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Pal S, Yuvaraj R, Krishnan H, Venkatraman B, Abraham J, Gopinathan A. Unraveling radiation resistance strategies in two bacterial strains from the high background radiation area of Chavara-Neendakara: A comprehensive whole genome analysis. PLoS One 2024; 19:e0304810. [PMID: 38857267 PMCID: PMC11164402 DOI: 10.1371/journal.pone.0304810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 05/18/2024] [Indexed: 06/12/2024] Open
Abstract
This paper reports the results of gamma irradiation experiments and whole genome sequencing (WGS) performed on vegetative cells of two radiation resistant bacterial strains, Metabacillus halosaccharovorans (VITHBRA001) and Bacillus paralicheniformis (VITHBRA024) (D10 values 2.32 kGy and 1.42 kGy, respectively), inhabiting the top-ranking high background radiation area (HBRA) of Chavara-Neendakara placer deposit (Kerala, India). The present investigation has been carried out in the context that information on strategies of bacteria having mid-range resistance for gamma radiation is inadequate. WGS, annotation, COG and KEGG analyses and manual curation of genes helped us address the possible pathways involved in the major domains of radiation resistance, involving recombination repair, base excision repair, nucleotide excision repair and mismatch repair, and the antioxidant genes, which the candidate could activate to survive under ionizing radiation. Additionally, with the help of these data, we could compare the candidate strains with that of the extremely radiation resistant model bacterium Deinococccus radiodurans, so as to find the commonalities existing in their strategies of resistance on the one hand, and also the rationale behind the difference in D10, on the other. Genomic analysis of VITHBRA001 and VITHBRA024 has further helped us ascertain the difference in capability of radiation resistance between the two strains. Significantly, the genes such as uvsE (NER), frnE (protein protection), ppk1 and ppx (non-enzymatic metabolite production) and those for carotenoid biosynthesis, are endogenous to VITHBRA001, but absent in VITHBRA024, which could explain the former's better radiation resistance. Further, this is the first-time study performed on any bacterial population inhabiting an HBRA. This study also brings forward the two species whose radiation resistance has not been reported thus far, and add to the knowledge on radiation resistant capabilities of the phylum Firmicutes which are abundantly observed in extreme environment.
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Affiliation(s)
- Sowptika Pal
- Molecular Endocrinology Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Ramani Yuvaraj
- Radiological and Environmental Safety Division, Indira Gandhi Centre for Atomic Research, Kalpakkam, Tamil Nadu, India
| | - Hari Krishnan
- Radiological and Environmental Safety Division, Indira Gandhi Centre for Atomic Research, Kalpakkam, Tamil Nadu, India
| | - Balasubramanian Venkatraman
- Radiological and Environmental Safety Division, Indira Gandhi Centre for Atomic Research, Kalpakkam, Tamil Nadu, India
| | - Jayanthi Abraham
- Microbial Biotechnology Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Anilkumar Gopinathan
- Molecular Endocrinology Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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Mishra S, Duarte GT, Horemans N, Ruytinx J, Gudkov D, Danchenko M. Complexity of responses to ionizing radiation in plants, and the impact on interacting biotic factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171567. [PMID: 38460702 DOI: 10.1016/j.scitotenv.2024.171567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/20/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
In nature, plants are simultaneously exposed to different abiotic (e.g., heat, drought, and salinity) and biotic (e.g., bacteria, fungi, and insects) stresses. Climate change and anthropogenic pressure are expected to intensify the frequency of stress factors. Although plants are well equipped with unique and common defense systems protecting against stressors, they may compromise their growth and development for survival in such challenging environments. Ionizing radiation is a peculiar stress factor capable of causing clustered damage. Radionuclides are both naturally present on the planet and produced by human activities. Natural and artificial radioactivity affects plants on molecular, biochemical, cellular, physiological, populational, and transgenerational levels. Moreover, the fitness of pests, pathogens, and symbionts is concomitantly challenged in radiologically contaminated areas. Plant responses to artificial acute ionizing radiation exposure and laboratory-simulated or field chronic exposure are often discordant. Acute or chronic ionizing radiation exposure may occasionally prime the defense system of plants to better tolerate the biotic stress or could often exhaust their metabolic reserves, making plants more susceptible to pests and pathogens. Currently, these alternatives are only marginally explored. Our review summarizes the available literature on the responses of host plants, biotic factors, and their interaction to ionizing radiation exposure. Such systematic analysis contributes to improved risk assessment in radiologically contaminated areas.
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Affiliation(s)
- Shubhi Mishra
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 950 07 Nitra, Slovakia
| | - Gustavo Turqueto Duarte
- Unit for Biosphere Impact Studies, Belgian Nuclear Research Centre SCK CEN, 2400 Mol, Belgium
| | - Nele Horemans
- Unit for Biosphere Impact Studies, Belgian Nuclear Research Centre SCK CEN, 2400 Mol, Belgium; Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Joske Ruytinx
- Department of Bio-engineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Dmitri Gudkov
- Institute of Hydrobiology, National Academy of Sciences of Ukraine, 04210 Kyiv, Ukraine
| | - Maksym Danchenko
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 950 07 Nitra, Slovakia.
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Wang W, Cui B, Nie Y, Sun L, Zhang F. Radiation injury and gut microbiota-based treatment. Protein Cell 2024; 15:83-97. [PMID: 37470727 PMCID: PMC10833463 DOI: 10.1093/procel/pwad044] [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: 05/15/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023] Open
Abstract
The exposure to either medical sources or accidental radiation can cause varying degrees of radiation injury (RI). RI is a common disease involving multiple human body parts and organs, yet effective treatments are currently limited. Accumulating evidence suggests gut microbiota are closely associated with the development and prevention of various RI. This article summarizes 10 common types of RI and their possible mechanisms. It also highlights the changes and potential microbiota-based treatments for RI, including probiotics, metabolites, and microbiota transplantation. Additionally, a 5P-Framework is proposed to provide a comprehensive strategy for managing RI.
