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Caffrey BJ, Pedrazo-Tardajos A, Liberti E, Gaunt B, Kim JS, Kirkland AI. Liquid Phase Electron Microscopy of Bacterial Ultrastructure. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2402871. [PMID: 39239997 DOI: 10.1002/smll.202402871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/05/2024] [Indexed: 09/07/2024]
Abstract
Recent advances in liquid phase scanning transmission electron microscopy (LP-STEM) have enabled the study of dynamic biological processes at nanometer resolutions, paving the way for live-cell imaging using electron microscopy. However, this technique is often hampered by the inherent thickness of whole cell samples and damage from electron beam irradiation. These restrictions degrade image quality and resolution, impeding biological interpretation. Using graphene encapsulation, scanning transmission electron microscopy (STEM), and energy-dispersive X-ray (EDX) spectroscopy to mitigate these issues provides unprecedented levels of intracellular detail in aqueous specimens. This study demonstrates the potential of LP-STEM to examine and identify internal cellular structures in thick biological samples. Specifically, it highlights the use of LP-STEM to investigate the radiation resistant, gram-positive bacterium, Deinococcus radiodurans using various imaging techniques.
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Affiliation(s)
- Brian J Caffrey
- The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 OQX, UK
| | - Adrián Pedrazo-Tardajos
- The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 OQX, UK
| | - Emanuela Liberti
- The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 OQX, UK
| | - Benjamin Gaunt
- The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 OQX, UK
- Nuffield Department of Women's & Reproductive Health, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Judy S Kim
- The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 OQX, UK
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
| | - Angus I Kirkland
- The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 OQX, UK
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
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2
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Szabla R, Li M, Warner V, Song Y, Junop M. DdrC, a unique DNA repair factor from D. radiodurans, senses and stabilizes DNA breaks through a novel lesion-recognition mechanism. Nucleic Acids Res 2024; 52:9282-9302. [PMID: 39036966 PMCID: PMC11347143 DOI: 10.1093/nar/gkae635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 07/03/2024] [Accepted: 07/11/2024] [Indexed: 07/23/2024] Open
Abstract
The bacterium Deinococcus radiodurans is known to survive high doses of DNA damaging agents. This resistance is the result of robust antioxidant systems which protect efficient DNA repair mechanisms that are unique to Deinococcus species. The protein DdrC has been identified as an important component of this repair machinery. DdrC is known to bind to DNA in vitro and has been shown to circularize and compact DNA fragments. The mechanism and biological relevance of this activity is poorly understood. Here, we show that the DdrC homodimer is a lesion-sensing protein that binds to two single-strand (ss) or double-strand (ds) breaks. The immobilization of DNA breaks in pairs consequently leads to the circularization of linear DNA and the compaction of nicked DNA. The degree of compaction is directly proportional with the number of available nicks. Previously, the structure of the DdrC homodimer was solved in an unusual asymmetric conformation. Here, we solve the structure of DdrC under different crystallographic environments and confirm that the asymmetry is an endogenous feature of DdrC. We propose a dynamic structural mechanism where the asymmetry is necessary to trap a pair of lesions. We support this model with mutant disruption and computational modeling experiments.
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Affiliation(s)
- Robert Szabla
- Department of Biochemistry, Western University, London, Ontario N6A 3K7, Canada
| | - Mingyi Li
- Department of Biochemistry, Western University, London, Ontario N6A 3K7, Canada
| | - Victoria Warner
- Department of Biochemistry, Western University, London, Ontario N6A 3K7, Canada
| | - Yifeng Song
- Department of Biochemistry, Western University, London, Ontario N6A 3K7, Canada
| | - Murray Junop
- Department of Biochemistry, Western University, London, Ontario N6A 3K7, Canada
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Anoud M, Delagoutte E, Helleu Q, Brion A, Duvernois-Berthet E, As M, Marques X, Lamribet K, Senamaud-Beaufort C, Jourdren L, Adrait A, Heinrich S, Toutirais G, Hamlaoui S, Gropplero G, Giovannini I, Ponger L, Geze M, Blugeon C, Couté Y, Guidetti R, Rebecchi L, Giovannangeli C, De Cian A, Concordet JP. Comparative transcriptomics reveal a novel tardigrade-specific DNA-binding protein induced in response to ionizing radiation. eLife 2024; 13:RP92621. [PMID: 38980300 PMCID: PMC11233135 DOI: 10.7554/elife.92621] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024] Open
Abstract
Tardigrades are microscopic animals renowned for their ability to withstand extreme conditions, including high doses of ionizing radiation (IR). To better understand their radio-resistance, we first characterized induction and repair of DNA double- and single-strand breaks after exposure to IR in the model species Hypsibius exemplaris. Importantly, we found that the rate of single-strand breaks induced was roughly equivalent to that in human cells, suggesting that DNA repair plays a predominant role in tardigrades' radio-resistance. To identify novel tardigrade-specific genes involved, we next conducted a comparative transcriptomics analysis across three different species. In all three species, many DNA repair genes were among the most strongly overexpressed genes alongside a novel tardigrade-specific gene, which we named Tardigrade DNA damage Response 1 (TDR1). We found that TDR1 protein interacts with DNA and forms aggregates at high concentration suggesting it may condensate DNA and preserve chromosome organization until DNA repair is accomplished. Remarkably, when expressed in human cells, TDR1 improved resistance to Bleomycin, a radiomimetic drug. Based on these findings, we propose that TDR1 is a novel tardigrade-specific gene conferring resistance to IR. Our study sheds light on mechanisms of DNA repair helping cope with high levels of DNA damage inflicted by IR.
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Affiliation(s)
- Marwan Anoud
- Département AVIV, MNHN, CNRS UMR7196, INSERM U1154ParisFrance
- Université Paris-SaclayOrsayFrance
| | | | - Quentin Helleu
- Département AVIV, MNHN, CNRS UMR7196, INSERM U1154ParisFrance
| | - Alice Brion
- Département AVIV, MNHN, CNRS UMR7196, INSERM U1154ParisFrance
| | | | - Marie As
- Département AVIV, MNHN, CNRS UMR7196, INSERM U1154ParisFrance
| | - Xavier Marques
- Département AVIV, MNHN, CNRS UMR7196, INSERM U1154ParisFrance
- CeMIM, MNHN, CNRS UMR7245ParisFrance
| | | | - Catherine Senamaud-Beaufort
- Génomique ENS, Institut de Biologie de l’ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSLParisFrance
| | - Laurent Jourdren
- Génomique ENS, Institut de Biologie de l’ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSLParisFrance
| | - Annie Adrait
- Univ. Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, CEAGrenobleFrance
| | - Sophie Heinrich
- Institut Curie, Inserm U1021-CNRS UMR 3347, Université Paris-Saclay, Université PSLOrsay CedexFrance
- Plateforme RADEXP, Institut CurieOrsayFrance
| | | | | | | | - Ilaria Giovannini
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
- NBFC, National Biodiversity Future CenterPalermoItaly
| | - Loic Ponger
- Département AVIV, MNHN, CNRS UMR7196, INSERM U1154ParisFrance
| | - Marc Geze
- CeMIM, MNHN, CNRS UMR7245ParisFrance
| | - Corinne Blugeon
- Génomique ENS, Institut de Biologie de l’ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSLParisFrance
| | - Yohann Couté
- Univ. Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, CEAGrenobleFrance
| | - Roberto Guidetti
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
- NBFC, National Biodiversity Future CenterPalermoItaly
| | - Lorena Rebecchi
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
- NBFC, National Biodiversity Future CenterPalermoItaly
| | | | - Anne De Cian
- Département AVIV, MNHN, CNRS UMR7196, INSERM U1154ParisFrance
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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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5
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Khan A, Liu G, Zhang G, Li X. Radiation-resistant bacteria in desiccated soil and their potentiality in applied sciences. Front Microbiol 2024; 15:1348758. [PMID: 38894973 PMCID: PMC11184166 DOI: 10.3389/fmicb.2024.1348758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
A rich diversity of radiation-resistant (Rr) and desiccation-resistant (Dr) bacteria has been found in arid habitats of the world. Evidence from scientific research has linked their origin to reactive oxygen species (ROS) intermediates. Rr and Dr. bacteria of arid regions have the potential to regulate imbalance radicals and evade a higher dose of radiation and oxidation than bacterial species of non-arid regions. Photochemical-activated ROS in Rr bacteria is run through photo-induction of electron transfer. A hypothetical model of the biogeochemical cycle based on solar radiation and desiccation. These selective stresses generate oxidative radicals for a short span with strong reactivity and toxic effects. Desert-inhibiting Rr bacteria efficiently evade ROS toxicity with an evolved antioxidant system and other defensive pathways. The imbalanced radicals in physiological disorders, cancer, and lung diseases could be neutralized by a self-sustaining evolved Rr bacteria antioxidant system. The direct link of evolved antioxidant system with intermediate ROS and indirect influence of radiation and desiccation provide useful insight into richness, ecological diversity, and origin of Rr bacteria capabilities. The distinguishing features of Rr bacteria in deserts present a fertile research area with promising applications in the pharmaceutical industry, genetic engineering, biological therapy, biological transformation, bioremediation, industrial biotechnology, and astrobiology.
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Affiliation(s)
- Asaf Khan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
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6
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Mishra S, Duarte GT, Horemans N, Ruytinx J, Gudkov D, Danchenko M. Complexity of responses to ionizing radiation in plants, and the impact on interacting biotic factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171567. [PMID: 38460702 DOI: 10.1016/j.scitotenv.2024.171567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/20/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
In nature, plants are simultaneously exposed to different abiotic (e.g., heat, drought, and salinity) and biotic (e.g., bacteria, fungi, and insects) stresses. Climate change and anthropogenic pressure are expected to intensify the frequency of stress factors. Although plants are well equipped with unique and common defense systems protecting against stressors, they may compromise their growth and development for survival in such challenging environments. Ionizing radiation is a peculiar stress factor capable of causing clustered damage. Radionuclides are both naturally present on the planet and produced by human activities. Natural and artificial radioactivity affects plants on molecular, biochemical, cellular, physiological, populational, and transgenerational levels. Moreover, the fitness of pests, pathogens, and symbionts is concomitantly challenged in radiologically contaminated areas. Plant responses to artificial acute ionizing radiation exposure and laboratory-simulated or field chronic exposure are often discordant. Acute or chronic ionizing radiation exposure may occasionally prime the defense system of plants to better tolerate the biotic stress or could often exhaust their metabolic reserves, making plants more susceptible to pests and pathogens. Currently, these alternatives are only marginally explored. Our review summarizes the available literature on the responses of host plants, biotic factors, and their interaction to ionizing radiation exposure. Such systematic analysis contributes to improved risk assessment in radiologically contaminated areas.
