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Khan A, Liu G, Zhang G, Li X. Radiation-resistant bacteria in desiccated soil and their potentiality in applied sciences. Front Microbiol 2024; 15:1348758. [PMID: 38894973 PMCID: PMC11184166 DOI: 10.3389/fmicb.2024.1348758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
A rich diversity of radiation-resistant (Rr) and desiccation-resistant (Dr) bacteria has been found in arid habitats of the world. Evidence from scientific research has linked their origin to reactive oxygen species (ROS) intermediates. Rr and Dr. bacteria of arid regions have the potential to regulate imbalance radicals and evade a higher dose of radiation and oxidation than bacterial species of non-arid regions. Photochemical-activated ROS in Rr bacteria is run through photo-induction of electron transfer. A hypothetical model of the biogeochemical cycle based on solar radiation and desiccation. These selective stresses generate oxidative radicals for a short span with strong reactivity and toxic effects. Desert-inhibiting Rr bacteria efficiently evade ROS toxicity with an evolved antioxidant system and other defensive pathways. The imbalanced radicals in physiological disorders, cancer, and lung diseases could be neutralized by a self-sustaining evolved Rr bacteria antioxidant system. The direct link of evolved antioxidant system with intermediate ROS and indirect influence of radiation and desiccation provide useful insight into richness, ecological diversity, and origin of Rr bacteria capabilities. The distinguishing features of Rr bacteria in deserts present a fertile research area with promising applications in the pharmaceutical industry, genetic engineering, biological therapy, biological transformation, bioremediation, industrial biotechnology, and astrobiology.
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Affiliation(s)
- Asaf Khan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
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Moris VC, Bruneau L, Berthe J, Heuskin AC, Penninckx S, Ritter S, Weber U, Durante M, Danchin EGJ, Hespeels B, Doninck KV. Ionizing radiation responses appear incidental to desiccation responses in the bdelloid rotifer Adineta vaga. BMC Biol 2024; 22:11. [PMID: 38273318 PMCID: PMC10809525 DOI: 10.1186/s12915-023-01807-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND The remarkable resistance to ionizing radiation found in anhydrobiotic organisms, such as some bacteria, tardigrades, and bdelloid rotifers has been hypothesized to be incidental to their desiccation resistance. Both stresses produce reactive oxygen species and cause damage to DNA and other macromolecules. However, this hypothesis has only been investigated in a few species. RESULTS In this study, we analyzed the transcriptomic response of the bdelloid rotifer Adineta vaga to desiccation and to low- (X-rays) and high- (Fe) LET radiation to highlight the molecular and genetic mechanisms triggered by both stresses. We identified numerous genes encoding antioxidants, but also chaperones, that are constitutively highly expressed, which may contribute to the protection of proteins against oxidative stress during desiccation and ionizing radiation. We also detected a transcriptomic response common to desiccation and ionizing radiation with the over-expression of genes mainly involved in DNA repair and protein modifications but also genes with unknown functions that were bdelloid-specific. A distinct transcriptomic response specific to rehydration was also found, with the over-expression of genes mainly encoding Late Embryogenesis Abundant proteins, specific heat shock proteins, and glucose repressive proteins. CONCLUSIONS These results suggest that the extreme resistance of bdelloid rotifers to radiation might indeed be a consequence of their capacity to resist complete desiccation. This study paves the way to functional genetic experiments on A. vaga targeting promising candidate proteins playing central roles in radiation and desiccation resistance.
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Affiliation(s)
- Victoria C Moris
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium.
- Laboratory of Molecular Biology & Evolution (MBE), Department of Biology, Université Libre de Bruxelles, 1000, Brussels, Belgium.
| | - Lucie Bruneau
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Jérémy Berthe
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Anne-Catherine Heuskin
- Namur Research Institute for Life Sciences (NARILIS), Laboratory of Analysis By Nuclear Reactions (LARN), University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Sébastien Penninckx
- Medical Physics Department, Institut Jules Bordet - Université Libre de Bruxelles, 90 Rue Meylemeersch, 1070, Brussels, Belgium
| | - Sylvia Ritter
- Biophysics Department, GSI Helmholtzzentrum Für Schwerionenforschung, Darmstadt, Germany
| | - Uli Weber
- Biophysics Department, GSI Helmholtzzentrum Für Schwerionenforschung, Darmstadt, Germany
| | - Marco Durante
- Biophysics Department, GSI Helmholtzzentrum Für Schwerionenforschung, Darmstadt, Germany
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Etienne G J Danchin
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 06903, Sophia Antipolis, France
| | - Boris Hespeels
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Karine Van Doninck
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
- Laboratory of Molecular Biology & Evolution (MBE), Department of Biology, Université Libre de Bruxelles, 1000, Brussels, Belgium
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3
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Gregory SP, Mackie JRM, Barnett MJ. Radioactive waste microbiology: predicting microbial survival and activity in changing extreme environments. FEMS Microbiol Rev 2024; 48:fuae001. [PMID: 38216518 PMCID: PMC10853057 DOI: 10.1093/femsre/fuae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/01/2023] [Accepted: 01/11/2024] [Indexed: 01/14/2024] Open
Abstract
The potential for microbial activity to occur within the engineered barrier system (EBS) of a geological disposal facility (GDF) for radioactive waste is acknowledged by waste management organizations as it could affect many aspects of the safety functions of a GDF. Microorganisms within an EBS will be exposed to changing temperature, pH, radiation, salinity, saturation, and availability of nutrient and energy sources, which can limit microbial survival and activity. Some of the limiting conditions are incorporated into GDF designs for safety reasons, including the high pH of cementitious repositories, the limited pore space of bentonite-based repositories, or the high salinity of GDFs in evaporitic geologies. Other environmental conditions such as elevated radiation, temperature, and desiccation, arise as a result of the presence of high heat generating waste (HHGW). Here, we present a comprehensive review of how environmental conditions in the EBS may limit microbial activity, covering HHGW and lower heat generating waste (LHGW) in a range of geological environments. We present data from the literature on the currently recognized limits to life for each of the environmental conditions described above, and nutrient availability to establish the potential for life in these environments. Using examples where each variable has been modelled for a particular GDF, we outline the times and locations when that variable can be expected to limit microbial activity. Finally, we show how this information for multiple variables can be used to improve our understanding of the potential for microbial activity to occur within the EBS of a GDF and, more broadly, to understand microbial life in changing environments exposed to multiple extreme conditions.
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Affiliation(s)
- Simon P Gregory
- British Geological Survey, Nicker Hill, Keyworth, Nottingham NG12 5GG, United Kingdom
| | - Jessica R M Mackie
- British Geological Survey, Nicker Hill, Keyworth, Nottingham NG12 5GG, United Kingdom
| | - Megan J Barnett
- British Geological Survey, Nicker Hill, Keyworth, Nottingham NG12 5GG, United Kingdom
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Pramanik D, Vaskimo L, Batenburg KJ, Kostenko A, Droppert K, Smets E, Gravendeel B. Orchid fruit and root movement analyzed using 2D photographs and a bioinformatics pipeline for processing sequential 3D scans. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11567. [PMID: 38369982 PMCID: PMC10873816 DOI: 10.1002/aps3.11567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 02/20/2024]
Abstract
Premise Most studies of the movement of orchid fruits and roots during plant development have focused on morphological observations; however, further genetic analysis is required to understand the molecular mechanisms underlying this phenomenon. A precise tool is required to observe these movements and harvest tissue at the correct position and time for transcriptomics research. Methods We utilized three-dimensional (3D) micro-computed tomography (CT) scans to capture the movement of fast-growing Erycina pusilla roots, and built an integrated bioinformatics pipeline to process 3D images into 3D time-lapse videos. To record the movement of slowly developing E. pusilla and Phalaenopsis equestris fruits, two-dimensional (2D) photographs were used. Results The E. pusilla roots twisted and resupinated multiple times from early development. The first period occurred in the early developmental stage (77-84 days after germination [DAG]) and the subsequent period occurred later in development (140-154 DAG). While E. pusilla fruits twisted 45° from 56-63 days after pollination (DAP), the fruits of P. equestris only began to resupinate a week before dehiscence (133 DAP) and ended a week after dehiscence (161 DAP). Discussion Our methods revealed that each orchid root and fruit had an independent direction and degree of torsion from the initial to the final position. Our innovative approaches produced detailed spatial and temporal information on the resupination of roots and fruits during orchid development.
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Affiliation(s)
- Dewi Pramanik
- Evolutionary EcologyNaturalis Biodiversity CenterDarwinweg 22333 CRLeidenThe Netherlands
- Institute of Biology Leiden, Faculty of ScienceLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
- Research Center for Horticulture, Research Organization for Agriculture and FoodNational Research and Innovation Agency (Badan Riset dan Inovasi Nasional/BRIN)Cibinong Science Center, Jl. Raya Jakarta‐Bogor, Pakansari, CibinongWest Java16915Indonesia
| | - Lotta Vaskimo
- Faculty of Science and TechnologyUniversity of Applied Sciences LeidenZernikedreef 112333 CKLeidenThe Netherlands
| | - K. Joost Batenburg
- Leiden Institute of Advanced Computer Science, Faculty of ScienceLeiden University, SnelliusNiels Bohrweg 12333 CALeidenThe Netherlands
- Computational ImagingCentrum Wiskunde en InformaticaScience Park 1231090 GBAmsterdamThe Netherlands
| | - Alexander Kostenko
- Computational ImagingCentrum Wiskunde en InformaticaScience Park 1231090 GBAmsterdamThe Netherlands
| | - Kevin Droppert
- Faculty of Science and TechnologyUniversity of Applied Sciences LeidenZernikedreef 112333 CKLeidenThe Netherlands
| | - Erik Smets
- Evolutionary EcologyNaturalis Biodiversity CenterDarwinweg 22333 CRLeidenThe Netherlands
- Institute of Biology Leiden, Faculty of ScienceLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
- Ecology, Evolution and Biodiversity Conservation, KU LeuvenKasteelpark Arenberg 31, BOX 24353001LeuvenBelgium
| | - Barbara Gravendeel
- Evolutionary EcologyNaturalis Biodiversity CenterDarwinweg 22333 CRLeidenThe Netherlands
- Institute of Biology Leiden, Faculty of ScienceLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
- Radboud Institute for Biological and Environmental SciencesRadboud UniversityHeyendaalseweg 1356500 GLNijmegenThe Netherlands
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Jenkins SV, Jung S, Jamshidi-Parsian A, Borrelli MJ, Dings RPM, Griffin RJ. Morphological Effects and In Vitro Biological Mechanisms of Radiation-Induced Cell Killing by Gold Nanomaterials. ACS APPLIED MATERIALS & INTERFACES 2023; 15:58241-58250. [PMID: 38059477 DOI: 10.1021/acsami.3c15358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Gold nanomaterials have been shown to augment radiation therapy both in vitro and in vivo. However, studies on these materials are mostly phenomenological due to nanoparticle heterogeneity and the complexity of biological systems. Even accurate quantification of the particle dose still results in bulk average biases; the effect on individual cells is not measured but rather the effect on the overall population. To perform quantitative nanobiology, we coated glass coverslips uniformly at varying densities with Au nanoparticle preparations with different morphologies (45 nm cages, 25 nm spheres, and 30 nm rods). Consequently, the effect of a specific number of particles per unit area in contact with breast cancer cells growing on the coated surfaces was ascertained. Gold nanocages showed the highest degree of radiosensitization on a per particle basis, followed by gold nanospheres and gold nanorods, respectively. All three materials showed little cytotoxic effect at 0 Gy, but clonogenic survival decreased proportionally with the radiation dose and particle coverage density. A similar trend was seen in vivo in the combined treatment antitumor response in 4T1 tumor-bearing animals. The presence of gold affected the type and quantity of reactive oxygen species generated, specifically superoxide and hydroxyl radicals, and the concentration of nanocages correlated with the development of more numerous double-stranded DNA breaks and increased protein oxidation as measured by carbonylation. This work demonstrates the dependence on morphology and concentration of radiation enhancement by gold nanomaterials and may lead to a novel method to differentiate intra- and extracellular functionalities of gold nanomedicine treatment strategies. It further provides insights that can guide the rational development of gold nanomaterial-based radiosensitizers for clinical use.
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Affiliation(s)
- Samir V Jenkins
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Seunghyun Jung
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Azemat Jamshidi-Parsian
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Michael J Borrelli
- Department of Radiology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Ruud P M Dings
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Robert J Griffin
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
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Nicolas E, Simion P, Guérineau M, Terwagne M, Colinet M, Virgo J, Lingurski M, Boutsen A, Dieu M, Hallet B, Van Doninck K. Horizontal acquisition of a DNA ligase improves DNA damage tolerance in eukaryotes. Nat Commun 2023; 14:7638. [PMID: 37993452 PMCID: PMC10665377 DOI: 10.1038/s41467-023-43075-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/30/2023] [Indexed: 11/24/2023] Open
Abstract
Bdelloid rotifers are part of the restricted circle of multicellular animals that can withstand a wide range of genotoxic stresses at any stage of their life cycle. In this study, bdelloid rotifer Adineta vaga is used as a model to decipher the molecular basis of their extreme tolerance. Proteomic analysis shows that a specific DNA ligase, different from those usually involved in DNA repair in eukaryotes, is strongly over-represented upon ionizing radiation. A phylogenetic analysis reveals its orthology to prokaryotic DNA ligase E, and its horizontal acquisition by bdelloid rotifers and plausibly other eukaryotes. The fungus Mortierella verticillata, having a single copy of this DNA Ligase E homolog, also exhibits an increased radiation tolerance with an over-expression of this DNA ligase E following X-ray exposure. We also provide evidence that A. vaga ligase E is a major contributor of DNA breaks ligation activity, which is a common step of all important DNA repair pathways. Consistently, its heterologous expression in human cell lines significantly improves their radio-tolerance. Overall, this study highlights the potential of horizontal gene transfers in eukaryotes, and their contribution to the adaptation to extreme conditions.