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Affiliation(s)
- Weihong Wang
- Department of Microbiota Medicine and Medical Center for Digestive Diseases, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
- Department of Microbiotherapy, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Bota Cui
- Department of Microbiota Medicine and Medical Center for Digestive Diseases, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
- Department of Microbiotherapy, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Yongzhan Nie
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an 710032, China
- National Clinical Research Center for Digestive Diseases, Xi’an 710032, China
| | - Lijuan Sun
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi’an 710069, China
| | - Faming Zhang
- Department of Microbiota Medicine and Medical Center for Digestive Diseases, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
- Department of Microbiotherapy, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China
- National Clinical Research Center for Digestive Diseases, Xi’an 710032, China
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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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Rahman AU, Ali A, Ahmad F, Ahmad S, Alharbi M, Alasmari AF, Fayyaz A, Rana QUA, Khan S, Hasan F, Badshah M, Shah AA. Unraveling the Radioprotective Mechanisms of UV-Resistant Bacillus subtilis ASM-1 Extracted Compounds through Molecular Docking. Pharmaceuticals (Basel) 2023; 16:1139. [PMID: 37631055 PMCID: PMC10459916 DOI: 10.3390/ph16081139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/26/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
Radioresistant microorganisms possess inimitable capabilities enabling them to thrive under extreme radiation. However, the existence of radiosensitive microorganisms inhabiting such an inhospitable environment is still a mystery. The current study examines the potential of radioresistant microorganisms to protect radiosensitive microorganisms in harsh environments. Bacillus subtilis strain ASM-1 was isolated from the Thal desert in Pakistan and evaluated for antioxidative and radioprotective potential after being exposed to UV radiation. The strain exhibited 54.91% survivability under UVB radiation (5.424 × 103 J/m2 for 8 min) and 50.94% to mitomycin-C (4 µg/mL). Extracellular fractions collected from ASM-1 extracts showed significant antioxidant potential, and chemical profiling revealed a pool of bioactive compounds, including pyrrolopyrazines, amides, alcoholics, and phenolics. The E-2 fraction showed the maximum antioxidant potential via DPPH assay (75%), and H2O2 scavenging assay (68%). A combination of ASM-1 supernatant with E-2 fraction (50 µL in a ratio of 2:1) provided substantial protection to radiosensitive cell types, Bacillus altitudinis ASM-9 (MT722073) and E. coli (ATCC 10536), under UVB radiation. Docking studies reveal that the compound supported by literature against the target proteins have strong binding affinities which further inferred its medical uses in health care treatment. This is followed by molecular dynamic simulations where it was observed among trajectories that there were no significant changes in major secondary structure elements, despite the presence of naturally flexible loops. This behavior can be interpreted as a strategy to enhance intermolecular conformational stability as the simulation progresses. Thus, our study concludes that Bacillus subtilis ASM-1 protects radiosensitive strains from radiation-induced injuries via biofilm formation and secretion of antioxidative and radioprotective compounds in the environment.
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Affiliation(s)
- Asim Ur Rahman
- Department of Microbiology, Quaid-i-Azam University, Islamabad 45320, Pakistan; (A.U.R.); (A.A.); (S.K.); (F.H.); (M.B.)
| | - Aftab Ali
- Department of Microbiology, Quaid-i-Azam University, Islamabad 45320, Pakistan; (A.U.R.); (A.A.); (S.K.); (F.H.); (M.B.)
| | - Faisal Ahmad
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan;
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan;
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut P.O. Box 36, Lebanon
- Department of Natural Sciences, Lebanese American University, Beirut P.O. Box 36, Lebanon
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (M.A.); (A.F.A.)
| | - Abdullah F. Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (M.A.); (A.F.A.)
| | - Amna Fayyaz
- Department of Environmental Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan;
| | - Qurrat ul ain Rana
- Department of Microbiology, Quaid-i-Azam University, Islamabad 45320, Pakistan; (A.U.R.); (A.A.); (S.K.); (F.H.); (M.B.)
- Joint Genome Institute, Lawrence Berkely National Laboratory, Berkley, CA 94720, USA
| | - Samiullah Khan
- Department of Microbiology, Quaid-i-Azam University, Islamabad 45320, Pakistan; (A.U.R.); (A.A.); (S.K.); (F.H.); (M.B.)
| | - Fariha Hasan
- Department of Microbiology, Quaid-i-Azam University, Islamabad 45320, Pakistan; (A.U.R.); (A.A.); (S.K.); (F.H.); (M.B.)
| | - Malik Badshah
- Department of Microbiology, Quaid-i-Azam University, Islamabad 45320, Pakistan; (A.U.R.); (A.A.); (S.K.); (F.H.); (M.B.)
| | - Aamer Ali Shah
- Department of Microbiology, Quaid-i-Azam University, Islamabad 45320, Pakistan; (A.U.R.); (A.A.); (S.K.); (F.H.); (M.B.)
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Sadowska-Bartosz I, Bartosz G. Antioxidant defense of Deinococcus radiodurans: how does it contribute to extreme radiation resistance? Int J Radiat Biol 2023; 99:1803-1829. [PMID: 37498212 DOI: 10.1080/09553002.2023.2241895] [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: 01/09/2023] [Revised: 06/28/2023] [Accepted: 07/08/2023] [Indexed: 07/28/2023]
Abstract
PURPOSE Deinococcus radiodurans is an extremely radioresistant bacterium characterized by D10 of 10 kGy, and able to grow luxuriantly under chronic ionizing radiation of 60 Gy/h. The aim of this article is to review the antioxidant system of D. radiodurans and its possible role in the unusual resistance of this bacterium to ionizing radiation. CONCLUSIONS The unusual radiation resistance of D. radiodurans has apparently evolved as a side effect of the adaptation of this extremophile to other damaging environmental factors, especially desiccation. The antioxidant proteins and low-molecular antioxidants (especially low-molecular weight Mn2+ complexes and carotenoids, in particular, deinoxanthin), as well as protein and non-protein regulators, are important for the antioxidant defense of this species. Antioxidant protection of proteins from radiation inactivation enables the repair of DNA damage caused by ionizing radiation.
