1
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Rai SN, Dutta T. Role of Yrn2 under oxidative stress in Deinococcus radiodurans. Biochem Biophys Res Commun 2024; 723:150169. [PMID: 38815487 DOI: 10.1016/j.bbrc.2024.150169] [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: 05/15/2024] [Revised: 05/18/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024]
Abstract
Among the two Y RNAs in Deinococcus radiodurans, the functional properties of Yrn2 are still not known. Yrn2 although consists of a long stem-loop for Rsr binding, differs from Yrn1 in the effector binding site. An initial study on Yrn2 delineated it to be a UV-induced noncoding RNA. Apart from that Yrn2 has scarcely been investigated. In the current study, we identified Yrn2 as an γ-radiation induced Y RNA, which is also induced upon H2O2 and mitomycin treatment. Ectopically expressed Yrn2 appeared to be nontoxic to the cell growth. An overabundance of Yrn2 was found to ameliorate cell survival under oxidative stress through the detoxification of intracellular reactive oxygen species with a subsequent decrease in total protein carbonylation. A significant accumulation of intracellular Mn(II) with unaltered Fe(II) and Zn(II) with detected while Yrn2 is overabundant in the cells. This study identified the role of a novel Yrn2 under oxidative stress in D. radiodurans.
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Affiliation(s)
- Shiv Narayan Rai
- RNA Biology Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Tanmay Dutta
- RNA Biology Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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2
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Petkowski JJ, Seager S, Bains W. Reasons why life on Earth rarely makes fluorine-containing compounds and their implications for the search for life beyond Earth. Sci Rep 2024; 14:15575. [PMID: 38971876 PMCID: PMC11227584 DOI: 10.1038/s41598-024-66265-w] [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: 02/10/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024] Open
Abstract
Life on Earth is known to rarely make fluorinated carbon compounds, as compared to other halocarbons. We quantify this rarity, based on our exhaustive natural products database curated from available literature. We build on explanations for the scarcity of fluorine chemistry in life on Earth, namely that the exclusion of the C-F bond stems from the unique physico-chemical properties of fluorine, predominantly its extreme electronegativity and strong hydration shell. We further show that the C-F bond is very hard to synthesize and when it is made by life its potential biological functions can be readily provided by alternative functional groups that are much less costly to incorporate into existing biochemistry. As a result, the overall evolutionary cost-to-benefit balance of incorporation of the C-F bond into the chemical repertoire of life is not favorable. We argue that the limitations of organofluorine chemistry are likely universal in that they do not exclusively apply to specifics of Earth's biochemistry. C-F bonds, therefore, will be rare in life beyond Earth no matter its chemical makeup.
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Affiliation(s)
- Janusz J Petkowski
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
- Faculty of Environmental Engineering, Wroclaw University of Science and Technology, 50-370, Wroclaw, Poland.
- JJ Scientific, Warsaw, Mazowieckie, Poland.
| | - Sara Seager
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - William Bains
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- School of Physics & Astronomy, Cardiff University, 4 The Parade, Cardiff, CF24 3AA, UK
- Rufus Scientific, Melbourn, Royston, Herts, UK
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3
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Geng F, Zhong L, Yang T, Chen J, Yang P, Jiang F, Yan T, Song B, Yu Z, Yu D, Zhang J, Cao J, Zhang S. A Frog Skin-Derived Peptide Targeting SCD1 Exerts Radioprotective Effects Against Skin Injury by Inhibiting STING-Mediated Inflammation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306253. [PMID: 38582510 PMCID: PMC11220654 DOI: 10.1002/advs.202306253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 03/22/2024] [Indexed: 04/08/2024]
Abstract
The extensive application of nuclear technology has increased the potential of uncontrolled radiation exposure to the public. Since skin is the largest organ, radiation-induced skin injury remains a serious medical concern. Organisms evolutionally develop distinct strategies to protect against environment insults and the related research may bring novel insights into therapeutics development. Here, 26 increased peptides are identified in skin tissues of frogs (Pelophylax nigromaculatus) exposed to electron beams, among which four promoted the wound healing of irradiated skin in rats. Specifically, radiation-induced frog skin peptide-2 (RIFSP-2), from histone proteolysis exerted membrane permeability property, maintained cellular homeostasis, and reduced pyroptosis of irradiated cells with decreased TBK1 phosphorylation. Subsequently, stearyl-CoA desaturase 1 (SCD1) is identified, a critical enzyme in biogenesis of monounsaturated fatty acids (MUFAs) as a direct target of RIFSP-2 based on streptavidin-biotin system. The lipidomic analysis further assured the restrain of MUFAs biogenesis by RIFSP-2 following radiation. Moreover, the decreased MUFA limited radiation-induced and STING-mediated inflammation response. In addition, genetic depletion or pharmacological inhibition of STING counteracted the decreased pyroptosis by RIFSP-2 and retarded tissue repair process. Altogether, RIFSP-2 restrains radiation-induced activation of SCD1-MUFA-STING axis. Thus, the stress-induced amphibian peptides can be a bountiful source of novel radiation mitigators.
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Affiliation(s)
- Fenghao Geng
- Laboratory of Radiation MedicineWest China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengdu610041China
- Laboratory of Radiation MedicineWest China Second University HospitalSichuan UniversityChengdu610041China
- Radiation Medicine Department of Institute of Preventive MedicineFourth Military Medical UniversityXi'an710032China
| | - Li Zhong
- School of Radiation Medicine and ProtectionState Key Laboratory of Radiation MedicineSoochow UniversitySuzhou215123China
| | - Tingyi Yang
- Laboratory of Radiation MedicineWest China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengdu610041China
| | - Jianhui Chen
- Laboratory of Radiation MedicineWest China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengdu610041China
| | - Ping Yang
- Laboratory of Radiation MedicineWest China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengdu610041China
| | - Fengdi Jiang
- Laboratory of Radiation MedicineWest China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengdu610041China
| | - Tao Yan
- Laboratory of Radiation MedicineWest China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengdu610041China
| | - Bin Song
- Laboratory of Radiation MedicineWest China Second University HospitalSichuan UniversityChengdu610041China
| | - Zuxiang Yu
- Laboratory of Radiation MedicineWest China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengdu610041China
| | - Daojiang Yu
- The Second Affiliated Hospital of Chengdu Medical CollegeChina National Nuclear Corporation 416 HospitalChengdu610051China
| | - Jie Zhang
- Radiation Medicine Department of Institute of Preventive MedicineFourth Military Medical UniversityXi'an710032China
| | - Jianping Cao
- School of Radiation Medicine and ProtectionState Key Laboratory of Radiation MedicineSoochow UniversitySuzhou215123China
| | - Shuyu Zhang
- Laboratory of Radiation MedicineWest China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengdu610041China
- Laboratory of Radiation MedicineWest China Second University HospitalSichuan UniversityChengdu610041China
- The Second Affiliated Hospital of Chengdu Medical CollegeChina National Nuclear Corporation 416 HospitalChengdu610051China
- NHC Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital)Mianyang621099China
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4
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Cordova A, Niese B, Sweet P, Kamat P, Phillip JM, Gordon V, Contreras LM. Quantitative morphological analysis of Deinococcus radiodurans elucidates complex dose-dependent nucleoid condensation during recovery from ionizing radiation. Appl Environ Microbiol 2024:e0010824. [PMID: 38864629 DOI: 10.1128/aem.00108-24] [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: 01/20/2024] [Accepted: 05/19/2024] [Indexed: 06/13/2024] Open
Abstract
The extremophile Deinococcus radiodurans maintains a highly organized and condensed nucleoid as its default state, possibly contributing to its high tolerance to ionizing radiation (IR). Previous studies of the D. radiodurans nucleoid were limited by reliance on manual image annotation and qualitative metrics. Here, we introduce a high-throughput approach to quantify the geometric properties of cells and nucleoids using confocal microscopy, digital reconstructions of cells, and computational modeling. We utilize this novel approach to investigate the dynamic process of nucleoid condensation in response to IR stress. Our quantitative analysis reveals that at the population level, exposure to IR induced nucleoid compaction and decreased the size of D. radiodurans cells. Morphological analysis and clustering identified six distinct sub-populations across all tested experimental conditions. Results indicate that exposure to IR induced fractional redistributions of cells across sub-populations to exhibit morphologies associated with greater nucleoid condensation and decreased the abundance of sub-populations associated with cell division. Nucleoid-associated proteins (NAPs) may link nucleoid compaction and stress tolerance, but their roles in regulating compaction in D. radiodurans are unknown. Imaging of genomic mutants of known and suspected NAPs that contribute to nucleoid condensation found that deletion of nucleic acid-binding proteins, not previously described as NAPs, can remodel the nucleoid by driving condensation or decondensation in the absence of stress and that IR increased the abundance of these morphological states. Thus, our integrated analysis introduces a new methodology for studying environmental influences on bacterial nucleoids and provides an opportunity to further investigate potential regulators of nucleoid condensation.IMPORTANCEDeinococcus radiodurans, an extremophile known for its stress tolerance, constitutively maintains a highly condensed nucleoid. Qualitative studies have described nucleoid behavior under a variety of conditions. However, a lack of quantitative data regarding nucleoid organization and dynamics has limited our understanding of the regulatory mechanisms controlling nucleoid organization in D. radiodurans. Here, we introduce a quantitative approach that enables high-throughput quantitative measurements of subcellular spatial characteristics in bacterial cells. Applying this to wild-type or single-protein-deficient populations of D. radiodurans subjected to ionizing radiation, we identified significant stress-responsive changes in cell shape, nucleoid organization, and morphology. These findings highlight this methodology's adaptability and capacity for quantitatively analyzing the cellular response to stressors for screening cellular proteins involved in bacterial nucleoid organization.
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Affiliation(s)
- Antonio Cordova
- Interdisciplinary Life Sciences Graduate Program, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas, USA
| | - Brandon Niese
- Department of Physics, Center for Nonlinear Dynamics, The University of Texas at Austin, Austin, Texas, USA
| | - Philip Sweet
- Interdisciplinary Life Sciences Graduate Program, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Pratik Kamat
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jude M Phillip
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Biomedical Engineering, Institute for Nanobiotechnology, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Vernita Gordon
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas, USA
- Department of Physics, Center for Nonlinear Dynamics, The University of Texas at Austin, Austin, Texas, USA
- LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, Texas, USA
| | - Lydia M Contreras
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas, USA
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, USA
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5
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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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6
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Caro-Astorga J, Meyerowitz JT, Stork DA, Nattermann U, Piszkiewicz S, Vimercati L, Schwendner P, Hocher A, Cockell C, DeBenedictis E. Polyextremophile engineering: a review of organisms that push the limits of life. Front Microbiol 2024; 15:1341701. [PMID: 38903795 PMCID: PMC11188471 DOI: 10.3389/fmicb.2024.1341701] [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: 11/20/2023] [Accepted: 05/16/2024] [Indexed: 06/22/2024] Open
Abstract
Nature exhibits an enormous diversity of organisms that thrive in extreme environments. From snow algae that reproduce at sub-zero temperatures to radiotrophic fungi that thrive in nuclear radiation at Chernobyl, extreme organisms raise many questions about the limits of life. Is there any environment where life could not "find a way"? Although many individual extremophilic organisms have been identified and studied, there remain outstanding questions about the limits of life and the extent to which extreme properties can be enhanced, combined or transferred to new organisms. In this review, we compile the current knowledge on the bioengineering of extremophile microbes. We summarize what is known about the basic mechanisms of extreme adaptations, compile synthetic biology's efforts to engineer extremophile organisms beyond what is found in nature, and highlight which adaptations can be combined. The basic science of extremophiles can be applied to engineered organisms tailored to specific biomanufacturing needs, such as growth in high temperatures or in the presence of unusual solvents.
