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Liu J, Li S, She TT, Huang J, Lian WH, Mo YJ, Zhang DY, Dong L, Li WJ. Rufibacter psychrotolerans sp. nov., a Cold-Tolerating Novel Species Isolated from Desert Soil. Curr Microbiol 2024; 81:313. [PMID: 39160426 DOI: 10.1007/s00284-024-03842-2] [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: 06/10/2024] [Accepted: 08/11/2024] [Indexed: 08/21/2024]
Abstract
Strain SYSU D00308T, a short-rod-shaped bacterium, was isolated from a sandy soil collected from the Gurbantunggut Desert, Xinjiang, PR China. Strain SYSU D00308T was Gram-stain-negative, aerobic, pink-pigmented, non-motile, catalase- and oxidase-positive. The strain grew at 4-37 ℃, pH 5.0-8.0 and 0-1.5% (w/v) NaCl. 16S rRNA gene sequencing analyses demonstrated that strain SYSU D00308T belonged to the genus Rufibacter and exhibited the highest sequence similarity (97.4%) to Rufibacter glacialis MDT1-10-3T. Summed features 3, 4, and iso-C15:0 were the major fatty acids, and menaquinone 7 (MK-7) was the sole respiratory menaquinone. The polar lipid profiles comprised phosphatidylethanolamine, an unidentified glycolipid, an unidentified phospholipid, two unidentified aminophospholipids, and two unidentified lipids. The genome size and DNA G + C content of strain SYSU D00308T were 5,176,683 bp and 54.8%, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between SYSU D00308T and members of the genus Rufibacter were 77.7-81.8% and 20.4-23.4% respectively, which were less than the corresponding thresholds (ANI: 95-96%; dDDH: 70%) for prokaryotic species definition. According to the genotypic, phenotypic and phylogenetic characteristics, strain SYSU D00308T represents a novel species of the genus Rufibacter. We propose the name, Rufibacter psychrotolerans sp. nov., with SYSU D00308T (= CGMCC 1.18621T = KCTC 82275T = MCCC 1K04970T) as the type strain.
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Affiliation(s)
- Jun Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, People's Republic of China
| | - Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, People's Republic of China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Key Laboratory of Biodiversity Conservation and Application in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Ting-Ting She
- Guangdong University of Education, Guangzhou, 510275, People's Republic of China
| | - Jie Huang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, People's Republic of China
| | - Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, People's Republic of China
| | - Yi-Jun Mo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, People's Republic of China
| | - Dong-Ya Zhang
- Microbiome Research Center, Moon (Guangzhou) Biotech Co., Ltd., Guangzhou, 510700, People's Republic of China
| | - Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, People's Republic of China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Key Laboratory of Biodiversity Conservation and Application in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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Wang Y, Liu J, Yi Y, Zhu L, Liu M, Zhang Z, Xie Q, Jiang L. Insights into the synthesis, engineering, and functions of microbial pigments in Deinococcus bacteria. Front Microbiol 2024; 15:1447785. [PMID: 39119139 PMCID: PMC11306087 DOI: 10.3389/fmicb.2024.1447785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 07/05/2024] [Indexed: 08/10/2024] Open
Abstract
The ability of Deinococcus bacteria to survive in harsh environments, such as high radiation, extreme temperature, and dryness, is mainly attributed to the generation of unique pigments, especially carotenoids. Although the limited number of natural pigments produced by these bacteria restricts their industrial potential, metabolic engineering and synthetic biology can significantly increase pigment yield and expand their application prospects. In this study, we review the properties, biosynthetic pathways, and functions of key enzymes and genes related to these pigments and explore strategies for improving pigment production through gene editing and optimization of culture conditions. Additionally, studies have highlighted the unique role of these pigments in antioxidant activity and radiation resistance, particularly emphasizing the critical functions of deinoxanthin in D. radiodurans. In the future, Deinococcus bacterial pigments will have broad application prospects in the food industry, drug production, and space exploration, where they can serve as radiation indicators and natural antioxidants to protect astronauts' health during long-term space flights.
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Affiliation(s)
- Yuxian Wang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Jiayu Liu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Yuanyang Yi
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences/ Xinjiang Key Laboratory of Special Environmental Microbiology, Urumqi, China
- College of Life Sciences, Xinjiang Normal University, Urumqi, China
| | - Liying Zhu
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, China
| | - Minghui Liu
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
| | - Zhidong Zhang
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences/ Xinjiang Key Laboratory of Special Environmental Microbiology, Urumqi, China
| | - Qiong Xie
- China Astronaut Research and Training Center, Beijing, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
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Chen Z, Hu J, Dai J, Zhou C, Hua Y, Hua X, Zhao Y. Precise CRISPR/Cpf1 genome editing system in the Deinococcus radiodurans with superior DNA repair mechanisms. Microbiol Res 2024; 284:127713. [PMID: 38608339 DOI: 10.1016/j.micres.2024.127713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/20/2024] [Accepted: 04/06/2024] [Indexed: 04/14/2024]
Abstract
Deinococcus radiodurans, with its high homologous recombination (HR) efficiency of double-stranded DNA breaks (DSBs), is a model organism for studying genome stability maintenance and an attractive microbe for industrial applications. Here, we developed an efficient CRISPR/Cpf1 genome editing system in D. radiodurans by evaluating and optimizing double-plasmid strategies and four Cas effector proteins from various organisms, which can precisely introduce different types of template-dependent mutagenesis without off-target toxicity. Furthermore, the role of DNA repair genes in determining editing efficiency in D. radiodurans was evaluated by introducing the CRISPR/Cpf1 system into 13 mutant strains lacking various DNA damage response and repair factors. In addition to the crucial role of RecA-dependent HR required for CRISPR/Cpf1 editing, D. radiodurans showed higher editing efficiency when lacking DdrB, the single-stranded DNA annealing (SSA) protein involved in the RecA-independent DSB repair pathway. This suggests a possible competition between HR and SSA pathways in the CRISPR editing of D. radiodurans. Moreover, off-target effects were observed during the genome editing of the pprI knockout strain, a master DNA damage response gene in Deinococcus species, which suggested that precise regulation of DNA damage response is critical for a high-fidelity genome editing system.
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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
| | - Jing Hu
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jingli Dai
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Congli Zhou
- 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
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 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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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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Yuzon JD, Schultzhaus Z, Wang Z. Transcriptomic and genomic effects of gamma-radiation exposure on strains of the black yeast Exophiala dermatitidis evolved to display increased ionizing radiation resistance. Microbiol Spectr 2023; 11:e0221923. [PMID: 37676019 PMCID: PMC10581076 DOI: 10.1128/spectrum.02219-23] [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: 05/25/2023] [Accepted: 07/15/2023] [Indexed: 09/08/2023] Open
Abstract
IMPORTANCE Ionizing radiation poses a significant threat to living organisms and human health, given its destructive nature and widespread use in fields such as medicine and the potential for nuclear disasters. Melanized fungi exhibit remarkable survival capabilities, enduring doses up to 1,000-fold higher than mammals. Through adaptive laboratory evolution, we validated the protective role of constitutive upregulation of DNA repair genes in the black yeast Exophiala dermatitidis, enhancing survival after radiation exposure. Surprisingly, we found that evolved strains lacking melanin still achieved high levels of radioresistance. Our study unveiled the significance of robust activation and enhancement of redox homeostasis, as evidenced by the profound transcriptional changes and increased accumulation of mutations, in substantially improving ionizing radiation resistance in the absence of melanin. These findings underscore the delicate balance between DNA repair and redox homeostasis for an organism's ability to endure and recover from radiation exposure.
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Affiliation(s)
- Jennifer D. Yuzon
- National Research Council Postdoctoral Research Associate, US Naval Research Laboratory, Washington, USA
| | - Zachary Schultzhaus
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, USA
| | - Zheng Wang
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, USA
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Maxson ME, Das L, Goldberg MF, Porcelli SA, Chan J, Jacobs WR. Mycobacterium tuberculosis Central Metabolism Is Key Regulator of Macrophage Pyroptosis and Host Immunity. Pathogens 2023; 12:1109. [PMID: 37764917 PMCID: PMC10535942 DOI: 10.3390/pathogens12091109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/17/2023] [Accepted: 08/26/2023] [Indexed: 09/29/2023] Open
Abstract
Metabolic dysregulation in Mycobacterium tuberculosis results in increased macrophage apoptosis or pyroptosis. However, mechanistic links between Mycobacterium virulence and bacterial metabolic plasticity remain ill defined. In this study, we screened random transposon insertions of M. bovis BCG to identify mutants that induce pyroptotic death of the infected macrophage. Analysis of the transposon insertion sites identified a panel of fdr (functioning death repressor) genes, which were shown in some cases to encode functions central to Mycobacterium metabolism. In-depth studies of one fdr gene, fdr8 (BCG3787/Rv3727), demonstrated its important role in the maintenance of M. tuberculosis and M. bovis BCG redox balance in reductive stress conditions in the host. Our studies expand the subset of known Mycobacterium genes linking bacterial metabolic plasticity to virulence and also reveal that the broad induction of pyroptosis by an intracellular bacterial pathogen is linked to enhanced cellular immunity in vivo.
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Affiliation(s)
- Michelle E. Maxson
- Program in Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada;
| | - Lahari Das
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (L.D.); (S.A.P.)
| | | | - Steven A. Porcelli
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (L.D.); (S.A.P.)
| | - John Chan
- Department of Medicine, New Jersey Medical School, 205 South Orange Avenue, Newark, NJ 07103, USA;
| | - William R. Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (L.D.); (S.A.P.)
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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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Asaka R, Ohshima K, Kawasaki S, Maoka T, Tode C, Wang-Otomo ZY, Takaichi S. Major Carotenoids of Meiothermus ruber Are Deinoxanthin Glucoside Esters, Not Meiothermoxanthin Glucoside Esters. JOURNAL OF NATURAL PRODUCTS 2022; 85:2266-2273. [PMID: 36129462 DOI: 10.1021/acs.jnatprod.2c00271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Meiothermus ruber DSMZ 1279T was isolated from a hot spring in Kamchatka and was red in color. The major carotenoid present was reported to be 1'-(β-d-glucopyranosyloxy)-3,4,3',4'-tetradehydro-1',2'-dihydro-β,ψ-caroten-2-one after saponification (Burgess et al. J. Nat. Prod. 1999, 62, 859-863). In this study, we purified the major carotenoids in this species without saponification. We then reidentified the major carotenoids present using spectroscopic data, including electronic circular dichroism (ECD), 1H NMR, rotating-frame nuclear Overhauser effect spectroscopy (ROESY), 13C NMR, heteronuclear single-quantum correlation spectroscopy (HSQC), heteronuclear multiple-bond correlation spectroscopy (HMBC), and MS, and enzymatic hydrolysis of fatty acid moieties and found deinoxanthin glucoside iso fatty acid esters. The bound fatty acids present included four iso types, and their composition differed from cellular lipids. Moreover, the previously identified carotenoid glucoside was a saponification artifact of deinoxanthin glucoside esters. Ketomyxocoxanthin glucoside esters and 1'-hydroxytorulene glucoside esters were also present. On the basis of the identification of carotenoids and the whole genome sequence of M. ruber, we propose a carotenoid biosynthetic pathway and note the corresponding genes.
