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de Groot A, Blanchard L. DNA repair and oxidative stress defense systems in radiation-resistant Deinococcus murrayi. Can J Microbiol 2023; 69:416-431. [PMID: 37552890 DOI: 10.1139/cjm-2023-0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Deinococcus murrayi is a bacterium isolated from hot springs in Portugal, and named after Dr. Robert G.E. Murray in recognition of his research on the genus Deinococcus. Like other Deinococcus species, D. murrayi is extremely resistant to ionizing radiation. Repair of massive DNA damage and limitation of oxidative protein damage are two important factors contributing to the robustness of Deinococcus bacteria. Here, we identify, among others, the DNA repair and oxidative stress defense proteins in D. murrayi, and highlight special features of D. murrayi. For DNA repair, D. murrayi does not contain a standalone uracil-DNA glycosylase (Ung), but it encodes a protein in which Ung is fused to a DNA photolyase domain (PhrB). UvrB and UvrD contain large insertions corresponding to inteins. One of its endonuclease III enzymes lacks a [4Fe-4S] cluster. Deinococcus murrayi possesses a homolog of the error-prone DNA polymerase IV. Concerning oxidative stress defense, D. murrayi encodes a manganese catalase in addition to a heme catalase. Its organic hydroperoxide resistance protein Ohr is atypical because the redox active cysteines are present in a CXXC motif. These and other characteristics of D. murrayi show further diversity among Deinococcus bacteria with respect to resistance-associated mechanisms.
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Affiliation(s)
- Arjan de Groot
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13115, France
| | - Laurence Blanchard
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13115, France
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2
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Li Y, Chen Z, Zhang Y, Wang Z, Zhang C, Deng Z, Huang L, Wang X, Fan J, Zhou S. Response of partial nitritation and denitrification processes to high levels of free ammonia in a pilot mature landfill leachate treatment system: Stability and microbial community dynamics. BIORESOURCE TECHNOLOGY 2023; 387:129571. [PMID: 37506935 DOI: 10.1016/j.biortech.2023.129571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/16/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
The high levels of free ammonia (FA) challenge the application of partial nitritation (PN) and denitrification (DN) in the treatment of ammonia-rich wastewater. This study explored the impact of high levels of FA on the PN and DN stability and microbial community dynamics. By reducing reflux and increasing influent load, the concentrations of FA in PN and DN reactors increased from 28.9 mg/L and 140.0 mg/L to 1099.8 mg/L and 868.4 mg/L, respectively. During this process, the performance of PN and DN remained stable. The microbial analysis revealed that the Nitrosomonas exhibited strong tolerance to high levels of FA, and its relative abundance was positively correlated with amoABC (R2 0.984) and hao (R2 0.999) genes. The increase in microbial diversity could enhance the resistance ability of PN against the FA impact. In contrast, high levels of FA had scant influence on the microbial community and performance of DN.
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Affiliation(s)
- Yonggan Li
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China
| | - Zhenguo Chen
- School of Environment, South China Normal University, Guangzhou 510006, China
| | - Yangzhong Zhang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China
| | - Zhiyu Wang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China
| | - Chuchu Zhang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China
| | - Zexi Deng
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China
| | - Linxiang Huang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China
| | - Xiaojun Wang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China; Hua an Biotech Co., Ltd., Foshan 528300, China.
| | - Junhao Fan
- Hua an Biotech Co., Ltd., Foshan 528300, China
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A Novel Glycoside Hydrolase DogH Utilizing Soluble Starch to Maltose Improve Osmotic Tolerance in Deinococcus radiodurans. Int J Mol Sci 2023; 24:ijms24043437. [PMID: 36834856 PMCID: PMC9967864 DOI: 10.3390/ijms24043437] [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: 12/26/2022] [Revised: 01/25/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
Deinococcus radiodurans is a microorganism that can adjust, survive or thrive in hostile conditions and has been described as "the strongest microorganism in the world". The underlying mechanism behind the exceptional resistance of this robust bacterium still remains unclear. Osmotic stress, caused by abiotic stresses such as desiccation, salt stress, high temperatures and freezing, is one of the main stresses suffered by microorganisms, and it is also the basic response pathway by which organisms cope with environmental stress. In this study, a unique trehalose synthesis-related gene, dogH (Deinococcus radiodurans orphan glycosyl hydrolase-like family 10), which encodes a novel glycoside hydrolase, was excavated using a multi-omics combination method. The content accumulation of trehalose and its precursors under hypertonic conditions was quantified by HPLC-MS. Ours results showed that the dogH gene was strongly induced by sorbitol and desiccation stress in D. radiodurans. DogH glycoside hydrolase hydrolyzes α-1,4-glycosidic bonds by releasing maltose from starch in the regulation of soluble sugars, thereby increasing the concentration of TreS (trehalose synthase) pathway precursors and trehalose biomass. The maltose and alginate content in D. radiodurans amounted to 48 μg mg protein-1 and 45 μg mg protein-1, respectively, which were 9 and 28 times higher than those in E. coli, respectively. The accumulation of greater intracellular concentrations of osmoprotectants may be the true reason for the higher osmotic stress tolerance of D. radiodurans.
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Xu L, Chen Y, Wang Z, Zhang Y, He Y, Zhang A, Chen H, Xue G. Discovering dominant ammonia assimilation: Implication for high-strength nitrogen removal in full scale biological treatment of landfill leachate. CHEMOSPHERE 2023; 312:137256. [PMID: 36395888 DOI: 10.1016/j.chemosphere.2022.137256] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/14/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Landfill leachate containing high-strength nitrogen is generated in domestic waste landfilling. The integration of anoxic and aerobic process (AO) based on nitrification and denitrification, has been a mainstream process of biological nitrogen removal (BNR). But the high-strength organics as well as aerobic effluent reflux might change the biochemical environment designed and operated as AO. In view of the nitrogen balance in a full scale landfill leachate treatment plant with two-stage AO, we found that approximately 90% removal of total nitrogen (TN) and ammonia (NH4+-N) focused on primary anoxic and aerobic stage. Meanwhile, the less nitrate and nitrite in the aerobic effluent were incapable of sustaining denitrification or anaerobic ammonia oxidation (anammox). The high reflux flow from aerobic to anoxic process enabled the similar microbial community and functional genes in anoxic and aerobic process units. However, the functional genes involving ammonia assimilation in all process units showcased the highest abundance compared to those correlated with other BNR pathways, including nitrification and denitrification, assimilatory and dissimilatory nitrate reduction, nitrogen fixation and anammox. The ammonia assimilation dominated the removals of TN and NH4+-N, rather than other BNR mechanism. The insight of dominant ammonia assimilation is favorable for illustrating the authentic BNR mechanism of landfill leachate in AO, thereby guiding the optimization of engineering design and operation.
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Affiliation(s)
- Lei Xu
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Yuting Chen
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Zheng Wang
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Yu Zhang
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Yueling He
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Ai Zhang
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Hong Chen
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Gang Xue
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200000, China.
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Lee JH, Jung JH, Kim MK, Lim S. Deinococcus taeanensis sp. nov., a Radiation-Resistant Bacterium Isolated from a Coastal Dune. Curr Microbiol 2022; 79:334. [PMID: 36161362 PMCID: PMC9510100 DOI: 10.1007/s00284-022-03044-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/14/2022] [Indexed: 11/28/2022]
Abstract
A Gram-stain-negative, nonspore-forming, nonmotile, aerobic, rod-shaped, and very pale orange-colored bacterial strain, designated TS293T, was isolated from a sand sample obtained from a coastal dune after exposure to 3kGy of gamma (γ)-radiation. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the isolate was a member of the genus Deinococcus and clustered with D. deserti VCD115T. The genome of strain TS293T was 4.62 Mbp long (68.2% G + C content and 4124 predicted genes) divided into a 2.86Mb main chromosome and five plasmids. Many genes considered to be important to the γ-radiation and oxidative stress resistance of Deinococcus were conserved in TS293T, but genome features that could differentiate TS293T from D. deserti and D. radiodurans, the type species of the Deinococcus genus, were also detected. Strain TS293T showed resistance to γ-radiation with D10 values (i.e., the dose required to reduce the bacterial population by tenfold) of 3.1kGy. The predominant fatty acids of strain TS293T were summed feature 3 (C16:1ω6c and/or C16:1ω7c) and iso-C16:0. The major polar lipids were two unidentified phosphoglycolipids and one unidentified glycolipid. The main respiratory quinone was menaquinone-8. Based on the phylogenetic, genomic, physiological, and chemotaxonomic characteristics, strain TS293T represents a novel species, for which the name Deinococcus taeanensis sp. nov. is proposed. The type strain is TS293T (= KCTC 43191T = JCM 34027T).