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Affiliation(s)
| | | | - Devon A. Stork
- Pioneer Research Laboratories, San Francisco, CA, United States
| | - Una Nattermann
- Pioneer Research Laboratories, San Francisco, CA, United States
| | | | - Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States
| | | | - Antoine Hocher
- London Institute of Medical Sciences, London, United Kingdom
| | - Charles Cockell
- UK Centre for Astrobiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Erika DeBenedictis
- The Francis Crick Institute, London, United Kingdom
- Pioneer Research Laboratories, San Francisco, CA, United States
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7
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Williamson AJ, Binet M, Sergeant C. Radionuclide biogeochemistry: from bioremediation toward the treatment of aqueous radioactive effluents. Crit Rev Biotechnol 2024; 44:698-716. [PMID: 37258417 DOI: 10.1080/07388551.2023.2194505] [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: 11/02/2021] [Revised: 10/07/2022] [Accepted: 01/29/2023] [Indexed: 06/02/2023]
Abstract
Civilian and military nuclear programs of several nations over more than 70 years have led to significant quantities of heterogenous solid, organic, and aqueous radioactive wastes bearing actinides, fission products, and activation products. While many physicochemical treatments have been developed to remediate, decontaminate and reduce waste volumes, they can involve high costs (energy input, expensive sorbants, ion exchange resins, chemical reducing/precipitation agents) or can lead to further secondary waste forms. Microorganisms can directly influence radionuclide solubility, via sorption, accumulation, precipitation, redox, and volatilization pathways, thus offering a more sustainable approach to remediation or effluent treatments. Much work to date has focused on fundamentals or laboratory-scale remediation trials, but there is a paucity of information toward field-scale bioremediation and, to a lesser extent, toward biological liquid effluent treatments. From the few biostimulation studies that have been conducted at legacy weapon production/test sites and uranium mining and milling sites, some marked success via bioreduction and biomineralisation has been observed. However, rebounding of radionuclide mobility from (a)biotic scale-up factors are often encountered. Radionuclide, heavy metal, co-contaminant, and/or matrix effects provide more challenging conditions than traditional industrial wastewater systems, thus innovative solutions via indirect interactions with stable element biogeochemical cycles, natural or engineered cultures or communities of metal and irradiation tolerant strains and reactor design inspirations from existing metal wastewater technologies, are required. This review encompasses the current state of the art in radionuclide biogeochemistry fundamentals and bioremediation and establishes links toward transitioning these concepts toward future radioactive effluent treatments.
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Affiliation(s)
| | - Marie Binet
- EDF R&D, LNHE (Laboratoire National d'Hydraulique et Environnement), Chatou, France
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8
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Rai SN, Dutta T. A novel ionizing radiation-induced small RNA, DrsS, promotes the detoxification of reactive oxygen species in Deinococcus radiodurans. Appl Environ Microbiol 2024; 90:e0153823. [PMID: 38587394 PMCID: PMC11107164 DOI: 10.1128/aem.01538-23] [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: 09/27/2023] [Accepted: 02/27/2024] [Indexed: 04/09/2024] Open
Abstract
A plethora of gene regulatory mechanisms with eccentric attributes in Deinoccocus radiodurans confer it to possess a distinctive ability to survive under ionizing radiation. Among the many regulatory processes, small RNA (sRNA)-mediated regulation of gene expression is prevalent in bacteria but barely investigated in D. radiodurans. In the current study, we identified a novel sRNA, DrsS, through RNA-seq analysis in D. radiodurans cells while exposed to ionizing radiation. Initial sequence analysis for promoter identification revealed that drsS is potentially co-transcribed with sodA and dr_1280 from a single operon. Elimination of the drsS allele in D. radiodurans chromosome resulted in an impaired growth phenotype under γ-radiation. DrsS has also been found to be upregulated under oxidative and genotoxic stresses. Deletion of the drsS gene resulted in the depletion of intracellular concentration of both Mn2+ and Fe2+ by ~70% and 40%, respectively, with a concomitant increase in carbonylation of intracellular protein. Complementation of drsS gene in ΔdrsS cells helped revert its intracellular Mn2+ and Fe2+ concentration and alleviated carbonylation of intracellular proteins. Cells with deleted drsS gene exhibited higher sensitivity to oxidative stress than wild-type cells. Extrachromosomally expressed drsS in ΔdrsS cells retrieved its oxidative stress resistance properties by catalase-mediated detoxification of reactive oxygen species (ROS). In vitro binding assays indicated that DsrS directly interacts with the coding region of the katA transcript, thus possibly protecting it from cellular endonucleases in vivo. This study identified a novel small RNA DrsS and investigated its function under oxidative stress in D. radiodurans. IMPORTANCE Deinococcus radiodurans possesses an idiosyncratic quality to survive under extreme ionizing radiation and, thus, has evolved with diverse mechanisms which promote the mending of intracellular damages caused by ionizing radiation. As sRNAs play a pivotal role in modulating gene expression to adapt to altered conditions and have been delineated to participate in almost all physiological processes, understanding the regulatory mechanism of sRNAs will unearth many pathways that lead to radioresistance in D. radiodurans. In that direction, DrsS has been identified to be a γ-radiation-induced sRNA, which is also induced by oxidative and genotoxic stresses. DrsS appeared to activate catalase under oxidative stress and detoxify intracellular ROS. This sRNA has also been shown to balance intracellular Mn(II) and Fe concentrations protecting intracellular proteins from carbonylation. This novel mechanism of DrsS identified in D. radiodurans adds substantially to our knowledge of how this bacterium exploits sRNA for its survival under stresses.
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Affiliation(s)
- Shiv Narayan Rai
- RNA Biology Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India
| | - Tanmay Dutta
- RNA Biology Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India
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9
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Rolland SGM, Memar N, Gartner A. Tardigrades: Trained to be hardy in the face of DNA damage. Curr Biol 2024; 34:R504-R507. [PMID: 38772339 DOI: 10.1016/j.cub.2024.04.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Tardigrades withstand ionizing irradiation levels ∼500 times higher than humans can tolerate. Two recent papers shed light on how this might be achieved - via the transcriptional induction of DNA repair genes, the induction of a radioprotective DNA-binding protein, and possibly also the heightened capacity of repair proteins.
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Affiliation(s)
- Stéphane G M Rolland
- Center for Genomic Integrity, Institute for Basic Science, UNIST-gil 50, Ulsan 44919, Republic of Korea
| | - Nadin Memar
- Center for Genomic Integrity, Institute for Basic Science, UNIST-gil 50, Ulsan 44919, Republic of Korea
| | - Anton Gartner
- Center for Genomic Integrity, Institute for Basic Science, UNIST-gil 50, Ulsan 44919, Republic of Korea; Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Graduate School for Health Sciences and Technology, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
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10
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Morales-Hidalgo M, Povedano-Priego C, Martinez-Moreno MF, Ruiz-Fresneda MA, Lopez-Fernandez M, Jroundi F, Merroun ML. Insights into the Impact of Physicochemical and Microbiological Parameters on the Safety Performance of Deep Geological Repositories. Microorganisms 2024; 12:1025. [PMID: 38792854 PMCID: PMC11123828 DOI: 10.3390/microorganisms12051025] [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: 04/23/2024] [Revised: 05/06/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
Currently, the production of radioactive waste from nuclear industries is increasing, leading to the development of reliable containment strategies. The deep geological repository (DGR) concept has emerged as a suitable storage solution, involving the underground emplacement of nuclear waste within stable geological formations. Bentonite clay, known for its exceptional properties, serves as a critical artificial barrier in the DGR system. Recent studies have suggested the stability of bentonite within DGR relevant conditions, indicating its potential to enhance the long-term safety performance of the repository. On the other hand, due to its high resistance to corrosion, copper is one of the most studied reference materials for canisters. This review provides a comprehensive perspective on the influence of nuclear waste conditions on the characteristics and properties of DGR engineered barriers. This paper outlines how evolving physico-chemical parameters (e.g., temperature, radiation) in a nuclear repository may impact these barriers over the lifespan of a repository and emphasizes the significance of understanding the impact of microbial processes, especially in the event of radionuclide leakage (e.g., U, Se) or canister corrosion. Therefore, this review aims to address the long-term safety of future DGRs, which is critical given the complexity of such future systems.
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Affiliation(s)
- Mar Morales-Hidalgo
- Department of Microbiology, Faculty of Sciences, University of Granada, 18071 Granada, Spain; (C.P.-P.); (M.F.M.-M.); (M.A.R.-F.); (M.L.-F.); (M.L.M.)
| | | | | | | | | | - Fadwa Jroundi
- Department of Microbiology, Faculty of Sciences, University of Granada, 18071 Granada, Spain; (C.P.-P.); (M.F.M.-M.); (M.A.R.-F.); (M.L.-F.); (M.L.M.)
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11
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Mota C, Webster M, Saidi M, Kapp U, Zubieta C, Giachin G, Manso JA, de Sanctis D. Metal ion activation and DNA recognition by the Deinococcus radiodurans manganese sensor DR2539. FEBS J 2024. [PMID: 38652591 DOI: 10.1111/febs.17140] [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: 02/15/2024] [Revised: 03/14/2024] [Accepted: 04/10/2024] [Indexed: 04/25/2024]
Abstract
The accumulation of manganese ions is crucial for scavenging reactive oxygen species and protecting the proteome of Deinococcus radiodurans (Dr). However, metal homeostasis still needs to be tightly regulated to avoid toxicity. DR2539, a dimeric transcription regulator, plays a key role in Dr manganese homeostasis. Despite comprising three well-conserved domains - a DNA-binding domain, a dimerisation domain, and an ancillary domain - the mechanisms underlying both, metal ion activation and DNA recognition remain elusive. In this study, we present biophysical analyses and the structure of the dimerisation and DNA-binding domains of DR2539 in its holo-form and in complex with the 21 base pair pseudo-palindromic repeat of the dr1709 promoter region, shedding light on these activation and recognition mechanisms. The dimer presents eight manganese binding sites that induce structural conformations essential for DNA binding. The analysis of the protein-DNA interfaces elucidates the significance of Tyr59 and helix α3 sequence in the interaction with the DNA. Finally, the structure in solution as determined by small-angle X-ray scattering experiments and supported by AlphaFold modeling provides a model illustrating the conformational changes induced upon metal binding.
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Affiliation(s)
- Cristiano Mota
- ESRF - The European Synchrotron, Grenoble, France
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | | | | | - Ulrike Kapp
- ESRF - The European Synchrotron, Grenoble, France
| | | | | | - José Antonio Manso
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
- I3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
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Sharma DK, Soni I, Misra HS, Rajpurohit YS. Natural transformation-specific DprA coordinate DNA double-strand break repair pathways in heavily irradiated D. radiodurans. Appl Environ Microbiol 2024; 90:e0194823. [PMID: 38193676 PMCID: PMC10880594 DOI: 10.1128/aem.01948-23] [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: 10/30/2023] [Accepted: 12/02/2023] [Indexed: 01/10/2024] Open
Abstract
Deinococcus radiodurans exhibits remarkable survival under extreme conditions, including ionizing radiation, desiccation, and various DNA-damaging agents. It employs unique repair mechanisms, such as single-strand annealing (SSA) and extended synthesis-dependent strand annealing (ESDSA), to efficiently restore damaged genome. In this study, we investigate the role of the natural transformation-specific protein DprA in DNA repair pathways following acute gamma radiation exposure. Our findings demonstrate that the absence of DprA leads to rapid repair of gamma radiation-induced DNA double-strand breaks primarily occur through SSA repair pathway. Additionally, our findings suggest that the DprA protein may hinder both the SSA and ESDSA repair pathways, albeit in distinct manners. Overall, our results highlight the crucial function of DprA in the selection between SSA and ESDSA pathways for DNA repair in heavily irradiated D. radiodurans.IMPORTANCEDeinococcus radiodurans exhibits an extraordinary ability to endure and thrive in extreme environments, including exposure to radiation, desiccation, and damaging chemicals, as well as intense UV radiation. The bacterium has evolved highly efficient repair mechanisms capable of rapidly mending hundreds of DNA fragments in its genome. Our research indicates that natural transformation (NT)-specific dprA genes play a pivotal role in regulating DNA repair in response to radiation. Remarkably, we found that DprA is instrumental in selecting DNA double-strand break repair pathways, a novel function that has not been reported before. This unique regulatory mechanism highlights the indispensable role of DprA beyond its native function in NT and underscores its ubiquitous presence across various bacterial species, regardless of their NT proficiency. These findings shed new light on the resilience and adaptability of Deinococcus radiodurans, opening avenues for further exploration into its exceptional survival strategies.