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Affiliation(s)
- Shubhi Mishra
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 950 07 Nitra, Slovakia
| | - Gustavo Turqueto Duarte
- Unit for Biosphere Impact Studies, Belgian Nuclear Research Centre SCK CEN, 2400 Mol, Belgium
| | - Nele Horemans
- Unit for Biosphere Impact Studies, Belgian Nuclear Research Centre SCK CEN, 2400 Mol, Belgium; Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Joske Ruytinx
- Department of Bio-engineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Dmitri Gudkov
- Institute of Hydrobiology, National Academy of Sciences of Ukraine, 04210 Kyiv, Ukraine
| | - Maksym Danchenko
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 950 07 Nitra, Slovakia.
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7
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Misra HS, Rajpurohit YS. DNA damage response and cell cycle regulation in bacteria: a twist around the paradigm. Front Microbiol 2024; 15:1389074. [PMID: 38605710 PMCID: PMC11007091 DOI: 10.3389/fmicb.2024.1389074] [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: 02/20/2024] [Accepted: 03/13/2024] [Indexed: 04/13/2024] Open
Abstract
The co-protease activity in the RecA-ssDNA complex cleaves the autorepressor LexA, resulting in the derepression of a large number of genes under LexA control. This process is called the SOS response, and genes that are expressed in response to DNA damage are called SOS genes. The proteins encoded by the SOS genes are involved in both DNA repair and maintaining the functions of crucial cell division proteins (e.g., FtsZ) under check until the damaged DNA is presumably repaired. This mechanism of SOS response is the only known mechanism of DNA damage response and cell cycle regulation in bacteria. However, there are bacteria that do not obey this rule of DNA damage response and cell cycle regulation, yet they respond to DNA damage, repair it, and survive. That means such bacteria would have some alternate mechanism(s) of DNA damage response and cell cycle regulation beyond the canonical pathway of the SOS response. In this study, we present the perspectives that bacteria may have other mechanisms of DNA damage response and cell cycle regulation mediated by bacterial eukaryotic type Ser/Thr protein kinases as an alternate to the canonical SOS response and herewith elaborate on them with a well-studied example in the radioresistant bacterium Deinococcus radiodurans.
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Affiliation(s)
- Hari Sharan Misra
- School of Sciences, Gandhi Institute of Technology and Management (GITAM), Visakhapatnam, India
| | - Yogendra Singh Rajpurohit
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Life Sciences, Homi Bhabha National Institute (DAE Deemed to be University), Mumbai, India
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8
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Thweatt JL, Harman CE, Araújo MN, Marlow JJ, Oliver GC, Sabuda MC, Sevgen S, Wilpiszeki RL. Chapter 6: The Breadth and Limits of Life on Earth. ASTROBIOLOGY 2024; 24:S124-S142. [PMID: 38498824 DOI: 10.1089/ast.2021.0131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Scientific ideas about the potential existence of life elsewhere in the universe are predominantly informed by knowledge about life on Earth. Over the past ∼4 billion years, life on Earth has evolved into millions of unique species. Life now inhabits nearly every environmental niche on Earth that has been explored. Despite the wide variety of species and diverse biochemistry of modern life, many features, such as energy production mechanisms and nutrient requirements, are conserved across the Tree of Life. Such conserved features help define the operational parameters required by life and therefore help direct the exploration and evaluation of habitability in extraterrestrial environments. As new diversity in the Tree of Life continues to expand, so do the known limits of life on Earth and the range of environments considered habitable elsewhere. The metabolic processes used by organisms living on the edge of habitability provide insights into the types of environments that would be most suitable to hosting extraterrestrial life, crucial for planning and developing future astrobiology missions. This chapter will introduce readers to the breadth and limits of life on Earth and show how the study of life at the extremes can inform the broader field of astrobiology.
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Affiliation(s)
- Jennifer L Thweatt
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA. (Former)
| | - C E Harman
- Planetary Systems Branch, NASA Ames Research Center, Moffett Field, California, USA
| | - M N Araújo
- Biochemistry Department, University of São Paulo, São Carlos, Brazil
| | - Jeffrey J Marlow
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Gina C Oliver
- Department of Geology, San Bernardino Valley College, San Bernardino, California, USA
| | - Mary C Sabuda
- Department of Earth and Environmental Sciences, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
- Biotechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - Serhat Sevgen
- Institute of Marine Sciences, Middle East Technical University, Erdemli, Mersin, Turkey
- Blue Marble Space Institute of Science, Seattle, Washington, USA
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9
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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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10
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Shi C, Wang L, Xu H, Zhao Y, Tian B, Hua Y. Characterization of a Novel N4-Methylcytosine Restriction-Modification System in Deinococcus radiodurans. Int J Mol Sci 2024; 25:1660. [PMID: 38338939 PMCID: PMC10855626 DOI: 10.3390/ijms25031660] [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: 12/21/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Deinococcus radiodurans is an extremophilic microorganism that possesses a unique DNA damage repair system, conferring a strong resistance to radiation, desiccation, oxidative stress, and chemical damage. Recently, we discovered that D. radiodurans possesses an N4-methylation (m4C) methyltransferase called M.DraR1, which recognizes the 5'-CCGCGG-3' sequence and methylates the second cytosine. Here, we revealed its cognate restriction endonuclease R.DraR1 and recognized that it is the only endonuclease specially for non-4C-methylated 5'-CCGCGG-3' sequence so far. We designated the particular m4C R.DraR1-M.DraR1 as the DraI R-M system. Bioinformatics searches displayed the rarity of the DraI R-M homologous system. Meanwhile, recombination and transformation efficiency experiments demonstrated the important role of the DraI R-M system in response to oxidative stress. In addition, in vitro activity experiments showed that R.DraR1 could exceptionally cleave DNA substrates with a m5C-methlated 5'-CCGCGG-3' sequence instead of its routine activity, suggesting that this particular R-M component possesses a broader substrate choice. Furthermore, an imbalance of the DraI R-M system led to cell death through regulating genes involved in the maintenance of cell survival such as genome stability, transporter, and energy production. Thus, our research revealed a novel m4C R-M system that plays key roles in maintaining cell viability and defending foreign DNA in D. radiodurans.
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Affiliation(s)
- Chenxiang Shi
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (C.S.); (H.X.); (Y.Z.); (B.T.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Liangyan Wang
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (C.S.); (H.X.); (Y.Z.); (B.T.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Hong Xu
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (C.S.); (H.X.); (Y.Z.); (B.T.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Ye Zhao
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (C.S.); (H.X.); (Y.Z.); (B.T.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Bing Tian
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (C.S.); (H.X.); (Y.Z.); (B.T.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Yuejin Hua
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (C.S.); (H.X.); (Y.Z.); (B.T.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
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Ujaoney AK, Anaganti N, Padwal MK, Basu B. Tracing the serendipitous genesis of radiation resistance. Mol Microbiol 2024; 121:142-151. [PMID: 38082498 DOI: 10.1111/mmi.15208] [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: 06/05/2023] [Revised: 11/01/2023] [Accepted: 11/27/2023] [Indexed: 01/15/2024]
Abstract
Free-living organisms frequently encounter unfavorable abiotic environmental factors. Those who adapt and cope with sudden changes in the external environment survive. Desiccation is one of the most common and frequently encountered stresses in nature. On the contrary, ionizing radiations are limited to high local concentrations of naturally occurring radioactive materials and related anthropogenic activities. Yet, resistance to high doses of ionizing radiation is evident across the tree of life. The evolution of desiccation resistance has been linked to the evolution of ionizing radiation resistance, although, evidence to support the idea that the evolution of desiccation tolerance is a necessary precursor to ionizing radiation resistance is lacking. Moreover, the presence of radioresistance in hyperthermophiles suggests multiple paths lead to radiation resistance. In this minireview, we focus on the molecular aspects of damage dynamics and damage response pathways comprising protective and restorative functions with a definitive survival advantage, to explore the serendipitous genesis of ionizing radiation resistance.
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Affiliation(s)
- Aman Kumar Ujaoney
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Narasimha Anaganti
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Mahesh Kumar Padwal
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Bhakti Basu
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
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12
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de Groot A, Blanchard L. DNA repair and oxidative stress defense systems in radiation-resistant Deinococcus murrayi. Can J Microbiol 2023; 69:416-431. [PMID: 37552890 DOI: 10.1139/cjm-2023-0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Deinococcus murrayi is a bacterium isolated from hot springs in Portugal, and named after Dr. Robert G.E. Murray in recognition of his research on the genus Deinococcus. Like other Deinococcus species, D. murrayi is extremely resistant to ionizing radiation. Repair of massive DNA damage and limitation of oxidative protein damage are two important factors contributing to the robustness of Deinococcus bacteria. Here, we identify, among others, the DNA repair and oxidative stress defense proteins in D. murrayi, and highlight special features of D. murrayi. For DNA repair, D. murrayi does not contain a standalone uracil-DNA glycosylase (Ung), but it encodes a protein in which Ung is fused to a DNA photolyase domain (PhrB). UvrB and UvrD contain large insertions corresponding to inteins. One of its endonuclease III enzymes lacks a [4Fe-4S] cluster. Deinococcus murrayi possesses a homolog of the error-prone DNA polymerase IV. Concerning oxidative stress defense, D. murrayi encodes a manganese catalase in addition to a heme catalase. Its organic hydroperoxide resistance protein Ohr is atypical because the redox active cysteines are present in a CXXC motif. These and other characteristics of D. murrayi show further diversity among Deinococcus bacteria with respect to resistance-associated mechanisms.
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Affiliation(s)
- Arjan de Groot
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13115, France
| | - Laurence Blanchard
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13115, France
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13
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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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14
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Chen Y, Zhang T, Lai Q, Zhang M, Yu M, Zeng R, Jin M. Characterization and Comparative Genomic Analysis of a Deep-Sea Bacillus Phage Reveal a Novel Genus. Viruses 2023; 15:1919. [PMID: 37766325 PMCID: PMC10535572 DOI: 10.3390/v15091919] [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: 08/23/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
As the most abundant biological entities, viruses are the major players in marine ecosystems. However, our knowledge on virus diversity and virus-host interactions in the deep sea remains very limited. In this study, vB_BteM-A9Y, a novel bacteriophage infecting Bacillus tequilensis, was isolated from deep-sea sediments in the South China Sea. vB_BteM-A9Y has a hexametric head and a long, complex contractile tail, which are typical features of myophages. vB_BteM-A9Y initiated host lysis at 60 min post infection with a burst size of 75 PFU/cell. The phage genome comprises 38,634 base pairs and encodes 54 predicted open reading frames (ORFs), of which 27 ORFs can be functionally annotated by homology analysis. Interestingly, abundant ORFs involved in DNA damage repair were identified in the phage genome, suggesting that vB_BteM-A9Y encodes multiple pathways for DNA damage repair, which may help to maintain the stability of the host/phage genome. A BLASTn search of the whole genome sequence of vB_BteM-A9Y against the GenBank revealed no existing homolog. Consistently, a phylogenomic tree and proteome-based phylogenetic tree analysis showed that vB_BteM-A9Y formed a unique branch. Further comparative analysis of genomic nucleotide similarity and ORF homology of vB_BteM-A9Y with its mostly related phages showed that the intergenomic similarity between vB_BteM-A9Y and these phages was 0-33.2%. Collectively, based on the comprehensive morphological, phylogenetic, and comparative genomic analysis, we propose that vB_BteM-A9Y belongs to a novel genus under Caudoviricetes. Therefore, our study will increase our knowledge on deep-sea virus diversity and virus-host interactions, as well as expanding our knowledge on phage taxonomy.