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Affiliation(s)
- Ji Hee Lee
- Division of Pathogen Resource Management, Korea Disease Control and Prevention Agency, Cheongju, 28160, Republic of Korea
| | - Jong-Hyun Jung
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Min-Kyu Kim
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Sangyong Lim
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea.
- Department of Radiation Science, University of Science and Technology, Daejeon, 34113, Republic of Korea.
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Xia W, Zong J, Zheng K, Wang Y, Zhang D, Guo S, Sun G. DgCspC gene overexpression improves cotton yield and tolerance to drought and salt stress comparison with wild-type plants. FRONTIERS IN PLANT SCIENCE 2022; 13:985900. [PMID: 36147229 PMCID: PMC9485673 DOI: 10.3389/fpls.2022.985900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
Drought and high salinity are key limiting factors for cotton quality and yield. Therefore, research is increasingly focused on mining effective genes to improve the stress resistance of cotton. Few studies have demonstrated that bacterial Cold shock proteins (Csps) overexpression can enhance plants stress tolerance. Here, we first identified and cloned a gene DgCspC encoding 88 amino acids (aa) with an open reading frame (ORF) of 264 base pairs (bp) from a Deinococcus gobiensis I-0 with high resistance to strong radiation, drought, and high temperature. In this study, heterologous expression of DgCspC promoted cotton growth, as exhibited by larger leaf size and higher plant height than the wild-type plants. Moreover, transgenic cotton lines showed higher tolerance to drought and salts stresses than wild-type plants, as revealed by susceptibility phenotype and physiological indexes. Furthermore, the enhanced stresses tolerance was attributed to high capacity of cellular osmotic regulation and ROS scavenging resulted from DgCspC expression modulating relative genes upregulated to cause proline and betaine accumulation. Meanwhile, photosynthetic efficiency and yield were significantly higher in the transgenic cotton than in the wild-type control under field conditions. This study provides a newly effective gene resource to cultivate new cotton varieties with high stresses resistance and yield.
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Affiliation(s)
- Wenwen Xia
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- Hainan Yazhou Bay Seed Lab, Sanya, China
| | - Jiahang Zong
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agriculture, Xinjiang Agricultural University, Urumqi, China
| | - Kai Zheng
- College of Agriculture, Xinjiang Agricultural University, Urumqi, China
| | - Yuan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dongling Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sandui Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guoqing Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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Thiol Reductases in Deinococcus Bacteria and Roles in Stress Tolerance. Antioxidants (Basel) 2022; 11:antiox11030561. [PMID: 35326211 PMCID: PMC8945050 DOI: 10.3390/antiox11030561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/11/2022] [Accepted: 03/13/2022] [Indexed: 12/10/2022] Open
Abstract
Deinococcus species possess remarkable tolerance to extreme environmental conditions that generate oxidative damage to macromolecules. Among enzymes fulfilling key functions in metabolism regulation and stress responses, thiol reductases (TRs) harbour catalytic cysteines modulating the redox status of Cys and Met in partner proteins. We present here a detailed description of Deinococcus TRs regarding gene occurrence, sequence features, and physiological functions that remain poorly characterised in this genus. Two NADPH-dependent thiol-based systems are present in Deinococcus. One involves thioredoxins, disulfide reductases providing electrons to protein partners involved notably in peroxide scavenging or in preserving protein redox status. The other is based on bacillithiol, a low-molecular-weight redox molecule, and bacilliredoxin, which together protect Cys residues against overoxidation. Deinococcus species possess various types of thiol peroxidases whose electron supply depends either on NADPH via thioredoxins or on NADH via lipoylated proteins. Recent data gained on deletion mutants confirmed the importance of TRs in Deinococcus tolerance to oxidative treatments, but additional investigations are needed to delineate the redox network in which they operate, and their precise physiological roles. The large palette of Deinococcus TR representatives very likely constitutes an asset for the maintenance of redox homeostasis in harsh stress conditions.
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Molecular Identification of Keratinase DgokerA from Deinococcus gobiensis for Feather Degradation. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12010464] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Keratin is a tough fibrous structural protein that is difficult to digest with pepsin and trypsin because of the presence of a large number of disulfide bonds. Keratin is widely found in agricultural waste. In recent years, especially, the development of the poultry industry has resulted in a large accumulation of feather keratin resources, which seriously pollute the environment. Keratinase can specifically attack disulfide bridges in keratin, converting them from complex to simplified forms. The keratinase thermal stability has drawn attention to various biotechnological industries. It is significant to identify keratinases and improve their thermostability from microorganism in extreme environments. In this study, the keratinases DgoKerA was identified in Deinococcus gobiensis I-0 from the Gobi desert. The amino acid sequence analysis revealed that DgoKerA was 58.68% identical to the keratinase MtaKerA from M. thermophila WR-220 and 40.94% identical to the classical BliKerA sequence from B. licheniformis PWD-1. In vitro enzyme activity analysis showed that DgoKerA exhibited an optimum temperature of 60 °C, an optimum pH of 7 and a specific enzyme activity of 51147 U/mg. DgoKerA can degrade intact feathers at 60 °C and has good potential for industrial applications. The molecular modification of DgoKerA was also carried out using site-directed mutagenesis, in which the mutant A350S enzyme activity was increased by nearly 30%, and the results provide a theoretical basis for the development and optimization of keratinase applications.
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Guo J, Song X, Zheng C, Sun S, Zhuang B, Tao B. Transcriptome analysis and identification of candidate genes involved in glyphosate resistance in the fungus Fusarium verticillioides. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2021; 56:658-669. [PMID: 34218722 DOI: 10.1080/03601234.2021.1936990] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Glyphosate is a broad-spectrum herbicide that has been widely used for nonselective weed control in soybean fields. In the present study, RNA-seq of an Fusarium verticillioides isolate exhibiting resistance to 120 mM glyphosate revealed gene expression occurring in the presence of glyphosate and led to the identification and screening of candidate genes. A transcriptome analysis revealed 5,548 and 5,361 differentially expressed genes (DEGs) in the glyphosate resistant (GR) Fusarium verticillioides isolate treated with 45 and 90 mM glyphosate, respectively. The gene ontology (GO) pathways associated with these differentially expressed genes primarily included metabolic process, amine metabolic process, cellular aromatic compound metabolism and stress response. The primary Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways included biosynthesis of secondary metabolites, carbon metabolism, glycolysis/gluconeogenesis, and nitrogen metabolism. The glyphosate degradation-related gene fv04, which belongs to the 3-isopropylalate dehydratase of the aconitase superfamily, was cloned to generate the prokaryotic expression vector pET-29b-fv04, which could be stably expressed in E. coli and promote the degradation of 52.3% of 500 mg/L glyphosate in 72 h. The results of the present study provide new ideas and insights for the acquisition of glyphosate resistance resources.