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Affiliation(s)
- Dhirendra Kumar Sharma
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute (DAE- Deemed University), Mumbai, India
| | - Ishu Soni
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute (DAE- Deemed University), Mumbai, India
| | - Hari S. Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Yogendra Singh Rajpurohit
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute (DAE- Deemed University), Mumbai, India
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Park JH, Lee S, Shin E, Abdi Nansa S, Lee SJ. The Transposition of Insertion Sequences in Sigma-Factor- and LysR-Deficient Mutants of Deinococcus geothermalis. Microorganisms 2024; 12:328. [PMID: 38399731 PMCID: PMC10892881 DOI: 10.3390/microorganisms12020328] [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: 01/17/2024] [Revised: 01/29/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Some insertion sequence (IS) elements were actively transposed using oxidative stress conditions, including gamma irradiation and hydrogen peroxide treatment, in Deinococcus geothermalis, a radiation-resistant bacterium. D. geothermalis wild-type (WT), sigma factor gene-disrupted (∆dgeo_0606), and LysR gene-disrupted (∆dgeo_1692) mutants were examined for IS induction that resulted in non-pigmented colonies after gamma irradiation (5 kGy) exposure. The loss of pigmentation occurred because dgeo_0524, which encodes a phytoene desaturase in the carotenoid pathway, was disrupted by the transposition of IS elements. The types and loci of the IS elements were identified as ISDge2 and ISDge6 in the ∆dgeo_0606 mutant and ISDge5 and ISDge7 in the ∆dgeo_1692 mutant, but were not identified in the WT strain. Furthermore, 80 and 100 mM H2O2 treatments induced different transpositions of IS elements in ∆dgeo_0606 (ISDge5, ISDge6, and ISDge7) and WT (ISDge6). However, no IS transposition was observed in the ∆dgeo_1692 mutant. The complementary strain of the ∆dgeo_0606 mutation showed recovery effects in the viability assay; however, the growth-delayed curve did not return because the neighboring gene dgeo_0607 was overexpressed, probably acting as an anti-sigma factor. The expression levels of certain transposases, recognized as pivotal contributors to IS transposition, did not precisely correlate with active transposition in varying oxidation environments. Nevertheless, these findings suggest that specific IS elements integrated into dgeo_0524 in a target-gene-deficient and oxidation-source-dependent manner.
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Affiliation(s)
| | | | | | | | - Sung-Jae Lee
- Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea; (J.H.P.); (S.L.); (E.S.); (S.A.N.)
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Bratkic A, Jazbec A, Toplak N, Koren S, Lojen S, Tinta T, Kostanjsek R, Snoj L. The colonization of an irradiated environment: the case of microbial biofilm in a nuclear reactor. Int J Radiat Biol 2024; 100:108-121. [PMID: 37812192 DOI: 10.1080/09553002.2023.2258206] [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: 11/25/2022] [Accepted: 08/19/2023] [Indexed: 10/10/2023]
Abstract
The investigation of the microbial community change in the biofilm, growing on the walls of a containment tank of TRIGA nuclear reactor revealed a thriving community in an oligotrophic and heavy-metal-laden environment, periodically exposed to high pulses of ionizing radiation (IR). We observed a vertical IR resistance/tolerance stratification of microbial genera, with higher resistance and less diversity closer to the reactor core. One of the isolated Bacillus strains survived 15 kGy of combined gamma and proton radiation, which was surprising. It appears that there is a succession of genera that colonizes or re-colonizes new or IR-sterilized surfaces, led by Bacilli and/or Actinobacteria, upon which a photoautotrophic and diazotrophic community is established within a fortnight. The temporal progression of the biofilm community was evaluated also as a proxy for microbial response to radiological contamination events. This indicated there is a need for better dose-response models that could describe microbial response to contamination events. Overall, TRIGA nuclear reactor offers a unique insight into IR microbiology and provides useful means to study relevant microbial dose-thresholds during and after radiological contamination.
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Affiliation(s)
- Arne Bratkic
- Department of Environmental Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Anze Jazbec
- Reactor Physics Division, Jožef Stefan Institute, Ljubljana, Slovenia
| | | | | | - Sonja Lojen
- Department of Environmental Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Tinkara Tinta
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
| | - Rok Kostanjsek
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Luka Snoj
- Reactor Physics Division, Jožef Stefan Institute, Ljubljana, Slovenia
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15
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Aureli L, Coleine C, Delgado-Baquerizo M, Ahren D, Cemmi A, Di Sarcina I, Onofri S, Selbmann L. Geography and environmental pressure are predictive of class-specific radioresistance in black fungi. Environ Microbiol 2023; 25:2931-2942. [PMID: 37775957 DOI: 10.1111/1462-2920.16510] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/13/2023] [Indexed: 10/01/2023]
Abstract
Black fungi are among the most resistant organisms to ionizing radiation on Earth. However, our current knowledge is based on studies on a few isolates, while the overall radioresistance limits across this microbial group and the relationship with local environmental conditions remain largely undetermined. To address this knowledge gap, we assessed the survival of 101 strains of black fungi isolated across a worldwide spatial distribution to gamma radiation doses up to 100 kGy. We found that intra and inter-specific taxonomy, UV radiation, and precipitation levels primarily influence the radioresistance in black fungi. Altogether, this study provides insights into the adaptive mechanisms of black fungi to extreme environments and highlights the role of local adaptation in shaping the survival capabilities of these extreme-tolerant organisms.
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Affiliation(s)
- Lorenzo Aureli
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
- Department of Biology, Lund University, Lund, Sweden
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Manuel Delgado-Baquerizo
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Sevilla, Spain
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Dag Ahren
- Department of Biology, Lund University, Lund, Sweden
- Department of Biology, National Bioinformatics Infrastructure Sweden (NBIS), Lund University, Lund, Sweden
| | - Alessia Cemmi
- Fusion and Technology for Nuclear Safety and Security Department, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA FSN-FISS-SNI), Rome, Italy
| | - Ilaria Di Sarcina
- Fusion and Technology for Nuclear Safety and Security Department, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA FSN-FISS-SNI), Rome, Italy
| | - 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
- Mycological Section, Italian Antarctic National Museum (MNA), Genoa, Italy
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De Mandal S, Srinivasan S, Jeon J. Complete genome sequence of Deinococcus rubellus Ant6 isolated from the fish muscle in the Antarctic Ocean. Front Bioeng Biotechnol 2023; 11:1257705. [PMID: 37908375 PMCID: PMC10614293 DOI: 10.3389/fbioe.2023.1257705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/25/2023] [Indexed: 11/02/2023] Open
Affiliation(s)
- Surajit De Mandal
- Department of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
| | - Sathiyaraj Srinivasan
- Department of Bio and Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul, Republic of Korea
| | - Junhyun Jeon
- Department of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
- Plant Immunity Research Center, Seoul National University, Seoul, Republic of Korea
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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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Foster L, Boothman C, Harrison S, Jenkinson P, Pittman JK, Lloyd JR. Identification of algal rich microbial blooms in the Sellafield Pile Fuel Storage Pond and the application of ultrasonic treatment to control the formation of blooms. Front Microbiol 2023; 14:1261801. [PMID: 37860139 PMCID: PMC10582928 DOI: 10.3389/fmicb.2023.1261801] [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: 07/19/2023] [Accepted: 09/19/2023] [Indexed: 10/21/2023] Open
Abstract
The presence of microorganisms in a range of nuclear facilities has been known for many years. In this study the microbial community inhabiting the Pile Fuel Storage Pond (PFSP), which is a legacy open-aired facility on the Sellafield nuclear site, Cumbria, UK, was determined to help target microbial bloom management strategies in this facility. The PFSP is currently undergoing decommissioning and the development of prolonged dense microbial blooms reduces the visibility within the water. Such impairment in the pond water visibility can lead to delays in pond operations, which also has financial implications. Efforts to control the microbial population within the PFSP are ongoing, with the installation of ultrasonic treatment units. Here next generation sequencing techniques focussing on broad targets for both eukaryotic and prokaryotic organisms were used to identify the microbial community. On-site monitoring of photosynthetic pigments indicated when microbial blooms formed and that eukaryotic algae were most likely to be responsible for these events. The sequencing data suggested that the blooms were dominated by members of the class Chrysophyceae, a group of golden algae, while evidence of cyanobacteria and other photosynthetic bacteria was limited, further supporting eukaryotic organisms causing the blooms. The results of sequencing data from 2018 was used to inform a change in the operational settings of the ultrasonic units, while monitoring of the microbial community and photosynthetic pigments trends was extended. Since the changes were made to the ultrasonic treatment, the visibility in the pond was significantly improved, with an absence of a spring bloom in 2020 and an overall reduction in the number of days lost due to microbial blooms annually. This work extends our knowledge of the diversity of microbes able to colonise nuclear fuel storage ponds, and also suggests that sequencing data can help to optimise the performance of ultrasonic treatments, to control algal proliferation in the PFSP facility and other inhospitable engineered systems.
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Affiliation(s)
- Lynn Foster
- Research Centre for Radwaste Disposal and Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, United Kingdom
| | - Christopher Boothman
- Research Centre for Radwaste Disposal and Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, United Kingdom
| | - Scott Harrison
- National Nuclear Laboratory, Central Laboratory, Sellafield, Seascale, United Kingdom
| | | | - Jon K. Pittman
- Research Centre for Radwaste Disposal and Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, United Kingdom
| | - Jonathan R. Lloyd
- Research Centre for Radwaste Disposal and Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, United Kingdom
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19
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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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20
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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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Wu S, Tian C, Tu Z, Guo J, Xu F, Qin W, Chang H, Wang Z, Hu T, Sun X, Ning H, Li Y, Gou W, Hou W. Protective effect of total flavonoids of Engelhardia roxburghiana Wall. leaves against radiation-induced intestinal injury in mice and its mechanism. JOURNAL OF ETHNOPHARMACOLOGY 2023; 311:116428. [PMID: 36997130 DOI: 10.1016/j.jep.2023.116428] [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: 11/16/2022] [Revised: 02/05/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Irradiation-induced intestinal injury (RIII) often occurs during radiotherapy in patients, which would result in abdominal pain, diarrhea, nausea, vomiting, and even death. Engelhardia roxburghiana Wall. leaves, a traditional Chinese herb, has unique anti-inflammatory, anti-tumor, antioxidant, and analgesic effects, is used to treat damp-heat diarrhea, hernia, and abdominal pain, and has the potential to protect against RIII. AIM OF THE STUDY To explore the protective effects of the total flavonoids of Engelhardia roxburghiana Wall. leaves (TFERL) on RIII and provide some reference for the application of Engelhardia roxburghiana Wall. leaves in the field of radiation protection. MATERIALS AND METHODS The effect of TFERL on the survival rate of mice was observed after a lethal radiation dose (7.2 Gy) by ionizing radiation (IR). To better observe the protective effects of the TFERL on RIII, a mice model of RIII induced by IR (13 Gy) was established. Small intestinal crypts, villi, intestinal stem cells (ISC) and the proliferation of ISC were observed by haematoxylin and eosin (H&E) and immunohistochemistry (IHC). Quantitative real-time PCR (qRT-PCR) was used to detect the expression of genes related to intestinal integrity. Superoxide dismutase (SOD), reduced glutathione (GSH), interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) in the serum of mice were assessed. In vitro, cell models of RIII induced by IR (2, 4, 6, 8 Gy) were established. Normal human intestinal epithelial cells HIEC-6 cells were treated with TFERL/Vehicle, and the radiation protective effect of TFERL on HIEC-6 cells was detected by clone formation assay. DNA damage was detected by comet assay and immunofluorescence assay. Reactive oxygen species (ROS), cell cycle and apoptosis rate were detected by flow cytometry. Oxidative stress, apoptosis and ferroptosis-related proteins were detected by western blot. Finally, the colony formation assay was used to detect the effect of TFERL on the radiosensitivity of colorectal cancer cells. RESULTS TFERL treatment can increase the survival rate and time of the mice after a lethal radiation dose. In the mice model of RIII induced by IR, TFERL alleviated RIII by reducing intestinal crypt/villi structural damage, increasing the number and proliferation of ISC, and maintaining the integrity of the intestinal epithelium after total abdominal irradiation. Moreover, TFERL promoted the proliferation of irradiated HIEC-6 cells, and reduced radiation-induced apoptosis and DNA damage. Mechanism studies have found that TFERL promotes the expression of NRF2 and its downstream antioxidant proteins, and silencing NRF2 resulted in the loss of radioprotection by TFERL, suggesting that TFERL exerts radiation protection by activating the NRF2 pathway. Surprisingly, TFERL reduced the number of clones of colon cancer cells after irradiation, suggesting that TFERL can increase the radiosensitivity of colon cancer cells. CONCLUSION Our data showed that TFERL inhibited oxidative stress, reduced DNA damage, reduced apoptosis and ferroptosis, and improved IR-induced RIII. This study may offer a fresh approach to using Chinese herbs for radioprotection.