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Affiliation(s)
- Izabela Sadowska-Bartosz
- Laboratory of Analytical Biochemistry, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
| | - Grzegorz Bartosz
- Department of Bioenergetics, Food Analysis and Microbiology, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
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Wei X, Huang Z, Jiang L, Li Y, Zhang X, Leng Y, Jiang C. Charting the landscape of the environmental exposome. IMETA 2022; 1:e50. [PMID: 38867899 PMCID: PMC10989948 DOI: 10.1002/imt2.50] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/13/2022] [Accepted: 07/30/2022] [Indexed: 06/14/2024]
Abstract
The exposome depicts the total exposures in the lifetime of an organism. Human exposome comprises exposures from environmental and humanistic sources. Biological, chemical, and physical environmental exposures pose potential health threats, especially to susceptible populations. Although still in its nascent stage, we are beginning to recognize the vast and dynamic nature of the exposome. In this review, we systematically summarize the biological and chemical environmental exposomes in three broad environmental matrices-air, soil, and water; each contains several distinct subcategories, along with a brief introduction to the physical exposome. Disease-related environmental exposures are highlighted, and humans are also a major source of disease-related biological exposures. We further discuss the interactions between biological, chemical, and physical exposomes. Finally, we propose a list of outstanding challenges under the exposome research framework that need to be addressed to move the field forward. Taken together, we present a detailed landscape of environmental exposome to prime researchers to join this exciting new field.
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Affiliation(s)
- Xin Wei
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouZhejiangChina
| | - Zinuo Huang
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouZhejiangChina
| | - Liuyiqi Jiang
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouZhejiangChina
| | - Yueer Li
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouZhejiangChina
| | - Xinyue Zhang
- Department of GeneticsStanford UniversityStanfordCaliforniaUSA
| | - Yuxin Leng
- Department of Intensive Care UnitPeking University Third HospitalBeijingChina
| | - Chao Jiang
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouZhejiangChina
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
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Martin-Pozas T, Nováková A, Jurado V, Fernandez-Cortes A, Cuezva S, Saiz-Jimenez C, Sanchez-Moral S. Diversity of Microfungi in a High Radon Cave Ecosystem. Front Microbiol 2022; 13:869661. [PMID: 35572646 PMCID: PMC9093739 DOI: 10.3389/fmicb.2022.869661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
Castañar Cave is a clear example of an oligotrophic ecosystem with high hygrothermal stability both seasonal and interannual and the particularity of registering extraordinary levels of environmental radiation. These environmental conditions make the cave an ideal laboratory to evaluate both the responses of the subterranean environment to sudden changes in the matter and energy fluxes with the exterior and also any impact derived from its use as a tourist resource under a very restrictive access regime. In 2008, a fungal outbreak provoked by a vomit contaminated the sediments which were removed and subsequently treated with hydrogen peroxide. Fungal surveys were carried out in 2008 and 2009. The visits were resumed in 2014. Here, 12 years after the outbreak, we present an exhaustive study on the cave sediments in order to know the distribution of the different fungal taxa, as well as the prevalence and spatio-temporal evolution of the fungi caused by the vomit over the years under the conditions of relative isolation and high radiation that characterize this cave.
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Affiliation(s)
- Tamara Martin-Pozas
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), Madrid, Spain
| | - Alena Nováková
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the CAS, Prague, Czechia
| | - Valme Jurado
- Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Institute of Natural Resources and Agricultural Biology (IRNAS-CSIC), Seville, Spain
| | | | - Soledad Cuezva
- Department of Geology, Geography and Environment, University of Alcala, Alcala de Henares, Spain
| | - Cesareo Saiz-Jimenez
- Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Institute of Natural Resources and Agricultural Biology (IRNAS-CSIC), Seville, Spain
| | - Sergio Sanchez-Moral
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), Madrid, Spain
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High Proportions of Radiation-Resistant Strains in Culturable Bacteria from the Taklimakan Desert. BIOLOGY 2022; 11:biology11040501. [PMID: 35453702 PMCID: PMC9030528 DOI: 10.3390/biology11040501] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/19/2022] [Accepted: 03/23/2022] [Indexed: 12/18/2022]
Abstract
Simple Summary Radiation-resistant extremophiles have frequently been found in the Taklimakan Desert, which is known for its harsh conditions. However, there is no systemic study investigating the diversity and proportion of radiation-resistant strains among culturable bacteria. The results of this study revealed the distribution of culturable bacteria in the Taklimakan Desert and indicated high proportions of radiation-resistant strains in the culturable bacteria. The study helps to better understand the ecological origin of radio-resistance and to quantitatively describe the desert as a common habitat for radiation-resistant extremophiles. Abstract The Taklimakan Desert located in China is the second-largest shifting sand desert in the world and is known for its harsh conditions. Types of γ-rays or UV radiation-resistant bacterial strains have been isolated from this desert. However, there is no information regarding the proportions of the radiation-resistant strains in the total culturable microbes. We isolated 352 bacterial strains from nine sites across the Taklimakan Desert from north to south. They belong to Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. The phylum Actinobacteria was the most predominant in abundance and Firmicutes had the highest species richness. Bacteroidetes had the lowest abundance and was found in four sites only, while the other three phyla were found in every site but with different distribution profiles. After irradiating with 1000 J/m2 and 6000 J/m2 UV-C, the strains with survival rates higher than 10% occupied 72.3% and 36.9% of all culturable bacteria, respectively. The members from Proteobacteria had the highest proportions, with survival rates higher than 10%. After radiation with 10 kGy γ-rays, Kocuria sp. TKL1057 and Planococcus sp. TKL1152 showed higher radiation-resistant capabilities than Deinococcus radiodurans R1. Besides obtaining several radiation-resistant extremophiles, this study measured the proportions of the radiation-resistant strains in the total culturable microbes for the first time. This study may help to better understand the origin of radioresistance, especially by quantitatively comparing proportions of radiation-resistant extremophiles from different environments in the future.