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Affiliation(s)
- Emilien Nicolas
- Université Libre de Bruxelles, Molecular Biology and Evolution, Brussels, 1050, Belgium.
| | - Paul Simion
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
- Université de Rennes, Ecosystèmes, biodiversité, évolution (ECOBIO UMR 6553), CNRS, Rennes, France
| | - Marc Guérineau
- Université Libre de Bruxelles, Molecular Biology and Evolution, Brussels, 1050, Belgium
| | - Matthieu Terwagne
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
| | - Mathilde Colinet
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
| | - Julie Virgo
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
| | - Maxime Lingurski
- Université Libre de Bruxelles, Molecular Biology and Evolution, Brussels, 1050, Belgium
| | - Anaïs Boutsen
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium
| | - Marc Dieu
- Université de Namur, MaSUN-mass spectrometry facility, Namur, 5000, Belgium
| | - Bernard Hallet
- Université Catholique de Louvain, Louvain Institute of Biomolecular Science and Technology, Louvain-la-Neuve, 1348, Belgium.
| | - Karine Van Doninck
- Université Libre de Bruxelles, Molecular Biology and Evolution, Brussels, 1050, Belgium.
- Université de Namur, Laboratory of Evolutionary Genetics and Ecology, Namur, 5000, Belgium.
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7
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de Groot A, Blanchard L. DNA repair and oxidative stress defense systems in radiation-resistant Deinococcus murrayi. Can J Microbiol 2023; 69:416-431. [PMID: 37552890 DOI: 10.1139/cjm-2023-0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Deinococcus murrayi is a bacterium isolated from hot springs in Portugal, and named after Dr. Robert G.E. Murray in recognition of his research on the genus Deinococcus. Like other Deinococcus species, D. murrayi is extremely resistant to ionizing radiation. Repair of massive DNA damage and limitation of oxidative protein damage are two important factors contributing to the robustness of Deinococcus bacteria. Here, we identify, among others, the DNA repair and oxidative stress defense proteins in D. murrayi, and highlight special features of D. murrayi. For DNA repair, D. murrayi does not contain a standalone uracil-DNA glycosylase (Ung), but it encodes a protein in which Ung is fused to a DNA photolyase domain (PhrB). UvrB and UvrD contain large insertions corresponding to inteins. One of its endonuclease III enzymes lacks a [4Fe-4S] cluster. Deinococcus murrayi possesses a homolog of the error-prone DNA polymerase IV. Concerning oxidative stress defense, D. murrayi encodes a manganese catalase in addition to a heme catalase. Its organic hydroperoxide resistance protein Ohr is atypical because the redox active cysteines are present in a CXXC motif. These and other characteristics of D. murrayi show further diversity among Deinococcus bacteria with respect to resistance-associated mechanisms.
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Affiliation(s)
- Arjan de Groot
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13115, France
| | - Laurence Blanchard
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13115, France
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Butterworth SJ, Barton F, Lloyd JR. Extremophilic microbial metabolism and radioactive waste disposal. Extremophiles 2023; 27:27. [PMID: 37839067 PMCID: PMC10577106 DOI: 10.1007/s00792-023-01312-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023]
Abstract
Decades of nuclear activities have left a legacy of hazardous radioactive waste, which must be isolated from the biosphere for over 100,000 years. The preferred option for safe waste disposal is a deep subsurface geological disposal facility (GDF). Due to the very long geological timescales required, and the complexity of materials to be disposed of (including a wide range of nutrients and electron donors/acceptors) microbial activity will likely play a pivotal role in the safe operation of these mega-facilities. A GDF environment provides many metabolic challenges to microbes that may inhabit the facility, including high temperature, pressure, radiation, alkalinity, and salinity, depending on the specific disposal concept employed. However, as our understanding of the boundaries of life is continuously challenged and expanded by the discovery of novel extremophiles in Earth's most inhospitable environments, it is becoming clear that microorganisms must be considered in GDF safety cases to ensure accurate predictions of long-term performance. This review explores extremophilic adaptations and how this knowledge can be applied to challenge our current assumptions on microbial activity in GDF environments. We conclude that regardless of concept, a GDF will consist of multiple extremes and it is of high importance to understand the limits of polyextremophiles under realistic environmental conditions.
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Affiliation(s)
- Sarah Jane Butterworth
- Department of Earth and Environmental Sciences, Research Centre for Radwaste Disposal and Williamson Research Centre, The University of Manchester, Manchester, UK
| | - Franky Barton
- Department of Earth and Environmental Sciences, Research Centre for Radwaste Disposal and Williamson Research Centre, The University of Manchester, Manchester, UK.
| | - Jonathan Richard Lloyd
- Department of Earth and Environmental Sciences, Research Centre for Radwaste Disposal and Williamson Research Centre, The University of Manchester, Manchester, UK.
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Daly MJ. The scientific revolution that unraveled the astonishing DNA repair capacity of the Deinococcaceae: 40 years on. Can J Microbiol 2023; 69:369-386. [PMID: 37267626 DOI: 10.1139/cjm-2023-0059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The family Deinococcaceae exhibits exceptional radiation resistance and possesses all the necessary traits for surviving in radiation-exposed environments. Their survival strategy involves the coupling of metabolic and DNA repair functions, resulting in an extraordinarily efficient homologous repair of DNA double-strand breaks (DSBs) caused by radiation or desiccation. The keys to their survival lie in the hyperaccumulation of manganous (Mn2+)-metabolite antioxidants that protect their DNA repair proteins under extreme oxidative stress and the persistent structural linkage by Holliday junctions of their multiple genome copies per cell that facilitates DSB repair. This coupling of metabolic and DNA repair functions has made polyploid Deinococcus bacteria a useful tool in environmental biotechnology, radiobiology, aging, and planetary protection. The review highlights the groundbreaking contributions of the late Robert G.E. Murray to the field of Deinococcus research and the emergent paradigm-shifting discoveries that revolutionized our understanding of radiation survivability and oxidative stress defense, demonstrating that the proteome, rather than the genome, is the primary target responsible for survivability. These discoveries have led to the commercial development of irradiated vaccines using Deinococcus Mn-peptide antioxidants and have significant implications for various fields.
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Affiliation(s)
- Michael J Daly
- Uniformed Services University of the Health Sciences (USUHS), School of Medicine, Department of Pathology, Bethesda, MD 20814-4799, USA
- Committee on Planetary Protection (CoPP), National Academies of Sciences, Washington, DC 20001, USA
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10
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Subramani G, Srinivasan S. Involvement of Nucleotide Excision Repair and Rec-Dependent Pathway Genes for UV Radiation Resistance in Deinococcus irradiatisoli 17bor-2. Genes (Basel) 2023; 14:1803. [PMID: 37761943 PMCID: PMC10531146 DOI: 10.3390/genes14091803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/16/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Strain Deinococcus irradiatisoli 17bor-2 was isolated from a soil sample exposed to γ radiation at Seoul Women's University, Republic of Korea. The genus Deinococcus is a Gram-negative, coccus-shaped, and extremophilic bacterium, well renowned as being a radiation-resistant bacterium. Therefore, the mechanism behind the resistance to radiation and the gene responsible for the resistance could be helpful for detailed experimental studies with biotechnological applications. To study the involvement of genes in UV radiation resistance in strain 17bor-2, the genomic DNA of the strain was sequenced and constructed using the Pacific Biosciences RS II system. In addition, the complete genome sequence of strain 17bor-2 was annotated and interpreted using the Genomes-Expert Review (IMG-ER) system, along with Prodigal and JGI GenePRIMP analysis. The genome analysis of strain 17bor-2 revealed evidence of excinuclease UvrABC genes, which are key enzymes in the nucleotide excision repair (NER) mechanism, as well as genes from the recA-dependent and recQ pathways. The genome of strain Deinococcus irradiatisoli 17bor-2 was a circular chromosome comprising 3,052,043 bp with a GC content of 67.0%, including 2911 coding sequences (CDs), 49 tRNA genes, and 9 rRNA genes. In addition, their complete genome sequence annotation features provided evidence that radiation resistance genes play a central part in adaptation against extreme environmental conditions. In recent decades, excision repair genes have been indicated in considerable detail for both prokaryote and eukaryote resistance against UV-C radiation.
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Affiliation(s)
| | - Sathiyaraj Srinivasan
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 01797, Republic of Korea;
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11
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Rollo F, Martins GD, Gouveia AG, Ithurbide S, Servant P, Romão CV, Moe E. Insights into the role of three Endonuclease III enzymes for oxidative stress resistance in the extremely radiation resistant bacterium Deinococcus radiodurans. Front Microbiol 2023; 14:1266785. [PMID: 37771704 PMCID: PMC10523315 DOI: 10.3389/fmicb.2023.1266785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 08/29/2023] [Indexed: 09/30/2023] Open
Abstract
The extremely radiation and desiccation resistant bacterium Deinococcus radiodurans possesses three genes encoding Endonuclease III-like enzymes (DrEndoIII1, DrEndoIII2, DrEndoIII3). In vitro enzymatic activity measurements revealed that DrEndoIII2 is the main Endonuclease III in this organism, while DrEndoIII1 and 3 possess unusual and, so far, no detectable EndoIII activity, respectively. In order to understand the role of these enzymes at a cellular level, DrEndoIII knockout mutants were constructed and subjected to various oxidative stress related conditions. The results showed that the mutants are as resistant to ionizing and UV-C radiation as well as H2O2 exposure as the wild type. However, upon exposure to oxidative stress induced by methyl viologen, the knockout strains were more resistant than the wild type. The difference in resistance may be attributed to the observed upregulation of the EndoIII homologs gene expression upon addition of methyl viologen. In conclusion, our data suggest that all three EndoIII homologs are crucial for cell survival in stress conditions, since the knockout of one of the genes tend to be compensated for by overexpression of the genes encoding the other two.
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Affiliation(s)
- Filipe Rollo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Guilherme D. Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - André G. Gouveia
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Solenne Ithurbide
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif sur Yvette, France
| | - Pascale Servant
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif sur Yvette, France
| | - Célia V. Romão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Elin Moe
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
- Department of Chemistry, UiT - The Arctic University of Norway, Tromsø, Norway
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12
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Chen Y, Zhang Q, Wang D, Shu YG, Shi H. Memory Effect on the Survival of Deinococcus radiodurans after Exposure in Near Space. Microbiol Spectr 2023; 11:e0347422. [PMID: 36749041 PMCID: PMC10100890 DOI: 10.1128/spectrum.03474-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 01/16/2023] [Indexed: 02/08/2023] Open
Abstract
Near space (20 to 100 km in altitude) is an extreme environment with high radiation and extreme cold, making it difficult for organisms to survive. However, many studies had shown that there were still microbes living in this extremely harsh environment. It was particularly important to study which factors affected the survival of microorganisms living in near space after exposure to irradiation, as this was related to many studies, such as studies of radioresistance mechanisms, panspermia hypothesis, long-distance microbial transfer, and developing extraterrestrial habitats. Survival after radiation was probably influenced by the growth condition before radiation, which is called the memory effect. In this research, we used different growth conditions to affect the growth of Deinococcus radiodurans and lyophilized bacteria in exponential phase to maintain the physiological state at this stage. Then high-altitude scientific balloon exposure experiments were carried out by using the Chinese Academy of Sciences Balloon-Borne Astrobiology Platform (CAS-BAP) at Dachaidan, Qinghai, China (37°44'N, 95°21'E). The aim was to investigate which factors influence survival after near-space exposure. The results suggested that there was a memory effect on the survival of D. radiodurans after exposure. If the differences in growth rate were caused by differences in nutrition, the survival rate and growth rate were positively correlated. Moreover, the addition of paraquat and Mn2+ during the growth phase can also increase survival. This finding may help to deepen the understanding of the mechanics of radiation protection and provide relevant evidence for many studies, such as of long-distance transfer of microorganisms in near space. IMPORTANCE Earth's near space is an extreme environment with high radiation and extreme cold. Which factors affect the survival of microbes in near space is related to many studies, such as studies of radioresistance mechanisms, panspermia hypothesis, long-distance microbial transfer, and developing extraterrestrial habitats. We performed several exposure experiments with Deinococcus radiodurans in near space to investigate which factors influence the survival rate after near-space exposure; that is, there was a relationship between survival after radiation and the growth condition before radiation. The results suggested that there was a memory effect on the survival of D. radiodurans after exposure. This finding may help to deepen the understanding of the mechanism of radiation protection and provide relevant evidence for many studies, such as of long-distance transfer of microorganisms in near space.