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Affiliation(s)
- Yuan Chen
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (Y.C.); (Q.L.); (M.Z.); (M.Y.)
| | - Tianyou Zhang
- Fujian Provincial Center for Disease Control and Prevention, Fuzhou 350000, China;
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (Y.C.); (Q.L.); (M.Z.); (M.Y.)
| | - Menghui Zhang
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (Y.C.); (Q.L.); (M.Z.); (M.Y.)
| | - Meishun Yu
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (Y.C.); (Q.L.); (M.Z.); (M.Y.)
| | - Runying Zeng
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (Y.C.); (Q.L.); (M.Z.); (M.Y.)
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519000, China
| | - Min Jin
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (Y.C.); (Q.L.); (M.Z.); (M.Y.)
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519000, China
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15
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Ujaoney AK, Anaganti N, Padwal MK, Basu B. Deinococcus lineage and Rad52 family-related protein DR0041 is involved in DNA protection and compaction. Int J Biol Macromol 2023; 248:125885. [PMID: 37473881 DOI: 10.1016/j.ijbiomac.2023.125885] [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: 05/08/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 07/22/2023]
Abstract
DR0041 ORF encodes an uncharacterized Deinococcus lineage protein. We earlier reported presence of DR0041 protein in DNA repair complexes of Ssb and RecA in Deinococcus radiodurans. Here, we systematically examined the role of DR0041 in DNA metabolism using various experimental methodologies including electrophoretic mobility assays, nuclease assays, strand exchange assays and transmission electron microscopy. Interaction between DR0041 and the C-terminal acidic tail of Ssb was assessed through co-expression and in vivo cross-linking studies. A knockout mutant was constructed to understand importance of DR0041 ORF for various physiological processes. Results highlight binding of DR0041 protein to single-stranded and double-stranded DNA, interaction with Ssb-coated single-stranded DNA without interference with RecA-mediated strand exchange, protection of DNA from exonucleases, and compaction of high molecular weight DNA molecules into tightly condensed forms. Bridging and compaction of sheared DNA by DR0041 protein might have implications in the preservation of damaged DNA templates to maintain genome integrity upon exposure to gamma irradiation. Our results suggest that DR0041 protein is dispensable for growth under standard growth conditions and following gamma irradiation but contributes to protection of DNA during transformation. We discuss the role of DR0041 protein from the perspective of protection of broken DNA templates and functional redundancy.
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Affiliation(s)
- Aman Kumar Ujaoney
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Narasimha Anaganti
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Mahesh Kumar Padwal
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Bhakti Basu
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India.
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16
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Gómez LA, Molina RE, Soto RI, Flores MR, Coloma-Rivero RF, Montero DA, Oñate ÁA. Unraveling the Role of the Zinc-Dependent Metalloproteinase/HTH-Xre Toxin/Antitoxin (TA) System of Brucella abortus in the Oxidative Stress Response: Insights into the Stress Response and Virulence. Toxins (Basel) 2023; 15:536. [PMID: 37755962 PMCID: PMC10538038 DOI: 10.3390/toxins15090536] [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: 06/20/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/28/2023] Open
Abstract
Toxin/antitoxin (TA) systems have been scarcely studied in Brucella abortus, the causative agent of brucellosis, which is one of the most prevalent zoonotic diseases worldwide. In this study, the roles of a putative type II TA system composed by a Zinc-dependent metalloproteinase (ZnMP) and a transcriptional regulator HTH-Xre were evaluated. The deletion of the open reading frame (ORF) BAB1_0270, coding for ZnMP, used to produce a mutant strain, allowed us to evaluate the survival and gene expression of B. abortus 2308 under oxidative conditions. Our results showed that the B. abortus mutant strain exhibited a significantly reduced capacity to survive under hydrogen peroxide-induced oxidative stress. Furthermore, this mutant strain showed a decreased expression of genes coding for catalase (katE), alkyl hydroperoxide reductase (ahpC) and transcriptional regulators (oxyR and oxyR-like), as well as genes involved in the general stress response, phyR and rpoE1, when compared to the wild-type strain. These findings suggest that this type II ZnMP/HTH-Xre TA system is required by B. abortus to resist oxidative stress. Additionally, previous evidence has demonstrated that this ZnMP also participates in the acidic stress resistance and virulence of B. abortus 2308. Therefore, we propose a hypothetical regulatory function for this ZnMP/HTH-Xre TA system, providing insight into the stress response and its potential roles in the pathogenesis of B. abortus.
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Affiliation(s)
- Leonardo A Gómez
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, University of Concepción, Concepción 4030000, Chile
| | - Raúl E Molina
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, University of Concepción, Concepción 4030000, Chile
| | - Rodrigo I Soto
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, University of Concepción, Concepción 4030000, Chile
| | - Manuel R Flores
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, University of Concepción, Concepción 4030000, Chile
| | - Roberto F Coloma-Rivero
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, University of Concepción, Concepción 4030000, Chile
| | - David A Montero
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, University of Concepción, Concepción 4030000, Chile
| | - Ángel A Oñate
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, University of Concepción, Concepción 4030000, Chile
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17
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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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18
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Chaudhary R, Mishra S, Maurya GK, Rajpurohit YS, Misra HS. FtsZ phosphorylation brings about growth arrest upon DNA damage in Deinococcus radiodurans. FASEB Bioadv 2023; 5:27-42. [PMID: 36643897 PMCID: PMC9832530 DOI: 10.1096/fba.2022-00082] [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: 07/21/2022] [Revised: 09/30/2022] [Accepted: 10/18/2022] [Indexed: 01/12/2023] Open
Abstract
The polymerization/depolymerization dynamics of FtsZ play a pivotal role in cell division in the majority of the bacteria. Deinococcus radiodurans, a radiation-resistant bacterium, shows an arrest of growth in response to DNA damage with no change in the level of FtsZ. This bacterium does not deploy LexA/RecA type of DNA damage response and cell cycle regulation, and its genome does not encode SulA homologues of Escherichia coli, which attenuate FtsZ functions in response to DNA damage in other bacteria. A radiation-responsive Ser/Thr quinoprotein kinase (RqkA), characterized for its role in radiation resistance in this bacterium, could phosphorylate several cognate proteins, including FtsZ (drFtsZ) at Serine 235 (S235) and Serine 335 (S335) residues. Here, we reported the detailed characterization of S235 and S335 phosphorylation effects in the regulation of drFtsZ functions and demonstrated that the phospho-mimetic replacements of these residues in drFtsZ had grossly affected its functions that could result in cell cycle arrest in response to DNA damage in D. radiodurans. Interestingly, the phospho-ablative replacements were found to be nearly similar to drFtsZ, whereas the phospho-mimetic mutant lost the wild-type protein's signature characteristics, including its dynamics under normal conditions. The kinetics of post-bleaching recovery for drFtsZ and phospho-mimetic mutant were nearly similar at 2 h post-irradiation recovery but were found to be different under normal conditions. These results highlighted the role of S/T phosphorylation in the regulation of drFtsZ functions and cell cycle arrest in response to DNA damage, which is demonstrated for the first time, in any bacteria.
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Affiliation(s)
- Reema Chaudhary
- Molecular Biology DivisionBhabha Atomic Research CentreMumbaiIndia
- Life SciencesHomi Bhabha National InstituteMumbaiIndia
| | - Shruti Mishra
- Molecular Biology DivisionBhabha Atomic Research CentreMumbaiIndia
- Life SciencesHomi Bhabha National InstituteMumbaiIndia
| | | | - Yogendra S. Rajpurohit
- Molecular Biology DivisionBhabha Atomic Research CentreMumbaiIndia
- Life SciencesHomi Bhabha National InstituteMumbaiIndia
| | - Hari S. Misra
- Molecular Biology DivisionBhabha Atomic Research CentreMumbaiIndia
- Life SciencesHomi Bhabha National InstituteMumbaiIndia
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19
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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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20
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Banneville AS, Bouthier de la Tour C, De Bonis S, Hognon C, Colletier JP, Teulon JM, Le Roy A, Pellequer JL, Monari A, Dehez F, Confalonieri F, Servant P, Timmins J. Structural and functional characterization of DdrC, a novel DNA damage-induced nucleoid associated protein involved in DNA compaction. Nucleic Acids Res 2022; 50:7680-7696. [PMID: 35801857 PMCID: PMC9303277 DOI: 10.1093/nar/gkac563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/18/2022] [Accepted: 06/17/2022] [Indexed: 01/19/2023] Open
Abstract
Deinococcus radiodurans is a spherical bacterium well-known for its outstanding resistance to DNA-damaging agents. Exposure to such agents leads to drastic changes in the transcriptome of D. radiodurans. In particular, four Deinococcus-specific genes, known as DNA Damage Response genes, are strongly up-regulated and have been shown to contribute to the resistance phenotype of D. radiodurans. One of these, DdrC, is expressed shortly after exposure to γ-radiation and is rapidly recruited to the nucleoid. In vitro, DdrC has been shown to compact circular DNA, circularize linear DNA, anneal complementary DNA strands and protect DNA from nucleases. To shed light on the possible functions of DdrC in D. radiodurans, we determined the crystal structure of the domain-swapped DdrC dimer at a resolution of 2.5 Å and further characterized its DNA binding and compaction properties. Notably, we show that DdrC bears two asymmetric DNA binding sites located on either side of the dimer and can modulate the topology and level of compaction of circular DNA. These findings suggest that DdrC may be a DNA damage-induced nucleoid-associated protein that enhances nucleoid compaction to limit the dispersion of the fragmented genome and facilitate DNA repair after exposure to severe DNA damaging conditions.