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11
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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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12
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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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13
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Cheptsov VS, Belov AA, Vorobyova EA, Pavlov AK, Lomasov VN. Effects of Radiation Intensity, Mineral Matrix, and Pre-Irradiation on the Bacterial Resistance to Gamma Irradiation under Low Temperature Conditions. Microorganisms 2021; 9:198. [PMID: 33477915 PMCID: PMC7833375 DOI: 10.3390/microorganisms9010198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 12/03/2022] Open
Abstract
Ionizing radiation is one of the main factors limiting the survival of microorganisms in extraterrestrial conditions. The survivability of microorganisms under irradiation depends significantly on the conditions, in which the irradiation occurs. In particular, temperature, pressure, oxygen and water concentrations are of great influence. However, the influence of factors such as the radiation intensity (in low-temperature conditions) and the type of mineral matrix, in which microorganisms are located, has been practically unstudied. It has been shown that the radioresistance of bacteria can increase after their exposure to sublethal doses and subsequent repair of damage under favorable conditions, however, such studies are also few and the influence of other factors of extraterrestrial space (temperature, pressure) was not studied in them. The viability of bacteria Arthrobacter polychromogenes, Kocuria rosea and Xanthomonas sp. after irradiation with gamma radiation at a dose of 1 kGy under conditions of low pressure (1 Torr) and low temperature (-50 °C) at different radiation intensities (4 vs. 0.8 kGy/h) with immobilization of bacteria on various mineral matrices (montmorillonite vs. analogue of lunar dust) has been studied. Native, previously non-irradiated strains, and strains that were previously irradiated with gamma radiation and subjected to 10 passages of cultivation on solid media were irradiated. The number of survived cells was determined by culturing on a solid medium. It has been shown that the radioresistance of bacteria depends significantly on the type of mineral matrix, on which they are immobilized, wherein montmorillonite contributes to an increased survivability in comparison with a silicate matrix. Survivability of the studied bacteria was found to increase with decreasing radiation intensity, despite the impossibility of active reparation processes under experimental conditions. Considering the low intensity of radiation on various space objects in comparison with radiobiological experiments, this suggests a longer preservation of the viable microorganisms outside the Earth than is commonly believed. An increase in bacterial radioresistance was revealed even after one cycle of irradiation of the strains and their subsequent cultivation under favourable conditions. This indicates the possibility of hypothetical microorganisms on Mars increasing their radioresistance.
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Affiliation(s)
- Vladimir S. Cheptsov
- Soil Science Faculty, Lomonosov Moscow State University, Leninskie Gory, 1, 12, 119234 Moscow, Russia; (A.A.B.); (E.A.V.)
- Space Research Institute, Russian Academy of Sciences, Profsoyuznaya str., 84/32, 117997 Moscow, Russia
- Network of Researchers on the Chemical Evolution of Life, Leeds LS7 3RB, UK
| | - Andrey A. Belov
- Soil Science Faculty, Lomonosov Moscow State University, Leninskie Gory, 1, 12, 119234 Moscow, Russia; (A.A.B.); (E.A.V.)
- Network of Researchers on the Chemical Evolution of Life, Leeds LS7 3RB, UK
| | - Elena A. Vorobyova
- Soil Science Faculty, Lomonosov Moscow State University, Leninskie Gory, 1, 12, 119234 Moscow, Russia; (A.A.B.); (E.A.V.)
- Network of Researchers on the Chemical Evolution of Life, Leeds LS7 3RB, UK
| | - Anatoli K. Pavlov
- Ioffe Physical-Technical Institute of the Russian Academy of Sciences, Polytechnicheskaya Street, 26, 194021 Saint-Petersburg, Russia;
| | - Vladimir N. Lomasov
- STC “Nuclear Physics”, Peter the Great St. Petersburg State Polytechnic University, Polytechnicheskaya Street, 29, 195251 Saint-Petersburg, Russia;
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14
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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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15
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Han R, Fang J, Jiang J, Gaidamakova EK, Tkavc R, Daly MJ, Contreras LM. Signal Recognition Particle RNA Contributes to Oxidative Stress Response in Deinococcus radiodurans by Modulating Catalase Localization. Front Microbiol 2020; 11:613571. [PMID: 33391243 PMCID: PMC7775534 DOI: 10.3389/fmicb.2020.613571] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
The proper functioning of many proteins requires their transport to the correct cellular compartment or their secretion. Signal recognition particle (SRP) is a major protein transport pathway responsible for the co-translational movement of integral membrane proteins as well as periplasmic proteins. Deinococcus radiodurans is a ubiquitous bacterium that expresses a complex phenotype of extreme oxidative stress resistance, which depends on proteins involved in DNA repair, metabolism, gene regulation, and antioxidant defense. These proteins are located extracellularly or subcellularly, but the molecular mechanism of protein localization in D. radiodurans to manage oxidative stress response remains unexplored. In this study, we characterized the SRP complex in D. radiodurans R1 and showed that the knockdown (KD) of the SRP RNA (Qpr6) reduced bacterial survival under hydrogen peroxide and growth under chronic ionizing radiation. Through LC-mass spectrometry (MS/MS) analysis, we detected 162 proteins in the periplasm of wild-type D. radiodurans, of which the transport of 65 of these proteins to the periplasm was significantly reduced in the Qpr6 KD strain. Through Western blotting, we further demonstrated the localization of the catalases in D. radiodurans, DR_1998 (KatE1) and DR_A0259 (KatE2), in both the cytoplasm and periplasm, respectively, and showed that the accumulation of KatE1 and KatE2 in the periplasm was reduced in the SRP-defective strains. Collectively, this study establishes the importance of the SRP pathway in the survival and the transport of antioxidant proteins in D. radiodurans under oxidative stress.
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Affiliation(s)
- Runhua Han
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Jaden Fang
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Jessie Jiang
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Elena K Gaidamakova
- Uniformed Services University of the Health Sciences, Department of Pathology, Bethesda, MD, United States.,The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Rok Tkavc
- Uniformed Services University of the Health Sciences, Department of Pathology, Bethesda, MD, United States.,The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States.,Uniformed Services University of the Health Sciences, Department of Microbiology and Immunology, Bethesda, MD, United States
| | - Michael J Daly
- Uniformed Services University of the Health Sciences, Department of Pathology, Bethesda, MD, United States
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular & Molecular Biology, The University of Texas at Austin, Austin, TX, United States
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16
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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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17
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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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18
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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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19
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Marušić K, Klarić MŠ, Sinčić L, Pucić I, Mihaljević B. Combined effects of gamma-irradiation, dose rate and mycobiota activity on cultural heritage – Study on model paper. Radiat Phys Chem Oxf Engl 1993 2020. [DOI: 10.1016/j.radphyschem.2019.108641] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Schultzhaus Z, Romsdahl J, Chen A, Tschirhart T, Kim S, Leary D, Wang Z. The response of the melanized yeast Exophiala dermatitidis to gamma radiation exposure. Environ Microbiol 2020; 22:1310-1326. [PMID: 32011087 DOI: 10.1111/1462-2920.14936] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/06/2020] [Accepted: 01/28/2020] [Indexed: 01/21/2023]
Abstract
The melanized yeast Exophiala dermatitidis is resistant to many environmental stresses and is used as a model for understanding the diverse roles of melanin in fungi. Here, we describe the extent of resistance of E. dermatitidis to acute γ-radiation exposure and the major mechanisms it uses to recover from this stress. We find that melanin does not protect E. dermatitidis from γ-radiation. Instead, environmental factors such as nutrient availability, culture age and culture density are much greater determinants of cell survival after exposure. We also observe a dramatic transcriptomic response to γ-radiation that mobilizes pathways involved in morphological development, protein degradation and DNA repair, and is unaffected by the presence of melanin. Together, these results suggest that the ability of E. dermatitidis to survive γ-radiation exposure is determined by the prior and the current metabolic state of the cells as well as DNA repair mechanisms, and that small changes in these conditions can lead to large effects in radiation resistance, which should be taken into account when understanding how diverse fungi recover from this unique stress.