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Affiliation(s)
- Yining Chen
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qing Zhang
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China
| | - Deyu Wang
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yao-Gen Shu
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
| | - Hualin Shi
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
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13
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Slaven JE, Wilkerson M, Soltis AR, Rittase WB, Bradfield DT, Bylicky M, Cary L, Tsioplaya A, Bouten R, Dalgard C, Day RM. Transcriptomic Profiling and Pathway Analysis of Mesenchymal Stem Cells Following Low Dose-Rate Radiation Exposure. Antioxidants (Basel) 2023; 12:antiox12020241. [PMID: 36829800 PMCID: PMC9951969 DOI: 10.3390/antiox12020241] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Low dose-rate radiation exposure can occur in medical imaging, as background from environmental or industrial radiation, and is a hazard of space travel. In contrast with high dose-rate radiation exposure that can induce acute life-threatening syndromes, chronic low-dose radiation is associated with Chronic Radiation Syndrome (CRS), which can alter environmental sensitivity. Secondary effects of chronic low dose-rate radiation exposure include circulatory, digestive, cardiovascular, and neurological diseases, as well as cancer. Here, we investigated 1-2 Gy, 0.66 cGy/h, 60Co radiation effects on primary human mesenchymal stem cells (hMSC). There was no significant induction of apoptosis or DNA damage, and cells continued to proliferate. Gene ontology (GO) analysis of transcriptome changes revealed alterations in pathways related to cellular metabolism (cholesterol, fatty acid, and glucose metabolism), extracellular matrix modification and cell adhesion/migration, and regulation of vasoconstriction and inflammation. Interestingly, there was increased hypoxia signaling and increased activation of pathways regulated by iron deficiency, but Nrf2 and related genes were reduced. The data were validated in hMSC and human lung microvascular endothelial cells using targeted qPCR and Western blotting. Notably absent in the GO analysis were alteration pathways for DNA damage response, cell cycle inhibition, senescence, and pro-inflammatory response that we previously observed for high dose-rate radiation exposure. Our findings suggest that cellular gene transcription response to low dose-rate ionizing radiation is fundamentally different compared to high-dose-rate exposure. We hypothesize that cellular response to hypoxia and iron deficiency are driving processes, upstream of the other pathway regulation.
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Affiliation(s)
- John E. Slaven
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Rd., Bethesda, MD 20814, USA
| | - Matthew Wilkerson
- Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Anthony R. Soltis
- Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - W. Bradley Rittase
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Rd., Bethesda, MD 20814, USA
| | - Dmitry T. Bradfield
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Rd., Bethesda, MD 20814, USA
| | - Michelle Bylicky
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Rd., Bethesda, MD 20814, USA
| | - Lynnette Cary
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Alena Tsioplaya
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Roxane Bouten
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Rd., Bethesda, MD 20814, USA
| | - Clifton Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Regina M. Day
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Rd., Bethesda, MD 20814, USA
- Correspondence: ; Tel.: +1-301-295-3236; Fax: +1-301-295-3220
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14
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Horne WH, Volpe RP, Korza G, DePratti S, Conze IH, Shuryak I, Grebenc T, Matrosova VY, Gaidamakova EK, Tkavc R, Sharma A, Gostinčar C, Gunde-Cimerman N, Hoffman BM, Setlow P, Daly MJ. Effects of Desiccation and Freezing on Microbial Ionizing Radiation Survivability: Considerations for Mars Sample Return. ASTROBIOLOGY 2022; 22:1337-1350. [PMID: 36282180 PMCID: PMC9618380 DOI: 10.1089/ast.2022.0065] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Increasingly, national space agencies are expanding their goals to include Mars exploration with sample return. To better protect Earth and its biosphere from potential extraterrestrial sources of contamination, as set forth in the Outer Space Treaty of 1967, international efforts to develop planetary protection measures strive to understand the danger of cross-contamination processes in Mars sample return missions. We aim to better understand the impact of the martian surface on microbial dormancy and survivability. Radiation resistance of microbes is a key parameter in considering survivability of microbes over geologic times on the frigid, arid surface of Mars that is bombarded by solar and galactic cosmic radiation. We tested the influence of desiccation and freezing on the ionizing radiation survival of six model microorganisms: vegetative cells of two bacteria (Deinococcus radiodurans, Escherichia coli) and a strain of budding yeast (Saccharomyces cerevisiae); and vegetative cells and endospores of three Bacillus bacteria (B. subtilis, B. megaterium, B. thuringiensis). Desiccation and freezing greatly increased radiation survival of vegetative polyploid microorganisms when applied separately, and when combined, desiccation and freezing increased radiation survival even more so. Thus, the radiation survival threshold of polyploid D. radiodurans cells can be extended from the already high value of 25 kGy in liquid culture to an astonishing 140 kGy when the cells are both desiccated and frozen. However, such synergistic radioprotective effects of desiccation and freezing were not observed in monogenomic or digenomic Bacillus cells and endospores, which are generally sterilized by 12 kGy. This difference is associated with a critical requirement for survivability under radiation, that is, repair of genome damage caused by radiation. Deinococcus radiodurans and S. cerevisiae accumulate similarly high levels of the Mn antioxidants that are required for extreme radiation resistance, as do endospores, though they greatly exceed spores in radioresistance because they contain multiple identical genome copies, which in D. radiodurans are joined by persistent Holliday junctions. We estimate ionizing radiation survival limits of polyploid DNA-based life-forms to be hundreds of millions of years of background radiation while buried in the martian subsurface. Our findings imply that forward contamination of Mars will essentially be permanent, and backward contamination is a possibility if life ever existed on Mars.
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Affiliation(s)
- William H. Horne
- School of Medicine, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, USA
- Department of Chemistry and Life Science, United States Military Academy, West Point, New York, USA
| | - Robert P. Volpe
- School of Medicine, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - George Korza
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Sarah DePratti
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Isabel H. Conze
- School of Medicine, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, USA
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Igor Shuryak
- Center for Radiological Research, Columbia University Irving Medical Center (CUIMC), New York, New York, USA
| | - Tine Grebenc
- Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Vera Y. Matrosova
- School of Medicine, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Elena K. Gaidamakova
- School of Medicine, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Rok Tkavc
- School of Medicine, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Ajay Sharma
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - Cene Gostinčar
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | | | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Michael J. Daly
- School of Medicine, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, USA
- Member, Committee on Planetary Protection (CoPP), National Academies of Sciences, Washington, DC, USA
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15
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Marín‐Tovar Y, Serrano‐Posada H, Díaz‐Vilchis A, Rudiño‐Piñera E. PCNA from
Thermococcus gammatolerans
: A protein involved in chromosomal
DNA
metabolism intrinsically resistant at high levels of ionizing radiation. Proteins 2022; 90:1684-1698. [DOI: 10.1002/prot.26346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/17/2022] [Accepted: 04/01/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Yerli Marín‐Tovar
- Laboratorio de Bioquímica Estructural, Departamento de Medicina Molecular y Bioprocesos Instituto de Biotecnología (IBt), Universidad Nacional Autónoma de México (UNAM) Cuernavaca Mexico
| | - Hugo Serrano‐Posada
- Consejo Nacional de Ciencia y Tecnología (CONACyT), Laboratorio de Biología Sintética, Estructural y Molecular, Laboratorio de Agrobiotecnología, Tecnoparque CLQ Universidad de Colima Colima Mexico
| | - Adelaida Díaz‐Vilchis
- Laboratorio de Bioquímica Estructural, Departamento de Medicina Molecular y Bioprocesos Instituto de Biotecnología (IBt), Universidad Nacional Autónoma de México (UNAM) Cuernavaca Mexico
| | - Enrique Rudiño‐Piñera
- Laboratorio de Bioquímica Estructural, Departamento de Medicina Molecular y Bioprocesos Instituto de Biotecnología (IBt), Universidad Nacional Autónoma de México (UNAM) Cuernavaca Mexico
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16
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Sabino CP, Ribeiro MS, Wainwright M, Dos Anjos C, Sellera FP, Dropa M, Nunes NB, Brancini GTP, Braga GUL, Arana-Chavez VE, Freitas RO, Lincopan N, Baptista MS. The Biochemical Mechanisms of Antimicrobial Photodynamic Therapy. Photochem Photobiol 2022; 99:742-750. [PMID: 35913428 DOI: 10.1111/php.13685] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/22/2022] [Indexed: 11/27/2022]
Abstract
The unbridled dissemination of multidrug-resistant pathogens is a major threat to global health and urgently demands novel therapeutic alternatives. Antimicrobial photodynamic therapy (aPDT) has been developed as a promising approach to treat localized infections regardless of drug resistance profile or taxonomy. Even though this technique has been known for more than a century, discussions and speculations regarding the biochemical mechanisms of microbial inactivation have never reached a consensus on what is the primary cause of cell death. Since photochemically generated oxidants promote ubiquitous reactions with various biomolecules, researchers simply assumed that all cellular structures are equally damaged. In this study, biochemical, molecular, biological, and advanced microscopy techniques were employed to investigate whether protein, membrane or DNA damage correlates better with dose-dependent microbial inactivation kinetics. We showed that although mild membrane permeabilization and late DNA damage occur, no correlation with inactivation kinetics was found. On the other hand, protein degradation was analyzed by 3 different methods and showed a dose-dependent trend that matches microbial inactivation kinetics. Our results provide a deeper mechanistic understanding of aPDT that can guide the scientific community towards the development of optimized photosensitizing drugs and also rationally propose synergistic combinations with antimicrobial chemotherapy.
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Affiliation(s)
- Caetano P Sabino
- BioLambda, Scientific and Commercial Ltd., São Paulo, SP, Brazil, 05595-000.,Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil, 05508-000
| | - Martha S Ribeiro
- Center for Lasers and Applications, Energy and Nuclear Research Institute, São Paulo, SP, Brazil, 05508-000
| | - Mark Wainwright
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK
| | - Carolina Dos Anjos
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, SP, Brazil, 05508-270.,Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Vaccine and Immunotherapy Center, Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | - Fábio P Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, SP, Brazil, 05508-270.,School of Veterinary Medicine, Metropolitan University of Santos, Santos, SP, Brazil, 11080-300
| | - Milena Dropa
- Public Health Laboratory, School of Public Health, University of São Paulo, São Paulo, Brazil
| | - Nathalia B Nunes
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, 14040-903, Brazil
| | - Guilherme T P Brancini
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, 14040-903, Brazil
| | - Gilberto U L Braga
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, 14040-903, Brazil
| | - Victor E Arana-Chavez
- Department of Biomaterials and Oral Biology, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Raul O Freitas
- Brazilian Synchrotron Light Laboratory, Brazilian Center for Research in Energy and Materials, 13083-970, Campinas, SP, Brazil, 13083-970
| | - Nilton Lincopan
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil, 05508-000.,Department of Microbiology, Institute for Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil, 05508-000
| | - Maurício S Baptista
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, Brazil, 05513-970
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17
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Deciphering the Biological Enigma-Genomic Evolution Underlying Anhydrobiosis in the Phylum Tardigrada and the Chironomid Polypedilum vanderplanki. INSECTS 2022; 13:insects13060557. [PMID: 35735894 PMCID: PMC9224920 DOI: 10.3390/insects13060557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/13/2022] [Accepted: 06/17/2022] [Indexed: 02/04/2023]
Abstract
Anhydrobiosis, an ametabolic dehydrated state triggered by water loss, is observed in several invertebrate lineages. Anhydrobiotes revive when rehydrated, and seem not to suffer the ultimately lethal cell damage that results from severe loss of water in other organisms. Here, we review the biochemical and genomic evidence that has revealed the protectant molecules, repair systems, and maintenance pathways associated with anhydrobiosis. We then introduce two lineages in which anhydrobiosis has evolved independently: Tardigrada, where anhydrobiosis characterizes many species within the phylum, and the genus Polypedilum, where anhydrobiosis occurs in only two species. Finally, we discuss the complexity of the evolution of anhydrobiosis within invertebrates based on current knowledge, and propose perspectives to enhance the understanding of anhydrobiosis.
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18
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Dollery SJ, Harro JM, Wiggins TJ, Wille BP, Kim PC, Tobin JK, Bushnell RV, Tasker NJPER, MacLeod DA, Tobin GJ. Select Whole-Cell Biofilm-Based Immunogens Protect against a Virulent Staphylococcus Isolate in a Stringent Implant Model of Infection. Vaccines (Basel) 2022; 10:vaccines10060833. [PMID: 35746441 PMCID: PMC9231243 DOI: 10.3390/vaccines10060833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/13/2022] [Accepted: 05/19/2022] [Indexed: 12/12/2022] Open
Abstract
Many microbes of concern to human health remain without vaccines. We have developed a whole-microbe inactivation technology that enables us to rapidly inactivate large quantities of a pathogen while retaining epitopes that were destroyed by previous inactivation methods. The method that we call UVC-MDP inactivation can be used to make whole-cell vaccines with increased potency. We and others are exploring the possibility of using improved irradiation-inactivation technologies to develop whole-cell vaccines for numerous antibiotic-resistant microbes. Here, we apply UVC-MDP to produce candidate MRSA vaccines which we test in a stringent tibia implant model of infection challenged with a virulent MSRA strain. We report high levels of clearance in the model and observe a pattern of protection that correlates with the immunogen protein profile used for vaccination.
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Affiliation(s)
- Stephen J. Dollery
- Biological Mimetics, Inc., Frederick, MD 21702, USA; (T.J.W.); (J.K.T.); (R.V.B.); (N.J.P.E.R.T.); (D.A.M.); (G.J.T.)
