review considers the paradigms of hormesis and oncogenesis in order to find a rationale that ties them all together. This relationship was thus characterized to be the microbiome.
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Affiliation(s)
- Ryan Clanton
- Department of Nuclear Engineering, Texas A&M University, College Station, TX 77843, USA; Texas A&M Institute for Preclinical Studies, Texas A&M University, College Station, TX 77843, USA
| | - David Saucier
- Department of Nuclear Engineering, Texas A&M University, College Station, TX 77843, USA
| | - John Ford
- Department of Nuclear Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Gamal Akabani
- Department of Nuclear Engineering, Texas A&M University, College Station, TX 77843, USA; Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA; Texas A&M Institute for Preclinical Studies, Texas A&M University, College Station, TX 77843, USA
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145
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Raven JA. Implications of mutation of organelle genomes for organelle function and evolution. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5639-50. [PMID: 26077836 DOI: 10.1093/jxb/erv298] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Organelle genomes undergo more variation, including that resulting from damage, than eukaryotic nuclear genomes, or bacterial genomes, under the same conditions. Recent advances in characterizing the changes to genomes of chloroplasts and mitochondria of Zea mays should, when applied more widely, help our understanding of how damage to organelle genomes relates to how organelle function is maintained through the life of individuals and in succeeding generations. Understanding of the degree of variation in the changes to organelle DNA and its repair among photosynthetic organisms might help to explain the variations in the rate of nucleotide substitution among organelle genomes. Further studies of organelle DNA variation, including that due to damage and its repair might also help us to understand why the extent of DNA turnover in the organelles is so much greater than that in their bacterial (cyanobacteria for chloroplasts, proteobacteria for mitochondria) relatives with similar rates of production of DNA-damaging reactive oxygen species. Finally, from the available data, even the longest-lived organelle-encoded proteins, and the RNAs needed for their synthesis, are unlikely to maintain organelle function for much more than a week after the complete loss of organelle DNA.
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Affiliation(s)
- John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK †School of Plant Biology, University of Western Australia, M048, 35 Stirling Highway, Crawley, WA 6009, Australia
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146
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Etemadifar Z. Response to Letter to the Editor from SMJ Mortazavi. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2015; 147:155-156. [PMID: 26026932 DOI: 10.1016/j.jenvrad.2015.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 05/11/2015] [Indexed: 06/04/2023]
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147
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Badri H, Monsieurs P, Coninx I, Nauts R, Wattiez R, Leys N. Temporal Gene Expression of the Cyanobacterium Arthrospira in Response to Gamma Rays. PLoS One 2015; 10:e0135565. [PMID: 26308624 PMCID: PMC4550399 DOI: 10.1371/journal.pone.0135565] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 07/23/2015] [Indexed: 12/16/2022] Open
Abstract
The edible cyanobacterium Arthrospira is resistant to ionising radiation. The cellular mechanisms underlying this radiation resistance are, however, still largely unknown. Therefore, additional molecular analysis was performed to investigate how these cells can escape from, protect against, or repair the radiation damage. Arthrospira cells were shortly exposed to different doses of 60Co gamma rays and the dynamic response was investigated by monitoring its gene expression and cell physiology at different time points after irradiation. The results revealed a fast switch from an active growth state to a kind of 'survival modus' during which the cells put photosynthesis, carbon and nitrogen assimilation on hold and activate pathways for cellular protection, detoxification, and repair. The higher the radiation dose, the more pronounced this global emergency response is expressed. Genes repressed during early response, suggested a reduction of photosystem II and I activity and reduced tricarboxylic acid (TCA) and Calvin-Benson-Bassham (CBB) cycles, combined with an activation of the pentose phosphate pathway (PPP). For reactive oxygen species detoxification and restoration of the redox balance in Arthrospira cells, the results suggested a powerful contribution of the antioxidant molecule glutathione. The repair mechanisms of Arthrospira cells that were immediately switched on, involve mainly proteases for damaged protein removal, single strand DNA repair and restriction modification systems, while recA was not induced. Additionally, the exposed cells showed significant increased expression of arh genes, coding for a novel group of protein of unknown function, also seen in our previous irradiation studies. This observation confirms our hypothesis that arh genes are key elements in radiation resistance of Arthrospira, requiring further investigation. This study provides new insights into phasic response and the cellular pathways involved in the radiation resistance of microbial cells, in particularly for photosynthetic organisms as the cyanobacterium Arthrospira.