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Affiliation(s)
- Jing Guo
- College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Xiuli Song
- Lingnan Normal University, Zhan Jiang, Guang Dong, PR China
| | - Caiyue Zheng
- College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Shiqi Sun
- College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Baolong Zhuang
- College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Bo Tao
- College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang, PR China
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Ma F, Zhou H, Yang Z, Wang C, An Y, Ni L, Liu M, Wang Y, Yu L. Gene expression profile analysis and target gene discovery of Mycobacterium tuberculosis biofilm. Appl Microbiol Biotechnol 2021; 105:5123-5134. [PMID: 34125278 DOI: 10.1007/s00253-021-11361-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 04/27/2021] [Accepted: 05/20/2021] [Indexed: 10/21/2022]
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (M. tuberculosis) is a fatal infectious disease to human health, and the drug tolerance and immune evasion of M. tuberculosis were reported to be related to its biofilm formation; however, the difficulty of M. tuberculosis biofilm culture and its unknown global mechanism impede its further research. Here, we developed a modified in vitro M. tuberculosis biofilm model with shorter culture time. Then we used Illumina RNA-seq technology to determine the global gene expression profile of M. tuberculosis H37Rv biofilms. Over 437 genes are expressed at significantly different levels in biofilm cells than in planktonic cells; among them, 153 were downregulated and 284 were upregulated. Go enrichment analysis and KEGG pathway analysis showed that genes involved in biosynthesis and metabolism of sulfur metabolism, steroid degradation, atrazine degradation, mammalian cell entry protein complex, etc. are involved in M. tuberculosis biofilm cells. Especially, ATP-binding cassette (ABC) transporters Rv1217c and Rv1218c were significantly upregulated in biofilm, whereas efflux pump inhibitors (EPIs) piperine and 1-(1-naphthylmethyl)-piperazine (NMP) inhibited biofilm formation and the expression of the Rv1217c and Rv1218c genes in a concentration-dependent manner, respectively, indicating Rv1217c and Rv1218c are potential target genes of M. tuberculosis biofilm. This study is the first RNA-Seq-based transcriptome profiling of M. tuberculosis biofilms and provides insights into a potential strategy for M. tuberculosis biofilm inhibition. KEY POINTS: • Characterize M. tuberculosis transcriptomes in biofilm cells by RNA-seq. • Inhibit the expression of Rv1217c and Rv1218c repressed biofilm formation.
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Affiliation(s)
- Fangxue Ma
- Key Laboratory for Zoonoses Research, Ministry of Education, Institute of Zoonosis, Department of Infectious Diseases, First Hospital of Jilin University, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Hong Zhou
- Key Laboratory for Zoonoses Research, Ministry of Education, Institute of Zoonosis, Department of Infectious Diseases, First Hospital of Jilin University, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Zhiqiang Yang
- Institute of Biomedical Sciences, School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Chao Wang
- Department of Immunology, Binzhou Medical University, Yantai, 264000, China
| | - Yanan An
- Department of Physiology, Binzhou Medical University, Yantai, 264000, China
| | - Lihui Ni
- Key Laboratory for Zoonoses Research, Ministry of Education, Institute of Zoonosis, Department of Infectious Diseases, First Hospital of Jilin University, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Mingyuan Liu
- Key Laboratory for Zoonoses Research, Ministry of Education, Institute of Zoonosis, Department of Infectious Diseases, First Hospital of Jilin University, College of Veterinary Medicine, Jilin University, Changchun, 130062, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Yang Wang
- Key Laboratory for Zoonoses Research, Ministry of Education, Institute of Zoonosis, Department of Infectious Diseases, First Hospital of Jilin University, College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
| | - Lu Yu
- Key Laboratory for Zoonoses Research, Ministry of Education, Institute of Zoonosis, Department of Infectious Diseases, First Hospital of Jilin University, College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
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11
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Liu Y, Zhang C, Wang Z, Lin M, Wang J, Wu M. Pleiotropic roles of late embryogenesis abundant proteins of Deinococcus radiodurans against oxidation and desiccation. Comput Struct Biotechnol J 2021; 19:3407-3415. [PMID: 34188783 PMCID: PMC8213827 DOI: 10.1016/j.csbj.2021.05.051] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/30/2021] [Accepted: 05/30/2021] [Indexed: 11/30/2022] Open
Abstract
Deinococcus radiodurans, an important extremophile, possesses extraordinary stress tolerance ability against lethal and mutagenic effects of DNA-damaging agents, such as γ-rays, ultraviolet, oxidation, and desiccation. How global regulators of this bacterium function in response to oxidation and desiccation has been an intense topic as elucidating such mechanisms may help to facilitate some beneficial applications in agriculture or medicine. Particularly, a variety of functional proteins have been characterized for D. radiodurans' behaviors under abiotic stresses. Interestingly, a group of Late Embryogenesis Abundant proteins (LEAs) in D. radiodurans have been characterized both biochemically and physiologically, which are shown indispensable for stabilizing crucial metabolic enzymes in a chaperone-like manner and thereby maintaining the metal ion homeostasis under oxidation and desiccation. The rapid progress in understanding deinococcal LEA proteins has substantially extended their functions in both plants and animals. Herein, we discuss the latest studies of radiodurans LEA proteins ranging from the classification to structures to functions. Importantly, the harnessing of these proteins may have unlimited potential for biotechnology, engineering and disease treatments.
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Affiliation(s)
- Yingying Liu
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58203-9037, USA
| | - Chen Zhang
- Laboratory of Microbiology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Zhihan Wang
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58203-9037, USA
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Min Wu
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58203-9037, USA
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12
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Zandalinas SI, Sengupta S, Fritschi FB, Azad RK, Nechushtai R, Mittler R. The impact of multifactorial stress combination on plant growth and survival. THE NEW PHYTOLOGIST 2021; 230:1034-1048. [PMID: 33496342 PMCID: PMC8048544 DOI: 10.1111/nph.17232] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/17/2021] [Indexed: 05/08/2023]
Abstract
Climate change-driven extreme weather events, combined with increasing temperatures, harsh soil conditions, low water availability and quality, and the introduction of many man-made pollutants, pose a unique challenge to plants. Although our knowledge of the response of plants to each of these individual conditions is vast, we know very little about how a combination of many of these factors, occurring simultaneously, that is multifactorial stress combination, impacts plants. Seedlings of wild-type and different mutants of Arabidopsis thaliana plants were subjected to a multifactorial stress combination of six different stresses, each applied at a low level, and their survival, physiological and molecular responses determined. Our findings reveal that, while each of the different stresses, applied individually, had a negligible effect on plant growth and survival, the accumulated impact of multifactorial stress combination on plants was detrimental. We further show that the response of plants to multifactorial stress combination is unique and that specific pathways and processes play a critical role in the acclimation of plants to multifactorial stress combination. Taken together our findings reveal that further polluting our environment could result in higher complexities of multifactorial stress combinations that in turn could drive a critical decline in plant growth and survival.
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Affiliation(s)
- Sara I. Zandalinas
- Division of Plant SciencesCollege of Agriculture Food and Natural Resources and Interdisciplinary Plant GroupChristopher S. Bond Life Sciences CenterUniversity of Missouri1201 Rollins StColumbiaMO65211USA
| | - Soham Sengupta
- Department of Biological Sciences and BioDiscovery InstituteCollege of ScienceUniversity of North Texas1155 Union Circle #305220DentonTX76203‐5017USA
| | - Felix B. Fritschi
- Division of Plant SciencesCollege of Agriculture Food and Natural Resources and Interdisciplinary Plant GroupChristopher S. Bond Life Sciences CenterUniversity of Missouri1201 Rollins StColumbiaMO65211USA
| | - Rajeev K. Azad
- Department of Biological Sciences and BioDiscovery InstituteCollege of ScienceUniversity of North Texas1155 Union Circle #305220DentonTX76203‐5017USA
- Department of MathematicsUniversity of North TexasDentonTX76203USA
| | - Rachel Nechushtai
- The Alexander Silberman Institute of Life ScienceThe Hebrew University of JerusalemEdmond J. Safra Campus at Givat RamJerusalem91904Israel
| | - Ron Mittler
- Division of Plant SciencesCollege of Agriculture Food and Natural Resources and Interdisciplinary Plant GroupChristopher S. Bond Life Sciences CenterUniversity of Missouri1201 Rollins StColumbiaMO65211USA
- Department of SurgeryUniversity of Missouri School of MedicineChristopher S. Bond Life Sciences Center University of Missouri1201 Rollins StColumbiaMO65211USA
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13
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Obulisamy PK, Mehariya S. Polyhydroxyalkanoates from extremophiles: A review. BIORESOURCE TECHNOLOGY 2021; 325:124653. [PMID: 33465644 DOI: 10.1016/j.biortech.2020.124653] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/27/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
Polyhydroxyalkanoates (PHAs) are group monomers/heteropolymers that are biodegradable and widely used in biomedical applications. They are considered as alternatives to fossil derived polymers and accumulated by microbes including extremophilic archaea as energy storage inclusions under nutrient limitations. The use of extremophilic archaea for PHA production is an economically viable option for conventional aerobic processes, but less is known about their pathways and PHA accumulation capacities. This review summarized: (a) specific adaptive mechanisms towards extreme environments by extremophiles and specific role of PHAs; (b) understanding of PHA synthesis/metabolism in archaea and specific functional genes; (c) genetic engineering and process engineering approaches required for high-rate PHA production using extremophilic archaea. To conclude, the future studies are suggested to understand the membrane lipids and PHAs accumulation to explain the adaptation mechanism of extremophiles and exploiting it for commercial production of PHAs.