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Affiliation(s)
- Ryo Asaka
- Department of Molecular Microbiology, Faculty of Science, Tokyo University of Agriculture, Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Kazuki Ohshima
- Department of Bioscience, Faculty of Science, Tokyo University of Agriculture, Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Shinji Kawasaki
- Department of Molecular Microbiology, Faculty of Science, Tokyo University of Agriculture, Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
- Department of Bioscience, Faculty of Science, Tokyo University of Agriculture, Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Takashi Maoka
- Research Institute for Production Development, Sakyo, Kyoto 606-0805, Japan
| | - Chisato Tode
- Kobe Pharmaceutical University, Higashinada, Kobe, Hyo̅go 658-8558, Japan
| | | | - Shinichi Takaichi
- Department of Molecular Microbiology, Faculty of Science, Tokyo University of Agriculture, Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
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Kapinusova G, Jani K, Smrhova T, Pajer P, Jarosova I, Suman J, Strejcek M, Uhlik O. Culturomics of Bacteria from Radon-Saturated Water of the World's Oldest Radium Mine. Microbiol Spectr 2022; 10:e0199522. [PMID: 36000901 PMCID: PMC9602452 DOI: 10.1128/spectrum.01995-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/04/2022] [Indexed: 12/31/2022] Open
Abstract
Balneotherapeutic water springs, such as those with thermal, saline, sulfur, or any other characteristics, have recently been the subject of phylogenetic studies with a closer focus on the description and/or isolation of phylogenetically novel or biotechnologically interesting microorganisms. Generally, however, most such microorganisms are rarely obtained in pure culture or are even, for now, unculturable under laboratory conditions. In this culture-dependent study of radioactive water springs of Jáchymov (Joachimstahl), Czech Republic, we investigated a combination of classical cultivation approaches with those imitating sampling source conditions. Using these environmentally relevant cultivation approaches, over 1,000 pure cultures were successfully isolated from 4 radioactive springs. Subsequent dereplication yielded 121 unique taxonomic units spanning 44 genera and 9 taxonomic classes, ~10% of which were identified as hitherto undescribed taxa. Genomes of the latter were sequenced and analyzed, with a special focus on endogenous defense systems to withstand oxidative stress and aid in radiotolerance. Due to their origin from radioactive waters, we determined the resistance of the isolates to oxidative stress. Most of the isolates were more resistant to menadione than the model strain Deinococcus radiodurans DSM 20539T. Moreover, isolates of the Deinococcacecae, Micrococcaceae, Bacillaceae, Moraxellaceae, and Pseudomonadaceae families even exhibited higher resistance in the presence of hydrogen peroxide. In summary, our culturomic analysis shows that subsurface water springs contain diverse bacterial populations, including as-yet-undescribed taxa and strains with promising biotechnological potential. Furthermore, this study suggests that environmentally relevant cultivation techniques increase the efficiency of cultivation, thus enhancing the chance of isolating hitherto uncultured microorganisms. IMPORTANCE The mine Svornost in Jáchymov (Joachimstahl), Czech Republic is a former silver-uranium mine and the world's first and for a long time only radium mine, nowadays the deepest mine devoted to the extraction of water which is saturated with radon and has therapeutic benefits given its chemical properties. This healing water, which is approximately 13 thousand years old, is used under medical supervision for the treatment of patients with neurological and rheumatic disorders. Our culturomic approach using low concentrations of growth substrates or the environmental matrix itself (i.e., water filtrate) in culturing media combined with prolonged cultivation time resulted in the isolation of a broad spectrum of microorganisms from 4 radioactive springs of Jáchymov which are phylogenetically novel and/or bear various adaptive or coping mechanisms to thrive under selective pressure and can thus provide a wide spectrum of capabilities potentially exploitable in diverse scientific, biotechnological, or medical disciplines.
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Affiliation(s)
- Gabriela Kapinusova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Kunal Jani
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Tereza Smrhova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Petr Pajer
- Military Health Institute, Ministry of Defence of the Czech Republic, Prague, Czech Republic
| | - Irena Jarosova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biotechnology, Prague, Czech Republic
| | - Jachym Suman
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Michal Strejcek
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Ondrej Uhlik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
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Tian C, Lv Y, Yang Z, Zhang R, Zhu Z, Ma H, Li J, Zhang Y. Microbial Community Structure and Metabolic Potential at the Initial Stage of Soil Development of the Glacial Forefields in Svalbard. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02116-3. [PMID: 36239777 DOI: 10.1007/s00248-022-02116-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
Microbial communities have been identified as the primary inhabitants of Arctic forefields. However, the metabolic potential of microbial communities in these newly exposed soils remains underexplored due to limited access. Here, we sampled the very edge of the glacial forefield in Svalbard and performed the 16S rRNA genes and metagenomic analysis to illustrate the ecosystem characteristics. Burkholderiales and Micrococcales were the dominant bacterial groups at the initial stage of soil development of glacial forefields. 214 metagenome-assembled genomes were recovered from glacier forefield microbiome datasets, including only 2 belonging to archaea. Analysis of these metagenome-assembled genomes revealed that 41% of assembled genomes had the genetic potential to use nitrate and nitrite as electron acceptors. Metabolic pathway reconstruction for these microbes suggested versatility for sulfide and thiosulfate oxidation, H2 and CO utilization, and CO2 fixation. Our results indicate the importance of anaerobic processes in elemental cycling in the glacial forefields. Besides, a range of genes related to adaption to low temperature and other stresses were detected, which revealed the presence of diverse mechanisms of adaption to the extreme environment of Svalbard. This research provides ecological insight into the initial stage of the soil developed during the retreating of glaciers.
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Affiliation(s)
- Chen Tian
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Key Laboratory for Polar Science, MNR, Polar Research Institute of China, Shanghai, People's Republic of China
- International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yongxin Lv
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, People's Republic of China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zhifeng Yang
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, USA
| | - Ruifeng Zhang
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Key Laboratory for Polar Science, MNR, Polar Research Institute of China, Shanghai, People's Republic of China
| | - Zhuoyi Zhu
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Key Laboratory for Polar Science, MNR, Polar Research Institute of China, Shanghai, People's Republic of China
| | - Hongmei Ma
- Key Laboratory for Polar Science, MNR, Polar Research Institute of China, Shanghai, People's Republic of China
| | - Jing Li
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yu Zhang
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
- Key Laboratory for Polar Science, MNR, Polar Research Institute of China, Shanghai, People's Republic of China.
- International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, People's Republic of China.
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Liu Y, Chen T, Cui X, Xu Y, Hu S, Zhao Y, Zhang W, Liu G, Zhang G. Sphingomonas radiodurans sp. nov., a novel radiation-resistant bacterium isolated from the north slope of Mount Everest. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005312] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated S9-5T, was isolated from moraine samples collected from the north slope of Mount Everest at an altitude of 5 500 m above sea level. A polyphasic study confirmed the affiliation of the strain with the genus
Sphingomonas
. Strain S9-5T was an aerobic, Gram-stain-negative, non-spore-forming, non-motile and rod-shaped bacterium that could grow at 10–40 °C, pH 5–8 and with 0–9 % (w/v) NaCl. Q-10 was its predominant respiratory menaquinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminophospholipid and eight unidentified lipids comprised the polar lipids of strain S9-5T. Its major fatty acids were summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c) and C16 : 0. The G+C content was 65.75mol%. Phylogenetic analysis based on 16S rRNA sequences showed that strain S9-5T was phylogenetically closely related to
Sphingomonas panaciterrae
DCY91T (98.17 %),
Sphingomonas olei
K-1-16T (98.11 %) and
Sphingomonas mucosissima
DSM 17494T (97.39 %). The average nucleotide identity values among strain S9-5T and
Sphingomonas panaciterrae
DCY91T,
Sphingomonas olei
K-1-16T and
Sphingomonas mucosissima
DSM 17494T were 78.82, 78.87 and 78.29 %, respectively. Based on the morphological, physiological and chemotaxonomic data, strain S9-5T (=JCM 34750T=GDMCC 1.2714T) should represent a novel species of the genus
Sphingomonas
, for which we propose the name Sphingomonas radiodurans sp. nov.
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Affiliation(s)
- Yang Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
| | - Tuo Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
| | - Xiaowen Cui
- College of Geography and Environment Science, Northwest Normal University, Lanzhou 730070, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Yeteng Xu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
| | - Shixin Hu
- Institute of Applied Magnetics, Key Laboratory for Magnetism and Magnetic Materials of the Ministry of Education, Lanzhou University, Lanzhou 730000, PR China
| | - Yidan Zhao
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
| | - Wei Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Gaosen Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
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12
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Avalos M, Garbeva P, Vader L, van Wezel GP, Dickschat JS, Ulanova D. Biosynthesis, evolution and ecology of microbial terpenoids. Nat Prod Rep 2021; 39:249-272. [PMID: 34612321 DOI: 10.1039/d1np00047k] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: through June 2021Terpenoids are the largest class of natural products recognised to date. While mostly known to humans as bioactive plant metabolites and part of essential oils, structurally diverse terpenoids are increasingly reported to be produced by microorganisms. For many of the compounds biological functions are yet unknown, but during the past years significant insights have been obtained for the role of terpenoids in microbial chemical ecology. Their functions include stress alleviation, maintenance of cell membrane integrity, photoprotection, attraction or repulsion of organisms, host growth promotion and defense. In this review we discuss the current knowledge of the biosynthesis and evolution of microbial terpenoids, and their ecological and biological roles in aquatic and terrestrial environments. Perspectives on their biotechnological applications, knowledge gaps and questions for future studies are discussed.
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Affiliation(s)
- Mariana Avalos
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands. .,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Lisa Vader
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.
| | - Gilles P van Wezel
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands. .,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Jeroen S Dickschat
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands.,University of Bonn, Kekulé-Institute of Organic Chemistry and Biochemistry, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Dana Ulanova
- Faculty of Agriculture and Marine Science, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi 783-8502, Japan.