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Affiliation(s)
- Zachary Schultzhaus
- National Research Council Postdoctoral Research Associate, National Research Laboratory, Washington, DC, USA
| | - Jillian Romsdahl
- National Research Council Postdoctoral Research Associate, National Research Laboratory, Washington, DC, USA
| | - Amy Chen
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Tanya Tschirhart
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Seongwon Kim
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Dagmar Leary
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Zheng Wang
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
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21
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Shuryak I. Review of resistance to chronic ionizing radiation exposure under environmental conditions in multicellular organisms. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2020; 212:106128. [PMID: 31818732 DOI: 10.1016/j.jenvrad.2019.106128] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/02/2019] [Accepted: 12/03/2019] [Indexed: 06/10/2023]
Abstract
Ionizing radiation resistance occurs among many phylogenetic groups and its mechanisms remain incompletely understood. Tolerances to acute and chronic irradiation do not always correlate because different mechanisms may be involved. The radioresistance phenomenon becomes even more complex in the field than in the laboratory because the effects of radioactive contamination on natural populations are intertwined with those of other factors, such as bioaccumulation of radionuclides, interspecific competition, seasonal variations in environmental conditions, and land use changes due to evacuation of humans from contaminated areas. Previous reviews of studies performed in radioactive sites like the Kyshtym, Chernobyl, and Fukushima accident regions, and of protracted irradiation experiments, often focused on detecting radiation effects at low doses in radiosensitive organisms. Here we review the literature with a different purpose: to identify organisms with high tolerance to chronic irradiation under environmental conditions, which maintained abundant populations and/or outcompeted more radiosensitive species at high dose rates. Taxa for which consistent evidence for radioresistance came from multiple studies conducted in different locations and at different times were found among plants (e.g. willow and birch trees, sedges), invertebrate and vertebrate animals (e.g. rotifers, some insects, crustaceans and freshwater fish). These organisms are not specialized "extremophiles", but tend to tolerate broad ranges of environmental conditions and stresses, have small genomes, reproduce quickly and/or disperse effectively over long distances. Based on these findings, resistance to radioactive contamination can be examined in a more broad context of chronic stress responses.
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Affiliation(s)
- Igor Shuryak
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168th Street, VC-11-234/5, New York, NY, USA.
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22
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Ogwu MC, Srinivasan S, Dong K, Ramasamy D, Waldman B, Adams JM. Community Ecology of Deinococcus in Irradiated Soil. MICROBIAL ECOLOGY 2019; 78:855-872. [PMID: 30980101 DOI: 10.1007/s00248-019-01343-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/12/2019] [Indexed: 05/24/2023]
Abstract
Deinococcus is a genus of soil bacteria known for radiation resistance. However, the effects of radiation exposure on its community structure are unknown. We exposed soil to three levels of gamma radiation, 0.1 kGy/h (low), 1 kGy/h (medium), and 3 kGy/h (high), once a week for 6 weeks and then extracted soil DNA for 16S rRNA amplicon sequencing. We found the following: (1) Increasing radiation dose produced a major increase in relative abundance of Deinococcus, reaching ~ 80% of reads at the highest doses. Differing abundances of the various Deinococcus species in relation to exposure levels indicate distinct "radiation niches." At 3 kGy/h, a single OTU identified as D. ficus overwhelmingly dominated the mesocosms. (2) Corresponding published genome data show that the dominant species at 3 kGy/h, D. ficus, has a larger and more complex genome than other Deinococcus species with a greater proportion of genes related to DNA and nucleotide metabolism, cell wall, membrane, and envelope biogenesis as well as more cell cycle control, cell division, and chromosome partitioning-related genes. Deinococcus ficus also has a higher guanine-cytosine ratio than most other Deinococcus. These features may be linked to genome stability and may explain its greater abundance in this apparently competitive system, under high-radiation exposures. (3) Genomic analysis suggests that Deinococcus, including D. ficus, are capable of utilizing diverse carbon sources derived from both microbial cells killed by the radiation (including C5-C12-containing compounds, like arabinose, lactose, N-acetyl-D-glucosamine) and plant-derived organic matter in the soil (e.g., cellulose and hemicellulose). (4) Overall, based on its metagenome, even the most highly irradiated (3 kGy/h) soil possesses a wide range of the activities necessary for a functional soil system. Future studies may consider the resilience and sustainability of such soils in a high-radiation environment.
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Affiliation(s)
- Matthew Chidozie Ogwu
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
- Department of Plant Biology and Biotechnology, University of Benin, PMB 1154, Ugbowo, Benin City, Edo State, Nigeria
| | - Sathiyaraj Srinivasan
- Department of Bio and Environmental Technology, Division of Environmental and Life Science, College of Natural Science, Seoul Women's University, 623 Hwarangno, Nowon-gu, Seoul, 139-774, Republic of Korea
| | - Ke Dong
- Department of Life Sciences, Kyonggi University, Suwon, 443-760, Republic of Korea
| | - Dhamodharan Ramasamy
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Bruce Waldman
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
- Department of Integrative Biology, Oklahoma State University, 501 Life Sciences West, Stillwater, OK, 74078, USA.
| | - Jonathan M Adams
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing, 210023, Qixia District, Jiangsu Province, People's Republic of China.