- Correspondence:
| | - Janette M. Harro
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD 21201, USA; (J.M.H.); (B.P.W.); (P.C.K.)
| | - Taralyn J. Wiggins
- Biological Mimetics, Inc., Frederick, MD 21702, USA; (T.J.W.); (J.K.T.); (R.V.B.); (N.J.P.E.R.T.); (D.A.M.); (G.J.T.)
| | - Brendan P. Wille
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD 21201, USA; (J.M.H.); (B.P.W.); (P.C.K.)
| | - Peter C. Kim
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD 21201, USA; (J.M.H.); (B.P.W.); (P.C.K.)
| | - John K. Tobin
- Biological Mimetics, Inc., Frederick, MD 21702, USA; (T.J.W.); (J.K.T.); (R.V.B.); (N.J.P.E.R.T.); (D.A.M.); (G.J.T.)
| | - Ruth V. Bushnell
- Biological Mimetics, Inc., Frederick, MD 21702, USA; (T.J.W.); (J.K.T.); (R.V.B.); (N.J.P.E.R.T.); (D.A.M.); (G.J.T.)
| | - Naomi J. P. E. R. Tasker
- Biological Mimetics, Inc., Frederick, MD 21702, USA; (T.J.W.); (J.K.T.); (R.V.B.); (N.J.P.E.R.T.); (D.A.M.); (G.J.T.)
| | - David A. MacLeod
- Biological Mimetics, Inc., Frederick, MD 21702, USA; (T.J.W.); (J.K.T.); (R.V.B.); (N.J.P.E.R.T.); (D.A.M.); (G.J.T.)
| | - Gregory J. Tobin
- Biological Mimetics, Inc., Frederick, MD 21702, USA; (T.J.W.); (J.K.T.); (R.V.B.); (N.J.P.E.R.T.); (D.A.M.); (G.J.T.)
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19
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Vanderwaeren L, Dok R, Voordeckers K, Vandemaele L, Verstrepen KJ, Nuyts S. An Integrated Approach Reveals DNA Damage and Proteotoxic Stress as Main Effects of Proton Radiation in S. cerevisiae. Int J Mol Sci 2022; 23:ijms23105493. [PMID: 35628303 PMCID: PMC9145671 DOI: 10.3390/ijms23105493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/09/2022] [Accepted: 05/12/2022] [Indexed: 02/01/2023] Open
Abstract
Proton radiotherapy (PRT) has the potential to reduce the normal tissue toxicity associated with conventional photon-based radiotherapy (X-ray therapy, XRT) because the active dose can be more directly targeted to a tumor. Although this dosimetric advantage of PRT is well known, the molecular mechanisms affected by PRT remain largely elusive. Here, we combined the molecular toolbox of the eukaryotic model Saccharomyces cerevisiae with a systems biology approach to investigate the physiological effects of PRT compared to XRT. Our data show that the DNA damage response and protein stress response are the major molecular mechanisms activated after both PRT and XRT. However, RNA-Seq revealed that PRT treatment evoked a stronger activation of genes involved in the response to proteotoxic stress, highlighting the molecular differences between PRT and XRT. Moreover, inhibition of the proteasome resulted in decreased survival in combination with PRT compared to XRT, not only further confirming that protons induced a stronger proteotoxic stress response, but also hinting at the potential of using proteasome inhibitors in combination with proton radiotherapy in clinical settings.
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Affiliation(s)
- Laura Vanderwaeren
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium; (L.V.); (R.D.); (L.V.)
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium;
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3000 Leuven, Belgium
| | - Rüveyda Dok
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium; (L.V.); (R.D.); (L.V.)
| | - Karin Voordeckers
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium;
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3000 Leuven, Belgium
| | - Laura Vandemaele
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium; (L.V.); (R.D.); (L.V.)
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium;
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3000 Leuven, Belgium
| | - Kevin J. Verstrepen
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium;
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3000 Leuven, Belgium
- Correspondence: (K.J.V.); (S.N.); Tel.: +32-(0)16-75-1393 (K.J.V.); +32-1634-7600 (S.N.); Fax: +32-1634-7623 (S.N.)
| | - Sandra Nuyts
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium; (L.V.); (R.D.); (L.V.)
- Department of Radiation Oncology, Leuven Cancer Institute, University Hospitals Leuven, 3000 Leuven, Belgium
- Correspondence: (K.J.V.); (S.N.); Tel.: +32-(0)16-75-1393 (K.J.V.); +32-1634-7600 (S.N.); Fax: +32-1634-7623 (S.N.)
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20
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Gawne PJ, Man F, Blower PJ, T M de Rosales R. Direct Cell Radiolabeling for in Vivo Cell Tracking with PET and SPECT Imaging. Chem Rev 2022; 122:10266-10318. [PMID: 35549242 PMCID: PMC9185691 DOI: 10.1021/acs.chemrev.1c00767] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The arrival of cell-based therapies is a revolution in medicine. However, its safe clinical application in a rational manner depends on reliable, clinically applicable methods for determining the fate and trafficking of therapeutic cells in vivo using medical imaging techniques─known as in vivo cell tracking. Radionuclide imaging using single photon emission computed tomography (SPECT) or positron emission tomography (PET) has several advantages over other imaging modalities for cell tracking because of its high sensitivity (requiring low amounts of probe per cell for imaging) and whole-body quantitative imaging capability using clinically available scanners. For cell tracking with radionuclides, ex vivo direct cell radiolabeling, that is, radiolabeling cells before their administration, is the simplest and most robust method, allowing labeling of any cell type without the need for genetic modification. This Review covers the development and application of direct cell radiolabeling probes utilizing a variety of chemical approaches: organic and inorganic/coordination (radio)chemistry, nanomaterials, and biochemistry. We describe the key early developments and the most recent advances in the field, identifying advantages and disadvantages of the different approaches and informing future development and choice of methods for clinical and preclinical application.
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Affiliation(s)
- Peter J Gawne
- School of Biomedical Engineering & Imaging Sciences, King's College London, St Thomas' Hospital, London, SE1 7EH, U.K
| | - Francis Man
- School of Biomedical Engineering & Imaging Sciences, King's College London, St Thomas' Hospital, London, SE1 7EH, U.K.,Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King's College London, London, SE1 9NH, U.K
| | - Philip J Blower
- School of Biomedical Engineering & Imaging Sciences, King's College London, St Thomas' Hospital, London, SE1 7EH, U.K
| | - Rafael T M de Rosales
- School of Biomedical Engineering & Imaging Sciences, King's College London, St Thomas' Hospital, London, SE1 7EH, U.K
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Thiol Reductases in Deinococcus Bacteria and Roles in Stress Tolerance. Antioxidants (Basel) 2022; 11:antiox11030561. [PMID: 35326211 PMCID: PMC8945050 DOI: 10.3390/antiox11030561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/11/2022] [Accepted: 03/13/2022] [Indexed: 12/10/2022] Open
Abstract
Deinococcus species possess remarkable tolerance to extreme environmental conditions that generate oxidative damage to macromolecules. Among enzymes fulfilling key functions in metabolism regulation and stress responses, thiol reductases (TRs) harbour catalytic cysteines modulating the redox status of Cys and Met in partner proteins. We present here a detailed description of Deinococcus TRs regarding gene occurrence, sequence features, and physiological functions that remain poorly characterised in this genus. Two NADPH-dependent thiol-based systems are present in Deinococcus. One involves thioredoxins, disulfide reductases providing electrons to protein partners involved notably in peroxide scavenging or in preserving protein redox status. The other is based on bacillithiol, a low-molecular-weight redox molecule, and bacilliredoxin, which together protect Cys residues against overoxidation. Deinococcus species possess various types of thiol peroxidases whose electron supply depends either on NADPH via thioredoxins or on NADH via lipoylated proteins. Recent data gained on deletion mutants confirmed the importance of TRs in Deinococcus tolerance to oxidative treatments, but additional investigations are needed to delineate the redox network in which they operate, and their precise physiological roles. The large palette of Deinococcus TR representatives very likely constitutes an asset for the maintenance of redox homeostasis in harsh stress conditions.
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22
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do Prado-Silva L, Brancini GT, Braga GÚ, Liao X, Ding T, Sant’Ana AS. Antimicrobial photodynamic treatment (aPDT) as an innovative technology to control spoilage and pathogenic microorganisms in agri-food products: An updated review. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108527] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Cai J, Pan C, Zhao Y, Xu H, Tian B, Wang L, Hua Y. DRJAMM Is Involved in the Oxidative Resistance in Deinococcus radiodurans. Front Microbiol 2022; 12:756867. [PMID: 35154022 PMCID: PMC8832034 DOI: 10.3389/fmicb.2021.756867] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 12/23/2021] [Indexed: 12/13/2022] Open
Abstract
Proteins containing JAB1/MPN/MOV34 metalloenzyme (JAMM/MPN+) domains that have Zn2+-dependent deubiquitinase (DUB) activity are ubiquitous across among all domains of life. Recently, a homolog in Deinococcus radiodurans, DRJAMM, was reported to possess the ability to cleave DRMoaD-MoaE. However, the detailed biochemical characteristics of DRJAMM in vitro and its biological mechanism in vivo remain unclear. Here, we show that DRJAMM has an efficient in vitro catalytic activity in the presence of Mn2+, Ca2+, Mg2+, and Ni2+ in addition to the well-reported Zn2+, and strong adaptability at a wide range of temperatures. Disruption of drJAMM led to elevated sensitivity in response to H2O2in vivo compared to the wild-type R1. In particular, the expression level of MoaE, a product of DRJAMM cleavage, was also increased under H2O2 stress, indicating that DRJAMM is needed in the antioxidant process. Moreover, DRJAMM was also demonstrated to be necessary for dimethyl sulfoxide respiratory system in D. radiodurans. These data suggest that DRJAMM plays key roles in the process of oxidative resistance in D. radiodurans with multiple-choice of metal ions and temperatures.
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A Geant4-DNA Evaluation of Radiation-Induced DNA Damage on a Human Fibroblast. Cancers (Basel) 2021; 13:cancers13194940. [PMID: 34638425 PMCID: PMC8508455 DOI: 10.3390/cancers13194940] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/21/2021] [Accepted: 09/26/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary DNA damage caused by ionizing radiation in a human fibroblast cell evaluated by the Geant4-DNA Monte Carlo toolkit is presented. A validation study using a computational geometric human DNA model was then carried out, and the calculated DNA damage as a function of particle type and energy is presented. The results of this work showed a significant improvement on past work and were consistent with recent radiobiological experimental data, such as damage yields. This work and the developed methodology could impact a broad number of research fields in which the understanding of radiation effects is crucial, such as cancer radiotherapy, space science, and medical physics. Abstract Accurately modeling the radiobiological mechanisms responsible for the induction of DNA damage remains a major scientific challenge, particularly for understanding the effects of low doses of ionizing radiation on living beings, such as the induction of carcinogenesis. A computational approach based on the Monte Carlo technique to simulate track structures in a biological medium is currently the most reliable method for calculating the early effects induced by ionizing radiation on DNA, the primary cellular target of such effects. The Geant4-DNA Monte Carlo toolkit can simulate not only the physical, but also the physico-chemical and chemical stages of water radiolysis. These stages can be combined with simplified geometric models of biological targets, such as DNA, to assess direct and indirect early DNA damage. In this study, DNA damage induced in a human fibroblast cell was evaluated using Geant4-DNA as a function of incident particle type (gammas, protons, and alphas) and energy. The resulting double-strand break yields as a function of linear energy transfer closely reproduced recent experimental data. Other quantities, such as fragment length distribution, scavengeable damage fraction, and time evolution of damage within an analytical repair model also supported the plausibility of predicting DNA damage using Geant4-DNA.The complete simulation chain application “molecularDNA”, an example for users of Geant4-DNA, will soon be distributed through Geant4.
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Eugénie N, Zivanovic Y, Lelandais G, Coste G, Bouthier de la Tour C, Bentchikou E, Servant P, Confalonieri F. Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium Deinococcus radiodurans by Integrative Genomic Analyses. Cells 2021; 10:cells10102536. [PMID: 34685516 PMCID: PMC8533742 DOI: 10.3390/cells10102536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 12/02/2022] Open
Abstract
Numerous genes are overexpressed in the radioresistant bacterium Deinococcus radiodurans after exposure to radiation or prolonged desiccation. It was shown that the DdrO and IrrE proteins play a major role in regulating the expression of approximately twenty genes. The transcriptional repressor DdrO blocks the expression of these genes under normal growth conditions. After exposure to genotoxic agents, the IrrE metalloprotease cleaves DdrO and relieves gene repression. At present, many questions remain, such as the number of genes regulated by DdrO. Here, we present the first ChIP-seq analysis performed at the genome level in Deinococcus species coupled with RNA-seq, which was achieved in the presence or not of DdrO. We also resequenced our laboratory stock strain of D. radiodurans R1 ATCC 13939 to obtain an accurate reference for read alignments and gene expression quantifications. We highlighted genes that are directly under the control of this transcriptional repressor and showed that the DdrO regulon in D. radiodurans includes numerous other genes than those previously described, including DNA and RNA metabolism proteins. These results thus pave the way to better understand the radioresistance pathways encoded by this bacterium and to compare the stress-induced responses mediated by this pair of proteins in diverse bacteria.