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Affiliation(s)
| | - Claire Bouthier de la Tour
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | | | - Cécilia Hognon
- LPCT, UMR 7019, Université de Lorraine, CNRS, Vandœuvre-lès-Nancy, France
| | | | | | - Aline Le Roy
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | | | - Antonio Monari
- LPCT, UMR 7019, Université de Lorraine, CNRS, Vandœuvre-lès-Nancy, France,Université Paris Cité, CNRS, Itodys, F-75006 Paris, France
| | - François Dehez
- LPCT, UMR 7019, Université de Lorraine, CNRS, Vandœuvre-lès-Nancy, France
| | - Fabrice Confalonieri
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Pascale Servant
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Joanna Timmins
- To whom correspondence should be addressed. Tel: +33 4 57 42 86 78;
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21
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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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22
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Zheng H, Liu B, Xu Y, Zhang Z, Man H, Liu J, Chen F. An Inducible Microbacterium Prophage vB_MoxS-R1 Represents a Novel Lineage of Siphovirus. Viruses 2022; 14:v14040731. [PMID: 35458461 PMCID: PMC9030533 DOI: 10.3390/v14040731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 12/02/2022] Open
Abstract
Lytic and lysogenic infections are the main strategies used by viruses to interact with microbial hosts. The genetic information of prophages provides insights into the nature of phages and their potential influences on hosts. Here, the siphovirus vB_MoxS-R1 was induced from a Microbacterium strain isolated from an estuarine Synechococcus culture. vB_MoxS-R1 has a high replication capability, with an estimated burst size of 2000 virions per cell. vB_MoxS-R1 represents a novel phage genus-based genomic analysis. Six transcriptional regulator (TR) genes were predicted in the vB_MoxS-R1 genome. Four of these TR genes are involved in stress responses, virulence and amino acid transportation in bacteria, suggesting that they may play roles in regulating the host cell metabolism in response to external environmental changes. A glycerophosphodiester phosphodiesterase gene related to phosphorus acquisition was also identified in the vB_MoxS-R1 genome. The presence of six TR genes and the phosphorus-acquisition gene suggests that prophage vB_MoxS-R1 has the potential to influence survival and adaptation of its host during lysogeny. Possession of four endonuclease genes in the prophage genome suggests that vB_MoxS-R1 is likely involved in DNA recombination or gene conversion and further influences host evolution.
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Affiliation(s)
- Hongrui Zheng
- Institute of Marine Science and Technology, Shandong University, Qingdao 266000, China; (H.Z.); (B.L.); (Z.Z.); (H.M.)
| | - Binbin Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266000, China; (H.Z.); (B.L.); (Z.Z.); (H.M.)
| | - Yongle Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266000, China; (H.Z.); (B.L.); (Z.Z.); (H.M.)
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361000, China
- Correspondence: (Y.X.); (J.L.)
| | - Zefeng Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266000, China; (H.Z.); (B.L.); (Z.Z.); (H.M.)
| | - Hongcong Man
- Institute of Marine Science and Technology, Shandong University, Qingdao 266000, China; (H.Z.); (B.L.); (Z.Z.); (H.M.)
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266000, China; (H.Z.); (B.L.); (Z.Z.); (H.M.)
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
- Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao 266237, China
- Correspondence: (Y.X.); (J.L.)
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA;
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23
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Thiol Reductases in Deinococcus Bacteria and Roles in Stress Tolerance. Antioxidants (Basel) 2022; 11:antiox11030561. [PMID: 35326211 PMCID: PMC8945050 DOI: 10.3390/antiox11030561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/11/2022] [Accepted: 03/13/2022] [Indexed: 12/10/2022] Open
Abstract
Deinococcus species possess remarkable tolerance to extreme environmental conditions that generate oxidative damage to macromolecules. Among enzymes fulfilling key functions in metabolism regulation and stress responses, thiol reductases (TRs) harbour catalytic cysteines modulating the redox status of Cys and Met in partner proteins. We present here a detailed description of Deinococcus TRs regarding gene occurrence, sequence features, and physiological functions that remain poorly characterised in this genus. Two NADPH-dependent thiol-based systems are present in Deinococcus. One involves thioredoxins, disulfide reductases providing electrons to protein partners involved notably in peroxide scavenging or in preserving protein redox status. The other is based on bacillithiol, a low-molecular-weight redox molecule, and bacilliredoxin, which together protect Cys residues against overoxidation. Deinococcus species possess various types of thiol peroxidases whose electron supply depends either on NADPH via thioredoxins or on NADH via lipoylated proteins. Recent data gained on deletion mutants confirmed the importance of TRs in Deinococcus tolerance to oxidative treatments, but additional investigations are needed to delineate the redox network in which they operate, and their precise physiological roles. The large palette of Deinococcus TR representatives very likely constitutes an asset for the maintenance of redox homeostasis in harsh stress conditions.
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24
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Rajpurohit YS, Sharma DK, Misra HS. Involvement of Serine / Threonine protein kinases in DNA damage response and cell division in bacteria. Res Microbiol 2021; 173:103883. [PMID: 34624492 DOI: 10.1016/j.resmic.2021.103883] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 11/29/2022]
Abstract
The roles of Serine/Threonine protein kinases (STPKs) in bacterial physiology, including bacterial responses to nutritional stresses and under pathogenesis have been well documented. STPKs roles in bacterial cell cycle regulation and DNA damage response have not been much emphasized, possibly because the LexA/RecA type SOS response became the synonym to DNA damage response and cell cycle regulation in bacteria. This review summarizes current knowledge of STPKs genetics, domain organization, and their roles in DNA damage response and cell division regulation in bacteria.
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Affiliation(s)
- Yogendra S Rajpurohit
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India; Life Sciences, Homi Bhabha National Institute (DAE- Deemed University), Mumbai, 400094, India.
| | - Dhirendra Kumar Sharma
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India; Life Sciences, Homi Bhabha National Institute (DAE- Deemed University), Mumbai, 400094, India
| | - Hari S Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India; Life Sciences, Homi Bhabha National Institute (DAE- Deemed University), Mumbai, 400094, India
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25
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Eugénie N, Zivanovic Y, Lelandais G, Coste G, Bouthier de la Tour C, Bentchikou E, Servant P, Confalonieri F. Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium Deinococcus radiodurans by Integrative Genomic Analyses. Cells 2021; 10:cells10102536. [PMID: 34685516 PMCID: PMC8533742 DOI: 10.3390/cells10102536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 12/02/2022] Open
Abstract
Numerous genes are overexpressed in the radioresistant bacterium Deinococcus radiodurans after exposure to radiation or prolonged desiccation. It was shown that the DdrO and IrrE proteins play a major role in regulating the expression of approximately twenty genes. The transcriptional repressor DdrO blocks the expression of these genes under normal growth conditions. After exposure to genotoxic agents, the IrrE metalloprotease cleaves DdrO and relieves gene repression. At present, many questions remain, such as the number of genes regulated by DdrO. Here, we present the first ChIP-seq analysis performed at the genome level in Deinococcus species coupled with RNA-seq, which was achieved in the presence or not of DdrO. We also resequenced our laboratory stock strain of D. radiodurans R1 ATCC 13939 to obtain an accurate reference for read alignments and gene expression quantifications. We highlighted genes that are directly under the control of this transcriptional repressor and showed that the DdrO regulon in D. radiodurans includes numerous other genes than those previously described, including DNA and RNA metabolism proteins. These results thus pave the way to better understand the radioresistance pathways encoded by this bacterium and to compare the stress-induced responses mediated by this pair of proteins in diverse bacteria.
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26
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Villa JK, Han R, Tsai CH, Chen A, Sweet P, Franco G, Vaezian R, Tkavc R, Daly MJ, Contreras LM. A small RNA regulates pprM, a modulator of pleiotropic proteins promoting DNA repair, in Deinococcus radiodurans under ionizing radiation. Sci Rep 2021; 11:12949. [PMID: 34155239 PMCID: PMC8217566 DOI: 10.1038/s41598-021-91335-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/20/2021] [Indexed: 02/05/2023] Open
Abstract
Networks of transcriptional and post-transcriptional regulators are critical for bacterial survival and adaptation to environmental stressors. While transcriptional regulators provide rapid activation and/or repression of a wide-network of genes, post-transcriptional regulators, such as small RNAs (sRNAs), are also important to fine-tune gene expression. However, the mechanisms of sRNAs remain poorly understood, especially in less-studied bacteria. Deinococcus radiodurans is a gram-positive bacterium resistant to extreme levels of ionizing radiation (IR). Although multiple unique regulatory systems (e.g., the Radiation and Desiccation Response (RDR)) have been identified in this organism, the role of post-transcriptional regulators has not been characterized within the IR response. In this study, we have characterized an sRNA, PprS (formerly Dsr2), as a post-transcriptional coordinator of IR recovery in D. radiodurans. PprS showed differential expression specifically under IR and knockdown of PprS resulted in reduced survival and growth under IR, suggesting its importance in regulating post-radiation recovery. We determined a number of potential RNA targets involved in several pathways including translation and DNA repair. Specifically, we confirmed that PprS binds within the coding region to stabilize the pprM (DR_0907) transcript, a RDR modulator. Overall, these results are the first to present an additional layer of sRNA-based control in DNA repair pathways associated with bacterial radioresistance.
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Affiliation(s)
- Jordan K Villa
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Runhua Han
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Chen-Hsun Tsai
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Angela Chen
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Philip Sweet
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Gabriela Franco
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Respina Vaezian
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Rok Tkavc
- Department of Pathology, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- Department of Microbiology and Immunology, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Michael J Daly
- Department of Pathology, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Department of Molecular and Cellular Biology, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Lydia M Contreras
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA.
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27
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Experimental evolution of extremophile resistance to ionizing radiation. Trends Genet 2021; 37:830-845. [PMID: 34088512 DOI: 10.1016/j.tig.2021.04.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 11/22/2022]
Abstract
A growing number of known species possess a remarkable characteristic - extreme resistance to the effects of ionizing radiation (IR). This review examines our current understanding of how organisms can adapt to and survive exposure to IR, one of the most toxic stressors known. The study of natural extremophiles such as Deinococcus radiodurans has revealed much. However, the evolution of Deinococcus was not driven by IR. Another approach, pioneered by Evelyn Witkin in 1946, is to utilize experimental evolution. Contributions to the IR-resistance phenotype affect multiple aspects of cell physiology, including DNA repair, removal of reactive oxygen species, the structure and packaging of DNA and the cell itself, and repair of iron-sulfur centers. Based on progress to date, we overview the diversity of mechanisms that can contribute to biological IR resistance arising as a result of either natural or experimental evolution.
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28
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de la Tour CB, Mathieu M, Servant P, Coste G, Norais C, Confalonieri F. Characterization of the DdrD protein from the extremely radioresistant bacterium Deinococcus radiodurans. Extremophiles 2021; 25:343-355. [PMID: 34052926 PMCID: PMC8254717 DOI: 10.1007/s00792-021-01233-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/16/2021] [Indexed: 10/25/2022]
Abstract
Here, we report the in vitro and in vivo characterization of the DdrD protein from the extraordinary stress-resistant bacterium, D. radiodurans. DdrD is one of the most highly induced proteins following cellular irradiation or desiccation. We confirm that DdrD belongs to the Radiation Desiccation Response (RDR) regulon protein family whose expression is regulated by the IrrE/DdrO proteins after DNA damage. We show that DdrD is a DNA binding protein that binds to single-stranded DNA In vitro, but not to duplex DNA unless it has a 5' single-stranded extension. In vivo, we observed no significant effect of the absence of DdrD on the survival of D. radiodurans cells after exposure to γ-rays or UV irradiation in different genetic contexts. However, genome reassembly is affected in a ∆ddrD mutant when cells recover from irradiation in the absence of nutrients. Thus, DdrD likely contributes to genome reconstitution after irradiation, but only under starvation conditions. Lastly, we show that the absence of the DdrD protein partially restores the frequency of plasmid transformation of a ∆ddrB mutant, suggesting that DdrD could also be involved in biological processes other than the response to DNA damage.