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13
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Wang X, Wang Y, Ling N, Shen Y, Zhang D, Liu D, Ou D, Wu Q, Ye Y. Effects of tolC on tolerance to bile salts and biofilm formation in Cronobacter malonaticus. J Dairy Sci 2021; 104:9521-9531. [PMID: 34099300 DOI: 10.3168/jds.2021-20128] [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: 01/05/2021] [Accepted: 03/29/2021] [Indexed: 12/21/2022]
Abstract
Bile salts is one of essential components of bile secreted into the intestine to confer antibacterial protection. Cronobacter species are associated with necrotizing enterocolitis in newborns and show a strong tolerance to bile salts. However, little attempt has been made to focus on the molecular basis of the tolerance to bile salts. In this study, we investigated the roles of tolC on growth, cell morphology, motility, and biofilm formation ability in Cronobacter malonaticus under bile salt stress. The results indicated that the absence of tolC significantly affected the colony morphology and outer membrane structure in a normal situation, compared with those of the wild type strain. The deletion of tolC caused the decline in resistance to bile salt stress, inhibition of growth, and observable reduction in relative growth rate and motility. Moreover, the bacterial stress response promoted the biofilm formation ability of the mutant strain. The expression of the AcrAB-TolC system (acrA, acrB, and tolC) was effectively upregulated compared with the control sample when exposed to different bile salt concentrations. The findings provide valuable information for deeply understanding molecular mechanisms about the roles of tolC under bile salt stress and the prevention and control of C. malonaticus.
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Affiliation(s)
- Xin Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Yaping Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Na Ling
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Yizhong Shen
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Danfeng Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Dengyu Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Dexin Ou
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
| | - Yingwang Ye
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China.
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14
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Sphingopyxis microcysteis sp. nov., a novel bioactive exopolysaccharides-bearing Sphingomonadaceae isolated from the Microcystis phycosphere. Antonie van Leeuwenhoek 2021; 114:845-857. [PMID: 33770293 DOI: 10.1007/s10482-021-01563-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 03/15/2021] [Indexed: 10/21/2022]
Abstract
During the study into the microbial biodiversity and bioactivity of the Microcystis phycosphere, a new yellow-pigmented, non-motile, rod-shaped bacterium containing polyhydroxybutyrate granules designated as strain Z10-6T was isolated from highly-toxic Microcystis aeruginosa Kützing M.TN-2. The new isolate produces active bioflocculating exopolysaccharides. Phylogenetic analysis based on 16S rRNA gene sequences indicated strain Z10-6T belongs to the genus Sphingopyxis with highest similarity to Sphingopyxis solisilvae R366T (98.86%), and the similarity to other Sphingopyxis members was less than 98.65%. However, both low values obtained by phylogenomic calculation of average nucleotide identity (ANI, 85.5%) and digital DNA-DNA hybridization (dDDH, 29.8%) separated the new species from its closest relative. The main polar lipids were sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified glycolipid and one unidentified aminophospholipid. The predominant fatty acids were summed feature 8, C17:1ω6c, summed feature 3, C16:0, C18:1ω7c 11-methyl and C14:0 2-OH. The respiratory quinone was ubiqunone-10, with spermidine as the major polyamine. The genomic DNA G + C content was 64.8 mol%. Several biosynthesis pathways encoding for potential new bacterial bioactive metabolites were found in the genome of strain Z10-6T. The polyphasic analyses clearly distinguished strain Z10-6T from its closest phylogenetic neighbors. Thus, it represents a novel species of the genus Sphingopyxis, for which the name Sphingopyxis microcysteis sp. nov. is proposed. The type strain is Z10-6T (= CCTCC AB2017276T = KCTC 62492T).
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15
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Metabolic Engineering of Extremophilic Bacterium Deinococcus radiodurans for the Production of the Novel Carotenoid Deinoxanthin. Microorganisms 2020; 9:microorganisms9010044. [PMID: 33375757 PMCID: PMC7823818 DOI: 10.3390/microorganisms9010044] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 12/27/2022] Open
Abstract
Deinoxanthin, a xanthophyll derived from Deinococcus species, is a unique organic compound that provides greater antioxidant effects compared to other carotenoids due to its superior scavenging activity against singlet oxygen and hydrogen peroxide. Therefore, it has attracted significant attention as a next-generation organic compound that has great potential as a natural ingredient in a food supplements. Although the microbial identification of deinoxanthin has been identified, mass production has not yet been achieved. Here, we report, for the first time, the development of an engineered extremophilic microorganism, Deinococcus radiodurans strain R1, that is capable of producing deinoxanthin through rational metabolic engineering and process optimization. The genes crtB and dxs were first introduced into the genome to reinforce the metabolic flux towards deinoxanthin. The optimal temperature was then identified through a comparative analysis of the mRNA expression of the two genes, while the carbon source was further optimized to increase deinoxanthin production. The final engineered D. radiodurans strain R1 was able to produce 394 ± 17.6 mg/L (102 ± 11.1 mg/g DCW) of deinoxanthin with a yield of 40.4 ± 1.2 mg/g sucrose and a productivity of 8.4 ± 0.2 mg/L/h from 10 g/L of sucrose. The final engineered strain and the strategies developed in the present study can act as the foundation for the industrial application of extremophilic microorganisms.
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16
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Mitra M, Nguyen KMAK, Box TW, Gilpin JS, Hamby SR, Berry TL, Duckett EH. Isolation and characterization of a novel Sphingobium yanoikuyae strain variant that uses biohazardous saturated hydrocarbons and aromatic compounds as sole carbon sources. F1000Res 2020; 9:767. [PMID: 32934808 PMCID: PMC7477647 DOI: 10.12688/f1000research.25284.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/14/2020] [Indexed: 01/09/2023] Open
Abstract
Background: Green micro-alga,
Chlamydomonas reinhardtii (a Chlorophyte), can be cultured in the laboratory heterotrophically or photo-heterotrophically in
Tris-
Phosphate-
Acetate (TAP) medium, which contains acetate as the carbon source.
Chlamydomonas can convert acetate in the TAP medium to glucose via the glyoxylate cycle, a pathway present in many microbes and higher plants. A novel bacterial strain, CC4533, was isolated from a contaminated TAP agar medium culture plate of a
Chlamydomonas wild type strain. In this article, we present our research on the isolation, and biochemical and molecular characterizations of CC4533. Methods: We conducted several microbiological tests and spectrophotometric analyses to biochemically characterize CC4533. The 16S rRNA gene of CC4533 was partially sequenced for taxonomic identification. We monitored the growth of CC4533 on Tris-Phosphate (TP) agar medium (lacks a carbon source) containing different sugars, aromatic compounds and saturated hydrocarbons, to see if CC4533 can use these chemicals as the sole source of carbon. Results: CC4533 is a Gram-negative, non-enteric yellow pigmented, aerobic, mesophilic bacillus. It is alpha-hemolytic and oxidase-positive. CC4533 can ferment glucose, sucrose and lactose, is starch hydrolysis-negative, resistant to penicillin, polymyxin B and chloramphenicol. CC4533 is sensitive to neomycin. Preliminary spectrophotometric analyses indicate that CC4533 produces b-carotenes. NCBI-BLAST analyses of the partial 16S rRNA gene sequence of CC4533 show 99.55% DNA sequence identity to that of
Sphingobium yanoikuyae strain PR86 and
S. yanoikuyae strain NRB095. CC4533 can use cyclo-chloroalkanes, saturated hydrocarbons present in car motor oil, polyhydroxyalkanoate, and mono- and poly-cyclic aromatic compounds, as sole carbon sources for growth. Conclusions: Taxonomically, CC4533 is very closely related to the alpha-proteobacterium
S. yanoikuyae, whose genome has been sequenced. Future research is needed to probe the potential of CC4533 for environmental bioremediation. Whole genome sequencing of CC4533 will confirm if it is a novel strain of
S. yanoikuyae or a new
Sphingobium species.
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Affiliation(s)
- Mautusi Mitra
- Biology Department, University of West Georgia, Carrollton, GA, 30118, USA
| | - Kevin Manoap-Anh-Khoa Nguyen
- Biology Department, University of West Georgia, Carrollton, GA, 30118, USA.,Department of Mechanical Engineering, Kennesaw State University, Marietta, GA, 30060, USA
| | - Taylor Wayland Box
- Biology Department, University of West Georgia, Carrollton, GA, 30118, USA
| | - Jesse Scott Gilpin
- Biology Department, University of West Georgia, Carrollton, GA, 30118, USA
| | - Seth Ryan Hamby
- Biology Department, University of West Georgia, Carrollton, GA, 30118, USA
| | - Taylor Lynne Berry
- Carrollton High School, Carrollton, GA, 30117, USA.,Department of Chemistry and Biochemistry, University of North Georgia, Dahlonega, GA, 30597, USA
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17
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Chen X, Jiang X, Xu M, Zhang M, Huang R, Huang J, Qi F. Co-production of farnesol and coenzyme Q 10 from metabolically engineered Rhodobacter sphaeroides. Microb Cell Fact 2019; 18:98. [PMID: 31151455 PMCID: PMC6544981 DOI: 10.1186/s12934-019-1145-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/20/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Farnesol is an acyclic sesquiterpene alcohol present in the essential oils of various plants in nature. It has been reported to be valuable in medical applications, such as alleviation of allergic asthma, gliosis, and edema as well as anti-cancerous and anti-inflammatory effects. Coenzyme Q10 (CoQ10), an essential cofactor in the aerobic respiratory electron transport chain, has attracted growing interest owing to its clinical benefits and important applications in the pharmaceutical, food, and health industries. In this work, co-production of (E,E)-farnesol (FOH) and CoQ10 was achieved by combining 3 different exogenous terpenes or sesquiterpene synthase with the RNA interference of psy (responsible for phytoene synthesis in Rhodobacter sphaeroides GY-2). RESULTS FOH production was significantly increased by overexpressing exogenous terpene synthase (TPS), phosphatidylglycerophosphatase B (PgpB), and sesquiterpene synthase (ATPS), as well as RNAi-mediated silencing of psy coding phytoene synthase (PSY) in R. sphaeroides strains. Rs-TPS, Rs-ATPS, and Rs-PgpB respectively produced 68.2%, 43.4%, and 21.9% higher FOH titers than that of the control strain. Interestingly, the CoQ10 production of these 3 recombinant R. sphaeroides strains was exactly opposite to that of FOH. However, CoQ10 production was almost unaffected in R. sphaeroides strains modified by psy RNA interference. The highest FOH production of 40.45 mg/L, which was twice as high as that of the control, was obtained from the TPS-PSYi strain, where the exogenous TPS was combined with the weakening of the phytoene synthesis pathway via psy RNA interference. CoQ10 production in TPS-PSYi, ATPS-PSYi, and PgpB-PSYi was decreased and lower than that of the control strain. CONCLUSIONS The original flux that contributed to phytoene synthesis was effectively redirected to provide precursors toward FOH or CoQ10 synthesis via psy RNA interference, which led to weakened carotenoid synthesis. The improved flux that was originally involved in CoQ10 production and phytoene synthesis was redirected toward FOH synthesis via metabolic modification. This is the first reported instance of FOH and CoQ10 co-production in R. sphaeroides using a metabolic engineering strategy.