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Affiliation(s)
| | - Sanjeet Mehariya
- Department of Engineering, University of Campania "Luigi Vanvitelli", Real Casa dell'Annunziata, Italy
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14
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Kumar J, Ghosh P, Kumar A. Ultraviolet-B Radiation Stress-Induced Toxicity and Alterations in Proteome of Deinococcus radiodurans. Microb Physiol 2020; 31:1-15. [PMID: 33341800 DOI: 10.1159/000512018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/27/2020] [Indexed: 11/19/2022]
Abstract
Deinococcus radiodurans is a polyextremophilic bacterium capable to survive and grow at high doses of ionizing radiation. Besides resistance to ionizing radiation, the bacterium is also resistant to toxic chemicals and desiccation. This study deals with the effects of non-ionizing radiation (ultraviolet-B) on survival, alterations in proteomic profile, and gene expression in D. radiodurans. Exposure of culture to UV-B caused decrease in the percentage survival with increasing duration, complete killing occurred after 16 h. D. radiodurans also showed enhancement in the generation of reactive oxygen species and activities of antioxidative enzymes. Separation of proteins by 2-dimensional gel electrophoresis revealed major changes in number and abundance of different proteins. Twenty-eight differentially abundant protein spots were identified by MALDI-TOF MS/MS analysis and divided into 8 groups including unknown proteins. Gene expression of a few identified proteins was also analyzed employing qRT-PCR, which showed differential expression corresponding to the respective proteins. In silico analysis of certain hypothetical proteins (HPs) suggested that these are novel and as yet not reported from D. radiodurans subjected to UV-B stress. These HPs may prove useful in future studies especially for assessing their significance in the adaptation and management of stress responses against UV-B stress.
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Affiliation(s)
- Jay Kumar
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Paushali Ghosh
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Ashok Kumar
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India,
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15
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Díaz-Riaño J, Posada L, Acosta IC, Ruíz-Pérez C, García-Castillo C, Reyes A, Zambrano MM. Computational search for UV radiation resistance strategies in Deinococcus swuensis isolated from Paramo ecosystems. PLoS One 2019; 14:e0221540. [PMID: 31790419 PMCID: PMC6886795 DOI: 10.1371/journal.pone.0221540] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/15/2019] [Indexed: 02/07/2023] Open
Abstract
Ultraviolet radiation (UVR) is widely known as deleterious for many organisms since it can cause damage to biomolecules either directly or indirectly via the formation of reactive oxygen species. The goal of this study was to analyze the capacity of high-mountain Espeletia hartwegiana plant phyllosphere microorganisms to survive UVR and to identify genes related to resistance strategies. A strain of Deinococcus swuensis showed a high survival rate of up to 60% after UVR treatment at 800J/m2 and was used for differential expression analysis using RNA-seq after exposing cells to 400J/m2 of UVR (with >95% survival rate). Differentially expressed genes were identified using the R-Bioconductor package NOISeq and compared with other reported resistance strategies reported for this genus. Genes identified as being overexpressed included transcriptional regulators and genes involved in protection against damage by UVR. Non-coding (nc)RNAs were also differentially expressed, some of which have not been previously implicated. This study characterized the immediate radiation response of D. swuensis and indicates the involvement of ncRNAs in the adaptation to extreme environmental conditions.
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Affiliation(s)
- Jorge Díaz-Riaño
- Corporación Corpogen Research Center, Bogotá D.C, Colombia
- Research group in Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de Los Andes, Bogotá D.C, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de Los Andes, Bogotá D.C, Colombia
| | | | | | - Carlos Ruíz-Pérez
- Research group in Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de Los Andes, Bogotá D.C, Colombia
| | - Catalina García-Castillo
- Research group in Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de Los Andes, Bogotá D.C, Colombia
| | - Alejandro Reyes
- Research group in Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de Los Andes, Bogotá D.C, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de Los Andes, Bogotá D.C, Colombia
- Center of Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, United States of America
- * E-mail: (AR); (MMZ)
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16
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Lim S, Jung JH, Blanchard L, de Groot A. Conservation and diversity of radiation and oxidative stress resistance mechanisms in Deinococcus species. FEMS Microbiol Rev 2019; 43:19-52. [PMID: 30339218 PMCID: PMC6300522 DOI: 10.1093/femsre/fuy037] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 10/17/2018] [Indexed: 12/17/2022] Open
Abstract
Deinococcus bacteria are famous for their extreme resistance to ionising radiation and other DNA damage- and oxidative stress-generating agents. More than a hundred genes have been reported to contribute to resistance to radiation, desiccation and/or oxidative stress in Deinococcus radiodurans. These encode proteins involved in DNA repair, oxidative stress defence, regulation and proteins of yet unknown function or with an extracytoplasmic location. Here, we analysed the conservation of radiation resistance-associated proteins in other radiation-resistant Deinococcus species. Strikingly, homologues of dozens of these proteins are absent in one or more Deinococcus species. For example, only a few Deinococcus-specific proteins and radiation resistance-associated regulatory proteins are present in each Deinococcus, notably the metallopeptidase/repressor pair IrrE/DdrO that controls the radiation/desiccation response regulon. Inversely, some Deinococcus species possess proteins that D. radiodurans lacks, including DNA repair proteins consisting of novel domain combinations, translesion polymerases, additional metalloregulators, redox-sensitive regulator SoxR and manganese-containing catalase. Moreover, the comparisons improved the characterisation of several proteins regarding important conserved residues, cellular location and possible protein–protein interactions. This comprehensive analysis indicates not only conservation but also large diversity in the molecular mechanisms involved in radiation resistance even within the Deinococcus genus.
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Affiliation(s)
- Sangyong Lim
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
| | - Jong-Hyun Jung
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
| | | | - Arjan de Groot
- Aix Marseille Univ, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, France
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17
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Draft Genome Sequence of the Radioresistant Bacterium Deinococcus aerius TR0125, Isolated from the High Atmosphere above Japan. GENOME ANNOUNCEMENTS 2018; 6:6/9/e00080-18. [PMID: 29496828 PMCID: PMC5834321 DOI: 10.1128/genomea.00080-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Deinococcus aerius strain TR0125 is a bacterium isolated from the high atmosphere above Japan that shows strong resistance to desiccation, UV-C, and gamma radiation. Here, we report the draft genome sequence of D. aerius (4.5 Mb), which may provide useful genetic information supporting its biochemical features.