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Affiliation(s)
- Claire Bouthier de la Tour
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198, Gif sur Yvette, France.
| | - Martine Mathieu
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198, Gif sur Yvette, France
| | - Pascale Servant
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198, Gif sur Yvette, France
| | - Geneviève Coste
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198, Gif sur Yvette, France
| | - Cédric Norais
- Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA.,SAT Lyon, Promega France, 24 Chemin des Verrieres, 69260, Charbonnières les Bains, France
| | - Fabrice Confalonieri
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198, Gif sur Yvette, France
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29
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Ujaoney AK, Padwal MK, Basu B. An in vivo Interaction Network of DNA-Repair Proteins: A Snapshot at Double Strand Break Repair in Deinococcus radiodurans. J Proteome Res 2021; 20:3242-3255. [PMID: 33929844 DOI: 10.1021/acs.jproteome.1c00078] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An extremophile Deinococcus radiodurans survives massive DNA damage by efficiently mending hundreds of double strand breaks through homology-dependent DNA repair pathways. Although DNA repair proteins that contribute to its impressive DNA repair capacity are fairly known, interactions among them or with proteins related to other relevant pathways remain unexplored. Here, we report in vivo cross-linking of the interactomes of key DNA repair proteins DdrA, DdrB, RecA, and Ssb (baits) in D. radiodurans cells recovering from gamma irradiation. The protein-protein interactions were systematically investigated through co-immunoprecipitation experiments coupled to mass spectrometry. From a total of 399 proteins co-eluted with the baits, we recovered interactions among diverse biological pathways such as DNA repair, transcription, translation, chromosome partitioning, cell division, antioxidation, protein folding/turnover, metabolism, cell wall architecture, membrane transporters, and uncharacterized proteins. Among these, about 80 proteins were relevant to the DNA damage resistance of the organism based on integration of data on inducible expression following DNA damage, radiation sensitive phenotype of deletion mutant, etc. Further, we cloned ORFs of 23 interactors in heterologous E. coli and expressed corresponding proteins with N-terminal His-tag, which were used for pull-down assays. A total of 95 interactions were assayed, in which we confirmed 25 previously unknown binary interactions between the proteins associated with radiation resistance, and 2 known interactions between DdrB and Ssb or DR_1245. Among these, five interactions were positive even under non-stress conditions. The confirmed interactions cover a wide range of biological processes such as DNA repair, negative regulation of cell division, chromosome partitioning, membrane anchorage, etc., and their functional relevance is discussed from the perspective of DNA repair. Overall, the study substantially advances our understanding on the cross-talk between different homology-dependent DNA repair pathways and other relevant biological processes that essentially contribute to the extraordinary DNA damage repair capability of D. radiodurans. The data sets generated and analyzed in this study have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD021822.
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Affiliation(s)
- Aman Kumar Ujaoney
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Mahesh Kumar Padwal
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Bhakti Basu
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
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30
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Rajpurohit YS, Sharma DK, Misra HS. PprA Protein Inhibits DNA Strand Exchange and ATP Hydrolysis of Deinococcus RecA and Regulates the Recombination in Gamma-Irradiated Cells. Front Cell Dev Biol 2021; 9:636178. [PMID: 33959605 PMCID: PMC8093518 DOI: 10.3389/fcell.2021.636178] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/23/2021] [Indexed: 11/14/2022] Open
Abstract
DrRecA and PprA proteins function are crucial for the extraordinary resistance to γ-radiation and DNA strand break repair in Deinococcus radiodurans. DrRecA mediated homologous recombination help in DNA strand break repair and cell survival, while the PprA protein confers radio-resistance via its roles in DNA repair, genome maintenance, and cell division. Genetically recA and pprA genes interact and constitute an epistatic group however, the mechanism underlying their functional interaction is not clear. Here, we showed the physical and functional interaction of DrRecA and PprA protein both in solution and inside the cells. The absence of the pprA gene increases the recombination frequency in gamma-irradiated D. radiodurans cells and genomic instability in cells growing under normal conditions. PprA negatively regulates the DrRecA functions by inhibiting DrRecA mediated DNA strand exchange and ATPase function in vitro. Furthermore, it is shown that the inhibitory effect of PprA on DrRecA catalyzed DNA strand exchange was not due to sequestration of homologous dsDNA and was dependent on PprA oligomerization and DNA binding property. Together, results suggest that PprA is a new member of recombination mediator proteins (RMPs), and able to regulate the DrRecA function in γ-irradiated cells by protecting the D. radiodurans genome from hyper-recombination and associated negative effects.
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Affiliation(s)
- Yogendra Singh Rajpurohit
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute (DAE- Deemed University), Mumbai, India
| | - Dhirendra Kumar Sharma
- 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.,Homi Bhabha National Institute (DAE- Deemed University), Mumbai, India
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31
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Coexistence of SOS-Dependent and SOS-Independent Regulation of DNA Repair Genes in Radiation-Resistant Deinococcus Bacteria. Cells 2021; 10:cells10040924. [PMID: 33923690 PMCID: PMC8072749 DOI: 10.3390/cells10040924] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 11/28/2022] Open
Abstract
Deinococcus bacteria are extremely resistant to radiation and able to repair a shattered genome in an essentially error-free manner after exposure to high doses of radiation or prolonged desiccation. An efficient, SOS-independent response mechanism to induce various DNA repair genes such as recA is essential for radiation resistance. This pathway, called radiation/desiccation response, is controlled by metallopeptidase IrrE and repressor DdrO that are highly conserved in Deinococcus. Among various Deinococcus species, Deinococcus radiodurans has been studied most extensively. Its genome encodes classical DNA repair proteins for error-free repair but no error-prone translesion DNA polymerases, which may suggest that absence of mutagenic lesion bypass is crucial for error-free repair of massive DNA damage. However, many other radiation-resistant Deinococcus species do possess translesion polymerases, and radiation-induced mutagenesis has been demonstrated. At least dozens of Deinococcus species contain a mutagenesis cassette, and some even two cassettes, encoding error-prone translesion polymerase DnaE2 and two other proteins, ImuY and ImuB-C, that are probable accessory factors required for DnaE2 activity. Expression of this mutagenesis cassette is under control of the SOS regulators RecA and LexA. In this paper, we review both the RecA/LexA-controlled mutagenesis and the IrrE/DdrO-controlled radiation/desiccation response in Deinococcus.
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32
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Redox signaling through zinc activates the radiation response in Deinococcus bacteria. Sci Rep 2021; 11:4528. [PMID: 33633226 PMCID: PMC7907104 DOI: 10.1038/s41598-021-84026-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 02/11/2021] [Indexed: 02/06/2023] Open
Abstract
Deinococcus bacteria are extremely resistant to radiation and other DNA damage- and oxidative stress-generating conditions. An efficient SOS-independent response mechanism inducing expression of several DNA repair genes is essential for this resistance, and is controlled by metalloprotease IrrE that cleaves and inactivates transcriptional repressor DdrO. Here, we identify the molecular signaling mechanism that triggers DdrO cleavage. We show that reactive oxygen species (ROS) stimulate the zinc-dependent metalloprotease activity of IrrE in Deinococcus. Sudden exposure of Deinococcus to zinc excess also rapidly induces DdrO cleavage, but is not accompanied by ROS production and DNA damage. Further, oxidative treatment leads to an increase of intracellular free zinc, indicating that IrrE activity is very likely stimulated directly by elevated levels of available zinc ions. We conclude that radiation and oxidative stress induce changes in redox homeostasis that result in IrrE activation by zinc in Deinococcus. We propose that a part of the zinc pool coordinated with cysteine thiolates is released due to their oxidation. Predicted regulation systems involving IrrE- and DdrO-like proteins are present in many bacteria, including pathogens, suggesting that such a redox signaling pathway including zinc as a second messenger is widespread and participates in various stress responses.
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33
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Narasimha A, Basu B. New insights into the activation of Radiation Desiccation Response regulon in Deinococcus radiodurans. J Biosci 2021. [DOI: 10.1007/s12038-020-00123-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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34
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Guesmi S, Pujic P, Nouioui I, Dubost A, Najjari A, Ghedira K, Igual JM, Miotello G, Cherif A, Armengaud J, Klenk HP, Normand P, Sghaier H. Ionizing-radiation-resistant Kocuria rhizophila PT10 isolated from the Tunisian Sahara xerophyte Panicum turgidum: Polyphasic characterization and proteogenomic arsenal. Genomics 2020; 113:317-330. [PMID: 33279651 DOI: 10.1016/j.ygeno.2020.11.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/17/2020] [Accepted: 11/29/2020] [Indexed: 10/22/2022]
Abstract
A new strain belonging to the genus Kocuria, designed PT10, was isolated from irradiated roots of the xerophyte Panicum turgidum. Isolate PT10 is a Gram-positive, coccoid, aerobic and ionizing-radiation (IR)-resistant actinobacterium. PT10 has shown an ability to survive under extreme conditions, such as gamma irradiation, desiccation and high concentration of hydrogen peroxide. Phenotypic, chemotaxonomic and comparative genome analyses support the assignment of strain PT10 (LMG 31102 = DSM 108617) as Kocuria rhizophila. The complete genome sequence of PT10 consists of one chromosome (2,656,287 bps), with a 70.7% G + C content and comprises 2481 protein-coding sequences. A total of 1487 proteins were identified by LC-MS/MS profiling. In silico analyses revealed that the proteome of the oxidation-tolerant PT10 possesses several features explaining its IR-resistant phenotype and many adaptive pathways implicated in response to environmental pressures - desiccation, cold, reactive oxygen species and other stressors.
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Affiliation(s)
- Sihem Guesmi
- National Agronomy Institute of Tunisia, 43, Avenue Charles Nicolle, 1082 Tunis, Mahrajène, Tunisia; Laboratory ″Energy and Matter for Development of Nuclear Sciences″ (LR16CNSTN02), National Center for Nuclear Sciences and Technology, Sidi Thabet Technopark, 2020, Tunisia.
| | - Petar Pujic
- Université de Lyon, Université Lyon 1, Lyon, France; CNRS, UMR 5557, Ecologie Microbienne, 69622 Villeurbanne, Cedex, INRA, UMR1418, Villeurbanne, France
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne NE1 7RU, UK; Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Afef Najjari
- Université de Tunis El Manar, Faculté des Sciences de Tunis, LR03ES03 Microorganismes et Biomolécules Actives, 2092 Tunis, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics - LR16IPT09, Institut Pasteur de Tunis, 13, Place Pasteur, Tunis 1002, Tunisia
| | - José M Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), c/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Guylaine Miotello
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Ameur Cherif
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Jean Armengaud
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne NE1 7RU, UK
| | | | - Haïtham Sghaier
- Laboratory ″Energy and Matter for Development of Nuclear Sciences″ (LR16CNSTN02), National Center for Nuclear Sciences and Technology, Sidi Thabet Technopark, 2020, Tunisia; Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia.