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Yamasaki A, Suzuki M, Funayama T, Moriwaki T, Sakashita T, Kobayashi Y, Zhang-Akiyama QM. High-Dose Irradiation Inhibits Motility and Induces Autophagy in Caenorhabditis elegans. Int J Mol Sci 2021; 22:ijms22189810. [PMID: 34575973 PMCID: PMC8467272 DOI: 10.3390/ijms22189810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
Radiation damages many cellular components and disrupts cellular functions, and was previously reported to impair locomotion in the model organism Caenorhabditis elegans. However, the response to even higher doses is not clear. First, to investigate the effects of high-dose radiation on the locomotion of C. elegans, we investigated the dose range that reduces whole-body locomotion or leads to death. Irradiation was performed in the range of 0-6 kGy. In the crawling analysis, motility decreased after irradiation in a dose-dependent manner. Exposure to 6 kGy of radiation affected crawling on agar immediately and caused the complete loss of motility. Both γ-rays and carbon-ion beams significantly reduced crawling motility at 3 kGy. Next, swimming in buffer was measured as a motility index to assess the response over time after irradiation and motility similarly decreased. However, swimming partially recovered 6 h after irradiation with 3 kGy of γ-rays. To examine the possibility of a recovery mechanism, in situ GFP reporter assay of the autophagy-related gene lgg-1 was performed. The fluorescence intensity was stronger in the anterior half of the body 7 h after irradiation with 3 kGy of γ-rays. GFP::LGG-1 induction was observed in the pharynx, neurons along the body, and the intestine. Furthermore, worms were exposed to region-specific radiation with carbon-ion microbeams and the trajectory of crawling was measured by image processing. Motility was lower after anterior-half body irradiation than after posterior-half body irradiation. This further supported that the anterior half of the body is important in the locomotory response to radiation.
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Affiliation(s)
- Akira Yamasaki
- Laboratory of Stress Response Biology, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan; (A.Y.); (T.M.)
- Department of Radiation-Applied Biology Research, Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology (QST-Takasaki), 1233 Watanuki, Takasaki 370-1292, Japan; (T.F.); (T.S.); (Y.K.)
| | - Michiyo Suzuki
- Department of Radiation-Applied Biology Research, Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology (QST-Takasaki), 1233 Watanuki, Takasaki 370-1292, Japan; (T.F.); (T.S.); (Y.K.)
- Correspondence: (M.S.); (Q.-M.Z.-A.); Tel.: +81-(0)27-346-9114 (M.S.); +81-(0)75-753-4097 (Q.-M.Z.-A.); Fax: +81-(0)27-346-9353 (M.S.); +81-(0)75-753-4087 (Q.-M.Z.-A.)
| | - Tomoo Funayama
- Department of Radiation-Applied Biology Research, Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology (QST-Takasaki), 1233 Watanuki, Takasaki 370-1292, Japan; (T.F.); (T.S.); (Y.K.)
| | - Takahito Moriwaki
- Laboratory of Stress Response Biology, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan; (A.Y.); (T.M.)
- Department of Molecular and Genetic Medicine, Kawasaki Medical School, Okayama 701-0192, Japan
| | - Tetsuya Sakashita
- Department of Radiation-Applied Biology Research, Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology (QST-Takasaki), 1233 Watanuki, Takasaki 370-1292, Japan; (T.F.); (T.S.); (Y.K.)
| | - Yasuhiko Kobayashi
- Department of Radiation-Applied Biology Research, Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology (QST-Takasaki), 1233 Watanuki, Takasaki 370-1292, Japan; (T.F.); (T.S.); (Y.K.)
| | - Qiu-Mei Zhang-Akiyama
- Laboratory of Stress Response Biology, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan; (A.Y.); (T.M.)
- Correspondence: (M.S.); (Q.-M.Z.-A.); Tel.: +81-(0)27-346-9114 (M.S.); +81-(0)75-753-4097 (Q.-M.Z.-A.); Fax: +81-(0)27-346-9353 (M.S.); +81-(0)75-753-4087 (Q.-M.Z.-A.)
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Kumar G, Dutta P, Parihar VK, Chamallamudi MR, Kumar N. Radiotherapy and Its Impact on the Nervous System of Cancer Survivors. CNS & NEUROLOGICAL DISORDERS-DRUG TARGETS 2021; 19:374-385. [PMID: 32640964 DOI: 10.2174/1871527319666200708125741] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 05/07/2020] [Accepted: 05/10/2020] [Indexed: 12/12/2022]
Abstract
Radiotherapy is routinely used for the treatment of nearly all brain tumors, but it may lead to progressive and debilitating impairments of cognitive function. The growing evidence supports the fact that radiation exposure to CNS disrupts diverse cognitive functions including learning, memory, processing speed, attention and executive functions. The present review highlights the types of radiotherapy and the possible mechanisms of cognitive deficits and neurotoxicity following radiotherapy. The review summarizes the articles from Scopus, PubMed, and Web of science search engines. Radiation therapy uses high-powered x-rays, particles, or radioactive seeds to kill cancer cells, with minimal damage to healthy cells. While radiotherapy has yielded relative success in the treatment of cancer, patients are often plagued with unwanted and even debilitating side effects from the treatment, which can lead to dose reduction or even cessation of treatment. Little is known about the underlying mechanisms responsible for the development of these behavioral toxicities; however, neuroinflammation is widely considered as one of the major mechanisms responsible for radiotherapy-induced toxicities. The present study reviews the different types of radiotherapy available for the treatment of various types of cancers and their associated neurological complications. It also summarizes the doses of radiations used in the variety of radiotherapy, and their early and delayed side effects. Special emphasis is given to the effects of various types of radiations or late side effects on cognitive impairments.
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Affiliation(s)
- Gautam Kumar
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal-576104, Karnataka, India
| | - Priyadarshini Dutta
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal-576104, Karnataka, India
| | - Vipan K Parihar
- Department of Radiation Oncology, University of California, Irvine, CA 92697- 2695, United States
| | - Mallikarjuna R Chamallamudi
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal-576104, Karnataka, India
| | - Nitesh Kumar
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal-576104, Karnataka, India
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Stachowski TR, Snell ME, Snell EH. A SAXS-based approach to rationally evaluate radical scavengers - toward eliminating radiation damage in solution and crystallographic studies. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1309-1320. [PMID: 34475280 PMCID: PMC8415334 DOI: 10.1107/s1600577521004045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/15/2021] [Indexed: 05/30/2023]
Abstract
X-ray-based techniques are a powerful tool in structural biology but the radiation-induced chemistry that results can be detrimental and may mask an accurate structural understanding. In the crystallographic case, cryocooling has been employed as a successful mitigation strategy but also has its limitations including the trapping of non-biological structural states. Crystallographic and solution studies performed at physiological temperatures can reveal otherwise hidden but relevant conformations, but are limited by their increased susceptibility to radiation damage. In this case, chemical additives that scavenge the species generated by radiation can mitigate damage but are not always successful and the mechanisms are often unclear. Using a protein designed to undergo a large-scale structural change from breakage of a disulfide bond, radiation damage can be monitored with small-angle X-ray scattering. Using this, we have quantitatively evaluated how three scavengers commonly used in crystallographic experiments - sodium nitrate, cysteine, and ascorbic acid - perform in solution at 10°C. Sodium nitrate was the most effective scavenger and completely inhibited fragmentation of the disulfide bond at a lower concentration (500 µM) compared with cysteine (∼5 mM) while ascorbic acid performed best at 5 mM but could only reduce fragmentation by ∼75% after a total accumulated dose of 792 Gy. The relative effectiveness of each scavenger matches their reported affinities for solvated electrons. Saturating concentrations of each scavenger shifted fragmentation from first order to a zeroth-order process, perhaps indicating the direct contribution of photoabsorption. The SAXS-based method can detect damage at X-ray doses far lower than those accessible crystallographically, thereby providing a detailed picture of scavenger processes. The solution results are also in close agreement with what is known about scavenger performance and mechanism in a crystallographic setting and suggest that a link can be made between the damage phenomenon in the two scenarios. Therefore, our engineered approach might provide a platform for more systematic and comprehensive screening of radioprotectants that can directly inform mitigation strategies for both solution and crystallographic experiments, while also clarifying fundamental radiation damage mechanisms.
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Affiliation(s)
- Timothy R. Stachowski
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St, Buffalo, NY 14203, USA
- Cell Stress Biology, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA
| | - Mary E. Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St, Buffalo, NY 14203, USA
| | - Edward H. Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St, Buffalo, NY 14203, USA
- Materials Design and Innovation, State University at New York at Buffalo, 700 Ellicott St, Buffalo, NY 14203, USA
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Li T, Cao Y, Li B, Dai R. The biological effects of radiation-induced liver damage and its natural protective medicine. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 167:87-95. [PMID: 34216638 DOI: 10.1016/j.pbiomolbio.2021.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 06/04/2021] [Accepted: 06/29/2021] [Indexed: 12/27/2022]
Abstract
The biological damage caused by the environmental factors such as radiation and its control methods are one of the frontiers of life science research that has received widespread attention. Ionizing radiation can directly interact with target molecules (such as DNA, proteins and lipids) or decomposed by radiation from water, leading to changes in oxidative events and biological activities in cells. Liver is a radiation-sensitive organ, and its radiosensitivity is second only to bone marrow, lymph, gastrointestinal tissue, gonads, embryos and kidneys. In addition, as a key organ of mammals, liver performs a series of functions, including the production of bile, the metabolism of nutrients, the elimination of waste, the storage of glycogen, and the synthesis of proteins. Therefore, liver is prone to various pathophysiological changes. In this review, the effects of radiation on liver injury, its pathogenesis, bystander effect and the natural traditional Chinese medicine to protect the radiation induced liver damage are discussed.
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Affiliation(s)
- Tianmei Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Yanlu Cao
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Bo Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China; Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, 100081, China.
| | - Rongji Dai
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
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Gabarty A, Abas A, Salem HM, El-Sonbaty SM, Farghaly DS, Awad HA. Assessment of combining biosynthesized silver nanoparticles using Bacillus thuringiensis and gamma irradiation for controlling Pectinophora gossypiella (saunders) (lepidoptera: Gelechiidae). Int J Radiat Biol 2021; 97:1299-1315. [PMID: 34032553 DOI: 10.1080/09553002.2021.1934747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
PURPOSE Combining gamma irradiation and nanotechnology has become one of the most promising new approaches for area-wide (AW) pest management in recent years. The laboratory trials were conducted to determine the combining effects of BT-AgNPs and gamma irradiation for controlling P. gossypiella. Radio-sensitivity of male pupae at different doses of gamma radiation and the effectiveness of biosynthesized silver nanoparticles using Bacillus thuringiensis on larval instar were assayed. Additionally, the ultrastructure changes on the alimentary canal of 4th instar larvae were studied to evaluate the impact of the combined approach at a cellular level. MATERIALS AND METHODS Laboratory- rearing technique was used for rearing Pectinophora gossypiella. The irradiation process was achieved at Co60 - Gamma Chamber (4000 A). Alanine dosimeters were used for measuring the average absorbed dose and dose mapping. Preparation of Silver nanoparticles (AgNPs) using Bacillus thuringiensis (Bt) and their characterization has been investigated. The treated 4th instar larvae by gamma irradiation or ∕and BT-AgNPs were dissected under the stereo microscope. The alimentary canal was obtained anatomically and Transmission Electron Microscope) was used in examining the stained sections. RESULTS Based on the nonhatching eggs produced by irradiated males' pupae, the values of effective doses were calculated. The effective doses ranged from 16 to 291 Gy for the ED25 - ED75. The sterility index reached 74.1% when irradiated with males by 291 Gy crossed with nonirradiated females and the adult emergence decreased to be 35.3%. The insecticidal potential of Bt-AgNPs on the 2nd and 4th larval instars was dose-dependent and its LC50 toxicity value was 0. 3 and 0. 4 mg/ml, respectively. The lethal concentration LC50 of the 2nd instar larvae increased the larval and pupal mortality to 55% and 44.4%, respectively, and reduced the adult emergence to be 55.6%. The combining effects of Bt-AgNPs with 291 Gy induced 100% pupae mortality and there was no adult emergence in F1 generation. Such effects also severed the ultrastructure deformity of the midgut of the 4th instar larvae after the two-day post-treatment. CONCLUSIONS The combining effects are recommended as an effective IPM program to control P. gossypiella by releasing sterile males (derived from pupae irradiated with 291 Gy) crossing with the normal females in the field, and reducing the fertility of the population to 31.2%. Subsequently, the resulted larvae treated with LC50 of Bt-AgNPs prevented the adult emergence and stopped the life cycle of P. gossypiella.
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Affiliation(s)
- Ahlam Gabarty
- Natural Products Department, National Center for Radiation Research and Technology, Egyptian Atomic Energy Authority, Cairo, Egypt
| | - Afaf Abas
- Department of Zoology and Entomology, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Hedaya M Salem
- Natural Products Department, National Center for Radiation Research and Technology, Egyptian Atomic Energy Authority, Cairo, Egypt
| | - Sawsan M El-Sonbaty
- Radiation Microbiology Research Department, National Center for Radiation Research and Technology, Egyptian Atomic Energy Authority, Cairo, Egypt
| | - Doaa S Farghaly
- Department of Zoology and Entomology, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Heba A Awad
- Department of Zoology and Entomology, Faculty of Science, Al-Azhar University, Cairo, Egypt
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Experimental evolution of extremophile resistance to ionizing radiation. Trends Genet 2021; 37:830-845. [PMID: 34088512 DOI: 10.1016/j.tig.2021.04.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 11/22/2022]
Abstract
A growing number of known species possess a remarkable characteristic - extreme resistance to the effects of ionizing radiation (IR). This review examines our current understanding of how organisms can adapt to and survive exposure to IR, one of the most toxic stressors known. The study of natural extremophiles such as Deinococcus radiodurans has revealed much. However, the evolution of Deinococcus was not driven by IR. Another approach, pioneered by Evelyn Witkin in 1946, is to utilize experimental evolution. Contributions to the IR-resistance phenotype affect multiple aspects of cell physiology, including DNA repair, removal of reactive oxygen species, the structure and packaging of DNA and the cell itself, and repair of iron-sulfur centers. Based on progress to date, we overview the diversity of mechanisms that can contribute to biological IR resistance arising as a result of either natural or experimental evolution.