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18
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Jiang S, Wang J, Liu X, Liu Y, Guo C, Zhang L, Han J, Wu X, Xue D, Gomaa AE, Feng S, Zhang H, Chen Y, Ping S, Chen M, Zhang W, Li L, Zhou Z, Zuo K, Li X, Yang Y, Lin M. DrwH, a novel WHy domain-containing hydrophobic LEA5C protein from Deinococcus radiodurans, protects enzymatic activity under oxidative stress. Sci Rep 2017; 7:9281. [PMID: 28839181 PMCID: PMC5570939 DOI: 10.1038/s41598-017-09541-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 07/24/2017] [Indexed: 11/09/2022] Open
Abstract
Water stress and hypersensitive response (WHy) domain is typically found as a component of atypical late embryogenesis abundant (LEA) proteins closely associated with resistance to multiple stresses in numerous organisms. Several putative LEA proteins have been identified in Deinococcus bacteria; however their precise function remains unclear. This work reports the characterization of a Deinococcus-specific gene encoding a novel WHy domain-containing hydrophobic LEA5C protein (named DrwH) in D. radiodurans R1. The expression of the drwH gene was induced by oxidative and salinity stresses. Inactivation of this gene resulted in increased sensitivity to oxidative and salinity stresses as well as reduced activities of antioxidant enzymes. The WHy domain of the DrwH protein differs structurally from that of a previously studied bacterial LEA5C protein, dWHy1, identified as a gene product from an Antarctic desert soil metagenome library. Further analysis indicated that in E. coli, the function of DrwH is related to oxidative stress tolerance, whereas dWHy1 is associated with freezing-thawing stress tolerance. Under oxidative stress induced by H2O2, DrwH protected the enzymatic activities of malate dehydrogenase (MDH) and lactate dehydrogenase (LDH). These findings provide new insight into the evolutionary and survival strategies of Deinococcus bacteria under extreme environmental conditions.
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Affiliation(s)
- Shijie Jiang
- Key Lab of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China.,Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoli Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingying Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cui Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liwen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiahui Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoli Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dong Xue
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ahmed E Gomaa
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shuai Feng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Heng Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yun Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuzhen Ping
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ming Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhengfu Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kaijing Zuo
- Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xufeng Li
- Key Lab of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Yi Yang
- Key Lab of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
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19
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Nelson DR, Khraiwesh B, Fu W, Alseekh S, Jaiswal A, Chaiboonchoe A, Hazzouri KM, O'Connor MJ, Butterfoss GL, Drou N, Rowe JD, Harb J, Fernie AR, Gunsalus KC, Salehi-Ashtiani K. The genome and phenome of the green alga Chloroidium sp. UTEX 3007 reveal adaptive traits for desert acclimatization. eLife 2017. [PMID: 28623667 PMCID: PMC5509433 DOI: 10.7554/elife.25783] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
To investigate the phenomic and genomic traits that allow green algae to survive in deserts, we characterized a ubiquitous species, Chloroidium sp. UTEX 3007, which we isolated from multiple locations in the United Arab Emirates (UAE). Metabolomic analyses of Chloroidium sp. UTEX 3007 indicated that the alga accumulates a broad range of carbon sources, including several desiccation tolerance-promoting sugars and unusually large stores of palmitate. Growth assays revealed capacities to grow in salinities from zero to 60 g/L and to grow heterotrophically on >40 distinct carbon sources. Assembly and annotation of genomic reads yielded a 52.5 Mbp genome with 8153 functionally annotated genes. Comparison with other sequenced green algae revealed unique protein families involved in osmotic stress tolerance and saccharide metabolism that support phenomic studies. Our results reveal the robust and flexible biology utilized by a green alga to successfully inhabit a desert coastline. DOI:http://dx.doi.org/10.7554/eLife.25783.001 Single-celled green algae, also known as green microalgae, play an important role for the world’s ecosystems, in part, because they can harness energy from sunlight to produce carbon-rich compounds. Microalgae are also important for biotechnology and people have harnessed them to make food, fuel and medicines. Green microalgae live in many types of habitats from streams to oceans, and they can also be found on the land, including in deserts. Like plants that live in the desert, these microalgae have likely evolved specific traits that allow them to live in these hot and dry regions. Yet, fewer scientists have studied microalgae compared to land plants, and until now it was not well understood how microalgae could survive in the desert. Nelson et al. analyzed green microalgae from different locations around the United Arab Emirates and found that one microalga, known as Chloroidium, is one of the most dominant algae in this area. This included samples from beaches, mangroves, desert oases, buildings and public fresh water sources. Chloroidium has a unique set of genes and proteins and grew particularly well in freshwater and saltwater. Rather than just harnessing sunlight, the microalgae were able to consume over 40 different varieties of carbon sources to produce energy. The microalgae also accumulated oily molecules with a similar composition to palm oil, which may help this species to survive in desert regions. A next step will be to develop biotechnological assets based on the information obtained. In the future, microalgae could be used to make an oil that represents an alternative to palm oil; this would reduce the demand for palm tree plantations, which pose a major threat to the natural environment. Moreover, understanding how microalgae can colonize a desert region will help us to understand the effects of climate change in the region. DOI:http://dx.doi.org/10.7554/eLife.25783.002
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Affiliation(s)
- David R Nelson
- Laboratory of Algal, Synthetic, and Systems Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Basel Khraiwesh
- Laboratory of Algal, Synthetic, and Systems Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Weiqi Fu
- Laboratory of Algal, Synthetic, and Systems Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Ashish Jaiswal
- Laboratory of Algal, Synthetic, and Systems Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Amphun Chaiboonchoe
- Laboratory of Algal, Synthetic, and Systems Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Khaled M Hazzouri
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Matthew J O'Connor
- Core Technology Platform, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Glenn L Butterfoss
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Nizar Drou
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Jillian D Rowe
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Jamil Harb
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.,Department of Biology and Biochemistry, Birzeit University, Birzeit, Palestine
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Kristin C Gunsalus
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Center for Genomics and Systems Biology and Department of Biology, New York University, New York, United States
| | - Kourosh Salehi-Ashtiani
- Laboratory of Algal, Synthetic, and Systems Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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20
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Ranawat P, Rawat S. Radiation resistance in thermophiles: mechanisms and applications. World J Microbiol Biotechnol 2017; 33:112. [DOI: 10.1007/s11274-017-2279-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 04/26/2017] [Indexed: 12/28/2022]
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21
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Gutiérrez-Preciado A, Vargas-Chávez C, Reyes-Prieto M, Ordoñez OF, Santos-García D, Rosas-Pérez T, Valdivia-Anistro J, Rebollar EA, Saralegui A, Moya A, Merino E, Farías ME, Latorre A, Souza V. The genomic sequence of Exiguobacterium chiriqhucha str. N139 reveals a species that thrives in cold waters and extreme environmental conditions. PeerJ 2017; 5:e3162. [PMID: 28439458 PMCID: PMC5399880 DOI: 10.7717/peerj.3162] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 03/08/2017] [Indexed: 02/05/2023] Open
Abstract
We report the genome sequence of Exiguobacterium chiriqhucha str. N139, isolated from a high-altitude Andean lake. Comparative genomic analyses of the Exiguobacterium genomes available suggest that our strain belongs to the same species as the previously reported E. pavilionensis str. RW-2 and Exiguobacterium str. GIC 31. We describe this species and propose the chiriqhucha name to group them. 'Chiri qhucha' in Quechua means 'cold lake', which is a common origin of these three cosmopolitan Exiguobacteria. The 2,952,588-bp E. chiriqhucha str. N139 genome contains one chromosome and three megaplasmids. The genome analysis of the Andean strain suggests the presence of enzymes that confer E. chiriqhucha str. N139 the ability to grow under multiple environmental extreme conditions, including high concentrations of different metals, high ultraviolet B radiation, scavenging for phosphorous and coping with high salinity. Moreover, the regulation of its tryptophan biosynthesis suggests that novel pathways remain to be discovered, and that these pathways might be fundamental in the amino acid metabolism of the microbial community from Laguna Negra, Argentina.