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Affiliation(s)
- Shaohua Wu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Chen Tian
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Zhengwei Tu
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Tianjin NanKai Hospital, Tianjin, 300100, China
| | - Jianghong Guo
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Feifei Xu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Weida Qin
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Huajie Chang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Zhiyun Wang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Tong Hu
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Xiao Sun
- Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Hongxin Ning
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Yiliang Li
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Wenfeng Gou
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China.
| | - Wenbin Hou
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China.
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Han JM, Song HY, Jung JH, Lim S, Seo HS, Kim WS, Lim ST, Byun EB. Deinococcus radiodurans-derived membrane vesicles protect HaCaT cells against H 2O 2-induced oxidative stress via modulation of MAPK and Nrf2/ARE pathways. Biol Proced Online 2023; 25:17. [PMID: 37328878 DOI: 10.1186/s12575-023-00211-4] [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: 03/10/2023] [Accepted: 06/07/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND Deinococcus radiodurans is a robust bacterium that can withstand harsh environments that cause oxidative stress to macromolecules due to its cellular structure and physiological functions. Cells release extracellular vesicles for intercellular communication and the transfer of biological information; their payload reflects the status of the source cells. Yet, the biological role and mechanism of Deinococcus radiodurans-derived extracellular vesicles remain unclear. AIM This study investigated the protective effects of membrane vesicles derived from D. radiodurans (R1-MVs) against H2O2-induced oxidative stress in HaCaT cells. RESULTS R1-MVs were identified as 322 nm spherical molecules. Pretreatment with R1-MVs inhibited H2O2-mediated apoptosis in HaCaT cells by suppressing the loss of mitochondrial membrane potential and reactive oxygen species (ROS) production. R1-MVs increased the superoxide dismutase (SOD) and catalase (CAT) activities, restored glutathione (GSH) homeostasis, and reduced malondialdehyde (MDA) production in H2O2-exposed HaCaT cells. Moreover, the protective effect of R1-MVs against H2O2-induced oxidative stress in HaCaT cells was dependent on the downregulation of mitogen-activated protein kinase (MAPK) phosphorylation and the upregulation of the nuclear factor E2-related factor 2 (Nrf2)/antioxidant response element (ARE) pathway. Furthermore, the weaker protective capabilities of R1-MVs derived from ΔDR2577 mutant than that of the wild-type R1-MVs confirmed our inferences and indicated that SlpA protein plays a crucial role in R1-MVs against H2O2-induced oxidative stress. CONCLUSION Taken together, R1-MVs exert significant protective effects against H2O2-induced oxidative stress in keratinocytes and have the potential to be applied in radiation-induced oxidative stress models.
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Affiliation(s)
- Jeong Moo Han
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-Si, Jeollabuk-Do, 56212, Republic of Korea
- Department of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul, 136-701, Republic of Korea
| | - Ha-Yeon Song
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-Si, Jeollabuk-Do, 56212, Republic of Korea
| | - Jong-Hyun Jung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-Si, Jeollabuk-Do, 56212, Republic of Korea
| | - Sangyong Lim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-Si, Jeollabuk-Do, 56212, Republic of Korea
- Department of Radiation Science, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Ho Seong Seo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-Si, Jeollabuk-Do, 56212, Republic of Korea
- Department of Radiation Science, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Woo Sik Kim
- Functional Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-Si, Jeollabuk-Do, 56212, Republic of Korea
| | - Seung-Taik Lim
- Department of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul, 136-701, Republic of Korea
| | - Eui-Baek Byun
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-Si, Jeollabuk-Do, 56212, Republic of Korea.
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The radioresistant and survival mechanisms of Deinococcus radiodurans. RADIATION MEDICINE AND PROTECTION 2023. [DOI: 10.1016/j.radmp.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
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24
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Górecki I, Kołodziejczyk A, Harasymczuk M, Młynarczyk G, Szymanek-Majchrzak K. The Impact of Harsh Stratospheric Conditions on Survival and Antibiotic Resistance Profile of Non-Spore Forming Multidrug Resistant Human Pathogenic Bacteria Causing Hospital-Associated Infections. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:2787. [PMID: 36833485 PMCID: PMC9956888 DOI: 10.3390/ijerph20042787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Bacteria are constantly being lifted to the stratosphere due to air movements caused by weather phenomena, volcanic eruptions, or human activity. In the upper parts of the atmosphere, they are exposed to extremely harsh and mutagenic conditions such as UV and space radiation or ozone. Most bacteria cannot withstand that stress, but for a fraction of them, it can act as a trigger for selective pressure and rapid evolution. We assessed the impact of stratospheric conditions on the survival and antibiotic resistance profile of common non-spore-forming human pathogenic bacteria, both sensitive and extremely dangerous multidrug-resistant variants, with plasmid-mediated mechanisms of resistance. Pseudomonas aeruginosa did not survive the exposure. In the case of strains that were recovered alive, the survival was extremely low: From 0.00001% of Klebsiella pneumoniae carrying the ndm-1 gene and methicillin-resistant Staphylococcus aureus mecA-positive with reduced susceptibility to vancomycin (MRSA/VISA), to a maximum of 0.001% of K. pneumoniae sensitive to all common antibiotics and S. aureus sensitive to vancomycin (MRSA/VSSA). We noticed a tendency towards increased antibiotic susceptibility after the stratospheric flight. Antimicrobial resistance is a current real, global, and increasing problem, and our results can inform current understandings of antibiotic resistance mechanisms and development in bacteria.
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Affiliation(s)
- Ignacy Górecki
- Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego, Str. 5, 02-004 Warsaw, Poland
| | - Agata Kołodziejczyk
- Analog Astronaut Training Center, Morelowa Str. 1F/4, 30-222 Cracow, Poland
- Space Technology Centre, AGH University of Technology, Czarnowiejska Str. 36, 30-054 Cracow, Poland
| | - Matt Harasymczuk
- Analog Astronaut Training Center, Morelowa Str. 1F/4, 30-222 Cracow, Poland
| | - Grażyna Młynarczyk
- Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego, Str. 5, 02-004 Warsaw, Poland
| | - Ksenia Szymanek-Majchrzak
- Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego, Str. 5, 02-004 Warsaw, Poland
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25
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de Toledo Arruda-Neto JD, Righi H, Cabrera Gomez JG, Ferreira da Silva L, Drigo E, da Costa Lemos AC. Radioresistance and radiosensitivity: a biophysical approach on bacterial cells robustness. Theory Biosci 2023; 142:13-28. [PMID: 36460936 DOI: 10.1007/s12064-022-00382-w] [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: 12/18/2021] [Accepted: 11/17/2022] [Indexed: 12/04/2022]
Abstract
The study of radiosensitivity and radioresistance of organisms exposed to ionizing radiation has acquired additional relevance since a new bio-concept, coined as The primacy of Proteome over Genome, was proposed and demonstrated elsewhere a few years ago. According to that finding, genome integrity would require an actively functioning Proteome. However, when exposure to radiation takes place, Reactive Oxygen Species (ROS) from water radiolysis induce protein carbonylation (PC), an irreversible oxidative Proteome damage. The bio-models used in that study were the radiosensitive Escherichia coli and the extraordinarily robust Deinococcus radiodurans. The production of ROS induces protective reactions rendering them non-reactive forms. Protective entities present in the cytosol, moieties smaller than 3 kDa, shield the Proteome against ROS, yielding protection against carbonylation. Shown in the present study is the fact that the fate of proteins functionality is determined by the magnitude of the Protein Carbonylation Yield (YPC), a quantity here analytically defined using published YPC numerical results. Analytical YPC expressions for E. coli and D. radiodurans were the input for a phenomenological approach, where the radiobiological magnitudes PP and PN, the probabilities for production of protein damage and ROS neutralization, respectively, were also analytically deduced. These highly relevant magnitudes, associated with key radiosensitivity and radioresistance issues, are addressed and discussed in this study. Among the plethora of information and conclusions derived from the present study, those endowed with higher conceptual degree, vis-à-vis the "Primacy of Proteome over Genome" concept, are as follows: (1) the ROS neutralization process in D. radiodurans reaches a maximum at a dose interval corresponding to the repairing shoulder. Therefore, it is a signature of the higher efficiency of the PC neutralization process. (2) ROS neutralization in D. radiodurans is nearly one order of magnitude higher than in E. coli, thus accounting for its extraordinary radioresistance. (3) Both physical (ROS-induced carbonyl radicals) and biological (protein modifications) processes are imbedded in the Protein Carbonylation Yield. The amalgamation of these two processes was accomplished by means of a statistical formalism.
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Affiliation(s)
| | - Henriette Righi
- Physics Institute-University of Sao Paulo, São Paulo, Brazil
- Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, Brazil
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26
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Olsson-Francis K, Doran PT, Ilyin V, Raulin F, Rettberg P, Kminek G, Mier MPZ, Coustenis A, Hedman N, Shehhi OA, Ammannito E, Bernardini J, Fujimoto M, Grasset O, Groen F, Hayes A, Gallagher S, Kumar K P, Mustin C, Nakamura A, Seasly E, Suzuki Y, Peng J, Prieto-Ballesteros O, Sinibaldi S, Xu K, Zaitsev M. The COSPAR Planetary Protection Policy for robotic missions to Mars: A review of current scientific knowledge and future perspectives. LIFE SCIENCES IN SPACE RESEARCH 2023; 36:27-35. [PMID: 36682826 DOI: 10.1016/j.lssr.2022.12.001] [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: 10/03/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Planetary protection guidance for martian exploration has become a notable point of discussion over the last decade. This is due to increased scientific interest in the habitability of the red planet with updated techniques, missions becoming more attainable by smaller space agencies, and both the private sector and governments engaging in activities to facilitate commercial opportunities and human-crewed missions. The international standards for planetary protection have been developed through consultation with the scientific community and the space agencies by the Committee on Space Research's (COSPAR) Panel on Planetary Protection, which provides guidance for compliance with the Outer Space Treaty of 1967. In 2021, the Panel evaluated recent scientific data and literature regarding the planetary protection requirements for Mars and the implications of this on the guidelines. In this paper, we discuss the COSPAR Planetary Protection Policy for Mars, review the new scientific findings and discuss the next steps required to enable the next generation of robotic missions to Mars.