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Affiliation(s)
- Xueduan Chen
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, Fujian, China
| | - Xianzhang Jiang
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, Fujian, China
| | - Man Xu
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, Fujian, China
| | - Mingliang Zhang
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, Fujian, China
| | - Runye Huang
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, Fujian, China
| | - Jianzhong Huang
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, Fujian, China.
| | - Feng Qi
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, Fujian, China. .,Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation & Fujian Provincial University Engineering Research Center of Industrial Biocatalysis, Fujian Normal University, Fuzhou, 350117, Fujian, China.
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18
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Floc'h K, Lacroix F, Barbieri L, Servant P, Galland R, Butler C, Sibarita JB, Bourgeois D, Timmins J. Bacterial cell wall nanoimaging by autoblinking microscopy. Sci Rep 2018; 8:14038. [PMID: 30232348 PMCID: PMC6145920 DOI: 10.1038/s41598-018-32335-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 09/06/2018] [Indexed: 01/02/2023] Open
Abstract
Spurious blinking fluorescent spots are often seen in bacteria during single-molecule localization microscopy experiments. Although this 'autoblinking' phenomenon is widespread, its origin remains unclear. In Deinococcus strains, we observed particularly strong autoblinking at the periphery of the bacteria, facilitating its comprehensive characterization. A systematic evaluation of the contributions of different components of the sample environment to autoblinking levels and the in-depth analysis of the photophysical properties of autoblinking molecules indicate that the phenomenon results from transient binding of fluorophores originating mostly from the growth medium to the bacterial cell wall, which produces single-molecule fluorescence through a Point Accumulation for Imaging in Nanoscale Topography (PAINT) mechanism. Our data suggest that the autoblinking molecules preferentially bind to the plasma membrane of bacterial cells. Autoblinking microscopy was used to acquire nanoscale images of live, unlabeled D. radiodurans and could be combined with PALM imaging of PAmCherry-labeled bacteria in two-color experiments. Autoblinking-based super-resolved images provided insight into the formation of septa in dividing bacteria and revealed heterogeneities in the distribution and dynamics of autoblinking molecules within the cell wall.
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Affiliation(s)
- Kevin Floc'h
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France
| | | | | | - Pascale Servant
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Remi Galland
- Institut Interdisciplinaire de Neurosciences, University of Bordeaux, Bordeaux, France.,Centre National de la Recherche Scientifique, UMR5297, Bordeaux, France
| | - Corey Butler
- Institut Interdisciplinaire de Neurosciences, University of Bordeaux, Bordeaux, France.,Centre National de la Recherche Scientifique, UMR5297, Bordeaux, France
| | - Jean-Baptiste Sibarita
- Institut Interdisciplinaire de Neurosciences, University of Bordeaux, Bordeaux, France.,Centre National de la Recherche Scientifique, UMR5297, Bordeaux, France
| | | | - Joanna Timmins
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France.
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19
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Li IC, Wu SY, Liou JF, Liu HH, Chen JH, Chen CC. Effects of Deinococcus spp. supplement on egg quality traits in laying hens. Poult Sci 2018; 97:319-327. [PMID: 29077878 DOI: 10.3382/ps/pex281] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/05/2017] [Indexed: 12/21/2022] Open
Abstract
To counter the ill effects of synthetic dyes, bacterial pigment production as an alternative is now one of the promising and emerging fields of research. This study was conducted to evaluate the applicability of Deinococcus genus on the egg quality traits in laying hens. In study I, 24 single comb White Leghorn layers were fed with various 1 wt % Deinococcus bacterial strains for 10 d. In study II, 84 brown Hendrix layers were fed with one of 4 diets containing 0, 0.2, 1, or 5 wt % Deinococcus sp. GKB-Aid 1995 powder for 12 wk. In study III, 60 White Leghorn laying hens were fed either with or without 1 wt % Deinococcus sp. GKB-Aid 1995 powder, 1 wt % Deinococcus sp. GKB-Aid 1995 granules, or 1 wt % Deinococcus sp. GKB-Aid 1995 oily granules for 10 successive d. In all of the experiments, feeding Deinococcus powder did not affect egg quality traits except for the yolk color. In particular, supplementation with all Deinococcus powder treatments changed the yolk color (P < 0.05) in study I, with the best pigmentation score obtained by D. grandis and Deinococcus sp. GKB-Aid 1995. Moreover, longer supplementation of Deinococcus sp. GKB-Aid 1995 in study II had a significant effect on feed conversion ratio. With these findings under consideration, the present study suggests that the Deinococcus species, especially Deinococcus sp. GKB-Aid 1995, can be an excellent candidate for improving egg yolk color in laying hens.
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Affiliation(s)
- I-Chen Li
- Grape King Bio Ltd, Zhong-Li Dist., Taoyuan City, Taiwan
| | - Szu-Yin Wu
- Grape King Bio Ltd, Zhong-Li Dist., Taoyuan City, Taiwan
| | - Jenn-Fa Liou
- Physiology Division, Livestock Research Institute, Council of Agriculture, Hsinhua, Tainan City, Taiwan
| | - Hsiao-Hui Liu
- Grape King Bio Ltd, Zhong-Li Dist., Taoyuan City, Taiwan
| | - Jiau-Hua Chen
- Department of Food Science and Technology, Chia Nan University, Tainan City, Taiwan
| | - Chin-Chu Chen
- Grape King Bio Ltd, Zhong-Li Dist., Taoyuan City, Taiwan.,Institute of Food Science and Technology, National Taiwan University, Taipei City, Taiwan.,Department of Food Science, Nutrition, and Nutraceutical Biotechnology, Shin Chien University, Taipei City, Taiwan.,Department of Applied Science, National Hsin-Chu University of Education, Hsinchu City, Taiwan.,Institute of Biotechnology, National Changhua University of Education, Changhua City, Taiwan.,Department of Bioscience Technology, Chung Yuan Christian University, Taoyuan City, Taiwan
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20
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Rodriguez-Concepcion M, Avalos J, Bonet ML, Boronat A, Gomez-Gomez L, Hornero-Mendez D, Limon MC, Meléndez-Martínez AJ, Olmedilla-Alonso B, Palou A, Ribot J, Rodrigo MJ, Zacarias L, Zhu C. A global perspective on carotenoids: Metabolism, biotechnology, and benefits for nutrition and health. Prog Lipid Res 2018; 70:62-93. [PMID: 29679619 DOI: 10.1016/j.plipres.2018.04.004] [Citation(s) in RCA: 469] [Impact Index Per Article: 78.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/16/2018] [Accepted: 04/18/2018] [Indexed: 12/22/2022]
Abstract
Carotenoids are lipophilic isoprenoid compounds synthesized by all photosynthetic organisms and some non-photosynthetic prokaryotes and fungi. With some notable exceptions, animals (including humans) do not produce carotenoids de novo but take them in their diets. In photosynthetic systems carotenoids are essential for photoprotection against excess light and contribute to light harvesting, but perhaps they are best known for their properties as natural pigments in the yellow to red range. Carotenoids can be associated to fatty acids, sugars, proteins, or other compounds that can change their physical and chemical properties and influence their biological roles. Furthermore, oxidative cleavage of carotenoids produces smaller molecules such as apocarotenoids, some of which are important pigments and volatile (aroma) compounds. Enzymatic breakage of carotenoids can also produce biologically active molecules in both plants (hormones, retrograde signals) and animals (retinoids). Both carotenoids and their enzymatic cleavage products are associated with other processes positively impacting human health. Carotenoids are widely used in the industry as food ingredients, feed additives, and supplements. This review, contributed by scientists of complementary disciplines related to carotenoid research, covers recent advances and provides a perspective on future directions on the subjects of carotenoid metabolism, biotechnology, and nutritional and health benefits.
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Affiliation(s)
| | - Javier Avalos
- Department of Genetics, Universidad de Sevilla, 41012 Seville, Spain
| | - M Luisa Bonet
- Laboratory of Molecular Biology, Nutrition and Biotechnology, Universitat de les Illes Balears, 07120 Palma de Mallorca, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 07120 Palma de Mallorca, Spain; Institut d'Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Albert Boronat
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain; Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Lourdes Gomez-Gomez
- Instituto Botánico, Universidad de Castilla-La Mancha, 02071 Albacete, Spain
| | - Damaso Hornero-Mendez
- Department of Food Phytochemistry, Instituto de la Grasa (IG-CSIC), 41013 Seville, Spain
| | - M Carmen Limon
- Department of Genetics, Universidad de Sevilla, 41012 Seville, Spain
| | - Antonio J Meléndez-Martínez
- Food Color & Quality Laboratory, Area of Nutrition & Food Science, Universidad de Sevilla, 41012 Seville, Spain
| | | | - Andreu Palou
- Laboratory of Molecular Biology, Nutrition and Biotechnology, Universitat de les Illes Balears, 07120 Palma de Mallorca, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 07120 Palma de Mallorca, Spain; Institut d'Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Joan Ribot
- Laboratory of Molecular Biology, Nutrition and Biotechnology, Universitat de les Illes Balears, 07120 Palma de Mallorca, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 07120 Palma de Mallorca, Spain; Institut d'Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Maria J Rodrigo
- Institute of Agrochemistry and Food Technology (IATA-CSIC), 46980 Valencia, Spain
| | - Lorenzo Zacarias
- Institute of Agrochemistry and Food Technology (IATA-CSIC), 46980 Valencia, Spain
| | - Changfu Zhu
- Department of Plant Production and Forestry Science, Universitat de Lleida-Agrotecnio, 25198 Lleida, Spain
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21
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Farci D, Slavov C, Piano D. Coexisting properties of thermostability and ultraviolet radiation resistance in the main S-layer complex of Deinococcus radiodurans. Photochem Photobiol Sci 2018; 17:81-88. [DOI: 10.1039/c7pp00240h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Deinococcus radiodurans is well known for its unusual resistance to different environmental stresses.
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Affiliation(s)
- Domenica Farci
- Department of Life and Environmental Sciences
- Laboratory of Plant Physiology and Photobiology
- University of Cagliari
- 09123 Cagliari
- Italy
| | - Chavdar Slavov
- Institute of Physical and Theoretical Chemistry
- Goethe University
- D-60438 Frankfurt am Main
- Germany
| | - Dario Piano
- Department of Life and Environmental Sciences
- Laboratory of Plant Physiology and Photobiology
- University of Cagliari
- 09123 Cagliari
- Italy
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22
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Antolak H, Oracz J, Otlewska A, Żyżelewicz D, Kręgiel D. Identification of Carotenoids and Isoprenoid Quinones from Asaia lannensis and Asaia bogorensis. Molecules 2017; 22:molecules22101608. [PMID: 28946700 PMCID: PMC6151773 DOI: 10.3390/molecules22101608] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 09/24/2017] [Accepted: 09/24/2017] [Indexed: 12/11/2022] Open
Abstract
The aim of the study was to identify and quantitatively assess of carotenoids and isoprenoid quinones biosynthesized by six different strains of acetic acid bacteria, belonging to genus Asaia, that are common beverage-spoiling bacteria in Europe. Bacterial cultures were conducted in a laboratory liquid culture minimal medium with 2% sucrose. Carotenoids and isoprenoid quinones were investigated using UHPLC-DAD-ESI-MS analysis. In general, tested strains of Asaia spp. were able to produce 10 carotenoids and 3 isoprenoid quinones: menaquinone-7, menaquinone-8, and ubiquinone-10. The main identified carotenoids in Asaia lannensis strains were phytofluene, neurosporene, α-carotene, while for Asaia bogorensis, neurosporene, canthaxanthin, and zeaxanthin were noted. What is more, tested Asaia spp. were able to produce myxoxanthophyll, which has so far been identified primarily in cyanobacteria. The results show that A. lannensis are characterized by statistically higher concentrations of produced carotenoids, as well as a greater variety of these compounds. We have noted that carotenoids were not only accumulated by bacterial cells, but also some strains of A. lannensis produced extracellular carotenoids.