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Affiliation(s)
- Ana Gutiérrez-Preciado
- Unidad de Genética Evolutiva, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Calle Catedrático José Beltrán Martínez, Paterna, Valencia, Spain
- Current affiliation: Ecologie Systématique Evolution, CNRS, AgroParisTech, Université Paris Sud (Paris XI), Orsay, France
| | - Carlos Vargas-Chávez
- Unidad de Genética Evolutiva, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Calle Catedrático José Beltrán Martínez, Paterna, Valencia, Spain
| | - Mariana Reyes-Prieto
- Unidad de Genética Evolutiva, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Calle Catedrático José Beltrán Martínez, Paterna, Valencia, Spain
| | - Omar F. Ordoñez
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Belgrano y Pasaje Caseros, San Miguel de Tucumán, Argentina
| | - Diego Santos-García
- Unidad de Genética Evolutiva, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Calle Catedrático José Beltrán Martínez, Paterna, Valencia, Spain
- Current affiliation: Department of Entomology, Hebrew University of Jerusalem, Rehovot, Israel
| | - Tania Rosas-Pérez
- Unidad de Genética Evolutiva, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Calle Catedrático José Beltrán Martínez, Paterna, Valencia, Spain
| | - Jorge Valdivia-Anistro
- Carrera de Biología, Faculta de Estudios Superiores Zaragoza, UNAM, Mexico City, Mexico
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México coyoacan, Mexico City, México
| | - Eria A. Rebollar
- Department of Biology, James Madison University, Harrisonburg, VI, United States of America
| | - Andrés Saralegui
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Andrés Moya
- Unidad de Genética Evolutiva, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Calle Catedrático José Beltrán Martínez, Paterna, Valencia, Spain
| | - Enrique Merino
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - María Eugenia Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Belgrano y Pasaje Caseros, San Miguel de Tucumán, Argentina
| | - Amparo Latorre
- Unidad de Genética Evolutiva, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Calle Catedrático José Beltrán Martínez, Paterna, Valencia, Spain
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México coyoacan, Mexico City, México
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22
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Mittler R. ROS Are Good. TRENDS IN PLANT SCIENCE 2017; 22:11-19. [PMID: 27666517 DOI: 10.1016/j.tplants.2016.08.002] [Citation(s) in RCA: 1415] [Impact Index Per Article: 202.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 07/29/2016] [Accepted: 08/07/2016] [Indexed: 05/17/2023]
Abstract
Reactive oxygen species (ROS) are thought to play a dual role in plant biology. They are required for many important signaling reactions, but are also toxic byproducts of aerobic metabolism. Recent studies revealed that ROS are necessary for the progression of several basic biological processes including cellular proliferation and differentiation. Moreover, cell death-that was previously thought to be the outcome of ROS directly killing cells by oxidation, in other words via oxidative stress-is now considered to be the result of ROS triggering a physiological or programmed pathway for cell death. This Opinion focuses on the possibility that ROS are beneficial to plants, supporting cellular proliferation, physiological function, and viability, and that maintaining a basal level of ROS in cells is essential for life.
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Affiliation(s)
- Ron Mittler
- Department of Biological Sciences and BioDiscovery Institute, College of Arts and Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA.
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23
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McClung DJ, Calixto A, Mosera MN, Kumar R, Neidle EL, Elliott KT. Novel heterologous bacterial system reveals enhanced susceptibility to DNA damage mediated by yqgF, a nearly ubiquitous and often essential gene. MICROBIOLOGY-SGM 2016; 162:1808-1821. [PMID: 27527105 DOI: 10.1099/mic.0.000355] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite its presence in most bacteria, yqgF remains one of only 13 essential genes of unknown function in Escherichia coli. Predictions of YqgF function often derive from sequence similarity to RuvC, the canonical Holliday junction resolvase. To clarify its role, we deleted yqgF from a bacterium where it is not essential, Acinetobacter baylyi ADP1. Loss of yqgF impaired growth and increased the frequency of transformation and allelic replacement (TAR). When E. coli yqgF was inserted in place of its A. baylyi chromosomal orthologue, wild-type growth and TAR were restored. Functional similarities of yqgF in both gamma-proteobacteria were further supported by defective 16S rRNA processing by the A. baylyi mutant, an effect previously shown in E. coli for a temperature-sensitive yqgF allele. However, our data question the validity of deducing YqgF function strictly by comparison to RuvC. A. baylyi studies indicated that YqgF and RuvC can function in opposition to one another. Relative to the wild type, the ΔyqgF mutant had increased TAR frequency and increased resistance to nalidixic acid, a DNA-damaging agent. In contrast, deletion of ruvC decreased TAR frequency and lowered resistance to nalidixic acid. YqgF, but not RuvC, appears to increase bacterial susceptibility to DNA damage, including UV radiation. Nevertheless, the effects of yqgF on growth and TAR frequency were found to depend on amino acids analogous to catalytically required residues of RuvC. This new heterologous system should facilitate future yqgF investigation by exploiting the viability of A. baylyi yqgF mutants. In addition, bioinformatic analysis showed that a non-essential gene immediately upstream of yqgF in A. baylyi and E. coli (yqgE) is similarly positioned in most gamma- and beta-proteobacteria. A small overlap in the coding sequences of these adjacent genes is typical. This conserved genetic arrangement raises the possibility of a functional partnership between yqgE and yqgF.
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Affiliation(s)
- Dylan J McClung
- Department of Biology, The College of New Jersey, Ewing, NJ, USA
| | - Abigail Calixto
- Department of Biology, The College of New Jersey, Ewing, NJ, USA
| | | | - Raagni Kumar
- Department of Biology, The College of New Jersey, Ewing, NJ, USA
| | - Ellen L Neidle
- Department of Microbiology, University of Georgia, Athens, GA, USA
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Draft Genome Sequence of the Radioresistant Bacterium Deinococcus grandis, Isolated from Freshwater Fish in Japan. GENOME ANNOUNCEMENTS 2016; 4:4/1/e01631-15. [PMID: 26868384 PMCID: PMC4751308 DOI: 10.1128/genomea.01631-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Deinococcus grandis is a radioresistant bacterium isolated from freshwater fish in Japan. Here we reported the draft genome sequence of D. grandis (4.1 Mb), which will be useful for elucidating the common principles of radioresistance in Deinococcus species through the comparative analysis of genomic sequences.
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Morozova D, Moeller R, Rettberg P, Wagner D. Enhanced Radiation Resistance of Methanosarcina soligelidi SMA-21, a New Methanogenic Archaeon Isolated from a Siberian Permafrost-Affected Soil in Direct Comparison to Methanosarcina barkeri. ASTROBIOLOGY 2015; 15:951-960. [PMID: 26544020 DOI: 10.1089/ast.2015.1319] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
UNLABELLED Permafrost-affected soils are characterized by a high abundance and diversity of methanogenic communities, which are considered suitable model organisms for potential life on Mars. Methanogens from Siberian permafrost have been proven to be highly resistant against divers stress conditions such as subzero temperatures, desiccation, and simulated thermophysical martian conditions. Here, we studied the radiation resistance of the currently described new species Methanosarcina soligelidi SMA-21, which was isolated from a Siberian permafrost-affected soil, in comparison to Methanosarcina barkeri, which is used as a reference organism from a nonpermafrost soil environment. Both strains were exposed to solar UV and ionizing radiation to assess their limits of survival. Methanosarcina soligelidi exhibit an increase in radiation resistance to UV (2.5- to 13.8-fold) and ionizing radiation (46.6-fold) compared to M. barkeri. The F10 (UVC) and D10 (X-rays) values of M. soligelidi are comparable to values for the well-known, highly radioresistant species Deinococcus radiodurans. In contrast, the radiation response of M. barkeri was highly sensitive to UV and ionizing radiation comparably to Escherichia coli and other radiosensitive microorganisms. This study showed that species of the same genus respond differently to UV and ionizing radiation, which might reflect the adaptation of Methanosarcina soligelidi SMA-21 to the harsh environmental conditions of the permafrost habitat. KEY WORDS Methanogenic archaea-Environmental UV-Ionizing radiation-Permafrost-Radiation resistance-Mars.