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Repar J, Zahradka D, Sović I, Zahradka K. Characterization of gross genome rearrangements in Deinococcus radiodurans recA mutants. Sci Rep 2021; 11:10939. [PMID: 34035321 PMCID: PMC8149714 DOI: 10.1038/s41598-021-89173-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/21/2021] [Indexed: 02/04/2023] Open
Abstract
Genome stability in radioresistant bacterium Deinococcus radiodurans depends on RecA, the main bacterial recombinase. Without RecA, gross genome rearrangements occur during repair of DNA double-strand breaks. Long repeated (insertion) sequences have been identified as hot spots for ectopic recombination leading to genome rearrangements, and single-strand annealing (SSA) postulated to be the most likely mechanism involved in this process. Here, we have sequenced five isolates of D. radiodurans recA mutant carrying gross genome rearrangements to precisely characterize the rearrangements and to elucidate the underlying repair mechanism. The detected rearrangements consisted of large deletions in chromosome II in all the sequenced recA isolates. The mechanism behind these deletions clearly differs from the classical SSA; it utilized short (4-11 bp) repeats as opposed to insertion sequences or other long repeats. Moreover, it worked over larger linear DNA distances from those previously tested. Our data are most compatible with alternative end-joining, a recombination mechanism that operates in eukaryotes, but is also found in Escherichia coli. Additionally, despite the recA isolates being preselected for different rearrangement patterns, all identified deletions were found to overlap in a 35 kb genomic region. We weigh the evidence for mechanistic vs. adaptive reasons for this phenomenon.
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Affiliation(s)
- Jelena Repar
- grid.4905.80000 0004 0635 7705Laboratory for Molecular Microbiology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Davor Zahradka
- grid.4905.80000 0004 0635 7705Laboratory for Molecular Microbiology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ivan Sović
- Digital BioLogic d.o.o, Ivanić-Grad, Croatia
| | - Ksenija Zahradka
- grid.4905.80000 0004 0635 7705Laboratory for Molecular Microbiology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
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Sah DK, Rai Y, Chauhan A, Kumari N, Chaturvedi MM, Bhatt AN. Sphingosine kinase inhibitor, SKI-II confers protection against the ionizing radiation by maintaining redox homeostasis most likely through Nrf2 signaling. Life Sci 2021; 278:119543. [PMID: 33933460 DOI: 10.1016/j.lfs.2021.119543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/15/2021] [Accepted: 04/23/2021] [Indexed: 10/21/2022]
Abstract
Exposure to ionizing radiation (IR) set a series of deleterious events causing acute radiation syndrome and mortality, posing the need for a potent and safe radio-protective drug. IR induces cell death predominantly by causing oxidative stress and macromolecular damage. The pre-existing antioxidant defence machinery of the cellular system plays a crucial role in protecting the cells against oxidative stress by activation of Nrf2. The current study was undertaken to investigate the radio-protective potential of sphingosine kinase inhibitor (SKI-II), which was demonstrated to activate Nrf2 signaling. The safety and efficacy of SKI-II were evaluated with cell cytotoxicity, proliferation index, and clonogenic survival assays in different cell lines, namely Raw 264.7, INT-407, IEC-6 and NIH/3T3 cell lines. A safe dose of SKI-II was found radio-protective in all the cell lines linked with the activated antioxidant defence system, thereby resulting in the amelioration of IR induced oxidative stress. SKI-II pretreatment also significantly reduced DNA damage, micronuclei expression, and accelerated DNA repair kinetics as compared to IR exposed cells. Reduced oxidative stress and enhanced DNA repair significantly reduced apoptosis and suppressed the pro-death signaling associated with IR exposure. Furthermore, the in-vitro observation was verified in the in-vivo model (C57 BL/6). The Intra-peritoneal (IP) administration of SKI-II, 2 h before a lethal dose of IR exposure (7.5 Gy) resulted in 75% survival. These results imply that SKI-II ameliorates IR-induced oxidative stress and cell death by inducing anti-oxidant defence system and DNA repair pathways, thus strengthening its potential to be used as radiation countermeasure.
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Affiliation(s)
- Dhananjay Kumar Sah
- Institute of Nuclear Medicine & Allied Sciences, DRDO, Delhi, India; Department of Zoology, University of Delhi, Delhi, India
| | - Yogesh Rai
- Institute of Nuclear Medicine & Allied Sciences, DRDO, Delhi, India
| | - Ankit Chauhan
- Institute of Nuclear Medicine & Allied Sciences, DRDO, Delhi, India
| | - Neeraj Kumari
- Institute of Nuclear Medicine & Allied Sciences, DRDO, Delhi, India
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Bruckbauer ST, Minkoff BB, Sussman MR, Cox MM. Proteome Damage Inflicted by Ionizing Radiation: Advancing a Theme in the Research of Miroslav Radman. Cells 2021; 10:cells10040954. [PMID: 33924085 PMCID: PMC8074248 DOI: 10.3390/cells10040954] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 02/03/2023] Open
Abstract
Oxidative proteome damage has been implicated as a major contributor to cell death and aging. Protein damage and aging has been a particular theme of the recent research of Miroslav Radman. However, the study of how cellular proteins are damaged by oxidative processes is still in its infancy. Here we examine oxidative changes in the proteomes of four bacterial populations—wild type E. coli, two isolates from E. coli populations evolved for high levels of ionizing radiation (IR) resistance, and D. radiodurans—immediately following exposure to 3000 Gy of ionizing radiation. By a substantial margin, the most prominent intracellular oxidation events involve hydroxylation of methionine residues. Significant but much less frequent are carbonylation events on tyrosine and dioxidation events on tryptophan. A few proteins are exquisitely sensitive to targeted oxidation events, notably the active site of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in E. coli. Extensive experimental evolution of E. coli for IR resistance has decreased overall proteome sensitivity to oxidation but not to the level seen in D. radiodurans. Many observed oxidation events may reflect aspects of protein structure and/or exposure of protein surfaces to water. Proteins such as GAPDH and possibly Ef-Tu may have an evolved sensitivity to oxidation by H2O2.
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Affiliation(s)
- Steven T. Bruckbauer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; (S.T.B.); (M.R.S.)
| | - Benjamin B. Minkoff
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Michael R. Sussman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; (S.T.B.); (M.R.S.)
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; (S.T.B.); (M.R.S.)
- Correspondence:
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Coexistence of SOS-Dependent and SOS-Independent Regulation of DNA Repair Genes in Radiation-Resistant Deinococcus Bacteria. Cells 2021; 10:cells10040924. [PMID: 33923690 PMCID: PMC8072749 DOI: 10.3390/cells10040924] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 11/28/2022] Open
Abstract
Deinococcus bacteria are extremely resistant to radiation and able to repair a shattered genome in an essentially error-free manner after exposure to high doses of radiation or prolonged desiccation. An efficient, SOS-independent response mechanism to induce various DNA repair genes such as recA is essential for radiation resistance. This pathway, called radiation/desiccation response, is controlled by metallopeptidase IrrE and repressor DdrO that are highly conserved in Deinococcus. Among various Deinococcus species, Deinococcus radiodurans has been studied most extensively. Its genome encodes classical DNA repair proteins for error-free repair but no error-prone translesion DNA polymerases, which may suggest that absence of mutagenic lesion bypass is crucial for error-free repair of massive DNA damage. However, many other radiation-resistant Deinococcus species do possess translesion polymerases, and radiation-induced mutagenesis has been demonstrated. At least dozens of Deinococcus species contain a mutagenesis cassette, and some even two cassettes, encoding error-prone translesion polymerase DnaE2 and two other proteins, ImuY and ImuB-C, that are probable accessory factors required for DnaE2 activity. Expression of this mutagenesis cassette is under control of the SOS regulators RecA and LexA. In this paper, we review both the RecA/LexA-controlled mutagenesis and the IrrE/DdrO-controlled radiation/desiccation response in Deinococcus.
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Dynamic Polyphosphate Metabolism Coordinating with Manganese Ions Defends against Oxidative Stress in the Extreme Bacterium Deinococcus radiodurans. Appl Environ Microbiol 2021; 87:AEM.02785-20. [PMID: 33452031 DOI: 10.1128/aem.02785-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/08/2021] [Indexed: 02/05/2023] Open
Abstract
Deinococcus radiodurans is an extreme bacterium with unparalleled resistance to oxidative stresses. Accumulation of intracellular Mn2+ complexing with small metabolites is the key contributor to the tolerance of D. radiodurans against oxidative stress. However, the intracellular reservoir of Mn ions and homeostatic regulation of the Mn complex in D. radiodurans remain unclear. We identified an evolutionarily ancient and negatively charged phosphate polymer (polyphosphate [PolyP]) in D. radiodurans We investigated PolyP metabolism in the response of D. radiodurans to oxidative stress. The genes dr1939, encoding polyphosphatase kinase (PPKDr; the subscript "Dr" refers to D. radiodurans), and dra0185, encoding exopolyphosphatase (PPXDr), were identified. PPXDr is a novel exopolyphosphatase with a cofactor preference to Mn2+, which enhances the dimerization and activity of PPXDr to allow the effective cleavage of PolyP-Mn. PPKDr and PPXDr exhibited different dynamic expression profiles under oxidative stress. First, ppkDr was upregulated leading to the accumulation of PolyP, which chelated large amounts of intracellular Mn ions. Subsequently, the expression level of ppkDr decreased while ppxDr was substantially upregulated and effectively hydrolyzed inactive PolyP-Mn to release phosphate (Pi) and Mn2+, which could form into Mn-Pi complexes to scavenge O2 - and protect proteins from oxidative damage. Hence, dynamic cellular PolyP metabolites complexed with free Mn ions highlight a defense strategy of D. radiodurans in response to oxidative stress.IMPORTANCE The Mn-phosphate complex (Mn-Pi) plays a key role in the cellular resistance of radioresistant bacteria. The evolutionarily ancient polyphosphate polymers (polyphosphate [PolyP]) could effectively chelate Mn2+ and donate phosphates. However, the intracellular reservoir of Mn ions and homeostatic regulation of the Mn-Pi complex remain unclear. Here, we investigated the relationship of PolyP metabolites and Mn2+ homeostasis and how they function to defend against oxidative stress in the radioresistant bacterium Deinococcus radiodurans We found that PPXDr (the subscript "Dr" refers to D. radiodurans) is a novel exopolyphosphatase with a cofactor preference for Mn2+, mediating PolyP-Mn degradation into Pi and Mn ions. The formed Mn-Pi complexes effectively protect proteins. The dynamic PolyP metabolism coordinating with Mn ions is a defense strategy of D. radiodurans in response to oxidative stress. The findings not only provide new insights into the resistance mechanism of the extreme bacterium D. radiodurans but also broaden our understanding of the functions of PolyP metabolism in organisms.
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Radioprotective Effect of Whey Hydrolysate Peptides against γ-Radiation-Induced Oxidative Stress in BALB/c Mice. Nutrients 2021; 13:nu13030816. [PMID: 33801268 PMCID: PMC7999902 DOI: 10.3390/nu13030816] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/22/2021] [Accepted: 02/26/2021] [Indexed: 12/27/2022] Open
Abstract
Radiation therapy is widely used in the treatment of tumor diseases, but it can also cause serious damage to the body, so it is necessary to find effective nutritional supplements. The main purpose of this study is to evaluate the protective effect of whey hydrolysate peptides (WHPs) against 60Coγ radiation damage in mice and explore the mechanism. BALB/c mice were given WHPs by oral gavage administration for 14 days. Then, some mice underwent a 30-day survival test after 8 Gy radiation, and other mice received 3.5 Gy radiation to analyze the changes in body weight, hematology and bone marrow DNA after three and 14 days. In addition, through further analysis of the level of oxidative stress and intestinal barrier function, the possible mechanism of the radioprotective effect of WHPs was explored. The study found WHPs can prolong survival time, restore body weight, and increase the number of peripheral blood white blood cells and bone marrow DNA content in irradiated mice. In addition, WHPs can significantly improve the antioxidant capacity, inhibit pro-inflammatory cytokines and protect the intestinal barrier. These results indicate that WHPs have a certain radioprotective effect in mice, and the main mechanism is related to reducing oxidative damage.
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Redox signaling through zinc activates the radiation response in Deinococcus bacteria. Sci Rep 2021; 11:4528. [PMID: 33633226 PMCID: PMC7907104 DOI: 10.1038/s41598-021-84026-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 02/11/2021] [Indexed: 02/06/2023] Open
Abstract
Deinococcus bacteria are extremely resistant to radiation and other DNA damage- and oxidative stress-generating conditions. An efficient SOS-independent response mechanism inducing expression of several DNA repair genes is essential for this resistance, and is controlled by metalloprotease IrrE that cleaves and inactivates transcriptional repressor DdrO. Here, we identify the molecular signaling mechanism that triggers DdrO cleavage. We show that reactive oxygen species (ROS) stimulate the zinc-dependent metalloprotease activity of IrrE in Deinococcus. Sudden exposure of Deinococcus to zinc excess also rapidly induces DdrO cleavage, but is not accompanied by ROS production and DNA damage. Further, oxidative treatment leads to an increase of intracellular free zinc, indicating that IrrE activity is very likely stimulated directly by elevated levels of available zinc ions. We conclude that radiation and oxidative stress induce changes in redox homeostasis that result in IrrE activation by zinc in Deinococcus. We propose that a part of the zinc pool coordinated with cysteine thiolates is released due to their oxidation. Predicted regulation systems involving IrrE- and DdrO-like proteins are present in many bacteria, including pathogens, suggesting that such a redox signaling pathway including zinc as a second messenger is widespread and participates in various stress responses.