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Affiliation(s)
- Hubert Antolak
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Science, Lodz University of Technology, 171/173 Wólczańska, 90-924 Lodz, Poland.
| | - Joanna Oracz
- Institute of Food Technology and Analysis, Faculty of Biotechnology and Food Science, Lodz University of Technology, 4/10 Stefanowskiego, 90-924 Lodz, Poland.
| | - Anna Otlewska
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Science, Lodz University of Technology, 171/173 Wólczańska, 90-924 Lodz, Poland.
| | - Dorota Żyżelewicz
- Institute of Food Technology and Analysis, Faculty of Biotechnology and Food Science, Lodz University of Technology, 4/10 Stefanowskiego, 90-924 Lodz, Poland.
| | - Dorota Kręgiel
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Science, Lodz University of Technology, 171/173 Wólczańska, 90-924 Lodz, Poland.
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23
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Leuko S, Bohmeier M, Hanke F, Böettger U, Rabbow E, Parpart A, Rettberg P, de Vera JPP. On the Stability of Deinoxanthin Exposed to Mars Conditions during a Long-Term Space Mission and Implications for Biomarker Detection on Other Planets. Front Microbiol 2017; 8:1680. [PMID: 28966605 PMCID: PMC5605620 DOI: 10.3389/fmicb.2017.01680] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/21/2017] [Indexed: 11/13/2022] Open
Abstract
Outer space, the final frontier, is a hostile and unforgiving place for any form of life as we know it. The unique environment of space allows for a close simulation of Mars surface conditions that cannot be simulated as accurately on the Earth. For this experiment, we tested the resistance of Deinococcus radiodurans to survive exposure to simulated Mars-like conditions in low-Earth orbit for a prolonged period of time as part of the Biology and Mars experiment (BIOMEX) project. Special focus was placed on the integrity of the carotenoid deinoxanthin, which may serve as a potential biomarker to search for remnants of life on other planets. Survival was investigated by evaluating colony forming units, damage inflicted to the 16S rRNA gene by quantitative PCR, and the integrity and detectability of deinoxanthin by Raman spectroscopy. Exposure to space conditions had a strong detrimental effect on the survival of the strains and the 16S rRNA integrity, yet results show that deinoxanthin survives exposure to conditions as they prevail on Mars. Solar radiation is not only strongly detrimental to the survival and 16S rRNA integrity but also to the Raman signal of deinoxanthin. Samples not exposed to solar radiation showed only minuscule signs of deterioration. To test whether deinoxanthin is able to withstand the tested parameters without the protection of the cell, it was extracted from cell homogenate and exposed to high/low temperatures, vacuum, germicidal UV-C radiation, and simulated solar radiation. Results obtained by Raman investigations showed a strong resistance of deinoxanthin against outer space and Mars conditions, with the only exception of the exposure to simulated solar radiation. Therefore, deinoxanthin proved to be a suitable easily detectable biomarker for the search of Earth-like organic pigment-containing life on other planets.
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Affiliation(s)
- Stefan Leuko
- German Aerospace Center, Research Group "Astrobiology", Radiation Biology Department, Institute of Aerospace MedicineKöln, Germany
| | - Maria Bohmeier
- German Aerospace Center, Research Group "Astrobiology", Radiation Biology Department, Institute of Aerospace MedicineKöln, Germany
| | - Franziska Hanke
- German Aerospace Center, Institute of Optical Sensor SystemsBerlin, Germany
| | - Ute Böettger
- German Aerospace Center, Institute of Optical Sensor SystemsBerlin, Germany
| | - Elke Rabbow
- German Aerospace Center, Research Group "Astrobiology", Radiation Biology Department, Institute of Aerospace MedicineKöln, Germany
| | - Andre Parpart
- German Aerospace Center, Research Group "Astrobiology", Radiation Biology Department, Institute of Aerospace MedicineKöln, Germany
| | - Petra Rettberg
- German Aerospace Center, Research Group "Astrobiology", Radiation Biology Department, Institute of Aerospace MedicineKöln, Germany
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24
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Jung KW, Lim S, Bahn YS. Microbial radiation-resistance mechanisms. J Microbiol 2017; 55:499-507. [PMID: 28664512 DOI: 10.1007/s12275-017-7242-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 06/19/2017] [Indexed: 11/28/2022]
Abstract
Organisms living in extreme environments have evolved a wide range of survival strategies by changing biochemical and physiological features depending on their biological niches. Interestingly, organisms exhibiting high radiation resistance have been discovered in the three domains of life (Bacteria, Archaea, and Eukarya), even though a naturally radiationintensive environment has not been found. To counteract the deleterious effects caused by radiation exposure, radiation- resistant organisms employ a series of defensive systems, such as changes in intracellular cation concentration, excellent DNA repair systems, and efficient enzymatic and non-enzymatic antioxidant systems. Here, we overview past and recent findings about radiation-resistance mechanisms in the three domains of life for potential usage of such radiationresistant microbes in the biotechnology industry.
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Affiliation(s)
- Kwang-Woo Jung
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Sangyong Lim
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea.
| | - Yong-Sun Bahn
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
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Zeng Y, Ma Y, Xiao F, Wang W, He S. Knockout of pprM Decreases Resistance to Desiccation and Oxidation in Deinococcus radiodurans. Indian J Microbiol 2017; 57:316-321. [PMID: 28904416 DOI: 10.1007/s12088-017-0653-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 05/27/2017] [Indexed: 10/19/2022] Open
Abstract
Deinococcus radiodurans has attracted a great interest in the past decades due to its extraordinary resistance to ionizing radiation and highly efficient DNA repair system. Recent studies indicated that pprM is a putative pleiotropic gene in D. radiodurans and plays an important role in radioresistance and antioxidation, but its underlying mechanisms are poorly elucidated. In this study, pprM mutation was generated to investigate resistance to desiccation and oxidative stress. The result showed that the survival of pprM mutant under desiccation was markedly retarded compared to the wild strain from day 7-28. Furthermore, knockout of pprM increases the intercellular accumulation of ROS and the sensibility to H2O2 stress in the bacterial growth inhibition assay. The absorbance spectrum experiment for detecting the carotenoid showed that deinoxanthin, a carotenoid that peculiarly exists in Deinococcus, was reduced in the pprM mutant in the pprM mutant. Quantitative real time PCR showed decreased expression of three genes viz. CrtI (DR0861, 50%),CrtB (DR0862, 40%) and CrtO (DR0093, 50%), which are involved in deinoxanthin synthesis, and of Dps (DNA protection during starving) gene (DRB0092) relevant to ion combining and DNA protection in cells. Our results suggest that pprM may affect antioxidative ability of D. radiodurans by regulating the synthesis of deinoxanthin and the concentration of metal ions. This may provide new clues for the treatment of antioxidants.
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Affiliation(s)
- Yang Zeng
- School of Public Health, University of South China, Hengyang, 421001 People's Republic of China
| | - Yun Ma
- Department of Biochemistry and Biology, University of South China, Hengyang, Hunan 421001 People's Republic of China
| | - Fangzhu Xiao
- School of Public Health, University of South China, Hengyang, 421001 People's Republic of China
| | - Wuzhou Wang
- Department of Biochemistry and Biology, University of South China, Hengyang, Hunan 421001 People's Republic of China
| | - Shuya He
- School of Public Health, University of South China, Hengyang, 421001 People's Republic of China.,Department of Biochemistry and Biology, University of South China, Hengyang, Hunan 421001 People's Republic of China
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26
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Farci D, Slavov C, Tramontano E, Piano D. The S-layer Protein DR_2577 Binds Deinoxanthin and under Desiccation Conditions Protects against UV-Radiation in Deinococcus radiodurans. Front Microbiol 2016; 7:155. [PMID: 26909071 PMCID: PMC4754619 DOI: 10.3389/fmicb.2016.00155] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 01/29/2016] [Indexed: 11/13/2022] Open
Abstract
Deinococcus radiodurans has the puzzling ability to withstand over a broad range of extreme conditions including high doses of ultraviolet radiation and deep desiccation. This bacterium is surrounded by a surface layer (S-layer) built of a regular repetition of several proteins, assembled to form a paracrystalline structure. Here we report that the deletion of a main constituent of this S-layer, the gene DR_2577, causes a decrease in the UVC resistance, especially in desiccated cells. Moreover, we show that the DR_2577 protein binds the carotenoid deinoxanthin, a strong protective antioxidant specific of this bacterium. A further spectroscopical characterization of the deinoxanthin-DR_2577 complex revealed features which could suggest a protective role of DR_2577. We propose that, especially under desiccation, the S-layer shields the bacterium from incident ultraviolet light and could behave as a first lane of defense against UV radiation.