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Affiliation(s)
- Daria Morozova
- 1 GFZ German Research Centre for Geosciences , Helmholtz Centre Potsdam, Section Geomicrobiology, Telegrafenberg, Potsdam, Germany
| | - Ralf Moeller
- 2 German Aerospace Center (DLR e.V.), Institute of Aerospace Medicine , Radiation Biology Department, Research Group Astrobiology, Köln, Germany
| | - Petra Rettberg
- 2 German Aerospace Center (DLR e.V.), Institute of Aerospace Medicine , Radiation Biology Department, Research Group Astrobiology, Köln, Germany
| | - Dirk Wagner
- 1 GFZ German Research Centre for Geosciences , Helmholtz Centre Potsdam, Section Geomicrobiology, Telegrafenberg, Potsdam, Germany
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26
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Gerber E, Bernard R, Castang S, Chabot N, Coze F, Dreux-Zigha A, Hauser E, Hivin P, Joseph P, Lazarelli C, Letellier G, Olive J, Leonetti JP. Deinococcus as new chassis for industrial biotechnology: biology, physiology and tools. J Appl Microbiol 2015; 119:1-10. [PMID: 25809882 PMCID: PMC4682472 DOI: 10.1111/jam.12808] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/20/2015] [Accepted: 03/03/2015] [Indexed: 11/28/2022]
Abstract
Deinococcus spp are among the most radiation-resistant micro-organisms that have been discovered. They show remarkable resistance to a range of damage caused by ionizing radiation, desiccation, UV radiation and oxidizing agents. Traditionally, Escherichia coli and Saccharomyces cerevisiae have been the two platforms of choice for engineering micro-organisms for biotechnological applications, because they are well understood and easy to work with. However, in recent years, researchers have begun using Deinococcus spp in biotechnologies and bioremediation due to their specific ability to grow and express novel engineered functions. More recently, the sequencing of several Deinococcus spp and comparative genomic analysis have provided new insight into the potential of this genus. Features such as the accumulation of genes encoding cell cleaning systems that eliminate organic and inorganic cell toxic components are widespread among Deinococcus spp. Other features such as the ability to degrade and metabolize sugars and polymeric sugars make Deinococcus spp. an attractive alternative for use in industrial biotechnology.
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Affiliation(s)
- E Gerber
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
| | - R Bernard
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
| | - S Castang
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
| | - N Chabot
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
| | - F Coze
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
| | - A Dreux-Zigha
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
| | - E Hauser
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
| | - P Hivin
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
| | - P Joseph
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
| | - C Lazarelli
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
| | - G Letellier
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
| | - J Olive
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
| | - J-P Leonetti
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
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Li Y, Zhu H, Lei X, Zhang H, Guan C, Chen Z, Zheng W, Xu H, Tian Y, Yu Z, Zheng T. The first evidence of deinoxanthin from Deinococcus sp. Y35 with strong algicidal effect on the toxic dinoflagellate Alexandrium tamarense. JOURNAL OF HAZARDOUS MATERIALS 2015; 290:87-95. [PMID: 25746568 DOI: 10.1016/j.jhazmat.2015.02.070] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Revised: 02/24/2015] [Accepted: 02/25/2015] [Indexed: 06/04/2023]
Abstract
Harmful algal blooms (HABs) could be deemed hazardous materials in aquatic environment. Alexandrium tamarense is a toxic HAB causing alga, which causes serious economic losses and health problems. In this study, the bacterium Deinococcus xianganensis Y35 produced a new algicide, showing a high algicidal effect on A. tamarense. The algicidal compound was identified as deinoxanthin, a red pigment, based on high resolution mass spectrometry and NMR after the active compound was isolated and purified. Deinoxanthin exhibited an obvious inhibitory effect on algal growth, and showed algicidal activity against A. tamarense with an EC50 of 5.636 μg/mL with 12h treatment time. Based on the unique structure and characteristics of deinoxanthin, the content of reactive oxygen species (ROS) increased after 0.5h exposure, the structure of organelles including chloroplasts and mitochondria were seriously damaged. All these results firstly confirmed that deinoxanthin as the efficient and eco-environmental algicidal compound has potential to be used for controlling harmful algal blooms through overproduction of ROS.
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Affiliation(s)
- Yi Li
- State Key Laboratory of Marine Environmental Science and Key Laboratory of MOE for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, China.
| | - Hong Zhu
- State Key Laboratory of Marine Environmental Science and Key Laboratory of MOE for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, China.
| | - Xueqian Lei
- State Key Laboratory of Marine Environmental Science and Key Laboratory of MOE for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, China.
| | - Huajun Zhang
- State Key Laboratory of Marine Environmental Science and Key Laboratory of MOE for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, China.
| | - Chengwei Guan
- State Key Laboratory of Marine Environmental Science and Key Laboratory of MOE for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, China.
| | - Zhangran Chen
- State Key Laboratory of Marine Environmental Science and Key Laboratory of MOE for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, China.
| | - Wei Zheng
- State Key Laboratory of Marine Environmental Science and Key Laboratory of MOE for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, China.
| | - Hong Xu
- State Key Laboratory of Marine Environmental Science and Key Laboratory of MOE for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, China.
| | - Yun Tian
- State Key Laboratory of Marine Environmental Science and Key Laboratory of MOE for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, China.
| | - Zhiming Yu
- Key Laboratory of Marine Ecology and Environmental Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Tianling Zheng
- State Key Laboratory of Marine Environmental Science and Key Laboratory of MOE for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, China.
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28
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Whole-genome optical mapping and finished genome sequence of Sphingobacterium deserti sp. nov., a new species isolated from the Western Desert of China. PLoS One 2015; 10:e0122254. [PMID: 25830331 PMCID: PMC4382152 DOI: 10.1371/journal.pone.0122254] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 02/20/2015] [Indexed: 11/19/2022] Open
Abstract
A novel Gram-negative bacterium, designated ZWT, was isolated from a soil sample of the Western Desert of China, and its phenotypic properties and phylogenetic position were investigated using a polyphasic approach. Growth occurred on TGY medium at 5-42°C with an optimum of 30°C, and at pH 7.0-11.0 with an optimum of pH 9.0. The predominant cellular fatty acids were summed feature 3 (C16:1ω7c/C16:1ω6c or C16:1ω6c/C16:1ω7c) (39.22%), iso-C15:0 (27.91%), iso-C17:0 3OH (15.21%), C16:0 (4.98%), iso-C15:0 3OH (3.03%), C16:0 3OH (5.39%) and C14:0 (1.74%). The major polar lipid of strain ZWT is phosphatidylethanolamine. The only menaquinone observed was MK-7. The GC content of the DNA of strain ZWT is 44.9 mol%. rDNA phylogeny, genome relatedness and chemotaxonomic characteristics all indicate that strain ZWT represents a novel species of the genus Sphingobacterium. We propose the name S. deserti sp. nov., with ZWT (= KCTC 32092T = ACCC 05744T) as the type strain. Whole genome optical mapping and next-generation sequencing was used to derive a finished genome sequence for strain ZWT, consisting of a circular chromosome of 4,615,818 bp in size. The genome of strain ZWT features 3,391 protein-encoding and 48 tRNA-encoding genes. Comparison of the predicted proteome of ZWT with those of other sphingobacteria identified 925 species-unique proteins that may contribute to the adaptation of ZWT to its native, extremely arid and inhospitable environment. As the first finished genome sequence for any Sphingobacterium, our work will serve as a useful reference for subsequent sequencing and mapping efforts for additional strains and species within this genus.