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Selveshwari S, Lele K, Dey S. Genomic signatures of UV resistance evolution in
Escherichia coli
depend on the growth phase during exposure. J Evol Biol 2021; 34:953-967. [DOI: 10.1111/jeb.13764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 12/27/2020] [Accepted: 01/13/2021] [Indexed: 11/28/2022]
Affiliation(s)
- S Selveshwari
- Population Biology Laboratory, Biology Division Indian Institute of Science Education and Research Pune Maharashtra India
| | - Kasturi Lele
- Population Biology Laboratory, Biology Division Indian Institute of Science Education and Research Pune Maharashtra India
| | - Sutirth Dey
- Population Biology Laboratory, Biology Division Indian Institute of Science Education and Research Pune Maharashtra India
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Berger D, Stångberg J, Baur J, Walters RJ. Elevated temperature increases genome-wide selection on de novo mutations. Proc Biol Sci 2021; 288:20203094. [PMID: 33529558 DOI: 10.1098/rspb.2020.3094] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Adaptation in new environments depends on the amount of genetic variation available for evolution, and the efficacy by which natural selection discriminates among this variation. However, whether some ecological factors reveal more genetic variation, or impose stronger selection pressures than others, is typically not known. Here, we apply the enzyme kinetic theory to show that rising global temperatures are predicted to intensify natural selection throughout the genome by increasing the effects of DNA sequence variation on protein stability. We test this prediction by (i) estimating temperature-dependent fitness effects of induced mutations in seed beetles adapted to ancestral or elevated temperature, and (ii) calculate 100 paired selection estimates on mutations in benign versus stressful environments from unicellular and multicellular organisms. Environmental stress per se did not increase mean selection on de novo mutation, suggesting that the cost of adaptation does not generally increase in new ecological settings to which the organism is maladapted. However, elevated temperature increased the mean strength of selection on genome-wide polymorphism, signified by increases in both mutation load and mutational variance in fitness. These results have important implications for genetic diversity gradients and the rate and repeatability of evolution under climate change.
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Affiliation(s)
- David Berger
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Josefine Stångberg
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Julian Baur
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Richard J Walters
- Centre for Environmental and Climate Research, Lund University, Sölvegatan 37, 223 62 Lund, Sweden
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Dollery SJ, Zurawski DV, Gaidamakova EK, Matrosova VY, Tobin JK, Wiggins TJ, Bushnell RV, MacLeod DA, Alamneh YA, Abu-Taleb R, Escatte MG, Meeks HN, Daly MJ, Tobin GJ. Radiation-Inactivated Acinetobacter baumannii Vaccine Candidates. Vaccines (Basel) 2021; 9:vaccines9020096. [PMID: 33514059 PMCID: PMC7912630 DOI: 10.3390/vaccines9020096] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/22/2021] [Accepted: 01/23/2021] [Indexed: 12/20/2022] Open
Abstract
Acinetobacter baumannii is a bacterial pathogen that is often multidrug-resistant (MDR) and causes a range of life-threatening illnesses, including pneumonia, septicemia, and wound infections. Some antibiotic treatments can reduce mortality if dosed early enough before an infection progresses, but there are few other treatment options when it comes to MDR-infection. Although several prophylactic strategies have been assessed, no vaccine candidates have advanced to clinical trials or have been approved. Herein, we rapidly produced protective whole-cell immunogens from planktonic and biofilm-like cultures of A. baumannii, strain AB5075 grown using a variety of methods. After selecting a panel of five cultures based on distinct protein profiles, replicative activity was extinguished by exposure to 10 kGy gamma radiation in the presence of a Deinococcus antioxidant complex composed of manganous (Mn2+) ions, a decapeptide, and orthophosphate. Mn2+ antioxidants prevent hydroxylation and carbonylation of irradiated proteins, but do not protect nucleic acids, yielding replication-deficient immunogenic A. baumannii vaccine candidates. Mice were immunized and boosted twice with 1.0 × 107 irradiated bacterial cells and then challenged intranasally with AB5075 using two mouse models. Planktonic cultures grown for 16 h in rich media and biofilm cultures grown in static cultures underneath minimal (M9) media stimulated immunity that led to 80–100% protection.
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Affiliation(s)
- Stephen J. Dollery
- Biological Mimetics, Inc., 124 Byte Drive, Frederick, MD 21702, USA; (J.K.T.); (T.J.W.); (R.V.B.); (D.A.M.); (G.J.T.)
- Correspondence:
| | - Daniel V. Zurawski
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (D.V.Z.); (Y.A.A.); (R.A.-T.); (M.G.E.)
| | - Elena K. Gaidamakova
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA; (E.K.G.); (V.Y.M.); (M.J.D.)
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Vera Y. Matrosova
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA; (E.K.G.); (V.Y.M.); (M.J.D.)
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - John K. Tobin
- Biological Mimetics, Inc., 124 Byte Drive, Frederick, MD 21702, USA; (J.K.T.); (T.J.W.); (R.V.B.); (D.A.M.); (G.J.T.)
| | - Taralyn J. Wiggins
- Biological Mimetics, Inc., 124 Byte Drive, Frederick, MD 21702, USA; (J.K.T.); (T.J.W.); (R.V.B.); (D.A.M.); (G.J.T.)
| | - Ruth V. Bushnell
- Biological Mimetics, Inc., 124 Byte Drive, Frederick, MD 21702, USA; (J.K.T.); (T.J.W.); (R.V.B.); (D.A.M.); (G.J.T.)
| | - David A. MacLeod
- Biological Mimetics, Inc., 124 Byte Drive, Frederick, MD 21702, USA; (J.K.T.); (T.J.W.); (R.V.B.); (D.A.M.); (G.J.T.)
| | - Yonas A. Alamneh
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (D.V.Z.); (Y.A.A.); (R.A.-T.); (M.G.E.)
| | - Rania Abu-Taleb
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (D.V.Z.); (Y.A.A.); (R.A.-T.); (M.G.E.)
| | - Mariel G. Escatte
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (D.V.Z.); (Y.A.A.); (R.A.-T.); (M.G.E.)
| | | | - Michael J. Daly
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA; (E.K.G.); (V.Y.M.); (M.J.D.)
| | - Gregory J. Tobin
- Biological Mimetics, Inc., 124 Byte Drive, Frederick, MD 21702, USA; (J.K.T.); (T.J.W.); (R.V.B.); (D.A.M.); (G.J.T.)
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Kumari N, Raghavan SC. G-quadruplex DNA structures and their relevance in radioprotection. Biochim Biophys Acta Gen Subj 2021; 1865:129857. [PMID: 33508382 DOI: 10.1016/j.bbagen.2021.129857] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND DNA, the genetic material of most of the organisms, is the crucial element of life. Integrity of DNA needs to be maintained for transmission of genetic material from one generation to another. All organisms are constantly challenged by the environmental conditions which can lead to the induction of DNA damage. Ionizing radiation (IR) has been known to induce DNA damage and IR sensitivity varies among different organisms. The causes for differential radiosensitivity among various organisms have not been studied in great detail. SCOPE OF REVIEW We discuss DNA secondary structure formation, GC content of the genome, role of G-quadruplex formation, and its relationship with radiosensitivity of the genome. MAJOR CONCLUSION In Deinococcus radiodurans, the bacterium that exhibits maximum radio resistance, multiple G-quadruplex forming motifs are reported. In human cells, G-quadruplex formation led to differential radiosensitivity. In this article, we have discussed, the role of secondary DNA structure formation like G-quadruplex in shielding the genome from radiation and its implications in understanding evolution of radio protective effect of an organism. We also discuss role of GC content and its correlation with radio resistance. GENERAL SIGNIFICANCE This review provides an insight into the role of G-quadruplexes in providing differential radiosensitivity at different site of the genome and in different organisms. It further discusses the possibility of higher GC content contributing towards reduced radiosensitivity in different organisms, evolution of radiosensitivity, and regulation of multiple cellular processes.
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Affiliation(s)
- Nitu Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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Schultzhaus Z, Chen A, Shuryak I, Wang Z. The Transcriptomic and Phenotypic Response of the Melanized Yeast Exophiala dermatitidis to Ionizing Particle Exposure. Front Microbiol 2021; 11:609996. [PMID: 33510728 PMCID: PMC7835796 DOI: 10.3389/fmicb.2020.609996] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/14/2020] [Indexed: 01/20/2023] Open
Abstract
Fungi can tolerate extremely high doses of ionizing radiation compared with most other eukaryotes, a phenomenon encompassing both the recovery from acute exposure and the growth of melanized fungi in chronically contaminated environments such as nuclear disaster sites. This observation has led to the use of fungi in radiobiology studies, with the goal of finding novel resistance mechanisms. However, it is still not entirely clear what underlies this phenomenon, as genetic studies have not pinpointed unique responses to ionizing radiation in the most resistant fungi. Additionally, little work has been done examining how fungi (other than budding yeast) respond to irradiation by ionizing particles (e.g., protons, α-particles), although particle irradiation may cause distinct cellular damage, and is more relevant for human risks. To address this paucity of data, in this study we have characterized the phenotypic and transcriptomic response of the highly radioresistant yeast Exophiala dermatitidis to irradiation by three separate ionizing radiation sources: protons, deuterons, and α-particles. The experiment was performed with both melanized and non-melanized strains of E. dermatitidis, to determine the effect of this pigment on the response. No significant difference in survival was observed between these strains under any condition, suggesting that melanin does not impart protection to acute irradiation to these particles. The transcriptomic response during recovery to particle exposure was similar to that observed after γ-irradiation, with DNA repair and replication genes upregulated, and genes involved in translation and ribosomal biogenesis being heavily repressed, indicating an attenuation of cell growth. However, a comparison of global gene expression showed clear clustering of particle and γ-radiation groups. The response elicited by particle irradiation was, in total, more complex. Compared to the γ-associated response, particle irradiation resulted in greater changes in gene expression, a more diverse set of differentially expressed genes, and a significant induction of gene categories such as autophagy and protein catabolism. Additionally, analysis of individual particle responses resulted in identification of the first unique expression signatures and individual genes for each particle type that could be used as radionuclide discrimination markers.
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Affiliation(s)
- Zachary Schultzhaus
- Center for Biomolecular Science and Engineering, United States Naval Research Laboratory, Washington, DC, United States
| | - Amy Chen
- Virginia Tech Carilion School of Medicine, Roanoke, VA, United States
| | - Igor Shuryak
- Center for Radiological Research, Columbia University Irving Medical Center, New York, NY, United States
| | - Zheng Wang
- Center for Biomolecular Science and Engineering, United States Naval Research Laboratory, Washington, DC, United States
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Paithankar JG, Ghodke TS, Patil RK. Insight into the evolutionary profile of radio-resistance among insects having intrinsically evolved defence against radiation toxicity. Int J Radiat Biol 2021; 98:1012-1024. [PMID: 33264042 DOI: 10.1080/09553002.2020.1859153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Ionizing radiation (IR) has wide-ranging applications in various fields. In agriculture, pest control is one of the important applications, because insect pests have become a threat to the global agriculture industry. IR are used routinely to prevent crop loss and to protect stored food commodities. Radio-sterilization and disinfestation treatments are commonly used procedures for insect pest control. From various studies on insect radio-sterilization and disinfestation, it has been established that compared to vertebrates' insects have high levels of radiation resistance. Therefore, to achieve adequate radio-sterilization/disinfestation; exposure to high doses of IR is necessary. However, studies over decades made a presumption that radiation resistance is general among insects. Recent studies have shown that some insect orders are having high IR resistance and some insect orders are sensitive to IR. These studies have clarified that radiation resistance is not uniform throughout insect class. The present review is an attempt to insight at the evolutionary profile of insect species studied for radio-sterilization and disinfestation treatment and are having the trait of radio-resistance. From various studies on insect radiation resistance and after phylogenetic analysis of insect species it appears that the evolutionary near species have drastically different levels of radio-resistance and trait of radiation resistance appears to be independent of insect evolution.