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35
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An RNA Repair Operon Regulated by Damaged tRNAs. Cell Rep 2020; 33:108527. [PMID: 33357439 PMCID: PMC7790460 DOI: 10.1016/j.celrep.2020.108527] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 11/03/2020] [Accepted: 11/23/2020] [Indexed: 12/11/2022] Open
Abstract
Many bacteria contain an RNA repair operon, encoding the RtcB RNA ligase and the RtcA RNA cyclase, that is regulated by the RtcR transcriptional activator. Although RtcR contains a divergent version of the CARF (CRISPR-associated Rossman fold) oligonucleotide-binding regulatory domain, both the specific signal that regulates operon expression and the substrates of the encoded enzymes are unknown. We report that tRNA fragments activate operon expression. Using a genetic screen in Salmonella enterica serovar Typhimurium, we find that the operon is expressed in the presence of mutations that cause tRNA fragments to accumulate. RtcA, which converts RNA phosphate ends to 2′, 3′-cyclic phosphate, is also required. Operon expression and tRNA fragment accumulation also occur upon DNA damage. The CARF domain binds 5′ tRNA fragments ending in cyclic phosphate, and RtcR oligomerizes upon binding these ligands, a prerequisite for operon activation. Our studies reveal a signaling pathway involving broken tRNAs and implicate the operon in tRNA repair. Hughes et al. demonstrate that a bacterial RNA repair operon, containing the RtcB RNA ligase and the RtcA RNA cyclase, is regulated by binding of 5′ tRNA halves ending in 2′, 3′-cyclic phosphate to the RtcR transcriptional activator. These studies show how tRNA fragments can regulate bacterial gene expression.
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36
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Jeong SW, Choi YJ. Extremophilic Microorganisms for the Treatment of Toxic Pollutants in the Environment. Molecules 2020; 25:E4916. [PMID: 33114255 PMCID: PMC7660605 DOI: 10.3390/molecules25214916] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 12/13/2022] Open
Abstract
As concerns about the substantial effect of various hazardous toxic pollutants on the environment and public health are increasing, the development of effective and sustainable treatment methods is urgently needed. In particular, the remediation of toxic components such as radioactive waste, toxic heavy metals, and other harmful substances under extreme conditions is quite difficult due to their restricted accessibility. Thus, novel treatment methods for the removal of toxic pollutants using extremophilic microorganisms that can thrive under extreme conditions have been investigated during the past several decades. In this review, recent trends in bioremediation using extremophilic microorganisms and related approaches to develop them are reviewed, with relevant examples and perspectives.
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Affiliation(s)
| | - Yong Jun Choi
- School of Environmental Engineering, University of Seoul, Seoul 02504, Korea;
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37
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Chen Z, Tang Y, Hua Y, Zhao Y. Structural features and functional implications of proteins enabling the robustness of Deinococcus radiodurans. Comput Struct Biotechnol J 2020; 18:2810-2817. [PMID: 33133422 PMCID: PMC7575645 DOI: 10.1016/j.csbj.2020.09.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 12/21/2022] Open
Abstract
Deinococcus radiodurans can survive under extreme conditions, including high doses of DNA damaging agents and ionizing radiation, desiccation, and oxidative stress. Both the efficient cellular DNA repair machinery and antioxidation systems contribute to the extreme resistance of this bacterium, making it an ideal organism for studying the cellular mechanisms of environmental adaptation. The number of stress-related proteins identified in this bacterium has mushroomed in the past two decades. The newly identified proteins reveal both commonalities and diversity of structure, mechanism, and function, which impact a wide range of cellular functions. Here, we review the unique and general structural features of these proteins and discuss how these studies improve our understanding of the environmental stress adaptation mechanisms of D. radiodurans.
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Affiliation(s)
- Zijing Chen
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuyue Tang
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuejin Hua
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ye Zhao
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
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38
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Sharma DK, Bihani SC, Siddiqui MQ, Misra HS, Rajpurohit YS. WD40 domain of RqkA regulates its kinase activity and role in extraordinary radioresistance of D. radiodurans. J Biomol Struct Dyn 2020; 40:1246-1259. [PMID: 32990194 DOI: 10.1080/07391102.2020.1824810] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
RqkA, a DNA damage responsive serine/threonine kinase, is characterized for its role in DNA repair and cell division in D. radiodurans. It has a unique combination of a kinase domain at N-terminus and a WD40 type domain at C-terminus joined through a linker. WD40 domain is comprised of eight β-propeller repeats held together via 'tryptophan-docking motifs' and forming a typical 'velcro' closure structure. RqkA mutants lacking the WD40 region (hereafter referred to as WD mutant) could not complement RqkA loss in γ radiation resistance in D. radiodurans and lacked γ radiation-mediated activation of kinase activity in vivo. WD mutants failed to phosphorylate its cognate substrate (e.g. DrRecA) in surrogate E. coli cells. Unlike wild-type enzyme, the kinase activity of its WD40 mutants was not stimulated by pyrroloquinoline quinine (PQQ) indicating the role of the WD motifs in PQQ interaction and stimulation of its kinase activity. Together, results highlighted the importance of the WD40 domain in the regulation of RqkA kinase signaling functions in vivo, and thus, the role of WD40 domain in the regulation of any STPK is first time demonstrated in bacteria.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dhirendra K Sharma
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Subhash C Bihani
- Radiation Biology and Health Science Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Mohammad Q Siddiqui
- Alberta RNA Research & Training Institute, Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Hari S Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute (DAE- Deemed University), Mumbai, India
| | - Yogendra S Rajpurohit
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute (DAE- Deemed University), Mumbai, India
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39
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Bruckbauer ST, Martin J, Minkoff BB, Veling MT, Lancaster I, Liu J, Trimarco JD, Bushnell B, Lipzen A, Wood EA, Sussman MR, Pennacchio C, Cox MM. Physiology of Highly Radioresistant Escherichia coli After Experimental Evolution for 100 Cycles of Selection. Front Microbiol 2020; 11:582590. [PMID: 33072055 PMCID: PMC7536353 DOI: 10.3389/fmicb.2020.582590] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 08/26/2020] [Indexed: 11/13/2022] Open
Abstract
Ionizing radiation (IR) is lethal to most organisms at high doses, damaging every cellular macromolecule via induction of reactive oxygen species (ROS). Utilizing experimental evolution and continuing previous work, we have generated the most IR-resistant Escherichia coli populations developed to date. After 100 cycles of selection, the dose required to kill 99% the four replicate populations (IR9-100, IR10-100, IR11-100, and IR12-100) has increased from 750 Gy to approximately 3,000 Gy. Fitness trade-offs, specialization, and clonal interference are evident. Long-lived competing sub-populations are present in three of the four lineages. In IR9, one lineage accumulates the heme precursor, porphyrin, leading to generation of yellow-brown colonies. Major genomic alterations are present. IR9 and IR10 exhibit major deletions and/or duplications proximal to the chromosome replication terminus. Contributions to IR resistance have expanded beyond the alterations in DNA repair systems documented previously. Variants of proteins involved in ATP synthesis (AtpA), iron-sulfur cluster biogenesis (SufD) and cadaverine synthesis (CadA) each contribute to IR resistance in IR9-100. Major genomic and physiological changes are emerging. An isolate from IR10 exhibits protein protection from ROS similar to the extremely radiation resistant bacterium Deinococcus radiodurans, without evident changes in cellular metal homeostasis. Selection is continuing with no limit to IR resistance in evidence as our E. coli populations approach levels of IR resistance typical of D. radiodurans.
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Affiliation(s)
- Steven T Bruckbauer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Joel Martin
- DOE Joint Genome Institute, Berkeley, CA, United States
| | - Benjamin B Minkoff
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States.,Center for Genomic Science Innovation, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Mike T Veling
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States
| | - Illissa Lancaster
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Jessica Liu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Joseph D Trimarco
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Anna Lipzen
- DOE Joint Genome Institute, Berkeley, CA, United States
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Michael R Sussman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States.,Center for Genomic Science Innovation, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | | | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
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40
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Abstract
Ro60 ribonucleoproteins (RNPs), composed of the ring-shaped Ro 60-kDa (Ro60) protein and noncoding RNAs called Y RNAs, are present in all three domains of life. Ro60 was first described as an autoantigen in patients with rheumatic disease, and Ro60 orthologs have been identified in 3% to 5% of bacterial genomes, spanning the majority of phyla. Their functions have been characterized primarily in Deinococcus radiodurans, the first sequenced bacterium with a recognizable ortholog. In D. radiodurans, the Ro60 ortholog enhances the ability of 3'-to-5' exoribonucleases to degrade structured RNA during several forms of environmental stress. Y RNAs are regulators that inhibit or allow the interactions of Ro60 with other proteins and RNAs. Studies of Ro60 RNPs in other bacteria hint at additional functions, since the most conserved Y RNA contains a domain that is a close tRNA mimic and Ro60 RNPs are often encoded adjacent to components of RNA repair systems.
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Affiliation(s)
- Soyeong Sim
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA; , , ,
| | - Kevin Hughes
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA; , , ,
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Xinguo Chen
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA; , , ,
| | - Sandra L Wolin
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA; , , ,
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41
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Bruckbauer ST, Minkoff BB, Yu D, Cryns VL, Cox MM, Sussman MR. Ionizing Radiation-induced Proteomic Oxidation in Escherichia coli. Mol Cell Proteomics 2020; 19:1375-1395. [PMID: 32536603 PMCID: PMC8015010 DOI: 10.1074/mcp.ra120.002092] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/10/2020] [Indexed: 12/12/2022] Open
Abstract
Recent work has begun to investigate the role of protein damage in cell death because of ionizing radiation (IR) exposure, but none have been performed on a proteome-wide basis, nor have they utilized MS (MS) to determine chemical identity of the amino acid side chain alteration. Here, we use Escherichia coli to perform the first MS analysis of IR-treated intact cells on a proteome scale. From quintuplicate IR-treated (1000 Gy) and untreated replicates, we successfully quantified 13,262 peptides mapping to 1938 unique proteins. Statistically significant, but low in magnitude (<2-fold), IR-induced changes in peptide abundance were observed in 12% of all peptides detected, although oxidative alterations were rare. Hydroxylation (+15.99 Da) was the most prevalent covalent adduct detected. In parallel with these studies on E. coli, identical experiments with the IR-resistant bacterium, Deinococcus radiodurans, revealed orders of magnitude less effect of IR on the proteome. In E. coli, the most significant target of IR by a wide margin was glyceraldehyde 3'-phosphate dehydrogenase (GAPDH), in which the thiol side chain of the catalytic Cys residue was oxidized to sulfonic acid. The same modification was detected in IR-treated human breast carcinoma cells. Sensitivity of GAPDH to reactive oxygen species (ROS) has been described previously in microbes and here, we present GAPDH as an immediate, primary target of IR-induced oxidation across all domains of life.