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Affiliation(s)
- Karen Olsson-Francis
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, UK.
| | - Peter T Doran
- Department of Geology and Geophysics, Louisiana State, Baton Rouge, Louisiana, USA
| | - Vyacheslav Ilyin
- Institute for Biomedical Problems, Russian Academy of Sciences, Moscow, Russia
| | - Francois Raulin
- Univ Paris Est Cr Univ Paris Est Créteil and Université Paris Cité, CNRS, LISA, F-94010 Créteil, France
| | - Petra Rettberg
- German Aerospace Center (DLR), Institute of Aerospace Medicine, Radiation Biology Department, Research Group Astrobiology, 51147 Cologne, Germany
| | | | - María-Paz Zorzano Mier
- Centro deAstrobiología (CAB), CSIC-INTA, Carretera de Ajalvir km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Athena Coustenis
- LESIA, Paris Observatory, PSL University, CNRS, Paris University, 92195 Meudon Cedex, France
| | - Niklas Hedman
- Committee, Policy and Legal Affairs Section, Office for Outer Space Affairs, United Nations Office at Vienna, Austria
| | | | | | - James Bernardini
- Office of Safety and Mission Assurance, NASA Headquarters, Washington, DC 20546, USA
| | - Masaki Fujimoto
- Japan Aerospace Exploration Agency (JAXA), Institute of Space and Astronautical Science (ISAS), Kanagawa, Japan
| | | | - Frank Groen
- Office of Safety and Mission Assurance, NASA Headquarters, Washington, DC 20546, USA
| | - Alex Hayes
- Cornell University, Ithaca, NY 14853-6801, USA
| | - Sarah Gallagher
- Institute of Earth and Space Exploration, Western University, London, Ontario, Canada
| | | | | | - Akiko Nakamura
- Department of Earth and Planetary Science, The University of Tokyo,7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Elaine Seasly
- Office of Safety and Mission Assurance, NASA Headquarters, Washington, DC 20546, USA
| | - Yohey Suzuki
- Department of Earth and Planetary Science, The University of Tokyo,7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Jing Peng
- China National Space Administration, Beijing, China
| | - Olga Prieto-Ballesteros
- Centro deAstrobiología (CAB), CSIC-INTA, Carretera de Ajalvir km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | | | - Kanyan Xu
- Laboratory of Space Microbiology, Shenzhou Space Biotechnology Group, Chinese Academy of Space Technology, Beijing, China
| | - Maxim Zaitsev
- Planetary Physics Dept., Space Research Inst. of Russian Acad. of Sciences, Moscow, Russia
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27
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Liu J, Dotsuta Y, Kitagaki T, Aoyagi N, Mei H, Takano M, Kozai N. Alteration of fuel debris simulants by Bacillus subtilis. J NUCL SCI TECHNOL 2023. [DOI: 10.1080/00223131.2022.2162995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Jiang Liu
- Collaborative Laboratories for Advanced Decommissioning Science, Japan Atomic Energy Agency (JAEA), Ibaraki, Japan
- Advanced Science Research Center, JAEA, Ibaraki, Japan
| | - Yuma Dotsuta
- Collaborative Laboratories for Advanced Decommissioning Science, Japan Atomic Energy Agency (JAEA), Ibaraki, Japan
- Advanced Science Research Center, JAEA, Ibaraki, Japan
| | - Toru Kitagaki
- Collaborative Laboratories for Advanced Decommissioning Science, Japan Atomic Energy Agency (JAEA), Ibaraki, Japan
- Advanced Science Research Center, JAEA, Ibaraki, Japan
| | - Noboru Aoyagi
- Advanced Science Research Center, JAEA, Ibaraki, Japan
| | - Huiyang Mei
- Advanced Science Research Center, JAEA, Ibaraki, Japan
| | - Masahide Takano
- Nuclear Science and Engineering Center, JAEA, Ibaraki, Japan
| | - Naofumi Kozai
- Collaborative Laboratories for Advanced Decommissioning Science, Japan Atomic Energy Agency (JAEA), Ibaraki, Japan
- Advanced Science Research Center, JAEA, Ibaraki, Japan
- Ningyo-toge Environmental Engineering Center, JAEA, Okayama, Japan
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28
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Shin E, Noh HS, Ye Q, Lee SJ. Hydrogen peroxide treatment induces the transposition of an insertion sequence in Deinococcus radiopugnans DY59. Front Microbiol 2023; 14:1110084. [PMID: 36937269 PMCID: PMC10017437 DOI: 10.3389/fmicb.2023.1110084] [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: 11/28/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
Deinococcus radiopugnans DY59 (formerly Deinococcus swuensis DY59) is a radiation-resistant bacterium isolated from soil. From the 3.5 Mb genomic DNA sequence of strain DY59 (December 2014), 31 insertion sequence (IS) elements of six IS families including IS1, IS4, IS5, IS66, IS630, and IS701 and five unclassified IS elements were detected. Upon induction of oxidative stress with 80 and 100 mM H2O2, the unique ISs of the IS4 family member were actively translocated into a carotenoid biosynthesis gene phytoene desaturase (QR90_10400), resulting in non-pigment phenotypic selection. Therefore, these active transpositions of a specific IS family member were induced by oxidative stress at 80 and 100 mM H2O2. Furthermore, D. radiopugnans DY59 exhibited extremely higher MIC values against H2O2 treatment. To explain this phenomenon, qRT-PCR was conducted to assess the expression levels of catalase and three LysR family regulators. Our findings indicated that the ISDrpg2 and ISDrpg3 elements of the IS4 family were actively transposed into the phytoene desaturase gene by H2O2 treatment via replicative transposition. However, high H2O2 resistance did not originate from H2O2-induced expression of catalase and LysR family regulators.
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29
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Complementary Roles of Two DNA Protection Proteins from Deinococcus geothermalis. Int J Mol Sci 2022; 24:ijms24010469. [PMID: 36613913 PMCID: PMC9820295 DOI: 10.3390/ijms24010469] [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: 11/10/2022] [Revised: 12/17/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
The roles of two interrelated DNA protection protein in starved cells (Dps)-putative Dps Dgeo_0257 and Dgeo_0281-as orthologous proteins to DrDps1 for DNA binding, protection, and metal ion sensing were characterised in a Deinococcus geothermalis strain. Dgeo_0257 exhibited high DNA-binding affinity and formed a multimeric structure but lacked the conserved amino acid sequence for ferroxidase activity. In contrast, the Dgeo_0281 (DgDps1) protein was abundant in the early exponential phase, had a lower DNA-binding activity than Dgeo_0257, and was mainly observed in its monomeric or dimeric forms. Electrophoretic mobility shift assays demonstrated that both purified proteins bound nonspecifically to DNA, and their binding ability was affected by certain metal ions. For example, in the presence of ferrous and ferric ions, neither Dgeo_0257 nor Dgeo_0281 could readily bind to DNA. In contrast, both proteins exhibited more stable DNA binding in the presence of zinc and manganese ions. Mutants in which the dps gene was disrupted exhibited higher sensitivity to oxidative stress than the wild-type strain. Furthermore, the expression levels of each gene showed an opposite correlation under H2O2 treatment conditions. Collectively, these findings indicate that the putative Dps Dgeo_0257 and DgDps1 from D. geothermalis are involved in DNA binding and protection in complementary interplay ways compared to known Dps.
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30
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Hou J, Dai J, Chen Z, Wang Y, Cao J, Hu J, Ye S, Hua Y, Zhao Y. Phosphorylation Regulation of a Histone-like HU Protein from Deinococcus radiodurans. Protein Pept Lett 2022; 29:891-899. [PMID: 35986527 PMCID: PMC9900698 DOI: 10.2174/0929866529666220819121911] [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: 03/03/2022] [Revised: 05/27/2022] [Accepted: 06/01/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Histone-like proteins are small molecular weight DNA-binding proteins that are widely distributed in prokaryotes. These proteins have multiple functions in cellular structures and processes, including the morphological stability of the nucleoid, DNA compactness, DNA replication, and DNA repair. Deinococcus radiodurans, an extremophilic microorganism, has extraordinary DNA repair capability and encodes an essential histone-like protein, DrHU. OBJECTIVE We aim to investigate the phosphorylation regulation role of a histone-like HU protein from Deinococcus radiodurans. METHODS LC-MS/MS analysis was used to determine the phosphorylation site of endogenous DrHU. The predicted structure of DrHU-DNA was obtained from homology modeling (Swissmodel) using Staphylococcus aureus HU-DNA structure (PDB ID: 4QJU) as the starting model. Two types of mutant proteins T37E and T37A were generated to explore their DNA binding affinity. Complemented-knockout strategy was used to generate the ΔDrHU/pk-T37A and ΔDrHU/pk-T37E strains for growth curves and phenotypical analyses. RESULTS AND DISCUSSION The phosphorylation site Thr37, which is present in most bacterial HU proteins, is located at the putative protein-DNA interaction interface of DrHU. Compared to the wild-type protein, one in which this threonine is replaced by glutamate to mimic a permanent state of phosphorylation (T37E) showed enhanced double-stranded DNA binding but a weakened protective effect against hydroxyl radical cleavage. Complementation of T37E in a DrHU-knockout strain caused growth defects and sensitized the cells to UV radiation and oxidative stress. CONCLUSIONS Phosphorylation modulates the DNA-binding capabilities of the histone-like HU protein from D. radiodurans, which contributes to the environmental adaptation of this organism.
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Affiliation(s)
- Jinfeng Hou
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310000, China
| | - Jingli Dai
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310000, China
| | - Zijing Chen
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310000, China
| | - Yudong Wang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310000, China
| | - Jiajia Cao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310000, China
| | - Jing Hu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310000, China
| | - Shumai Ye
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310000, China
| | - Yuejin Hua
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310000, China
| | - Ye Zhao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310000, China,Address correspondence to this author at the MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310000, China; E-mail:
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31
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Gao Y, Li N, Zhou Y, Zhang Z, Zhang Y, Fan P, Zhou H, Zhang T, Chang L, Gao H, Li Y, Kang X, Xie Q, Lyu Z, Xu P. iTRAQ-based proteomic analysis of Deinococcus radiodurans in response to 12C 6+ heavy ion irradiation. BMC Microbiol 2022; 22:264. [PMID: 36333788 PMCID: PMC9635210 DOI: 10.1186/s12866-022-02676-x] [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: 06/20/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Background Deinococcus radiodurans (D. radiodurans) is best known for its extreme resistance to diverse environmental stress factors, including ionizing radiation (IR), ultraviolet (UV) irradiation, oxidative stress, and high temperatures. Robust DNA repair system and antioxidant system have been demonstrated to contribute to extreme resistance in D. radiodurans. However, practically all studies on the mechanism underlying D. radiodurans’s extraordinary resistance relied on the treated strain during the post-treatment recovery lag phase to identify the key elements involved. The direct gene or protein changes of D. radiodurans after stress have not yet been characterized. Results In this study, we performed a proteomics profiling on D. radiodurans right after the heavy ion irradiation treatment, to discover the altered proteins that were quickly responsive to IR in D. radiodurans. Our study found that D. radiodurans shown exceptional resistance to 12C6+ heavy ion irradiation, in contrast to Escherichia coli (E.coli) strains. By using iTRAQ (Isobaric Tags for Relative and Absolute Quantitation)-based quantitative mass spectrometry analysis, the kinetics of proteome changes induced by various dosages of 12C6+ heavy ion irradiation were mapped. The results revealed that 452 proteins were differentially expressed under heavy ion irradiation, with the majority of proteins being upregulated, indicating the upregulation of functional categories of translation, TCA cycle (Tricarboxylic Acid cycle), and antioxidation regulation under heavy ion irradiation. Conclusions This study shows how D. radiodurans reacts to exposure to 12C6+ heavy ion irradiation in terms of its overall protein expression profile. Most importantly, comparing the proteome profiling of D. radiodurans directly after heavy ion irradiation with research on the post-irradiation recovery phase would potentially provide a better understanding of mechanisms underlying the extreme radioresistance in D. radiodurans. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02676-x.
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Affiliation(s)
- Yuan Gao
- grid.27871.3b0000 0000 9750 7019Central Laboratory of College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China ,grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Naikang Li
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China ,School of Life Sciences, Institute of Life Science and Green DevelopmentHebei University and Key Laboratory of Microbial Diversity Research and Application of Hebei Province, 180 East Wusi Road, Baoding, 071002 People’s Republic of China
| | - Yanxia Zhou
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China ,Beijing Institute of Food Inspection and Research, Beijing Municipal Center for Food Safety Monitoring and Risk Assessment, Beijing, 102206 People’s Republic of China
| | - Zhenpeng Zhang
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Yao Zhang
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Pengcheng Fan
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Hangfan Zhou
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Tao Zhang
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Lei Chang
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Huiying Gao
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Yanchang Li
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Xianjiang Kang
- School of Life Sciences, Institute of Life Science and Green DevelopmentHebei University and Key Laboratory of Microbial Diversity Research and Application of Hebei Province, 180 East Wusi Road, Baoding, 071002 People’s Republic of China
| | - Qiong Xie
- grid.418516.f0000 0004 1791 7464China Astronaut Research and Training Center, Beijing, 100094 People’s Republic of China
| | - Zhitang Lyu
- School of Life Sciences, Institute of Life Science and Green DevelopmentHebei University and Key Laboratory of Microbial Diversity Research and Application of Hebei Province, 180 East Wusi Road, Baoding, 071002 People’s Republic of China
| | - Ping Xu
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China ,School of Life Sciences, Institute of Life Science and Green DevelopmentHebei University and Key Laboratory of Microbial Diversity Research and Application of Hebei Province, 180 East Wusi Road, Baoding, 071002 People’s Republic of China ,grid.186775.a0000 0000 9490 772XAnhui Medical University, Hefei, 230032 People’s Republic of China ,grid.443382.a0000 0004 1804 268XMedical School of Guizhou University, Guiyang, 550025 People’s Republic of China ,grid.411866.c0000 0000 8848 7685Second Clinical Medicine Collage, Guangzhou University Chinese Medicine, Guangzhou, 510006 People’s Republic of China
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Kimura S, Sato M, Fan X, Ohmori M, Ehira S. The two-component response regulator OrrA confers dehydration tolerance by regulating avaKa expression in the cyanobacterium Anabaena sp. strain PCC 7120. Environ Microbiol 2022; 24:5165-5173. [PMID: 36054741 PMCID: PMC9804601 DOI: 10.1111/1462-2920.16162] [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: 06/28/2021] [Accepted: 08/06/2022] [Indexed: 01/05/2023]
Abstract
The cyanobacterium Anabaena sp. strain PCC 7120 exhibits dehydration tolerance. The regulation of gene expression in response to dehydration is crucial for the acquisition of dehydration tolerance, but the molecular mechanisms underlying dehydration responses remain unknown. In this study, the functions of the response regulator OrrA in the regulation of salt and dehydration responses were investigated. Disruption of orrA abolished or diminished the induction of hundreds of genes in response to salt stress and dehydration. Thus, OrrA is a principal regulator of both stress responses. In particular, OrrA plays a crucial role in dehydration tolerance because an orrA disruptant completely lost the ability to regrow after dehydration. Moreover, in the OrrA regulon, avaKa encoding a protein of unknown function was revealed to be indispensable for dehydration tolerance. OrrA and AvaK are conserved among the terrestrial cyanobacteria, suggesting their conserved functions in dehydration tolerance in cyanobacteria.