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Affiliation(s)
- Domenica Farci
- Laboratory of Plant Physiology and Photobiology, Department of Life and Environmental Sciences, University of Cagliari Cagliari, Italy
| | - Chavdar Slavov
- Department of Physical Chemistry, Institute of Physical and Theoretical Chemistry Frankfurt am Main, Germany
| | - Enzo Tramontano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari Cagliari, Italy
| | - Dario Piano
- Laboratory of Plant Physiology and Photobiology, Department of Life and Environmental Sciences, University of CagliariCagliari, Italy; International Institute of Molecular and Cell BiologyWarsaw, Poland
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27
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Hansler A, Chen Q, Ma Y, Gross SS. Untargeted metabolite profiling reveals that nitric oxide bioynthesis is an endogenous modulator of carotenoid biosynthesis in Deinococcus radiodurans and is required for extreme ionizing radiation resistance. Arch Biochem Biophys 2015; 589:38-52. [PMID: 26550929 DOI: 10.1016/j.abb.2015.10.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/12/2015] [Accepted: 10/12/2015] [Indexed: 10/22/2022]
Abstract
Deinococcus radiodurans (Drad) is the most radioresistant organism known. Although mechanisms that underlie the extreme radioresistance of Drad are incompletely defined, resistance to UV irradiation-induced killing was found to be greatly attenuated in an NO synthase (NOS) knockout strain of Drad (Δnos). We now show that endogenous NO production is also critical for protection of Drad against γ-irradiation (3000 Gy), a result of accelerated growth recovery, not protection against killing. NO-donor treatment rescued radiosensitization in Δnos Drad but did not influence radiosensitivity in wild type Drad. To discover molecular mechanisms by which endogenous NO confers radioresistance, metabolite profiling studies were performed. Untargeted LC-MS-based metabolite profiling in Drad quantified relative abundances of 1425 molecules and levels of 294 of these were altered by >5-fold (p < 0.01). Unexpectedly, these studies identified a dramatic perturbation in carotenoid biosynthetic intermediates in Δnos Drad, including a reciprocal switch in the pathway end-products from deoxydeinoxanthin to deinoxanthin. NO supplementation rescued these nos deletion-associated changes in carotenoid biosynthesis, and fully-restored radioresistance to wildtype levels. Because carotenoids were shown to be important contributors to radioprotection in Drad, our findings suggest that endogenously-produced NO serves to maintain a spectrum of carotenoids critical for Drad's ability to withstand radiation insult.
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Affiliation(s)
- Alex Hansler
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA
| | - Qiuying Chen
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA
| | - Yuliang Ma
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA
| | - Steven S Gross
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA.
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28
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Castillo H, Schoderbek D, Dulal S, Escobar G, Wood J, Nelson R, Smith G. Stress induction in the bacteria Shewanella oneidensis and Deinococcus radiodurans in response to below-background ionizing radiation. Int J Radiat Biol 2015; 91:749-56. [PMID: 26073528 DOI: 10.3109/09553002.2015.1062571] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE The 'Linear no-threshold' (LNT) model predicts that any amount of radiation increases the risk of organisms to accumulate negative effects. Several studies at below background radiation levels (4.5-11.4 nGy h(-1)) show decreased growth rates and an increased susceptibility to oxidative stress. The purpose of our study is to obtain molecular evidence of a stress response in Shewanella oneidensis and Deinococcus radiodurans grown at a gamma dose rate of 0.16 nGy h(-1), about 400 times less than normal background radiation. MATERIALS AND METHODS Bacteria cultures were grown at a dose rate of 0.16 or 71.3 nGy h(-1) gamma irradiation. Total RNA was extracted from samples at early-exponential and stationary phases for the rt-PCR relative quantification (radiation-deprived treatment/background radiation control) of the stress-related genes katB (catalase), recA (recombinase), oxyR (oxidative stress transcriptional regulator), lexA (SOS regulon transcriptional repressor), dnaK (heat shock protein 70) and SOA0154 (putative heavy metal efflux pump). RESULTS Deprivation of normal levels of radiation caused a reduction in growth of both bacterial species, accompanied by the upregulation of katB, recA, SOA0154 genes in S. oneidensis and the upregulation of dnaK in D. radiodurans. When cells were returned to background radiation levels, growth rates recovered and the stress response dissipated. CONCLUSIONS Our results indicate that below-background levels of radiation inhibited growth and elicited a stress response in two species of bacteria, contrary to the LNT model prediction.
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Affiliation(s)
- Hugo Castillo
- a Department of Biology , New Mexico State University , Las Cruces , NM , USA
| | - Donald Schoderbek
- b Department of Agriculture , Food, and Nutritional Science, University of Alberta , Edmonton , Alberta, Canada
| | - Santosh Dulal
- c School of Medicine, University of North Carolina , Chapel Hill NC
| | - Gabriela Escobar
- a Department of Biology , New Mexico State University , Las Cruces , NM , USA
| | - Jeffrey Wood
- d Department of Energy-Carlsbad Field Office , Carlsbad , NM , USA
| | - Roger Nelson
- d Department of Energy-Carlsbad Field Office , Carlsbad , NM , USA
| | - Geoffrey Smith
- a Department of Biology , New Mexico State University , Las Cruces , NM , USA
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Extraction of water-soluble polysaccharide and the antioxidant activity from Semen cassiae. J Food Drug Anal 2014; 22:492-499. [PMID: 28911465 PMCID: PMC9354996 DOI: 10.1016/j.jfda.2014.01.027] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 01/15/2014] [Accepted: 01/18/2014] [Indexed: 11/29/2022] Open
Abstract
Water-soluble polysaccharide was isolated from Semen cassiae using water for extraction and ethanol for deposition. The optimized conditions for polysaccharide isolation by orthogonal experiments were a sample to liquid ratio of 1:30 at 80°C for 3.5 hours; the yield of polysaccharide from Semen cassiae under these conditions was 5.46%. Different polysaccharides (SCPW-1, SCPW-2, SCPW-3, SCPW-4, SCPW-5, SCPS-1, SCPS-2) were obtained from the extract (i.e., crude polysaccharide) by DEAE-cellulose column chromatography. The polysaccharides obtained showed different structures by Fourier transform infrared therein the five elected from the seven kinds separated. The antioxidant activities of the extract were evaluated. The scavenging rates of the present extract on hydroxyl and superoxide were 43.32% and 64.97%, respectively, at a concentration of polysaccharide of 94.03 μg/mL, which was better than vitamin C at the same concentration. The scavenging rate of the present extract on 1,1-diphenyl-2-picrylhydrazyl was 13.33% at a polysaccharide concentration of 94.03 μg/mL, which was less than vitamin C at the same concentration.
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30
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Luan H, Meng N, Fu J, Chen X, Xu X, Feng Q, Jiang H, Dai J, Yuan X, Lu Y, Roberts AA, Luo X, Chen M, Xu S, Li J, Hamilton CJ, Fang C, Wang J. Genome-wide transcriptome and antioxidant analyses on gamma-irradiated phases of deinococcus radiodurans R1. PLoS One 2014; 9:e85649. [PMID: 24465634 PMCID: PMC3900439 DOI: 10.1371/journal.pone.0085649] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 11/29/2013] [Indexed: 11/18/2022] Open
Abstract
Adaptation of D. radiodurans cells to extreme irradiation environments requires dynamic interactions between gene expression and metabolic regulatory networks, but studies typically address only a single layer of regulation during the recovery period after irradiation. Dynamic transcriptome analysis of D. radiodurans cells using strand-specific RNA sequencing (ssRNA-seq), combined with LC-MS based metabolite analysis, allowed an estimate of the immediate expression pattern of genes and antioxidants in response to irradiation. Transcriptome dynamics were examined in cells by ssRNA-seq covering its predicted genes. Of the 144 non-coding RNAs that were annotated, 49 of these were transfer RNAs and 95 were putative novel antisense RNAs. Genes differentially expressed during irradiation and recovery included those involved in DNA repair, degradation of damaged proteins and tricarboxylic acid (TCA) cycle metabolism. The knockout mutant crtB (phytoene synthase gene) was unable to produce carotenoids, and exhibited a decreased survival rate after irradiation, suggesting a role for these pigments in radiation resistance. Network components identified in this study, including repair and metabolic genes and antioxidants, provided new insights into the complex mechanism of radiation resistance in D. radiodurans.
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Affiliation(s)
- Hemi Luan
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
- Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Nan Meng
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
| | - Jin Fu
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
| | - Xiaomin Chen
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
| | - Xun Xu
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
| | - Qiang Feng
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
| | - Hui Jiang
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
| | - Jun Dai
- College of Life Sciences, Wuhan University, Wuhan, China
- Key Laboratory of Fermentation Engineering, Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan, China
| | - Xune Yuan
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
| | - Yanping Lu
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
| | - Alexandra A. Roberts
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Xiao Luo
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
| | - Maoshan Chen
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
| | - Shengtao Xu
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
| | - Jun Li
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
| | - Chris J. Hamilton
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Chengxiang Fang
- College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail: (CF); (JW)
| | - Jun Wang
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail: (CF); (JW)
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31
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Yu LZH, Luo XS, Liu M, Huang Q. Diversity of ionizing radiation-resistant bacteria obtained from the Taklimakan Desert. J Basic Microbiol 2013; 55:135-40. [PMID: 25590873 DOI: 10.1002/jobm.201300390] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 08/23/2013] [Indexed: 11/06/2022]
Abstract
So far, little is known about the diversity of the radiation-resistant microbes of the hyperarid Taklimakan Desert. In this study, ionizing radiation (IR)-resistant bacteria from two sites in Xinjiang were investigated. After exposing the arid (water content of 0.8 ± 0.3%) and non-arid (water content of 21.3 ± 0.9%) sediment samples to IR of 3000 Gy using a (60)Co source, a total of 52 γ-radiation-resistant bacteria were isolated from the desert sample. The 16S rRNA genes of all isolates were sequenced. The phylogenetic tree places these isolates into five groups: Cytophaga-Flavobacterium-Bacteroides, Proteobacteria, Deinococcus-Thermus, Firmicutes, and Actinobacteria. Interestingly, this is the first report of radiation-resistant bacteria belonging to the genera Knoellia, Lysobacter, Nocardioides, Paracoccus, Pontibacter, Rufibacter and Microvirga. The 16s rRNA genes of four isolates showed low sequence similarities to those of the published species. Phenotypic analysis showed that all bacteria in this study are able to produce catalase, suggesting that these bacteria possess reactive oxygen species (ROS)-scavenging enzymes. These radiation-resistant bacteria also displayed diverse metabolic properties. Moreover, their radiation resistances were found to differ. The diversity of the radiation-resistant bacteria in the desert provides further ecological support for the hypothesis that the ionizing-radiation resistance phenotype is a consequence of the evolution of ROS-scavenging systems that protect cells against oxidative damage caused by desiccation.
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Affiliation(s)
- Li Zhi-Han Yu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
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32
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Liu C, Sun Z, Shen S, Lin L, Li T, Tian B, Hua Y. Identification and characterization of the geranylgeranyl diphosphate synthase in Deinococcus radiodurans. Lett Appl Microbiol 2013; 58:219-24. [PMID: 24151908 DOI: 10.1111/lam.12181] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 10/12/2013] [Accepted: 10/12/2013] [Indexed: 11/30/2022]
Abstract
UNLABELLED Deinococcus radiodurans strain R1 utilizes multiple antioxidants including a unique carotenoid, deinoxanthin, to fight again oxidative stress. Most of the enzymes involved in the deinoxanthin biosynthetic pathway have been identified. However, the enzyme catalysing the synthesis of geranylgeranyl diphosphate (GGPP), which is a precursor of carotenoid biosynthesis, has yet to be identified. Two putative isoprenyl diphosphate synthases (IPPS) homologues (DR1395 and DR932) were screened out by analysis of conserved amino acid regions, and their biochemical functions were investigated. Gene mutation, gene expression in Escherichia coli and analysis of carotenoid products were used to investigate the functions of these candidates. The results suggested that DR1395 encodes the protein for GGPP synthesis. Site-directed mutant analysis indicated that the amino acid composition of and around the first aspartate-rich motif is vital for GGPP synthase function. SIGNIFICANCE AND IMPACT OF THE STUDY Deinococcus radiodurans strain R1 produces a unique carotenoid product, deinoxanthin, as an antioxidant. In this study, DR1395 was identified as the gene encoding geranylgeranyl diphosphate synthase (GGPPS) for entrance to deinoxanthin biosynthesis in D. radiodurans. Moreover, site-directed mutagenesis studies on DR1395 identified the effect of amino acid composition of the aspartate-rich motif on the production of this carotenoid. This study demonstrated the entrance step in the deinoxanthin biosynthetic pathway. These results can be useful in genetic engineering strategies for deinoxanthin production including enhancement of GGPPS gene expression in D. radiodurans.