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Affiliation(s)
- Steven T Bruckbauer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Benjamin B Minkoff
- Center for Genomic Science Innovation, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Deyang Yu
- Department of Medicine, University of Wisconsin Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Wisconsin, USA
| | - Vincent L Cryns
- Department of Medicine, University of Wisconsin Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Wisconsin, USA
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA.
| | - Michael R Sussman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Center for Genomic Science Innovation, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA.
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42
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Late embryogenesis abundant group3 protein (DrLEA3) is involved in antioxidation in the extremophilic bacterium Deinococcus radiodurans. Microbiol Res 2020; 240:126559. [PMID: 32721821 DOI: 10.1016/j.micres.2020.126559] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/12/2020] [Accepted: 07/17/2020] [Indexed: 01/06/2023]
Abstract
Deinococcus radiodurans is able to survive under extreme conditions, including high doses of ionizing radiation, desiccation and oxidative stress. In addition to enhanced DNA repair capabilities, an effective antioxidation system plays an important role in its robustness. Previous studies have linked the radiation resistance of D. radiodurans to its prolonged desiccation tolerance phenotype, which both cause DNA damage. In the current study, we investigated the roles of dr_1172 in D. radiodurans, the gene encoding a typical group 3 LEA protein (DrLEA3) conserved within Deinococcus species. In addition to the increased transcriptional level under oxidative stress, the inactivation of dr_1172-sensitized cells to H2O2 treatments and the reduced cellular antioxidation activities suggested that dr_1172 is involved in the cellular defense against oxidative stress. Moreover, DrLEA3 was enriched at the cell membrane and bound to various types of metal ions. Cells devoid of DrLEA3 showed a decreased intracellular Mn/Fe concentration ratio, indicating that DrLEA3 also plays a role in maintaining metal ion homeostasis in vivo.
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43
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Joshi SR, Jagtap S, Basu B, Deobagkar DD, Ghosh P. Construction, analysis and validation of co-expression network to understand stress adaptation in Deinococcus radiodurans R1. PLoS One 2020; 15:e0234721. [PMID: 32579573 PMCID: PMC7314050 DOI: 10.1371/journal.pone.0234721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 06/02/2020] [Indexed: 01/12/2023] Open
Abstract
Systems biology based approaches have been effectively utilized to mine high throughput data. In the current study, we have performed system-level analysis for Deinococcus radiodurans R1 by constructing a gene co-expression network based on several microarray datasets available in the public domain. This condition-independent network was constructed by Weighted Gene Co-expression Network Analysis (WGCNA) with 61 microarray samples from 9 different experimental conditions. We identified 13 co-expressed modules, of which, 11 showed functional enrichments of one or more pathway/s or biological process. Comparative analysis of differentially expressed genes and proteins from radiation and desiccation stress studies with our co-expressed modules revealed the association of cyan with radiation response. Interestingly, two modules viz darkgreen and tan was associated with radiation as well as desiccation stress responses. The functional analysis of these modules showed enrichment of pathways important for adaptation of radiation or desiccation stress. To decipher the regulatory roles of these stress responsive modules, we identified transcription factors (TFs) and then calculated a Biweight mid correlation between modules hub gene and the identified TFs. We obtained 7 TFs for radiation and desiccation responsive modules. The expressions of 3 TFs were validated in response to gamma radiation using qRT-PCR. Along with the TFs, selected close neighbor genes of two important TFs, viz., DR_0997 (CRP) and DR_2287 (AsnC family transcriptional regulator) in the darkgreen module were also validated. In our network, among 13 hub genes associated with 13 modules, the functionality of 5 hub genes which are annotated as hypothetical proteins (hypothetical hub genes) in D. radiodurans genome has been revealed. Overall the study provided a better insight of pathways and regulators associated with relevant DNA damaging stress response in D. radiodurans.
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Affiliation(s)
- Suraj R. Joshi
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, India
- Molecular Biology Research Laboratory, Department of Zoology, Savitribai Phule Pune University, Pune, India
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Surabhi Jagtap
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, India
| | - Bhakti Basu
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Deepti D. Deobagkar
- Molecular Biology Research Laboratory, Department of Zoology, Savitribai Phule Pune University, Pune, India
| | - Payel Ghosh
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, India
- * E-mail: ,
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44
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Ithurbide S, Coste G, Lisboa J, Eugénie N, Bentchikou E, Bouthier de la Tour C, Liger D, Confalonieri F, Sommer S, Quevillon-Cheruel S, Servant P. Natural Transformation in Deinococcus radiodurans: A Genetic Analysis Reveals the Major Roles of DprA, DdrB, RecA, RecF, and RecO Proteins. Front Microbiol 2020; 11:1253. [PMID: 32625182 PMCID: PMC7314969 DOI: 10.3389/fmicb.2020.01253] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 05/18/2020] [Indexed: 11/14/2022] Open
Abstract
Horizontal gene transfer is a major driver of bacterial evolution and adaptation to environmental stresses, occurring notably via transformation of naturally competent organisms. The Deinococcus radiodurans bacterium, characterized by its extreme radioresistance, is also naturally competent. Here, we investigated the role of D. radiodurans players involved in different steps of natural transformation. First, we identified the factors (PilQ, PilD, type IV pilins, PilB, PilT, ComEC-ComEA, and ComF) involved in DNA uptake and DNA translocation across the external and cytoplasmic membranes and showed that the DNA-uptake machinery is similar to that described in the Gram negative bacterium Vibrio cholerae. Then, we studied the involvement of recombination and DNA repair proteins, RecA, RecF, RecO, DprA, and DdrB into the DNA processing steps of D. radiodurans transformation by plasmid and genomic DNA. The transformation frequency of the cells devoid of DprA, a highly conserved protein among competent species, strongly decreased but was not completely abolished whereas it was completely abolished in ΔdprA ΔrecF, ΔdprA ΔrecO, and ΔdprA ΔddrB double mutants. We propose that RecF and RecO, belonging to the recombination mediator complex, and DdrB, a specific deinococcal DNA binding protein, can replace a function played by DprA, or alternatively, act at a different step of recombination with DprA. We also demonstrated that a ΔdprA mutant is as resistant as wild type to various doses of γ-irradiation, suggesting that DprA, and potentially transformation, do not play a major role in D. radiodurans radioresistance.
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Affiliation(s)
- Solenne Ithurbide
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Geneviève Coste
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Johnny Lisboa
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Nicolas Eugénie
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Esma Bentchikou
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Claire Bouthier de la Tour
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Dominique Liger
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Fabrice Confalonieri
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Suzanne Sommer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Sophie Quevillon-Cheruel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Pascale Servant
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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45
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de Groot A, Siponen MI, Magerand R, Eugénie N, Martin-Arevalillo R, Doloy J, Lemaire D, Brandelet G, Parcy F, Dumas R, Roche P, Servant P, Confalonieri F, Arnoux P, Pignol D, Blanchard L. Crystal structure of the transcriptional repressor DdrO: insight into the metalloprotease/repressor-controlled radiation response in Deinococcus. Nucleic Acids Res 2020; 47:11403-11417. [PMID: 31598697 PMCID: PMC6868357 DOI: 10.1093/nar/gkz883] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 09/25/2019] [Accepted: 10/01/2019] [Indexed: 12/13/2022] Open
Abstract
Exposure to harmful conditions such as radiation and desiccation induce oxidative stress and DNA damage. In radiation-resistant Deinococcus bacteria, the radiation/desiccation response is controlled by two proteins: the XRE family transcriptional repressor DdrO and the COG2856 metalloprotease IrrE. The latter cleaves and inactivates DdrO. Here, we report the biochemical characterization and crystal structure of DdrO, which is the first structure of a XRE protein targeted by a COG2856 protein. DdrO is composed of two domains that fold independently and are separated by a flexible linker. The N-terminal domain corresponds to the DNA-binding domain. The C-terminal domain, containing three alpha helices arranged in a novel fold, is required for DdrO dimerization. Cleavage by IrrE occurs in the loop between the last two helices of DdrO and abolishes dimerization and DNA binding. The cleavage site is hidden in the DdrO dimer structure, indicating that IrrE cleaves DdrO monomers or that the interaction with IrrE induces a structural change rendering accessible the cleavage site. Predicted COG2856/XRE regulatory protein pairs are found in many bacteria, and available data suggest two different molecular mechanisms for stress-induced gene expression: COG2856 protein-mediated cleavage or inhibition of oligomerization without cleavage of the XRE repressor.
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Affiliation(s)
- Arjan de Groot
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13108, France
| | - Marina I Siponen
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13108, France
| | - Romaric Magerand
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13108, France
| | - Nicolas Eugénie
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, Gif-sur-Yvette cedex, F-91198, France
| | | | - Jade Doloy
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13108, France
| | - David Lemaire
- Aix Marseille Univ, CEA, CNRS, BIAM, Interaction Protein Metal Team, Saint Paul-Lez-Durance, F-13108, France
| | - Géraldine Brandelet
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13108, France
| | - François Parcy
- Univ. Grenoble Alpes, CNRS, CEA, INRA, IRIG-DBSCI-LPCV, Grenoble, F-38000, France
| | - Renaud Dumas
- Univ. Grenoble Alpes, CNRS, CEA, INRA, IRIG-DBSCI-LPCV, Grenoble, F-38000, France
| | - Philippe Roche
- Aix Marseille Univ, CNRS, Inserm, Institut Paoli Calmettes, CRCM, Marseille CEDEX 09, F-13273, France
| | - Pascale Servant
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, Gif-sur-Yvette cedex, F-91198, France
| | - Fabrice Confalonieri
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, Gif-sur-Yvette cedex, F-91198, France
| | - Pascal Arnoux
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13108, France
| | - David Pignol
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13108, France
| | - Laurence Blanchard
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13108, France
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Jayeola V, McClelland M, Porwollik S, Chu W, Farber J, Kathariou S. Identification of Novel Genes Mediating Survival of Salmonella on Low-Moisture Foods via Transposon Sequencing Analysis. Front Microbiol 2020; 11:726. [PMID: 32499760 PMCID: PMC7242855 DOI: 10.3389/fmicb.2020.00726] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/27/2020] [Indexed: 01/11/2023] Open
Abstract
Salmonella enterica is the leading foodborne pathogen associated with outbreaks involving low-moisture foods (LMFs). However, the genes involved in Salmonella's long-term survival on LMFs remain poorly characterized. In this study, in-shell pistachios were inoculated with Tn5-based mutant libraries of S. Enteritidis P125109, S. Typhimurium 14028s, and S. Newport C4.2 at approximate 108 CFU/g and stored at 25°C. Transposon sequencing analysis (Tn-seq) was then employed to determine the relative abundance of each Tn5 insertion site immediately after inoculation (T0), after drying (T1), and at 120 days (T120). In S. Enteritidis, S. Typhimurium, and S. Newport mutant libraries, the relative abundance of 51, 80, and 101 Tn5 insertion sites, respectively, was significantly lower at T1 compared to T0, while in libraries of S. Enteritidis and S. Typhimurium the relative abundance of 42 and 68 Tn5 insertion sites, respectively, was significantly lower at T120 compared to T1. Tn5 insertion sites with reduced relative abundance in this competition assay were localized in DNA repair, lipopolysaccharide biosynthesis and stringent response genes. Twelve genes among those under strong negative selection in the competition assay were selected for further study. Whole gene deletion mutants in ten of these genes, sspA, barA, uvrB, damX, rfbD, uvrY, lrhA, yifE, rbsR, and ompR, were impaired for individual survival on pistachios. The findings highlight the value of combined mutagenesis and sequencing to identify novel genes important for the survival of Salmonella in low-moisture foods.