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Affiliation(s)
- Satoshi Kimura
- Department of Biochemistry and Molecular Biology, Faculty of ScienceSaitama UniversitySaitamaJapan
| | - Miho Sato
- Department of Biological Sciences, Graduate school of ScienceTokyo Metropolitan UniversityTokyoJapan
| | - Xingyan Fan
- Department of Biological Sciences, Graduate school of ScienceTokyo Metropolitan UniversityTokyoJapan
| | - Masayuki Ohmori
- Department of Biochemistry and Molecular Biology, Faculty of ScienceSaitama UniversitySaitamaJapan
| | - Shigeki Ehira
- Department of Biochemistry and Molecular Biology, Faculty of ScienceSaitama UniversitySaitamaJapan,Department of Biological Sciences, Graduate school of ScienceTokyo Metropolitan UniversityTokyoJapan
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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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Liu Y, Cui X, Yang R, Zhang Y, Xu Y, Liu G, Zhang B, Wang J, Wang X, Zhang W, Chen T, Zhang G. Genomic Insights into the Radiation-Resistant Capability of Sphingomonas qomolangmaensis S5-59 T and Sphingomonas glaciei S8-45 T, Two Novel Bacteria from the North Slope of Mount Everest. Microorganisms 2022; 10:microorganisms10102037. [PMID: 36296313 PMCID: PMC9611098 DOI: 10.3390/microorganisms10102037] [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: 09/28/2022] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022] Open
Abstract
Mount Everest provides natural advantages to finding radiation-resistant extremophiles that are functionally mechanistic and possess commercial significance. (1) Background: Two bacterial strains, designated S5-59T and S8-45T, were isolated from moraine samples collected from the north slope of Mount Everest at altitudes of 5700m and 5100m above sea level. (2) Methods: The present study investigated the polyphasic features and genomic characteristics of S5-59T and S8-45T. (3) Results: The major fatty acids and the predominant respiratory menaquinone of S5-59T and S8-45T were summed as feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c) and ubiquinone-10 (Q-10). Phylogenetic analyses based on 16S rRNA sequences and average nucleotide identity values among these two strains and their reference type strains were below the species demarcation thresholds of 98.65% and 95%. Strains S5-59T and S8-45T harbored great radiation resistance. The genomic analyses showed that DNA damage repair genes, such as mutL, mutS, radA, radC, recF, recN, etc., were present in the S5-59T and S8-45T strains. Additionally, strain S5-59T possessed more genes related to DNA protection proteins. The pan-genome analysis and horizontal gene transfers revealed that strains of Sphingomonas had a consistently homologous genetic evolutionary radiation resistance. Moreover, enzymatic antioxidative proteins also served critical roles in converting ROS into harmless molecules that resulted in resistance to radiation. Further, pigments and carotenoids such as zeaxanthin and alkylresorcinols of the non-enzymatic antioxidative system were also predicted to protect them from radiation. (4) Conclusions: Type strains S5-59T (=JCM 35564T =GDMCC 1.3193T) and S8-45T (=JCM 34749T =GDMCC 1.2715T) represent two novel species of the genus Sphingomonas with the proposed name Sphingomonas qomolangmaensis sp. nov. and Sphingomonas glaciei sp. nov. The type strains, S5-59T and S8-45T, were assessed in a deeply genomic study of their radiation-resistant mechanisms and this thus resulted in a further understanding of their greater potential application for the development of anti-radiation protective drugs.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Xiaowen Cui
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- College of Geography and Environment Science, Northwest Normal University, Lanzhou 730070, China
| | - Ruiqi Yang
- College of Urban Environment, Lanzhou City University, Lanzhou 730070, China
| | - Yiyang Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Yeteng Xu
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- School of Stomatology, Lanzhou University, Lanzhou 730000, China
| | - Binglin Zhang
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Jinxiu Wang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Xinyue Wang
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Correspondence: (T.C.); (G.Z.)
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Correspondence: (T.C.); (G.Z.)
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Dollery SJ, Zurawski DV, Bushnell RV, Tobin JK, Wiggins TJ, MacLeod DA, Tasker NJPER, Alamneh YA, Abu-Taleb R, Czintos CM, Su W, Escatte MG, Meeks HN, Daly MJ, Tobin GJ. Whole-cell vaccine candidates induce a protective response against virulent Acinetobacter baumannii. Front Immunol 2022; 13:941010. [PMID: 36238282 PMCID: PMC9553005 DOI: 10.3389/fimmu.2022.941010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
Acinetobacter baumannii causes multi-system diseases in both nosocomial settings and a pre-disposed general population. The bacterium is not only desiccation-resistant but also notoriously resistant to multiple antibiotics and drugs of last resort including carbapenem, colistin, and sulbactam. The World Health Organization has categorized carbapenem-resistant A. baumannii at the top of its critical pathogen list in a bid to direct urgent countermeasure development. Several early-stage vaccines have shown a range of efficacies in healthy mice, but no vaccine candidates have advanced into clinical trials. Herein, we report our findings that both an ionizing γ-radiation-inactivated and a non-ionizing ultraviolet C-inactivated whole-cell vaccine candidate protects neutropenic mice from pulmonary challenge with virulent AB5075, a particularly pathogenic isolate. In addition, we demonstrate that a humoral response is sufficient for this protection via the passive immunization of neutropenic mice.
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Affiliation(s)
- Stephen J. Dollery
- Biological Mimetics, Inc., Frederick, MD, United States
- *Correspondence: Stephen J. Dollery,
| | - Daniel V. Zurawski
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | | | - John K. Tobin
- Biological Mimetics, Inc., Frederick, MD, United States
| | | | | | | | - Yonas A. Alamneh
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Rania Abu-Taleb
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Christine M. Czintos
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Wanwen Su
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Mariel G. Escatte
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Heather N. Meeks
- Defense Threat Reduction Agency, Fort Belvoir, VA, United States
| | - Michael J. Daly
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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36
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Park HR, Lee JH, Ji HJ, Lim S, Ahn KB, Seo HS. Radioprotection of deinococcal exopolysaccharide BRD125 by regenerating hematopoietic stem cells. Front Oncol 2022; 12:898185. [PMID: 36226052 PMCID: PMC9549790 DOI: 10.3389/fonc.2022.898185] [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: 03/17/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
There is a substantial need for the development of biomaterials for protecting hematopoietic stem cells and enhancing hematopoiesis after radiation damage. Bacterial exopolysaccharide (EPS) has been shown to be very attractive to researchers as a radioprotectant owing to its high antioxidant, anti-cancer, and limited adverse effects. In the present study, we isolated EPS from a novel strain, Deinococcus radiodurans BRD125, which produces EPS in high abundance, and investigated its applicability as a radioprotective biomaterial. We found that EPS isolated from EPS-rich D. radiodurans BRD125 (DeinoPol-BRD125) had an excellent free-radical scavenging effect and reduced irradiation-induced apoptosis. In addition, bone-marrow and spleen-cell apoptosis in irradiated mice were significantly reduced by DeinoPol-BRD125 administration. DeinoPol-BRD125 enhanced the expression of hematopoiesis-related cytokines such as GM-CSF, G-GSF, M-CSF, and SCF, thereby enhancing hematopoietic stem cells protection and regeneration. Taken together, our findings are the first to report the immunological mechanism of a novel radioprotectant, DeinoPol-BRD125, which might constitute an ideal radioprotective and radiation mitigating agent as a supplement drug during radiotherapy.
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Affiliation(s)
- Hae Ran Park
- Research Division for Radiation Science, Korea Atomic Energy Research Institute, Jeongeup, South Korea
- *Correspondence: Ho Seong Seo, ; Hae Ran Park,
| | - Ji Hee Lee
- Research Division for Radiation Science, Korea Atomic Energy Research Institute, Jeongeup, South Korea
- Division of Pathogen Resource Management, Center for Public Vaccine Development Support, National Institute of Infectious Diseases, National Institute of Health (NIH), Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Hyun Jung Ji
- Research Division for Radiation Science, Korea Atomic Energy Research Institute, Jeongeup, South Korea
- Department of Oral Microbiology and Immunology, DRI, and BK21 Plus Program, School of Dentistry, Seoul National University, Seoul, South Korea
| | - Sangyong Lim
- Research Division for Radiation Science, Korea Atomic Energy Research Institute, Jeongeup, South Korea
- Department of Radiation Science, University of Science and Technology, Daejeon, South Korea
| | - Ki Bum Ahn
- Research Division for Radiation Science, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - Ho Seong Seo
- Research Division for Radiation Science, Korea Atomic Energy Research Institute, Jeongeup, South Korea
- Department of Radiation Science, University of Science and Technology, Daejeon, South Korea
- *Correspondence: Ho Seong Seo, ; Hae Ran Park,
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37
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M S, N RP, Chakraborty A, Rajendrasozhan S. Proteomic profiling of Deinococcus radiodurans with response to thioredoxin reductase inhibitor and ionizing radiation treatment. J Proteomics 2022; 267:104697. [PMID: 35995383 DOI: 10.1016/j.jprot.2022.104697] [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: 07/04/2022] [Revised: 08/05/2022] [Accepted: 08/10/2022] [Indexed: 11/27/2022]
Abstract
This study explains the importance of cellular redox system in preserving the proteome of the radioresistant Deinococcus radiodurans. The thioredoxin reductase (TrxR) redox system was inhibited by ebselen (10 μM), and then the bacterium was exposed to 4 kGy of ionizing radiation. The differentially expressed proteins were analyzed using label-free quantitative (LFQ) proteomics. The 4 kGy radiation treatment increases the expression of stress response proteins like osmotically inducible protein OsmC, catalase, and metallophosphoesterase compared to control. Ebselen plus radiation treatment augments oxidoreductases proteins in D. radiodurans. Further, the proteins involved in glycolysis, tricarboxylic acetic acid (TCA) and proteins like proteases, peptidase, and peptide transporters were significantly decreased in the ebselen plus radiation group compared to radiation treated group. Further, ebselen plus radiation treatment increases the ATP-binding cassette (ABC) transporters involved in the efflux of toxic chemicals and nutrient uptake and the stress response related membrane protein like S-layer homology domain-containing protein in D. radiodurans. Thus, the results show that the altered redox status via inhibition of TrxR redox system significantly affects the expression of essential cellular proteins for the survival. The cellular content of D. radiodurans may be used to handle redox imbalances in the normal cells during cancer radiotherapy. SIGNIFICANCE: Deinococcus radiodurans is a popular radioresistance organism with efficient antioxidant systems and DNA repair mechanisms. There are many antioxidant systems and small molecules that responsible for its resistance. The importance of thiol based antioxidant systems in its resistance property has not fully studied yet. Thioredoxin reductase is an important disulfide containing protein that involved in maintaining redox homeostasis. The TrxR inhibition affects the cell survival and synthesis of molecules against ionizing radiation. In this study we are reporting the effects of TrxR inhibitor on proteome of D. radiodurans upon ionizing radiation. This study reveals the significance of TrxR antioxidant system on the proteome of D. radiodurans. The inhibition of TrxR antioxidant system and the subsequent disturbances in the proteome content makes the organism vulnerable to oxidative stress.