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Affiliation(s)
- C Liu
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
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Adaptation of the black yeast Wangiella dermatitidis to ionizing radiation: molecular and cellular mechanisms. PLoS One 2012; 7:e48674. [PMID: 23139812 PMCID: PMC3490873 DOI: 10.1371/journal.pone.0048674] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 09/27/2012] [Indexed: 11/25/2022] Open
Abstract
Observations of enhanced growth of melanized fungi under low-dose ionizing radiation in the laboratory and in the damaged Chernobyl nuclear reactor suggest they have adapted the ability to survive or even benefit from exposure to ionizing radiation. However, the cellular and molecular mechanism of fungal responses to such radiation remains poorly understood. Using the black yeast Wangiella dermatitidis as a model, we confirmed that ionizing radiation enhanced cell growth by increasing cell division and cell size. Using RNA-seq technology, we compared the transcriptomic profiles of the wild type and the melanin-deficient wdpks1 mutant under irradiation and non-irradiation conditions. It was found that more than 3000 genes were differentially expressed when these two strains were constantly exposed to a low dose of ionizing radiation and that half were regulated at least two fold in either direction. Functional analysis indicated that many genes for amino acid and carbohydrate metabolism and cell cycle progression were down-regulated and that a number of antioxidant genes and genes affecting membrane fluidity were up-regulated in both irradiated strains. However, the expression of ribosomal biogenesis genes was significantly up-regulated in the irradiated wild-type strain but not in the irradiated wdpks1 mutant, implying that melanin might help to contribute radiation energy for protein translation. Furthermore, we demonstrated that long-term exposure to low doses of radiation significantly increased survivability of both the wild-type and the wdpks1 mutant, which was correlated with reduced levels of reactive oxygen species (ROS), increased production of carotenoid and induced expression of genes encoding translesion DNA synthesis. Our results represent the first functional genomic study of how melanized fungal cells respond to low dose ionizing radiation and provide clues for the identification of biological processes, molecular pathways and individual genes regulated by radiation.
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Biological role of pigment production for the bacterial phytopathogen Pantoea stewartii subsp. stewartii. Appl Environ Microbiol 2012; 78:6859-65. [PMID: 22820327 DOI: 10.1128/aem.01574-12] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Pantoea stewartii subsp. stewartii, the causal agent of Stewart's wilt of sweet corn, produces a yellow carotenoid pigment. A nonpigmented mutant was selected from a bank of mutants generated by random transposon mutagenesis. The transposon insertion site was mapped to the crtB gene, encoding a putative phytoene synthase, an enzyme involved in the early steps of carotenoid biosynthesis. We demonstrate here that the carotenoid pigment imparts protection against UV radiation and also contributes to the complete antioxidant pathway of P. stewartii. Moreover, production of this pigment is regulated by the EsaI/EsaR quorum-sensing system and significantly contributes to the virulence of the pathogen in planta.
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Liu X, Gai Z, Tao F, Tang H, Xu P. Carotenoids play a positive role in the degradation of heterocycles by Sphingobium yanoikuyae. PLoS One 2012; 7:e39522. [PMID: 22745775 PMCID: PMC3380023 DOI: 10.1371/journal.pone.0039522] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 05/22/2012] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Microbial oxidative degradation is a potential way of removing pollutants such as heterocycles from the environment. During this process, reactive oxygen species or other oxidants are inevitably produced, and may cause damage to DNA, proteins, and membranes, thereby decreasing the degradation rate. Carotenoids can serve as membrane-integrated antioxidants, protecting cells from oxidative stress. FINDINGS Several genes involved in the carotenoid biosynthetic pathway were cloned and characterized from a carbazole-degrading bacterium Sphingobium yanoikuyae XLDN2-5. In addition, a yellow-pigmented carotenoid synthesized by strain XLDN2-5 was identified as zeaxanthin that was synthesized from β-carotene through β-cryptoxanthin. The amounts of zeaxanthin and hydrogen peroxide produced were significantly and simultaneously enhanced during the biodegradation of heterocycles (carbazole < carbazole + benzothiophene < carbazole + dibenzothiophene). These higher production levels were consistent with the transcriptional increase of the gene encoding phytoene desaturase, one of the key enzymes for carotenoid biosynthesis. CONCLUSIONS/SIGNIFICANCE Sphingobium yanoikuyae XLDN2-5 can enhance the synthesis of zeaxanthin, one of the carotenoids, which may modulate membrane fluidity and defense against intracellular oxidative stress. To our knowledge, this is the first report on the positive role of carotenoids in the biodegradation of heterocycles, while elucidating the carotenoid biosynthetic pathway in the Sphingobium genus.
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Affiliation(s)
- Xiaorui Liu
- State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People′s Republic of China
| | - Zhonghui Gai
- State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People′s Republic of China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People′s Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People′s Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People′s Republic of China
- * E-mail:
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Dartnell LR, Page K, Jorge-Villar SE, Wright G, Munshi T, Scowen IJ, Ward JM, Edwards HGM. Destruction of Raman biosignatures by ionising radiation and the implications for life detection on Mars. Anal Bioanal Chem 2012; 403:131-44. [DOI: 10.1007/s00216-012-5829-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 02/01/2012] [Accepted: 02/01/2012] [Indexed: 10/28/2022]
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Abaydulla G, Luo X, Shi J, Peng F, Liu M, Wang Y, Dai J, Fang C. Rufibacter tibetensis gen. nov., sp. nov., a novel member of the family Cytophagaceae isolated from soil. Antonie van Leeuwenhoek 2011; 101:725-31. [DOI: 10.1007/s10482-011-9686-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 12/11/2011] [Indexed: 10/14/2022]
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Lysenko VS, Chistyakov VA, Zimakov DV, Soier VG, Sazykina MA, Sazykina MI, Sazykin IS, Krasnov VP. Separation and mass spectrometry identification of carotenoid complex from radioresistant bacteria Deinococcus radiodurans. JOURNAL OF ANALYTICAL CHEMISTRY 2011. [DOI: 10.1134/s1061934811130144] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abstract
Deinococcus radiodurans is a robust bacterium best known for its capacity to repair massive DNA damage efficiently and accurately. It is extremely resistant to many DNA-damaging agents, including ionizing radiation and UV radiation (100 to 295 nm), desiccation, and mitomycin C, which induce oxidative damage not only to DNA but also to all cellular macromolecules via the production of reactive oxygen species. The extreme resilience of D. radiodurans to oxidative stress is imparted synergistically by an efficient protection of proteins against oxidative stress and an efficient DNA repair mechanism, enhanced by functional redundancies in both systems. D. radiodurans assets for the prevention of and recovery from oxidative stress are extensively reviewed here. Radiation- and desiccation-resistant bacteria such as D. radiodurans have substantially lower protein oxidation levels than do sensitive bacteria but have similar yields of DNA double-strand breaks. These findings challenge the concept of DNA as the primary target of radiation toxicity while advancing protein damage, and the protection of proteins against oxidative damage, as a new paradigm of radiation toxicity and survival. The protection of DNA repair and other proteins against oxidative damage is imparted by enzymatic and nonenzymatic antioxidant defense systems dominated by divalent manganese complexes. Given that oxidative stress caused by the accumulation of reactive oxygen species is associated with aging and cancer, a comprehensive outlook on D. radiodurans strategies of combating oxidative stress may open new avenues for antiaging and anticancer treatments. The study of the antioxidation protection in D. radiodurans is therefore of considerable potential interest for medicine and public health.
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Desertibacter roseus gen. nov., sp. nov., a gamma radiation-resistant bacterium in the family Rhodospirillaceae, isolated from desert sand. Int J Syst Evol Microbiol 2011; 61:1109-1113. [DOI: 10.1099/ijs.0.021246-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, rod-shaped, strictly aerobic bacterium, strain 2622T, was isolated from gamma-irradiated soil sampled from the Taklimakan desert in Xinjiang, China. Phylogenetic analyses showed that strain 2622T formed a distinct lineage in the family Rhodospirillaceae and shared 91.7 and 90.1 % 16S rRNA gene sequence similarity with its closest relatives, the type strains of Skermanella xinjiangensis and Skermanella aerolata, respectively. The DNA G+C content of strain 2622T was 71.4 mol% and the isoprenoid quinone was ubiquinone Q-10. Based on phenotypic and chemotaxonomic data and phylogenetic analysis, strain 2622T is considered to represent a novel species of a new genus in the family Rhodospirillaceae, for which the name Desertibacter roseus gen. nov., sp. nov. is proposed. The type strain of Desertibacter roseus is strain 2622T ( = CCTCC AB 208152T = KCTC 22436T).
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Tian B, Hua Y. Carotenoid biosynthesis in extremophilic Deinococcus–Thermus bacteria. Trends Microbiol 2010; 18:512-20. [DOI: 10.1016/j.tim.2010.07.007] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2010] [Revised: 07/19/2010] [Accepted: 07/30/2010] [Indexed: 10/19/2022]
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Protein damage and death by radiation in Escherichia coli and Deinococcus radiodurans. Proc Natl Acad Sci U S A 2010; 107:14373-7. [PMID: 20660760 DOI: 10.1073/pnas.1009312107] [Citation(s) in RCA: 179] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Deinococcus radiodurans is among a small number of bacterial species that are extremely resistant to ionizing radiation, UV light, toxic chemicals, and desiccation. We measured proteome oxidation (i.e., protein carbonylation, PC) in D. radiodurans as well as in standard and evolved resistant strains of Escherichia coli exposed to ionizing radiation or UVC light and found a consistent correlation with cell killing. The unique quantitative relationship between incurred PC and cell death holds over the entire range of killing for all tested bacteria and for both lethal agents, meaning that both bacterial species are equally sensitive to PC. We show that the extraordinary robustness of D. radiodurans depends on efficient proteome protection (but not DNA protection) against constitutive and radiation-induced PC consisting of low molecular weight cytosolic compounds. Remarkably, experimental evolution of resistance to ionizing radiation in E. coli coevolves with protection against PC. The decline in biosynthetic efficacy of the cellular proteome, as measured by the loss of reproduction of undamaged bacteriophage lambda in irradiated standard and evolved ionizing radiation-resistant E. coli, correlates with radiation-induced oxidative damage to host cells and their sensitivity to ionizing radiation. This correlation suggests that cell death by radiation is caused primarily by oxidative damage with consequential loss of maintenance activities including DNA repair.