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23
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Shuryak I, Tkavc R, Matrosova VY, Volpe RP, Grichenko O, Klimenkova P, Conze IH, Balygina IA, Gaidamakova EK, Daly MJ. Chronic gamma radiation resistance in fungi correlates with resistance to chromium and elevated temperatures, but not with resistance to acute irradiation. Sci Rep 2019; 9:11361. [PMID: 31388021 PMCID: PMC6684587 DOI: 10.1038/s41598-019-47007-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/10/2019] [Indexed: 02/07/2023] Open
Abstract
Exposure to chronic ionizing radiation (CIR) from nuclear power plant accidents, acts of terrorism, and space exploration poses serious threats to humans. Fungi are a group of highly radiation-resistant eukaryotes, and an understanding of fungal CIR resistance mechanisms holds the prospect of protecting humans. We compared the abilities of 95 wild-type yeast and dimorphic fungal isolates, representing diverse Ascomycota and Basidiomycota, to resist exposure to five environmentally-relevant stressors: CIR (long-duration growth under 36 Gy/h) and acute (10 kGy/h) ionizing radiation (IR), heavy metals (chromium, mercury), elevated temperature (up to 50 °C), and low pH (2.3). To quantify associations between resistances to CIR and these other stressors, we used correlation analysis, logistic regression with multi-model inference, and customized machine learning. The results suggest that resistance to acute IR in fungi is not strongly correlated with the ability of a given fungal isolate to grow under CIR. Instead, the strongest predictors of CIR resistance in fungi were resistance to chromium (III) and to elevated temperature. These results suggest fundamental differences between the mechanisms of resistance to chronic and acute radiation. Convergent evolution towards radioresistance among genetically distinct groups of organisms is considered here.
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Affiliation(s)
- Igor Shuryak
- Center for Radiological Research, Columbia University Irving Medical Center, New York, NY, USA.
| | - Rok Tkavc
- Department of Pathology, Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, USA.,Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, USA
| | - Vera Y Matrosova
- Department of Pathology, Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Robert P Volpe
- Department of Pathology, Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Olga Grichenko
- Department of Pathology, Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Polina Klimenkova
- Department of Pathology, Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Isabel H Conze
- Department of Pathology, Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, USA.,Department of Biology, University of Bielefeld, Bielefeld, Germany
| | - Irina A Balygina
- Department of Pathology, Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, USA.,Institute of Medicine and Psychology, Novosibirsk State University, Novosibirsk, Russia
| | - Elena K Gaidamakova
- Department of Pathology, Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Michael J Daly
- Department of Pathology, Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, USA
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24
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Metataxonomics of Tunisian phosphogypsum based on five bioinformatics pipelines: Insights for bioremediation. Genomics 2019; 112:981-989. [PMID: 31220587 DOI: 10.1016/j.ygeno.2019.06.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 06/15/2019] [Indexed: 11/23/2022]
Abstract
Phosphogypsum (PG) is an acidic by-product from the phosphate fertilizer industry and it is characterized by a low nutrient availability and the presence of radionuclides and heavy metals which pose a serious problem in its management. Here, we have applied Illumina MiSeq sequencing technology and five bioinformatics pipelines to explore the phylogenetic communities in Tunisian PG. Taking One Codex as a reference method, we present the results of 16S-rDNA-gene-based metataxonomics abundances with four other alternative bioinformatics pipelines (MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST), mothur, MICrobial Community Analysis (MICCA) and Quantitative Insights into Microbial Ecology (QIIME)), when analyzing the Tunisian PG. Importantly, based on 16S rDNA datasets, the functional capabilities of microbial communities of PG were deciphered. They suggested the presence of PG autochthonous bacteria valorizable into (1) removal of radioactive elements and toxic heavy metals, (2) promotion of plant growth, (3) oxidation and (4) reduction of sulfate. These bacteria can be explored further for applications in the bioremediation of by-products, like PG, by different processes.
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25
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Minkoff BB, Bruckbauer ST, Sabat G, Cox MM, Sussman MR. Covalent Modification of Amino Acids and Peptides Induced by Ionizing Radiation from an Electron Beam Linear Accelerator Used in Radiotherapy. Radiat Res 2019; 191:447-459. [PMID: 30849023 PMCID: PMC6506356 DOI: 10.1667/rr15288.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
To identify modifications to amino acids that are directly induced by ionizing radiation, free amino acids and 3-residue peptides were irradiated using a linear accelerator (Linac) radiotherapy device. Mass spectrometry was performed to detail the relative sensitivity to radiation as well as identify covalent, radiation-dependent adducts. The order of reactivity of the 20 common amino acids was generally in agreement with published literature except for His (most reactive of the 20) and Cys (less reactive). Novel and previously identified modifications on the free amino acids were detected. Amino acids were far less reactive when flanked by glycine residues in a tripeptide. Order of reactivity, with GVG most and GEG least, was substantially altered, as were patterns of modification. Radiation reactivity of amino acids is clearly and strongly affected by conversion of the α-amino and α-carboxyl groups to peptide bonds, and the presence of neighboring amino acid residues.
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Affiliation(s)
- Benjamin B. Minkoff
- Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Steven T. Bruckbauer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Grzegorz Sabat
- Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Michael R. Sussman
- Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
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26
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Schultzhaus Z, Chen A, Kim S, Shuryak I, Chang M, Wang Z. Transcriptomic analysis reveals the relationship of melanization to growth and resistance to gamma radiation in Cryptococcus neoformans. Environ Microbiol 2019; 21:2613-2628. [PMID: 30724440 DOI: 10.1111/1462-2920.14550] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/29/2019] [Accepted: 01/29/2019] [Indexed: 11/29/2022]
Abstract
The pathogenic fungus Cryptococcus neoformans produces melanin within its cell wall for infection and resistance against external stresses such as exposure to UV, temperature fluctuations and reactive oxygen species. It has been reported that melanin may also protect cells from ionizing radiation damage, against which C. neoformans is extremely resistant. This has tagged melanin as a potential radioprotective biomaterial. Here, we report the effect of melanin on the transcriptomic response of C. neoformans to gamma radiation. We did not observe a substantial protective effect of melanin against gamma radiation, and the general gene expression patterns in irradiated cells were independent of the presence of melanin. However, melanization itself dramatically altered the C. neoformans transcriptome, primarily by repressing genes involved in respiration and cell growth. We suggest that, in addition to providing a physical and chemical barrier against external stresses, melanin production alters the transcriptional landscape of C. neoformans with the result of increased resistance to uncertain environmental conditions. This observation demonstrates the importance of the melanization process in understanding the stress response of C. neoformans and for understanding fungal physiology.