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Affiliation(s)
- Jagdish Gopal Paithankar
- Division of Environmental Health and Toxicology, Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Mangalore, India
| | - Tanhaji Sandu Ghodke
- Centre for Applications of Radioisotopes and Radiation Technology (CARRT), Mangalore University, Mangalore, India.,Department of Applied Zoology, Mangalore University, Mangalore, India
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Romsdahl J, Schultzhaus Z, Chen A, Liu J, Ewing A, Hervey J, Wang Z. Adaptive evolution of a melanized fungus reveals robust augmentation of radiation resistance by abrogating non-homologous end-joining. Environ Microbiol 2020; 23:3627-3645. [PMID: 33078510 DOI: 10.1111/1462-2920.15285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/22/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023]
Abstract
Fungi have been observed to exhibit resistance to high levels of ionizing radiation despite sharing most DNA repair mechanisms with other eukaryotes. Radioresistance, in fact, is such a common feature in fungi that it is difficult to identify species that exhibit widely different radiosensitivities, which in turn has hampered the identification of genetic elements responsible for this resistance phenotype. Due to the inherent mutagenic properties of radiation exposure, however, this can be addressed through adaptive laboratory evolution for increased ionizing radiation resistance. Here, using the black yeast Exophiala dermatitidis, we demonstrate that resistance to γ-radiation can be greatly increased through repeated rounds of irradiation and outgrowth. Moreover, we find that the small genome size of fungi situates them as a relatively simple functional genomics platform for identification of mutations associated with ionizing radiation resistance. This enabled the identification of genetic mutations in genes encoding proteins with a broad range of functions from 10 evolved strains. Specifically, we find that greatly increased resistance to γ-radiation is achieved in E. dermatitidis through disruption of the non-homologous end-joining pathway, with three individual evolutionary paths converging to abolish this DNA repair process. This result suggests that non-homologous end-joining, even in haploid cells where homologous chromosomes are not present during much of the cell cycle, is an impediment to repair of radiation-induced lesions in this organism, and that the relative levels of homologous and non-homologous repair in a given fungal species may play a major role in its radiation resistance.
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Affiliation(s)
- Jillian Romsdahl
- National Research Council Postdoctoral Research Associate, Naval Research Laboratory, Washington, DC, USA
| | - Zachary Schultzhaus
- Center for Biomolecular Sciences and Engineering, US Naval Research Laboratory, Washington, DC, USA
| | - Amy Chen
- Virginia Tech Carilion School of Medicine, Roanoke, VA, USA
| | - Jing Liu
- Thomas Jefferson High School for Science and Technology, Alexandria, VA, USA
| | | | - Judson Hervey
- Center for Biomolecular Sciences and Engineering, US Naval Research Laboratory, Washington, DC, USA
| | - Zheng Wang
- Center for Biomolecular Sciences and Engineering, US Naval Research Laboratory, Washington, DC, USA
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46
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Guesmi S, Nouioui I, Pujic P, Dubost A, Najjari A, Ghedira K, Igual JM, Cherif A, Klenk HP, Sghaier H, Normand P. Draft genome sequence of Promicromonospora panici sp. nov., a novel ionizing-radiation-resistant actinobacterium isolated from roots of the desert plant Panicum turgidum. Extremophiles 2020; 25:25-38. [PMID: 33104875 DOI: 10.1007/s00792-020-01207-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 10/07/2020] [Indexed: 11/26/2022]
Abstract
A novel strain of the genus Promicromonospora, designated PT9T, was recovered from irradiated roots of the xerophyte Panicum turgidum collected from the Ksar Ghilane oasis in southern Tunisia. Strain PT9T is aerobic, non-spore-forming, Gram- positive actinomycete that produces branched hyphae and forms white to yellowish-white colonies. Chemotaxonomic features, including fatty acids, whole cell sugars and polar lipid profiles, support the assignment of PT9T to the genus Promicromonospora. The genomic relatedness indexes based on DNA-DNA hybridization and average nucleotide identity values revealed a significant genomic divergence between strain PT9T and all sequenced type strains of the taxon. Phylogenomic analysis showed that isolate PT9T was most closely related to Promicromonospora soli CGMCC 4.7398T. Phenotypic and phylogenomic analyses suggest that isolate PT9T represents a novel species of the genus Promicromonospora, for which the name Promicromonospora panici sp. nov. is proposed. The type strain is PT9T (LMG 31103T = DSM 108613T).The isolate PT9T is an ionizing-radiation-resistant actinobacterium (D10 value = 2.6 kGy), with resistance to desiccation and hydrogen peroxide. The complete genome sequence of PT9T consists of 6,582,650 bps with 71.2% G+C content and 6291 protein-coding sequences. This genome will help to decipher the microbial genetic bases for ionizing-radiation resistance mechanisms including the response to oxidative stress.
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Affiliation(s)
- Sihem Guesmi
- National Agronomy Institute of Tunisia, Avenue Charles Nicolle, 1082, Tunis, Mahrajène, Tunisia
- Laboratory "Energy and Matter for Development of Nuclear Sciences" (LR16CNSTN02), National Center for Nuclear Sciences and Technology, Sidi Thabet Technopark, 2020, Sidi Thabet, Tunisia
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Petar Pujic
- Université de Lyon, Université Lyon 1, Lyon, France
- CNRS, UMR 5557, Écologie Microbienne, UMR1418, INRA, 69622 Cedex, Villeurbanne, France
| | - Audrey Dubost
- Université de Lyon, Université Lyon 1, Lyon, France
- CNRS, UMR 5557, Écologie Microbienne, UMR1418, INRA, 69622 Cedex, Villeurbanne, France
| | - Afef Najjari
- Université de Tunis el Manar, Faculté des Sciences de Tunis, LR03ES03 Microorganismes et Biomolécules Actives, 2092, Tunis, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, Université de Tunis El Manar, 1002, Tunis, Tunisia
| | - José M Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), c/Cordel de Merinas 40-52, 37008, Salamanca, Spain
| | - Ameur Cherif
- University Manouba, ISBST, BVBGR-LR11ES31,, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Haïtham Sghaier
- Laboratory "Energy and Matter for Development of Nuclear Sciences" (LR16CNSTN02), National Center for Nuclear Sciences and Technology, Sidi Thabet Technopark, 2020, Sidi Thabet, Tunisia
- University Manouba, ISBST, BVBGR-LR11ES31,, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Philippe Normand
- Université de Lyon, Université Lyon 1, Lyon, France.
- CNRS, UMR 5557, Écologie Microbienne, UMR1418, INRA, 69622 Cedex, Villeurbanne, France.
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47
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Chang RL, Stanley JA, Robinson MC, Sher JW, Li Z, Chan YA, Omdahl AR, Wattiez R, Godzik A, Matallana-Surget S. Protein structure, amino acid composition and sequence determine proteome vulnerability to oxidation-induced damage. EMBO J 2020; 39:e104523. [PMID: 33073387 PMCID: PMC7705453 DOI: 10.15252/embj.2020104523] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 09/16/2020] [Accepted: 09/22/2020] [Indexed: 02/05/2023] Open
Abstract
Oxidative stress alters cell viability, from microorganism irradiation sensitivity to human aging and neurodegeneration. Deleterious effects of protein carbonylation by reactive oxygen species (ROS) make understanding molecular properties determining ROS susceptibility essential. The radiation‐resistant bacterium Deinococcus radiodurans accumulates less carbonylation than sensitive organisms, making it a key model for deciphering properties governing oxidative stress resistance. We integrated shotgun redox proteomics, structural systems biology, and machine learning to resolve properties determining protein damage by γ‐irradiation in Escherichia coli and D. radiodurans at multiple scales. Local accessibility, charge, and lysine enrichment accurately predict ROS susceptibility. Lysine, methionine, and cysteine usage also contribute to ROS resistance of the D. radiodurans proteome. Our model predicts proteome maintenance machinery, and proteins protecting against ROS are more resistant in D. radiodurans. Our findings substantiate that protein‐intrinsic protection impacts oxidative stress resistance, identifying causal molecular properties.
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Affiliation(s)
- Roger L Chang
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Julian A Stanley
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA
| | - Matthew C Robinson
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA
| | - Joel W Sher
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA
| | - Zhanwen Li
- Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, USA
| | - Yujia A Chan
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Ashton R Omdahl
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Adam Godzik
- Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, USA
| | - Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK
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48
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Chen Z, Tang Y, Hua Y, Zhao Y. Structural features and functional implications of proteins enabling the robustness of Deinococcus radiodurans. Comput Struct Biotechnol J 2020; 18:2810-2817. [PMID: 33133422 PMCID: PMC7575645 DOI: 10.1016/j.csbj.2020.09.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 12/21/2022] Open
Abstract
Deinococcus radiodurans can survive under extreme conditions, including high doses of DNA damaging agents and ionizing radiation, desiccation, and oxidative stress. Both the efficient cellular DNA repair machinery and antioxidation systems contribute to the extreme resistance of this bacterium, making it an ideal organism for studying the cellular mechanisms of environmental adaptation. The number of stress-related proteins identified in this bacterium has mushroomed in the past two decades. The newly identified proteins reveal both commonalities and diversity of structure, mechanism, and function, which impact a wide range of cellular functions. Here, we review the unique and general structural features of these proteins and discuss how these studies improve our understanding of the environmental stress adaptation mechanisms of D. radiodurans.
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Affiliation(s)
- Zijing Chen
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuyue Tang
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuejin Hua
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ye Zhao
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
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49
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Schultzhaus ZS, Schultzhaus JN, Romsdahl J, Chen A, Hervey IV WJ, Leary DH, Wang Z. Proteomics Reveals Distinct Changes Associated with Increased Gamma Radiation Resistance in the Black Yeast Exophiala dermatitidis. Genes (Basel) 2020; 11:genes11101128. [PMID: 32992890 PMCID: PMC7650708 DOI: 10.3390/genes11101128] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 12/12/2022] Open
Abstract
The yeast Exophiala dermatitidis exhibits high resistance to γ-radiation in comparison to many other fungi. Several aspects of this phenotype have been characterized, including its dependence on homologous recombination for the repair of radiation-induced DNA damage, and the transcriptomic response invoked by acute γ-radiation exposure in this organism. However, these findings have yet to identify unique γ-radiation exposure survival strategies-many genes that are induced by γ-radiation exposure do not appear to be important for recovery, and the homologous recombination machinery of this organism is not unique compared to more sensitive species. To identify features associated with γ-radiation resistance, here we characterized the proteomes of two E. dermatitidis strains-the wild type and a hyper-resistant strain developed through adaptive laboratory evolution-before and after γ-radiation exposure. The results demonstrate that protein intensities do not change substantially in response to this stress. Rather, the increased resistance exhibited by the evolved strain may be due in part to increased basal levels of single-stranded binding proteins and a large increase in ribosomal content, possibly allowing for a more robust, induced response during recovery. This experiment provides evidence enabling us to focus on DNA replication, protein production, and ribosome levels for further studies into the mechanism of γ-radiation resistance in E. dermatitidis and other fungi.
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Affiliation(s)
- Zachary S. Schultzhaus
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC 20375, USA; (Z.S.S.); (J.N.S.); (W.J.H.IV); (D.H.L.)
| | - Janna N. Schultzhaus
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC 20375, USA; (Z.S.S.); (J.N.S.); (W.J.H.IV); (D.H.L.)
| | - Jillian Romsdahl
- National Research Council, Postdoctoral Fellowship Program, US Naval Research Laboratory, Washington, DC 20744, USA;
| | - Amy Chen
- Virginia Tech Carilion School of Medicine, Roanoke, VA 24016, USA;
| | - W. Judson Hervey IV
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC 20375, USA; (Z.S.S.); (J.N.S.); (W.J.H.IV); (D.H.L.)
| | - Dagmar H. Leary
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC 20375, USA; (Z.S.S.); (J.N.S.); (W.J.H.IV); (D.H.L.)
| | - Zheng Wang
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC 20375, USA; (Z.S.S.); (J.N.S.); (W.J.H.IV); (D.H.L.)
- Correspondence: ; Tel.: +1-202-404-1007
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50
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Bruckbauer ST, Martin J, Minkoff BB, Veling MT, Lancaster I, Liu J, Trimarco JD, Bushnell B, Lipzen A, Wood EA, Sussman MR, Pennacchio C, Cox MM. Physiology of Highly Radioresistant Escherichia coli After Experimental Evolution for 100 Cycles of Selection. Front Microbiol 2020; 11:582590. [PMID: 33072055 PMCID: PMC7536353 DOI: 10.3389/fmicb.2020.582590] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 08/26/2020] [Indexed: 11/13/2022] Open
Abstract
Ionizing radiation (IR) is lethal to most organisms at high doses, damaging every cellular macromolecule via induction of reactive oxygen species (ROS). Utilizing experimental evolution and continuing previous work, we have generated the most IR-resistant Escherichia coli populations developed to date. After 100 cycles of selection, the dose required to kill 99% the four replicate populations (IR9-100, IR10-100, IR11-100, and IR12-100) has increased from 750 Gy to approximately 3,000 Gy. Fitness trade-offs, specialization, and clonal interference are evident. Long-lived competing sub-populations are present in three of the four lineages. In IR9, one lineage accumulates the heme precursor, porphyrin, leading to generation of yellow-brown colonies. Major genomic alterations are present. IR9 and IR10 exhibit major deletions and/or duplications proximal to the chromosome replication terminus. Contributions to IR resistance have expanded beyond the alterations in DNA repair systems documented previously. Variants of proteins involved in ATP synthesis (AtpA), iron-sulfur cluster biogenesis (SufD) and cadaverine synthesis (CadA) each contribute to IR resistance in IR9-100. Major genomic and physiological changes are emerging. An isolate from IR10 exhibits protein protection from ROS similar to the extremely radiation resistant bacterium Deinococcus radiodurans, without evident changes in cellular metal homeostasis. Selection is continuing with no limit to IR resistance in evidence as our E. coli populations approach levels of IR resistance typical of D. radiodurans.
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Affiliation(s)
- Steven T Bruckbauer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Joel Martin
- DOE Joint Genome Institute, Berkeley, CA, United States
| | - Benjamin B Minkoff
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States.,Center for Genomic Science Innovation, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Mike T Veling
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States
| | - Illissa Lancaster
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Jessica Liu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Joseph D Trimarco
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Anna Lipzen
- DOE Joint Genome Institute, Berkeley, CA, United States
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Michael R Sussman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States.,Center for Genomic Science Innovation, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | | | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
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