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Phylogenetic and evolutionary patterns in microbial carotenoid biosynthesis are revealed by comparative genomics. PLoS One 2010; 5:e11257. [PMID: 20582313 PMCID: PMC2889829 DOI: 10.1371/journal.pone.0011257] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Accepted: 05/28/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Carotenoids are multifunctional, taxonomically widespread and biotechnologically important pigments. Their biosynthesis serves as a model system for understanding the evolution of secondary metabolism. Microbial carotenoid diversity and evolution has hitherto been analyzed primarily from structural and biosynthetic perspectives, with the few phylogenetic analyses of microbial carotenoid biosynthetic proteins using either used limited datasets or lacking methodological rigor. Given the recent accumulation of microbial genome sequences, a reappraisal of microbial carotenoid biosynthetic diversity and evolution from the perspective of comparative genomics is warranted to validate and complement models of microbial carotenoid diversity and evolution based upon structural and biosynthetic data. METHODOLOGY/PRINCIPAL FINDINGS Comparative genomics were used to identify and analyze in silico microbial carotenoid biosynthetic pathways. Four major phylogenetic lineages of carotenoid biosynthesis are suggested composed of: (i) Proteobacteria; (ii) Firmicutes; (iii) Chlorobi, Cyanobacteria and photosynthetic eukaryotes; and (iv) Archaea, Bacteroidetes and two separate sub-lineages of Actinobacteria. Using this phylogenetic framework, specific evolutionary mechanisms are proposed for carotenoid desaturase CrtI-family enzymes and carotenoid cyclases. Several phylogenetic lineage-specific evolutionary mechanisms are also suggested, including: (i) horizontal gene transfer; (ii) gene acquisition followed by differential gene loss; (iii) co-evolution with other biochemical structures such as proteorhodopsins; and (iv) positive selection. CONCLUSIONS/SIGNIFICANCE Comparative genomics analyses of microbial carotenoid biosynthetic proteins indicate a much greater taxonomic diversity then that identified based on structural and biosynthetic data, and divides microbial carotenoid biosynthesis into several, well-supported phylogenetic lineages not evident previously. This phylogenetic framework is applicable to understanding the evolution of specific carotenoid biosynthetic proteins or the unique characteristics of carotenoid biosynthetic evolution in a specific phylogenetic lineage. Together, these analyses suggest a "bramble" model for microbial carotenoid biosynthesis whereby later biosynthetic steps exhibit greater evolutionary plasticity and reticulation compared to those closer to the biosynthetic "root". Structural diversification may be constrained ("trimmed") where selection is strong, but less so where selection is weaker. These analyses also highlight likely productive avenues for future research and bioprospecting by identifying both gaps in current knowledge and taxa which may particularly facilitate carotenoid diversification.
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Roth S, Feichtinger J, Hertel C. Response of Deinococcus radiodurans to low-pressure low-temperature plasma sterilization processes. J Appl Microbiol 2010; 109:1521-30. [PMID: 20553346 DOI: 10.1111/j.1365-2672.2010.04771.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS Characterize the response of Deinococcus radiodurans R1 cells to low-pressure low-temperature nitrogen-oxygen microwave plasma and identify repair processes during recovery. METHODS AND RESULTS Cells coated onto glass slides exhibited a biphasic plasma inactivation kinetics. Treatment with various plasmas and subsequent incubation in recovery medium prolonged the lag phase in a part of the survivors, during which the ability to grow on stress medium was recovered. This recovery strongly depended on transcriptional and translational processes and cell wall synthesis, as revealed by addition of specific inhibitors to the recovery medium. Genes involved in DNA repair, oxidative stress response, and cell wall synthesis were induced during recovery, as determined by quantitative RT-PCR. Damage to chromosomal DNA caused by plasma agents and repair during recovery was directly shown by quantitative PCR. Plasmas with less UV radiation emission were also effective in killing D. radiodurans cells but resulted in less DNA damage and lower induction of the investigated genes. CONCLUSIONS The response of D. radiodurans to plasma indicates that DNA, proteins, and cell wall are primary targets of plasma finally leading to the cell death. Protein oxidation is more important for killing of D. radiodurans cells than of Bacillus subtilis spores. Thus, the contaminating biological material affects the plasma composition to be used for sterilization. SIGNIFICANCE AND IMPACT OF THE STUDY The results in this study provide new insight into the interaction of plasma with bacterial cells. This knowledge contributes to the definition of useful parameters for novel plasma sterilization equipment to control process safety.
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Affiliation(s)
- S Roth
- Institute of Food Science and Biotechnology, Section Food Microbiology, University of Hohenheim, Stuttgart, Germany
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Genes involved in yellow pigmentation of Cronobacter sakazakii ES5 and influence of pigmentation on persistence and growth under environmental stress. Appl Environ Microbiol 2009; 76:1053-61. [PMID: 20038705 DOI: 10.1128/aem.01420-09] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cronobacter spp. are opportunistic food-borne pathogens that are responsible for rare but highly fatal cases of meningitis and necrotizing enterocolitis in neonates. While the operon responsible for yellow pigmentation in Cronobacter sakazakii strain ES5 was described recently, the involvement of additional genes in pigment expression and the influence of pigmentation on the fitness of Cronobacter spp. have not been investigated. Thus, the aim of this study was to identify further genes involved in pigment expression in Cronobacter sakazakii ES5 and to assess the influence of pigmentation on growth and persistence under conditions of environmental stress. A knockout library was created using random transposon mutagenesis. The screening of 9,500 mutants for decreased pigment production identified 30 colorless mutants. The mapping of transposon insertion sites revealed insertions in not only the carotenoid operon but also in various other genes involved in signal transduction, inorganic ions, and energy metabolism. To determine the effect of pigmentation on fitness, colorless mutants (DeltacrtE, DeltacrtX, and DeltacrtY) were compared to the yellow wild type using growth and inactivation experiments, a macrophage assay, and a phenotype array. Among other findings, the colorless mutants grew at significantly increased rates under osmotic stress compared to that of the yellow wild type while showing increased susceptibility to desiccation. Moreover, DeltacrtE and DeltacrtY exhibited increased sensitivity to UVB irradiation.
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Sun Z, Shen S, Tian B, Wang H, Xu Z, Wang L, Hua Y. Functional analysis of γ-carotene ketolase involved in the carotenoid biosynthesis ofDeinococcus radiodurans. FEMS Microbiol Lett 2009; 301:21-7. [DOI: 10.1111/j.1574-6968.2009.01794.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Bauermeister A, Bentchikou E, Moeller R, Rettberg P. Roles of PprA, IrrE, and RecA in the resistance of Deinococcus radiodurans to germicidal and environmentally relevant UV radiation. Arch Microbiol 2009; 191:913-8. [DOI: 10.1007/s00203-009-0522-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Revised: 10/06/2009] [Accepted: 10/12/2009] [Indexed: 02/01/2023]
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Tian B, Sun Z, Shen S, Wang H, Jiao J, Wang L, Hu Y, Hua Y. Effects of carotenoids from Deinococcus radiodurans on protein oxidation. Lett Appl Microbiol 2009; 49:689-94. [PMID: 19780959 DOI: 10.1111/j.1472-765x.2009.02727.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To evaluate the antioxidant effect of carotenoids from Deinococcus radiodurans on protein. METHODS AND RESULTS Deinococcus radiodurans strain R1 (ATCC 13939) and its mutant strain R1DeltacrtB were used for this study. The total carotenoids (R1ex) from D. radiodurans were obtained by extraction with acetone/methanol (7 : 2, by vol), and their antioxidant activity was measured using the DPPH (2,2-diphenyl-1-picrylhydrazyl) system. The protein oxidation level, in vitro and in the cell, was measured using the DNPH (2,4-dinitrophenyl hydrazine) method. The carotenoid extract R1ex scavenged 40.2% DPPH radicals compared to beta-carotene (31.7%) at a concentration of 0.5 mg ml(-1). The intracellular level of protein oxidation in mutant R1DeltacrtB, which does not contain carotenoid, was 0.0212 mmol mg(-1) protein which is significantly greater than that in the wild type (0.0169 mmol mg(-1) protein) following the treatment with H(2)O(2). The purified major carotenoid product (deinoxanthin) from the wild type showed a greater inhibition of oxidative damage in bovine serum albumin than lycopene or lutein. CONCLUSIONS Carotenoids prevent protein oxidation and contribute to the resistance to cell damage in D. radiodurans. SIGNIFICANCE AND IMPACT OF THE STUDY Our results provide the evidence that carotenoids can protect proteins in D. radiodurans against oxidative stress.
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Affiliation(s)
- B Tian
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
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2′-Methyl and 1′-xylosyl derivatives of 2′-hydroxyflexixanthin are major carotenoids of Hymenobacter species. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.03.117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Sun Z, Shen S, Wang C, Wang H, Hu Y, Jiao J, Ma T, Tian B, Hua Y. A novel carotenoid 1,2-hydratase (CruF) from two species of the non-photosynthetic bacterium Deinococcus. MICROBIOLOGY-SGM 2009; 155:2775-2783. [PMID: 19443548 DOI: 10.1099/mic.0.027623-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A novel carotenoid 1,2-hydratase (CruF) responsible for the C-1',2' hydration of gamma-carotene was identified in the non-photosynthetic bacteria Deinococcus radiodurans R1 and Deinococcus geothermalis DSM 11300. Gene expression and disruption experiments demonstrated that dr0091 and dgeo2309 encode CruF in D. radiodurans and D. geothermalis, respectively. Their homologues were also found in the genomes of cyanobacteria, and exhibited little homology to the hydroxyneurosporene synthase (CrtC) proteins found mainly in photosynthetic bacteria. Phylogenetic analysis showed that CruF homologues form a separate family, which is evolutionarily distant from the known CrtC family.
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Affiliation(s)
- Zongtao Sun
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, 310029 Hangzhou, China
| | - Shaochuan Shen
- State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Chemical Engineering and Materials Science, Zhejiang University of Technology, 310032 Hangzhou, China.,Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, 310029 Hangzhou, China
| | - Chao Wang
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, 310029 Hangzhou, China
| | - Hu Wang
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, 310029 Hangzhou, China
| | - Yaping Hu
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, 310029 Hangzhou, China
| | - Jiandong Jiao
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, 310029 Hangzhou, China
| | - Tingting Ma
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, 310029 Hangzhou, China
| | - Bing Tian
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, 310029 Hangzhou, China
| | - Yuejin Hua
- Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, 310029 Hangzhou, China
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