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Affiliation(s)
- Sudharsan M
- Department of Biochemistry and Biotechnology, Annamalai University, Annamalainagar, 608 002, Tamilnadu, India
| | - Rajendra Prasad N
- Department of Biochemistry and Biotechnology, Annamalai University, Annamalainagar, 608 002, Tamilnadu, India
| | - Anindita Chakraborty
- UGC-DAE Consortium for Scientific Research, Kolkata Centre, 700098, West Bengal, India
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38
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Xu H, Fang C, Shao C, Li L, Huang Q. Study of the synergistic effect of singlet oxygen with other plasma-generated ROS in fungi inactivation during water disinfection. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156576. [PMID: 35688233 DOI: 10.1016/j.scitotenv.2022.156576] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/22/2022] [Accepted: 06/05/2022] [Indexed: 06/15/2023]
Abstract
Cold atmospheric plasma (CAP) possesses the ability of high-efficiency disinfection. It is reported that mixtures of reactive oxygen species (ROS) including ·OH, 1O2, O2- and H2O2 generated from CAP have better antimicrobial ability than mimicked solution of mixture of single ROS type, but the reason is not clear. In this study, CAP was applied to treat yeasts in water in order to investigate the fungal inactivation efficiency and mechanism. The results showed that plasma treatment for 5 min could result in >2-log reduction of yeast cells, and application of varied ROS scavengers could significantly increase the yeast survival rate, indicating that ·OH and 1O2 played the pivotal role in yeast inactivation. Moreover, the synergistic effect of 1O2 with other plasma-generated ROS was revealed. 1O2 could diffuse into cells and induce the depolarization of mitochondrial membrane potential (MMP), and different levels of MMP depolarization determined different cell death modes. Mild damage of mitochondria during short-term plasma treatment could lead to apoptosis. For long-term plasma treatment, the cell membrane could be severely damaged by the plasma-generated ·OH, so a large amount of 1O2 could induce more depolarization of MMP, leading to increase of intracellular O2- and Fe2+ which subsequently caused cell inactivation. 1O2 could also induce protein aggregation and increase of RIP1/RIP3 necrosome, leading to necroptosis. With participation of 1O2, endogenous ·OH could also be generated via Fenton and Haber-Weiss reactions during plasma treatment, which potentiated necroptosis. Adding l-His could mitigate membrane damage, inhibit the drop of MMP and the formation of necrosome, and thus prevent the happening of necroptosis. These findings may deepen the understanding of plasma sterilization mechanisms and provide guidance for microbial killing in the environment.
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Affiliation(s)
- Hangbo Xu
- CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Institute of Intelligent Agriculture, Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS), Hefei 230031, China
| | - Cao Fang
- CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Institute of Intelligent Agriculture, Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS), Hefei 230031, China; Science Island Branch of Graduate School, University of Science and Technology of China, Hefei 230026, China
| | - Changsheng Shao
- CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Institute of Intelligent Agriculture, Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS), Hefei 230031, China; Science Island Branch of Graduate School, University of Science and Technology of China, Hefei 230026, China
| | - Lamei Li
- CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Institute of Intelligent Agriculture, Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS), Hefei 230031, China; Science Island Branch of Graduate School, University of Science and Technology of China, Hefei 230026, China
| | - Qing Huang
- CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Institute of Intelligent Agriculture, Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS), Hefei 230031, China.
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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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40
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Zeng N, Zhang N, Ma X, Wang Y, Zhang Y, Wang D, Pu F, Li B. Transcriptomics Integrated with Metabolomics: Assessing the Central Metabolism of Different Cells after Cell Differentiation in Aureobasidium pullulans NG. J Fungi (Basel) 2022; 8:jof8080882. [PMID: 36012870 PMCID: PMC9410427 DOI: 10.3390/jof8080882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/15/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
When organisms are stimulated by external stresses, oxidative stress is induced, resulting in the production of large amounts of reactive oxygen species (ROS) that inhibit cell growth and accelerate cellular aging until death. Understanding the molecular mechanisms of abiotic stress is important to enhance cellular resistance, and Aureobasidium pullulans, a highly resistant yeast-like fungus, can use cellular differentiation to resist environmental stress. Here, swollen cells (SCs) from two different differentiation periods in Aureobasidium pullulans NG showed significantly higher antioxidant capacity and stress defense capacity than yeast-like cells (YL). The transcriptome and the metabolome of both cells were analyzed, and the results showed that amino acid metabolism, carbohydrate metabolism, and lipid metabolism were significantly enriched in SCs. Glyoxylate metabolism was significantly upregulated in carbohydrate metabolism, replacing the metabolic hub of the citric acid (TCA) cycle, helping to coordinate multiple metabolic pathways and playing an important role in the resistance of Aureobasidium pullulans NG to environmental stress. Finally, we obtained 10 key genes and two key metabolites in SCs, which provide valuable clues for subsequent validation. In conclusion, these results provide valuable information for assessing central metabolism-mediating oxidative stress in Aureobasidium pullulans NG, and also provide new ideas for exploring the pathways of eukaryotic resistance to abiotic stress.
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Affiliation(s)
- Nan Zeng
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Ning Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
- Correspondence: (N.Z.); (B.L.)
| | - Xin Ma
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Yunjiao Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Yating Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Dandan Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Fangxiong Pu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Bingxue Li
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, China
- Correspondence: (N.Z.); (B.L.)
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Tollefsen KE, Alonzo F, Beresford NA, Brede DA, Dufourcq-Sekatcheff E, Gilbin R, Horemans N, Hurem S, Laloi P, Maremonti E, Oughton D, Simon O, Song Y, Wood MD, Xie L, Frelon S. Adverse outcome pathways (AOPs) for radiation-induced reproductive effects in environmental species: state of science and identification of a consensus AOP network. Int J Radiat Biol 2022; 98:1816-1831. [PMID: 35976054 DOI: 10.1080/09553002.2022.2110317] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Reproductive effects of ionizing radiation in organisms have been observed under laboratory and field conditions. Such assessments often rely on associations between exposure and effects, and thus lacking a detailed mechanistic understanding of causality between effects occurring at different levels of biological organization. The Adverse Outcome Pathway (AOP), a conceptual knowledge framework to capture, organize, evaluate and visualize the scientific knowledge of relevant toxicological effects, has the potential to evaluate the causal relationships between molecular, cellular, individual, and population effects. This paper presents the first development of a set of consensus AOPs for reproductive effects of ionizing radiation in wildlife. This work was performed by a group of experts formed during a workshop organized jointly by the Multidisciplinary European Low Dose Initiative (MELODI) and the European Radioecology Alliance (ALLIANCE) associations to present the AOP approach and tools. The work presents a series of taxon-specific case studies that were used to identify relevant empirical evidence, identify common AOP components and propose a set of consensus AOPs that could be organized into an AOP network with broader taxonomic applicability. CONCLUSION Expert consultation led to the identification of key biological events and description of causal linkages between ionizing radiation, reproductive impairment and reduction in population fitness. The study characterized the knowledge domain of taxon-specific AOPs, identified knowledge gaps pertinent to reproductive-relevant AOP development and reflected on how AOPs could assist applications in radiation (radioecological) research, environmental health assessment, and radiological protection. Future advancement and consolidation of the AOPs is planned to include structured weight of evidence considerations, formalized review and critical assessment of the empirical evidence prior to formal submission and review by the OECD sponsored AOP development program.
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Affiliation(s)
- Knut Erik Tollefsen
- Norwegian Institute for Water Research (NIVA), Oslo, Norway.,Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences (NMBU), Ås, Norway.,Centre for Environmental Radioactivity, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Frédéric Alonzo
- Health and Environment Division, Institute for Radiological Protection and Nuclear Safety (IRSN), Saint-Paul-Lez-Durance, France
| | - Nicholas A Beresford
- UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Bailrigg, UK.,School of Science, Engineering & Environment, University of Salford, Salford, UK
| | - Dag Anders Brede
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences (NMBU), Ås, Norway.,Centre for Environmental Radioactivity, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Elizabeth Dufourcq-Sekatcheff
- Health and Environment Division, Institute for Radiological Protection and Nuclear Safety (IRSN), Saint-Paul-Lez-Durance, France
| | - Rodolphe Gilbin
- Health and Environment Division, Institute for Radiological Protection and Nuclear Safety (IRSN), Saint-Paul-Lez-Durance, France
| | | | - Selma Hurem
- Centre for Environmental Radioactivity, Norwegian University of Life Sciences (NMBU), Ås, Norway.,Faculty of Veterinary medicine, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Patrick Laloi
- Health and Environment Division, Institute for Radiological Protection and Nuclear Safety (IRSN), Saint-Paul-Lez-Durance, France
| | - Erica Maremonti
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences (NMBU), Ås, Norway.,Centre for Environmental Radioactivity, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Deborah Oughton
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences (NMBU), Ås, Norway.,Centre for Environmental Radioactivity, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Olivier Simon
- Health and Environment Division, Institute for Radiological Protection and Nuclear Safety (IRSN), Saint-Paul-Lez-Durance, France
| | - You Song
- Norwegian Institute for Water Research (NIVA), Oslo, Norway.,Centre for Environmental Radioactivity, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Michael D Wood
- School of Science, Engineering & Environment, University of Salford, Salford, UK
| | - Li Xie
- Norwegian Institute for Water Research (NIVA), Oslo, Norway.,Centre for Environmental Radioactivity, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Sandrine Frelon
- Health and Environment Division, Institute for Radiological Protection and Nuclear Safety (IRSN), Saint-Paul-Lez-Durance, France
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42
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Dai Z, Zhang Z, Zhu L, Zhu Z, Jiang L. Complete Genome Sequencing Analysis of Deinococcus wulumuqiensis R12, an Extremely Radiation-Resistant Strain. Curr Microbiol 2022; 79:292. [PMID: 35972568 DOI: 10.1007/s00284-022-02984-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 07/20/2022] [Indexed: 11/03/2022]
Abstract
Genome sequencing was performed by the PacBio RS II platform and Illumina HiSeq 4000 platform to discover the metabolic profile of the Deinococcus wulumuqiensis R12, which was isolated from radiation-contaminated soils in Xinjiang Uygur Autonomous Region of northwest China. The genome of 3.5 Mbp comprises one circular chromosome and four circular plasmids with 3679 genes and a GC content of 66.97%. A total of 41 new transcriptional factors were identified using the DeepTFactor tool. Genomic analysis revealed the presence of genes for homologous recombination repair, which suggested high recombination efficiency in R12. Three Type I and one Type II RM systems, two CRISPR arrays, and one Cas-Type IC protein were found, allowing the development of endogenous CRISPR-Cas gene-editing tools. Additionally, we found that R12 has a broad spectrum of substrate utilization, which was validated by physiological experiments. Genes involved in the carotenoid biosynthesis pathway and the antioxidative system were also identified. Overall, the comprehensive description of the genome of R12 will facilitate the additional exploitation of this strain as a versatile cell factory for biotechnological applications.
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Affiliation(s)
- Zijie Dai
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Zhidong Zhang
- Xinjiang Key Laboratory of Special Environmental Microbiology, Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, Xinjiang, China
| | - Liying Zhu
- College of Chemical and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Zhengming Zhu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China. .,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, China.
| | - Ling Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China. .,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, China.