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Affiliation(s)
- Zachary Schultzhaus
- National Research Council Postdoctoral Research Associate, Naval Research Laboratory, Washington, DC, USA
| | - Amy Chen
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Seongwon Kim
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Igor Shuryak
- Center for Radiological Research, Columbia University Irving Medical Center, New York, NY, USA
| | - Melody Chang
- Thomas Jefferson High School for Science and Technology, Alexandria, VA, USA
| | - Zheng Wang
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
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27
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Podolich O, Kukharenko O, Haidak A, Zaets I, Zaika L, Storozhuk O, Palchikovska L, Orlovska I, Reva O, Borisova T, Khirunenko L, Sosnin M, Rabbow E, Kravchenko V, Skoryk M, Kremenskoy M, Demets R, Olsson-Francis K, Kozyrovska N, de Vera JPP. Multimicrobial Kombucha Culture Tolerates Mars-Like Conditions Simulated on Low-Earth Orbit. ASTROBIOLOGY 2019; 19:183-196. [PMID: 30484685 DOI: 10.1089/ast.2017.1746] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A kombucha multimicrobial culture (KMC) was exposed to simulated Mars-like conditions in low-Earth orbit (LEO). The study was part of the Biology and Mars Experiment (BIOMEX), which was accommodated in the European Space Agency's EXPOSE-R2 facility, outside the International Space Station. The aim of the study was to investigate the capability of a KMC microecosystem to survive simulated Mars-like conditions in LEO. During the 18-month exposure period, desiccated KMC samples, represented by living cellulose-based films, were subjected to simulated anoxic Mars-like conditions and ultraviolet (UV) radiation, as prevalent at the surface of present-day Mars. Postexposure analysis demonstrated that growth of both the bacterial and yeast members of the KMC community was observed after 60 days of incubation; whereas growth was detected after 2 days in the initial KMC. The KMC that was exposed to extraterrestrial UV radiation showed degradation of DNA, alteration in the composition and structure of the cellular membranes, and an inhibition of cellulose synthesis. In the "space dark control" (exposed to LEO conditions without the UV radiation), the diversity of the microorganisms that survived in the biofilm was reduced compared with the ground-based controls. This was accompanied by structural dissimilarities in the extracellular membrane vesicles. After a series of subculturing, the revived communities restored partially their structure and associated activities.
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Affiliation(s)
- Olga Podolich
- 1 Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Olga Kukharenko
- 1 Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Andriy Haidak
- 1 Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Iryna Zaets
- 1 Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Leonid Zaika
- 1 Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Olha Storozhuk
- 1 Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | | | - Iryna Orlovska
- 1 Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Oleg Reva
- 2 Department of Biochemistry, Genetics and Microbiology, Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, South Africa
| | | | | | | | - Elke Rabbow
- 5 German Aerospace Center (DLR) Cologne, Institute of Aerospace Medicine, Radiation Biology, Berlin, Germany
| | | | | | | | | | - Karen Olsson-Francis
- 8 School of Environment, Earth and Ecosystem Sciences, The Open University, Milton Keynes, United Kingdom
| | | | - Jean-Pierre Paul de Vera
- 9 Astrobiological Laboratories, German Aerospace Center (DLR) Berlin, Institute of Planetary Research, Management and Infrastructure, Berlin, Germany
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28
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Lim S, Jung JH, Blanchard L, de Groot A. Conservation and diversity of radiation and oxidative stress resistance mechanisms in Deinococcus species. FEMS Microbiol Rev 2019; 43:19-52. [PMID: 30339218 PMCID: PMC6300522 DOI: 10.1093/femsre/fuy037] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 10/17/2018] [Indexed: 12/17/2022] Open
Abstract
Deinococcus bacteria are famous for their extreme resistance to ionising radiation and other DNA damage- and oxidative stress-generating agents. More than a hundred genes have been reported to contribute to resistance to radiation, desiccation and/or oxidative stress in Deinococcus radiodurans. These encode proteins involved in DNA repair, oxidative stress defence, regulation and proteins of yet unknown function or with an extracytoplasmic location. Here, we analysed the conservation of radiation resistance-associated proteins in other radiation-resistant Deinococcus species. Strikingly, homologues of dozens of these proteins are absent in one or more Deinococcus species. For example, only a few Deinococcus-specific proteins and radiation resistance-associated regulatory proteins are present in each Deinococcus, notably the metallopeptidase/repressor pair IrrE/DdrO that controls the radiation/desiccation response regulon. Inversely, some Deinococcus species possess proteins that D. radiodurans lacks, including DNA repair proteins consisting of novel domain combinations, translesion polymerases, additional metalloregulators, redox-sensitive regulator SoxR and manganese-containing catalase. Moreover, the comparisons improved the characterisation of several proteins regarding important conserved residues, cellular location and possible protein–protein interactions. This comprehensive analysis indicates not only conservation but also large diversity in the molecular mechanisms involved in radiation resistance even within the Deinococcus genus.