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Affiliation(s)
- Hanène Badri
- Expert Groups for Molecular and Cellular Biology and Biosphere Impact Studies, Belgian Nuclear Research Centre SCK•CEN, Mol, Belgium
- Proteomics and Microbiology Group, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Pieter Monsieurs
- Expert Groups for Molecular and Cellular Biology and Biosphere Impact Studies, Belgian Nuclear Research Centre SCK•CEN, Mol, Belgium
| | - Ilse Coninx
- Expert Groups for Molecular and Cellular Biology and Biosphere Impact Studies, Belgian Nuclear Research Centre SCK•CEN, Mol, Belgium
| | - Robin Nauts
- Expert Groups for Molecular and Cellular Biology and Biosphere Impact Studies, Belgian Nuclear Research Centre SCK•CEN, Mol, Belgium
| | - Ruddy Wattiez
- Proteomics and Microbiology Group, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Natalie Leys
- Expert Groups for Molecular and Cellular Biology and Biosphere Impact Studies, Belgian Nuclear Research Centre SCK•CEN, Mol, Belgium
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148
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G-quadruplex forming structural motifs in the genome of Deinococcus radiodurans and their regulatory roles in promoter functions. Appl Microbiol Biotechnol 2015. [PMID: 26201493 DOI: 10.1007/s00253-015-6808-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Deinococcus radiodurans displays compromised radioresistance in the presence of guanine quadruplex (G4)-binding drugs (G4 drugs). Genome-wide scanning showed islands of guanine runs (G-motif) in the upstream regions of coding sequences as well as in the structural regions of many genes, indicating a role for G4 DNA in the regulation of genome functions in this bacterium. G-motifs present upstream to some of the DNA damage-responsive genes like lexA, pprI, recF, recQ, mutL and radA were synthesized, and the formation of G4 DNA structures was probed in vitro. The G-motifs present at the 67th position upstream to recQ and at the 121st position upstream to mutL produced parallel and mixed G4 DNA structures, respectively. Expression of β-galactosidase under recQ and mutL promoters containing respective G-motifs was inhibited by G4 drugs under normal growth conditions in D. radiodurans. However, when such cells were exposed to γ radiation, mutL promoter activity was stimulated while recQ promoter activity was inhibited in the presence of G4 drugs. Deletion of the G-motif from the recQ promoter could relax it from G4 drug repression. D. radiodurans cells treated with G4 drug showed reduction in recQ expression and γ radiation resistance, indicating an involvement of G4 DNA in the radioresistance of this bacterium. These results suggest that G-motifs from D. radiodurans genome form different types of G4 DNA structures at least in vitro, and the recQ and mutL promoters seem to be differentially regulated at the levels of G4 DNA structures.
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149
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Dai J, Dai W, Qiu C, Yang Z, Zhang Y, Zhou M, Zhang L, Fang C, Gao Q, Yang Q, Li X, Wang Z, Wang Z, Jia Z, Chen X. Unraveling adaptation of Pontibacter korlensis to radiation and infertility in desert through complete genome and comparative transcriptomic analysis. Sci Rep 2015; 5:10929. [PMID: 26057562 PMCID: PMC4460873 DOI: 10.1038/srep10929] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 04/27/2015] [Indexed: 11/10/2022] Open
Abstract
The desert is a harsh habitat for flora and microbial life due to its aridness and strong radiation. In this study, we constructed the first complete and deeply annotated genome of the genus Pontibacter (Pontibacter korlensis X14-1T = CCTCC AB 206081T, X14-1). Reconstruction of the sugar metabolism process indicated that strain X14-1 can utilize diverse sugars, including cellulose, starch and sucrose; this result is consistent with previous experiments. Strain X14-1 is also able to resist desiccation and radiation in the desert through well-armed systems related to DNA repair, radical oxygen species (ROS) detoxification and the OstAB and TreYZ pathways for trehalose synthesis. A comparative transcriptomic analysis under gamma radiation revealed that strain X14-1 presents high-efficacy operating responses to radiation, including the robust expression of catalase and the manganese transport protein. Evaluation of 73 novel genes that are differentially expressed showed that some of these genes may contribute to the strain’s adaptation to radiation and desiccation through ferric transport and preservation.
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Affiliation(s)
- Jun Dai
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan 430068, China
| | | | | | | | - Yi Zhang
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan 430068, China
| | - Mengzhou Zhou
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan 430068, China
| | - Lei Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chengxiang Fang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Qiang Gao
- BGI Shenzhen, Shenzhen 518083, China
| | - Qiao Yang
- East China Sea fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China
| | - Xin Li
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan 430068, China
| | - Zhi Wang
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan 430068, China
| | | | - Zhenhua Jia
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan 430068, China
| | - Xiong Chen
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan 430068, China
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150
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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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