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43
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Chen Y, Yang Z, Zhou X, Jin M, Dai Z, Ming D, Zhang Z, Zhu L, Jiang L. Sequence, structure, and function of the Dps DNA-binding protein from Deinococcus wulumuqiensis R12. Microb Cell Fact 2022; 21:132. [PMID: 35780107 PMCID: PMC9250271 DOI: 10.1186/s12934-022-01857-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 06/21/2022] [Indexed: 11/28/2022] Open
Abstract
Deinococcus wulumuqiensis R12, which was isolated from arid irradiated soil in Xinjiang province of China, belongs to a genus that is well-known for its extreme resistance to ionizing radiation and oxidative stress. The DNA-binding protein Dps has been studied for its great contribution to oxidative resistance. To explore the role of Dps in D. wulumuqiensis R12, the Dps sequence and homology-modeled structure were analyzed. In addition, the dps gene was knocked out and proteomics was used to verify the functions of Dps in D. wulumuqiensis R12. Docking data and DNA binding experiments in vitro showed that the R12 Dps protein has a better DNA binding ability than the Dps1 protein from D. radiodurans R1. When the dps gene was deleted in D. wulumuqiensis R12, its resistance to H2O2 and UV rays was greatly reduced, and the cell envelope was destroyed by H2O2 treatment. Additionally, the qRT-PCR and proteomics data suggested that when the dps gene was deleted, the catalase gene was significantly down-regulated. The proteomics data indicated that the metabolism, transport and oxidation–reduction processes of D. wulumuqiensis R12 were down-regulated after the deletion of the dps gene. Overall, the data conformed that Dps protein plays an important role in D. wulumuqiensis R12.
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Affiliation(s)
- Yao Chen
- College of Food Science and Light Industry, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Zhihan Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Xue Zhou
- College of Food Science and Light Industry, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Mengmeng Jin
- College of Food Science and Light Industry, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Zijie Dai
- College of Food Science and Light Industry, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Dengming Ming
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Zhidong Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China. .,Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences/Xinjiang Key Laboratory of Special Environmental Microbiology, Ürümqi, 830091, Xinjiang, China.
| | - Liying Zhu
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, China.
| | - Ling Jiang
- College of Food Science and Light Industry, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China.
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44
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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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Yang R, Zhang B, Xu Y, Zhang G, Liu Y, Zhang D, Zhang W, Chen T, Liu G. Genomic insights revealed the environmental adaptability of Planococcus halotolerans Y50 isolated from petroleum-contaminated soil on the Qinghai-Tibet Plateau. Gene 2022; 823:146368. [PMID: 35240255 DOI: 10.1016/j.gene.2022.146368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/28/2022]
Abstract
The Tibetan Plateau niche provides unprecedented opportunities to find microbes that are functional and commercial significance. The present study investigated the physiological and genomic characteristics of Planococcus halotolerans Y50 that was isolated from a petroleum-contaminated soil sample from the Qinghai-Tibet Plateau, and it displayed psychrotolerant, antiradiation, and oil-degraded characteristics. Whole genome sequencing indicated that strain Y50 has a 3.52 Mb genome and 44.7% G + C content, and it possesses 3377 CDSs. The presence of a wide range of UV damage repair genes uvrX and uvsE, DNA repair genes radA and recN, superoxide dismutase, peroxiredoxin and dioxygenase genes provided the genomic basis for the adaptation of the plateau environment polluted by petroleum. Related experiments also verified that the Y50 strain could degrade n-alkanes from C11-C23, and approximately 30% of the total petroleum at 25 °C within 7 days. Meanwhile, strain Y50 could withstand 5 × 103 J/m2 UVC and 10 KGy gamma ray radiation, and it had strong antioxidant and high radical scavengers for superoxide anion, hydroxyl radical and DPPH. In addition, pan-genome analysis and horizontal gene transfers revealed that strains with different niches have obtained various genes through horizontal gene transfer in the process of evolution, and the more similar their geographical locations, the more similar their members are genetically and ecologically. In conclusion, P. halotolerans Y50 possesses high potential of applications in the bioremediation of alpine hydrocarbons contaminated environment.
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Affiliation(s)
- Ruiqi Yang
- College of Urban Environment, Lanzhou City University, Lanzhou 730070, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000, China
| | - Binglin Zhang
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy Sciences, Lanzhou 730000, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000, China.
| | - Yeteng Xu
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy Sciences, Lanzhou 730000, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000, China
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000, China; Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Yang Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000, China; Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Dongming Zhang
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), KTH Royal Institute of Technology, Stockholm, Sweden
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000, China; Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy Sciences, Lanzhou 730000, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000, China; Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
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46
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A Novel Small RNA, DsrO, in Deinococcus radiodurans Promotes Methionine Sulfoxide Reductase ( msrA) Expression for Oxidative Stress Adaptation. Appl Environ Microbiol 2022; 88:e0003822. [PMID: 35575549 PMCID: PMC9195949 DOI: 10.1128/aem.00038-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Reactive oxygen species (ROS) can cause destructive damage to biological macromolecules and protein dysfunction in bacteria. Methionine sulfoxide reductase (Msr) with redox-active Cys and/or seleno-cysteine (Sec) residues can restore physiological functions of the proteome, which is essential for oxidative stress tolerance of the extremophile Deinococcus radiodurans. However, the underlying mechanism regulating MsrA enzyme activity in D. radiodurans under oxidative stress has remained elusive. Here, we identified the function of MsrA in response to oxidative stress. msrA expression in D. radiodurans was significantly upregulated under oxidative stress. The msrA mutant showed a deficiency in antioxidative capacity and an increased level of dabsyl-Met-S-SO, indicating increased sensitivity to oxidative stress. Moreover, msrA mRNA was posttranscriptionally regulated by a small RNA, DsrO. Analysis of the molecular interaction between DsrO and msrA mRNA demonstrated that DsrO increased the half-life of msrA mRNA and then upregulated MsrA enzyme activity under oxidative stress compared to the wild type. msrA expression was also transcriptionally regulated by the DNA-repairing regulator DrRRA, providing a connection for further analysis of protein restoration during DNA repair. Overall, our results provide direct evidence that DsrO and DrRRA regulate msrA expression at two levels to stabilize msrA mRNA and increase MsrA protein levels, revealing the protective roles of DsrO signaling in D. radiodurans against oxidative stress. IMPORTANCE The repair of oxidized proteins is an indispensable function allowing the extremophile D. radiodurans to grow in adverse environments. Msr proteins and various oxidoreductases can reduce oxidized Cys and Met amino acid residues of damaged proteins to recover protein function. Consequently, it is important to investigate the molecular mechanism maintaining the high reducing activity of MsrA protein in D. radiodurans during stresses. Here, we showed the protective roles of an sRNA, DsrO, in D. radiodurans against oxidative stress. DsrO interacts with msrA mRNA to improve msrA mRNA stability, and this increases the amount of MsrA protein. In addition, we also showed that DrRRA transcriptionally regulated msrA gene expression. Due to the importance of DrRRA in regulating DNA repair, this study provides a clue for further analysis of MsrA activity during DNA repair. This study indicates that protecting proteins from oxidation is an effective strategy for extremophiles to adapt to stress conditions.
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47
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Sudharsan M, Prasad NR, Kanimozhi G, Rishiikeshwer B, Brindha G, Chakraborty A. Redox status and metabolomic profiling of thioredoxin reductase inhibitors and 4 kGy ionizing radiation-exposed Deinococcus radiodurans. Microbiol Res 2022; 261:127070. [DOI: 10.1016/j.micres.2022.127070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 12/24/2022]
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48
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Liu Y, Chen T, Cui X, Xu Y, Hu S, Zhao Y, Zhang W, Liu G, Zhang G. Sphingomonas radiodurans sp. nov., a novel radiation-resistant bacterium isolated from the north slope of Mount Everest. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005312] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated S9-5T, was isolated from moraine samples collected from the north slope of Mount Everest at an altitude of 5 500 m above sea level. A polyphasic study confirmed the affiliation of the strain with the genus
Sphingomonas
. Strain S9-5T was an aerobic, Gram-stain-negative, non-spore-forming, non-motile and rod-shaped bacterium that could grow at 10–40 °C, pH 5–8 and with 0–9 % (w/v) NaCl. Q-10 was its predominant respiratory menaquinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminophospholipid and eight unidentified lipids comprised the polar lipids of strain S9-5T. Its major fatty acids were summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c) and C16 : 0. The G+C content was 65.75mol%. Phylogenetic analysis based on 16S rRNA sequences showed that strain S9-5T was phylogenetically closely related to
Sphingomonas panaciterrae
DCY91T (98.17 %),
Sphingomonas olei
K-1-16T (98.11 %) and
Sphingomonas mucosissima
DSM 17494T (97.39 %). The average nucleotide identity values among strain S9-5T and
Sphingomonas panaciterrae
DCY91T,
Sphingomonas olei
K-1-16T and
Sphingomonas mucosissima
DSM 17494T were 78.82, 78.87 and 78.29 %, respectively. Based on the morphological, physiological and chemotaxonomic data, strain S9-5T (=JCM 34750T=GDMCC 1.2714T) should represent a novel species of the genus
Sphingomonas
, for which we propose the name Sphingomonas radiodurans sp. nov.
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Affiliation(s)
- Yang Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
| | - Tuo Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
| | - Xiaowen Cui
- College of Geography and Environment Science, Northwest Normal University, Lanzhou 730070, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Yeteng Xu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
| | - Shixin Hu
- Institute of Applied Magnetics, Key Laboratory for Magnetism and Magnetic Materials of the Ministry of Education, Lanzhou University, Lanzhou 730000, PR China
| | - Yidan Zhao
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
| | - Wei Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Gaosen Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
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49
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Ye Q, Shin E, Lee C, Choi N, Kim Y, Yoon KS, Lee SJ. Transposition of insertion sequences by dielectric barrier discharge plasma and gamma irradiation in the radiation-resistant bacterium Deinococcus geothermalis. J Microbiol Methods 2022; 196:106473. [DOI: 10.1016/j.mimet.2022.106473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/19/2022] [Accepted: 04/19/2022] [Indexed: 12/27/2022]
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50
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Small-Molecule Mn Antioxidants in Caenorhabditis elegans and Deinococcus radiodurans Supplant MnSOD Enzymes during Aging and Irradiation. mBio 2022; 13:e0339421. [PMID: 35012337 PMCID: PMC8749422 DOI: 10.1128/mbio.03394-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Denham Harman's oxidative damage theory identifies superoxide (O2•-) radicals as central agents of aging and radiation injury, with Mn2+-dependent superoxide dismutase (MnSOD) as the principal O2•--scavenger. However, in the radiation-resistant nematode Caenorhabditis elegans, the mitochondrial antioxidant enzyme MnSOD is dispensable for longevity, and in the model bacterium Deinococcus radiodurans, it is dispensable for radiation resistance. Many radiation-resistant organisms accumulate small-molecule Mn2+-antioxidant complexes well-known for their catalytic ability to scavenge O2•-, along with MnSOD, as exemplified by D. radiodurans. Here, we report experiments that relate the MnSOD and Mn-antioxidant content to aging and oxidative stress resistances and which indicate that C. elegans, like D. radiodurans, may rely on Mn-antioxidant complexes as the primary defense against reactive oxygen species (ROS). Wild-type and ΔMnSOD D. radiodurans and C. elegans were monitored for gamma radiation sensitivities over their life spans while gauging Mn2+-antioxidant content by electron paramagnetic resonance (EPR) spectroscopy, a powerful new approach to determining the in vivo Mn-antioxidant content of cells as they age. As with D. radiodurans, MnSOD is dispensable for radiation survivability in C. elegans, which hyperaccumulates Mn-antioxidants exceptionally protective of proteins. Unexpectedly, ΔMnSOD mutants of both the nematodes and bacteria exhibited increased gamma radiation survival compared to the wild-type. In contrast, the loss of MnSOD renders radiation-resistant bacteria sensitive to atmospheric oxygen during desiccation. Our results support the concept that the disparate responses to oxidative stress are explained by the accumulation of Mn-antioxidant complexes which protect, complement, and can even supplant MnSOD. IMPORTANCE The current theory of cellular defense against oxidative damage identifies antioxidant enzymes as primary defenders against ROS, with MnSOD being the preeminent superoxide (O2•-) scavenger. However, MnSOD is shown to be dispensable both for radiation resistance and longevity in model organisms, the bacterium Deinococcus radiodurans and the nematode Caenorhabditis elegans. Measured by electron paramagnetic resonance (EPR) spectroscopy, small-molecule Mn-antioxidant content was shown to decline in unison with age-related decreases in cell proliferation and radioresistance, which again are independent of MnSOD presence. Most notably, the Mn-antioxidant content of C. elegans drops precipitously in the last third of its life span, which links with reports that the steady-state level of oxidized proteins increases exponentially during the last third of the life span in animals. This leads us to propose that global responses to oxidative stress must be understood through an extended theory that includes small-molecule Mn-antioxidants as potent O2•--scavengers that complement, and can even supplant, MnSOD.
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