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Affiliation(s)
- Victor Jayeola
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, United States
| | - Steffen Porwollik
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, United States
| | - Weiping Chu
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, United States
| | - Jeffrey Farber
- Department of Food Science, University of Guelph, Guelph, ON, Canada
| | - Sophia Kathariou
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
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Husseini ZN, Hosseini Tafreshi SA, Aghaie P, Toghyani MA. CaCl 2 pretreatment improves gamma toxicity tolerance in microalga Chlorella vulgaris. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 192:110261. [PMID: 32018153 DOI: 10.1016/j.ecoenv.2020.110261] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 06/10/2023]
Abstract
The Chlorella vulgaris has been generally recognized as a promising microalgal model to study stress-related responses due to its ability to withstand against ionizing and non-ionizing radiation. The objective of the present study was to investigate the effect of CaCl2 pre-treatment at different concentrations on the responses of microalga C. vulgaris under gamma radiation toxicity. Changes in growth, physiological parameters and biochemical compositions of the algae pretreated with 0.17 (normal), 5, and 10 mM CaCl2 were analyzed under 300 Gy gamma irradiation and compared to those of gamma-free control. The results showed that parameters including specific growth rate, cell size, chlorophyll and protein contents, ascorbate peroxidase (APX), and superoxide dismutase (SOD) activity, Ferric Reducing Antioxidant Power (FRAP), and the ratios of nucleic acid to protein negatively affected by gamma irradiation. All these parameters, except for the ratios of nucleic acid to protein significantly increased in the algae when pretreated with a CaCl2 content higher than normal concentration. The analysis also showed that parameters including catalase activity, proline, and carotenoid content, the level of lipid peroxidation, and electrolyte leakage (EL) significantly increased under gamma irradiation but not affected significantly under different CaCl2 pre-treatments. Additionally, specific growth rate, chlorophyll a and protein content, APX and SOD activity, FRAP, lipid peroxidation, electrolyte leakage, and the ratios of nucleic acid to protein were the only parameters that significantly affected by the interaction of gamma toxicity and CaCl2 pretreatment. Overall, the results suggested that regardless of the CaCl2 effect, the algal cells responded to gamma radiation more efficiently by increasing proline, carotenoids content, and CAT activity. More important, it was concluded that calcium had an essential role in modifying the detrimental effect of gamma toxicity on the algae mainly by increasing the activity of ascorbate peroxidase and superoxide dismutase and maintaining the reducing antioxidant power (FRAP) of the cells at a high level.
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Affiliation(s)
- Zainab Naser Husseini
- Biotechnology Division, Department of Cell and Molecular Biology, Faculty of Chemistry, University of Kashan, Kashan, Iran. 8731753153, Iran
| | - Seyed Ali Hosseini Tafreshi
- Biotechnology Division, Department of Cell and Molecular Biology, Faculty of Chemistry, University of Kashan, Kashan, Iran. 8731753153, Iran.
| | - Peyman Aghaie
- Department of Biology, Faculty of Science, Payame Noor Universtiy, Po Box 19395-3697, Tehran, Iran
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Lai L, Huang C, Zhou F, Xia F, Xiong G. Finite elements analysis of the temporomandibular joint disc in patients with intra-articular disorders. BMC Oral Health 2020; 20:93. [PMID: 32228551 PMCID: PMC7106847 DOI: 10.1186/s12903-020-01074-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 03/11/2020] [Indexed: 11/28/2022] Open
Abstract
Background Intra-articular disorders (ID) or anterior and/or medial displacement of the temporomandibular joint disorder (TMJ) disc are the most common form of TMJ dysfunction (TMD). TMD causes changes in the friction coefficient during TMJ movement. Herein, we provided a three-dimensional (3D) finite-elements model (FEM) including the maxilla, disc, and mandible and evaluated the stress distribution with different friction coefficient. Methods Fourteen volunteers without TMD and 20 patients with MRI-diagnosed TMD were selected. CT and MRI data were collected to build the 3D FEA model of the mandible and TMJ disc. Stress distribution with different friction coefficient was measured. Result In the normal model, stress distribution on the TMJ disc was 2.07 ± 0.17, 1.49 ± 0.14, and 1.41 ± 0.14 MPa with 0.001, 0.3, and 0.4 friction coefficient, respectively. In the TMD model, stress distribution was 3.87 ± 0.15, 7.23 ± 0.22, and 7.77 ± 0.19 MPa respectively. Conclusion When the friction coefficient of the side with anterior displacement increased, stress on the disc, condyle and mandible of the opposite side increased. Simultaneously, stress values of the disc, condyle and mandible were higher than those of the normal lateral joint.
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Affiliation(s)
- Linfeng Lai
- Department of Oral Surgery, The Dingling Clinical Institute of Wenzhou Medical University (Wenzhou Central Hospital), Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Chenyao Huang
- Department of Oral Surgery, The Dingling Clinical Institute of Wenzhou Medical University (Wenzhou Central Hospital), Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Fan Zhou
- Department of Oral Surgery, The Dingling Clinical Institute of Wenzhou Medical University (Wenzhou Central Hospital), Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Fujian Xia
- Department of Oral Surgery, The Dingling Clinical Institute of Wenzhou Medical University (Wenzhou Central Hospital), Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Guofeng Xiong
- Department of Oral Surgery, The Dingling Clinical Institute of Wenzhou Medical University (Wenzhou Central Hospital), Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China.
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49
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Hosseini Tafreshi SA, Aghaie P, Toghyani MA, Ramazani-Moghaddam-Arani A. Improvement of ionizing gamma irradiation tolerance of Chlorella vulgaris by pretreatment with polyethylene glycol. Int J Radiat Biol 2020; 96:919-928. [PMID: 32159411 DOI: 10.1080/09553002.2020.1741717] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Purpose: To evaluate the effects of polyethylene glycol (PEG) 6000 pretreatment on growth and physiological responses of eukaryotic microalga Chlorella vulgaris exposed to ionizing irradiation.Materials and methods: The microalgal cells pretreated with different PEG concentrations (0, 5, 10 and 20%) and then exposed to 300 Gray gamma irradiation at a dose rate of 0.5 Gy s-1. The various growth and physiological parameters including algal growth, cell size, the degree of electrolyte leakage (EL) and lipid peroxidation, the content of pigments and proline and the activity of antioxidant enzymes under gamma-free or 300 Gray gamma irradiation conditions were examined.Results: The results showed that PEG stimulated a higher growth and cell size under both stress-free and gamma-stress conditions. The maximum growth and cell size was reported when the algae was pretreated with 10% PEG. A relative increase of catalase activity was observed in all samples after exposing to gamma irradiation. However, the highest value was recorded for the gamma-radiated algae pretreated with 10% PEG. In the absence of PEG, gamma irradiation induced a significant reduction in ascorbate peroxidase activity, but with PEG pretreatment, the enzyme activity remained constant or even increased after gamma irradiation. On the other hand, although gamma irradiation stress generally suppressed the activity of superoxide dismutase in all cells, pretreating the algae with PEG could diminish this suppressing effect at all applied concentrations. Compared to the PEG-free controls, a lower rate of chlorophylls and membrane integrity loss was shown in the PEG-treated algae when exposed to gamma stress. Total carotenoid content in PEG-treated algae was also similar under both gamma-free and gamma-radiated conditions. A PEG-independent increase in proline accumulation was reported under gamma-irradiation treatment.Conclusions: Overall, the results suggested that PEG pretreatment could improve gamma-irradiation tolerance in C. vulgaris probably by stimulating a range of enzymatic and non-enzymatic reactive oxygen species scavenging systems. The microalgae may also consume PEG to break down and use it as an alternative source of carbon during stress which should be further studied in detail.
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Affiliation(s)
- Seyed Ali Hosseini Tafreshi
- Biotechnology Division, Department of Cell and Molecular Biology, Faculty of Chemistry, University of Kashan, Kashan, Iran
| | - Peyman Aghaie
- Department of Biology, Faculty of Science, Payame Noor University, Tehran, Iran
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Choo K, Kim M, Nansa SA, Bae MK, Lee C, Lee SJ. Redox potential change by the cystine importer affected on enzymatic antioxidant protection in Deinococcus geothermalis. Antonie van Leeuwenhoek 2020; 113:779-790. [PMID: 31993844 DOI: 10.1007/s10482-020-01388-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 01/21/2020] [Indexed: 10/25/2022]
Abstract
Radiation resistant bacteria genus Deinococcus species were well studied on DNA repair and anti-oxidative stress response mechanisms. There are many protection factors as enzymatic and nonenzymatic involved. One of them is intracellular redox potential as like thiol compounds including cysteine acts as primary protectant against oxidation stress. A gene cluster consisting of the genes Dgeo_1986 and Dgeo_1987 of Deinococcus geothermalis was identified as a cystine importer. The expression levels of dgeo_1986 and dgeo_1987 were up-regulated by over 60-fold and 4-fold during the late exponential (L) growth phase, respectively. The double-knockout mutant of dgeo_1986 and dgeo_1987 was reduced in cystine and thiol concentrations and leading to enhanced sensitivity against H2O2 stress. The expression of catalase (Dgeo_2728) as an enzymatic anti-oxidant is more induced in the wild-type strain than the Δdgeo_1986-87 strain at the late growth phase. The expression level of the oxidative stress response regulator OxyR (Dgeo_1888) is dependent on the intracellular redox balance. That is, when the intracellular thiol content was reduced in the wild-type strain during the L phase, OxyR was clearly induced. Interestingly, the expression level of OxyR was higher in the Δdgeo_1986-87 strain than in the wild-type strain upon H2O2 treatment. Although OxyR was induced by H2O2 treatment in Δdgeo_1986-87 strain, where intracellular redox potential of cystine was reduced as a thiol compound due to reduced cystine import, the relative level of expression of catalase was unexpectedly down-regulated. Therefore, the catalase induction system as an enzymatic antioxidant protection should be affected via the cystine importer but not rely on the OxyR controlled manner.
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Affiliation(s)
- Kyungsil Choo
- Department of Biology, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Korea
| | - Minwook Kim
- Department of Biology, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Korea.,Department of Developmental Biology, Pittsburgh Liver Research Center, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Sama Abdi Nansa
- Department of Biology, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Korea
| | - Min K Bae
- Department of Biology, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Korea
| | - Chanjae Lee
- Department of Biology, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Korea
| | - Sung-Jae Lee
- Department of Biology, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Korea.
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