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Affiliation(s)
- Sangyong Lim
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
| | - Jong-Hyun Jung
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
| | | | - Arjan de Groot
- Aix Marseille Univ, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, France
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29
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Shuryak I. Review of microbial resistance to chronic ionizing radiation exposure under environmental conditions. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2019; 196:50-63. [PMID: 30388428 DOI: 10.1016/j.jenvrad.2018.10.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 10/21/2018] [Indexed: 06/08/2023]
Abstract
Ionizing radiation (IR) produces multiple types of damage to nucleic acids, proteins and other crucial cellular components. Nevertheless, various microorganisms from phylogenetically distant taxa (bacteria, archaea, fungi) can resist IR levels many orders of magnitude above natural background. This intriguing phenomenon of radioresistance probably arose independently many times throughout evolution as a byproduct of selective pressures from other stresses (e.g. desiccation, UV radiation, chemical oxidants). Most of the literature on microbial radioresistance is based on acute γ-irradiation experiments performed in the laboratory, typically involving pure cultures grown under near-optimal conditions. There is much less information about the upper limits of radioresistance in the field, such as in radioactively-contaminated areas, where several radiation types (e.g. α and β, as well as γ) and other stressors (e.g. non-optimal temperature and nutrient levels, toxic chemicals, interspecific competition) act over multiple generations. Here we discuss several examples of radioresistant microbes isolated from extremely radioactive locations (e.g. Chernobyl and Mayak nuclear plant sites) and estimate the radiation dose rates they were able to tolerate. Some of these organisms (e.g. the fungus Cladosporium cladosporioides, the cyanobacterium Geitlerinema amphibium) are widely-distributed and colonize a variety of habitats. These examples suggest that resistance to chronic IR and chemical contamination is not limited to rare specialized strains from extreme environments, but can occur among common microbial taxa, perhaps due to overlap between mechanisms of resistance to IR and other stressors.
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Affiliation(s)
- Igor Shuryak
- Center for Radiological Research, Columbia University, 630 West 168(th) street, VC-11-234/5, New York, NY, 10032, USA.
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30
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Survival of Radioresistant Bacteria on Europa’s Surface after Pulse Ejection of Subsurface Ocean Water. GEOSCIENCES 2018. [DOI: 10.3390/geosciences9010009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We briefly present preliminary results of our study of the radioresistant bacteria in a low temperature and pressure and high-radiation environment and hypothesize the ability of microorganisms to survive extraterrestrial high-radiation environments, such as the icy surface of Jupiter’s moon, Europa. In this study, samples containing a strain of Deinococcus radiodurans VKM B-1422T embedded into a simulated version of Europa’s ice were put under extreme environmental (−130 °C, 0.01 mbar) and radiation conditions using a specially designed experimental vacuum chamber. The samples were irradiated with 5, 10, 50, and 100 kGy doses and subsequently studied for residual viable cells. We estimate the limit of the accumulated dose that viable cells in those conditions could withstand at 50 kGy. Combining our numerical modelling of the accumulated dose in ice with observations of water eruption events on Europa, we hypothesize that in the case of such events, it is possible that putative extraterrestrial organisms might retain viability in a dormant state for up to 10,000 years, and could be sampled and studied by future probe missions.
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31
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Pacelli C, Bryan RA, Onofri S, Selbmann L, Zucconi L, Shuryak I, Dadachova E. Survival and redox activity of Friedmanniomyces endolithicus, an Antarctic endemic black meristematic fungus, after gamma rays exposure. Fungal Biol 2018; 122:1222-1227. [PMID: 30449360 DOI: 10.1016/j.funbio.2018.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/08/2018] [Accepted: 10/12/2018] [Indexed: 11/29/2022]
Abstract
Despite living organisms are not exposed to acute ionizing radiation under natural conditions, some exhibit a high radiation resistance. Understanding this phenomenon is important for assessing the impact of radiation-related accidents, occupational exposures and space missions. In this context, in this study we analyzed the effect of gamma rays on the Antarctic cryptoendolithic melanized fungus Friedmanniomyces endolithicus CCFEE 5208 and demonstrated its resistance to acute doses of gamma radiation (up to 400 Gy), accompanied by increase in metabolic activity.
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Affiliation(s)
- Claudia Pacelli
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy; Albert Einstein College of Medicine, Bronx, New York, USA
| | - Ruth A Bryan
- Albert Einstein College of Medicine, Bronx, New York, USA
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy.
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy; Italian National Antarctic Museum (MNA), Mycological Section, Genoa, Italy
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Igor Shuryak
- Center for Radiological Research, Columbia University, New York, USA
| | - Ekaterina Dadachova
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Canada
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32
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Paithankar JG, Raghu SV, Patil RK. Concomitant changes in radiation resistance and trehalose levels during life stages of Drosophila melanogaster suggest radio-protective function of trehalose. Int J Radiat Biol 2018; 94:576-589. [PMID: 29613812 DOI: 10.1080/09553002.2018.1460499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
PURPOSE During development, various life stages of Drosophila melanogaster (D. melanogaster) show different levels of resistance to gamma irradiation, with the early pupal stage being the most radiation sensitive. This provides us an opportunity to explore the biochemical basis of such variations. The present study was carried out to understand the mechanisms underlying radiation resistance during life stages of D. melanogaster. MATERIALS AND METHODS Homogenates from all the life stages of D. melanogaster were prepared at stipulated age. These homogenates were used for the determination of (1) enzymatic antioxidants: superoxide dismutase (SOD), catalase, D. melanogaster glutathione peroxidase (DmGPx), and glutathione S-transferase (GST); (2) reducing non-enzymatic antioxidants: total antioxidant capacity (TAC), reduced glutathione (GSH) and non-reducing non-enzymatic antioxidant trehalose; and (3) levels of protein carbonyl (PC) content. Age-dependent changes in radiation resistance and associated biochemical changes were also studied in young (2 d) and old (20 and 30 d) flies. RESULTS TAC and GSH were found high in the early pupal stage, whereas catalase and DmGPx were found to increase in the early pupal stage. The non-feeding third instar (NFTI) larvae were found to have high levels of SOD and GST, besides NFTI larvae showed high levels of trehalose. A remarkable decrease was observed in radiation resistance and trehalose levels during the early pupal stage. The PC level was the highest during early pupal stage and was the lowest in NFTI larvae. Older flies showed high level of PC compared with young flies. CONCLUSION In vitro increments in trehalose concentration correspond to reduced formation of PCs, suggesting a protective role of trehalose against free radicals. A strong correlation between levels of trehalose and PC formation suggests amelioration of proteome damage due to ionizing radiation (IR). Stages with high trehalose levels showed protected proteome and high radiation resistance, suggesting a significant role for this disaccharide in radiation resistance.
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Affiliation(s)
| | | | - Rajashekhar K Patil
- a Department of Applied Zoology , Mangalore University , Mangalore , Karnataka , India.,b Centre for Radioisotopes and Radiation Technology (CARRT) , Mangalore University , Mangalore , Karnataka , India
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