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Rummel JD, Beaty DW, Jones MA, Bakermans C, Barlow NG, Boston PJ, Chevrier VF, Clark BC, de Vera JPP, Gough RV, Hallsworth JE, Head JW, Hipkin VJ, Kieft TL, McEwen AS, Mellon MT, Mikucki JA, Nicholson WL, Omelon CR, Peterson R, Roden EE, Sherwood Lollar B, Tanaka KL, Viola D, Wray JJ. A new analysis of Mars "Special Regions": findings of the second MEPAG Special Regions Science Analysis Group (SR-SAG2). ASTROBIOLOGY 2014; 14:887-968. [PMID: 25401393 DOI: 10.1089/ast.2014.1227] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
A committee of the Mars Exploration Program Analysis Group (MEPAG) has reviewed and updated the description of Special Regions on Mars as places where terrestrial organisms might replicate (per the COSPAR Planetary Protection Policy). This review and update was conducted by an international team (SR-SAG2) drawn from both the biological science and Mars exploration communities, focused on understanding when and where Special Regions could occur. The study applied recently available data about martian environments and about terrestrial organisms, building on a previous analysis of Mars Special Regions (2006) undertaken by a similar team. Since then, a new body of highly relevant information has been generated from the Mars Reconnaissance Orbiter (launched in 2005) and Phoenix (2007) and data from Mars Express and the twin Mars Exploration Rovers (all 2003). Results have also been gleaned from the Mars Science Laboratory (launched in 2011). In addition to Mars data, there is a considerable body of new data regarding the known environmental limits to life on Earth-including the potential for terrestrial microbial life to survive and replicate under martian environmental conditions. The SR-SAG2 analysis has included an examination of new Mars models relevant to natural environmental variation in water activity and temperature; a review and reconsideration of the current parameters used to define Special Regions; and updated maps and descriptions of the martian environments recommended for treatment as "Uncertain" or "Special" as natural features or those potentially formed by the influence of future landed spacecraft. Significant changes in our knowledge of the capabilities of terrestrial organisms and the existence of possibly habitable martian environments have led to a new appreciation of where Mars Special Regions may be identified and protected. The SR-SAG also considered the impact of Special Regions on potential future human missions to Mars, both as locations of potential resources and as places that should not be inadvertently contaminated by human activity.
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Affiliation(s)
- John D Rummel
- 1 Department of Biology, East Carolina University , Greenville, North Carolina, USA
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30
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Adachi M, Hirayama H, Shimizu R, Satoh K, Narumi I, Kuroki R. Interaction of double-stranded DNA with polymerized PprA protein from Deinococcus radiodurans. Protein Sci 2014; 23:1349-58. [PMID: 25044036 DOI: 10.1002/pro.2519] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/11/2014] [Accepted: 07/11/2014] [Indexed: 11/06/2022]
Abstract
Pleiotropic protein promoting DNA repair A (PprA) is a key protein that facilitates the extreme radioresistance of Deinococcus radiodurans. To clarify the role of PprA in the radioresistance mechanism, the interaction between recombinant PprA expressed in Escherichia coli with several double-stranded DNAs (i.e., super coiled, linear, or nicked circular dsDNA) was investigated. In a gel-shift assay, the band shift of supercoiled pUC19 DNA caused by the binding of PprA showed a bimodal distribution, which was promoted by the addition of 1 mM Mg, Ca, or Sr ions. The dissociation constant of the PprA-supercoiled pUC19 DNA complex, calculated from the relative portions of shifted bands, was 0.6 μM with Hill coefficient of 3.3 in the presence of 1 mM Mg acetate. This indicates that at least 281 PprA molecules are required to saturate a supercoiled pUC19 DNA, which is consistent with the number (280) of bound PprA molecules estimated by the UV absorption of the PprA-pUC19 complex purified by gel filtration. This saturation also suggests linear polymerization of PprA along the dsDNA. On the other hand, the bands of linear dsDNA and nicked circular dsDNA that eventually formed PprA complexes did not saturate, but created larger molecular complexes when the PprA concentration was >1.3 μM. This result implies that DNA-bound PprA aids association of the termini of damaged DNAs, which is regulated by the concentration of PprA. These findings are important for the understanding of the mechanism underlying effective DNA repair involving PprA.
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Affiliation(s)
- Motoyasu Adachi
- Molecular Biology Research Division, Quantum Beam Science Center, Japan Atomic Energy Agency, Ibaraki, 319-1195, Japan
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31
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Egas C, Barroso C, Froufe HJC, Pacheco J, Albuquerque L, da Costa MS. Complete genome sequence of the Radiation-Resistant bacterium Rubrobacter radiotolerans RSPS-4. Stand Genomic Sci 2014; 9:1062-75. [PMID: 25197483 PMCID: PMC4148983 DOI: 10.4056/sigs.5661021] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rubrobacter radiotolerans strain RSPS-4 is a slightly thermophilic member of the phylum “Actinobacteria” isolated from a hot spring in São Pedro do Sul, Portugal. This aerobic and halotolerant bacterium is also extremely resistant to gamma and UV radiation, which are the main reasons for the interest in sequencing its genome. Here, we present the complete genome sequence of strain RSPS-4 as well as its assembly and annotation. We also compare the gene sequence of this organism with that of the type strain of the species R. radiotolerans isolated from a hot spring in Japan. The genome of strain RSPS-4 comprises one circular chromosome of 2,875,491 bp with a G+C content of 66.91%, and 3 circular plasmids of 190,889 bp, 149,806 bp and 51,047 bp, harboring 3,214 predicted protein coding genes, 46 tRNA genes and a single rRNA operon.
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Affiliation(s)
- C Egas
- Next Generation Sequencing Unit, Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
| | - C Barroso
- Next Generation Sequencing Unit, Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
| | - H J C Froufe
- Next Generation Sequencing Unit, Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
| | - J Pacheco
- Next Generation Sequencing Unit, Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
| | - L Albuquerque
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - M S da Costa
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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Wang Y, Lin W, Li J, Pan Y. Changes of cell growth and magnetosome biomineralization in Magnetospirillum magneticum AMB-1 after ultraviolet-B irradiation. Front Microbiol 2013; 4:397. [PMID: 24391631 PMCID: PMC3867805 DOI: 10.3389/fmicb.2013.00397] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 12/04/2013] [Indexed: 11/28/2022] Open
Abstract
Effects of ultraviolet radiation on microorganisms are of great interest in field of microbiology and planetary sciences. In the present study, we used Magnetospirillum magneticum AMB-1 as a model organism to examine the influence of ultraviolet-B (UV-B) radiation on cell growth and magnetite biomineralization of magnetotactic bacteria (MTB). Live AMB-1 cells were exposed to UV-B radiation for 60, 300 and 900 s, which correspond to radiation doses of 120 J/m2, 600 J/m2, and 1800 J/m2, respectively. After irradiation, the amounts of cyclobutane pyrimidine dimers (CPD) and reactive oxygen species (ROS) of the cells were increased, and cell growth was stunted up to ~170 h, depending on the UV-B radiation doses. The UV-B irradiated cells also produced on average more magnetite crystals with larger grain sizes and longer chains, which results in changes of their magnetic properties.
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Affiliation(s)
- Yinzhao Wang
- Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of the Earth's Deep Interior, Institute of Geology and Geophysics, Chinese Academy of Sciences Beijing, China ; France-China Bio-Mineralization and Nano-Structures Laboratory, Chinese Academy of Sciences Beijing, China
| | - Wei Lin
- Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of the Earth's Deep Interior, Institute of Geology and Geophysics, Chinese Academy of Sciences Beijing, China ; France-China Bio-Mineralization and Nano-Structures Laboratory, Chinese Academy of Sciences Beijing, China
| | - Jinhua Li
- Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of the Earth's Deep Interior, Institute of Geology and Geophysics, Chinese Academy of Sciences Beijing, China ; France-China Bio-Mineralization and Nano-Structures Laboratory, Chinese Academy of Sciences Beijing, China
| | - Yongxin Pan
- Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of the Earth's Deep Interior, Institute of Geology and Geophysics, Chinese Academy of Sciences Beijing, China ; France-China Bio-Mineralization and Nano-Structures Laboratory, Chinese Academy of Sciences Beijing, China
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33
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Wray GA. Genomics and the Evolution of Phenotypic Traits. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-110512-135828] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Evolutionary genetics has entered an unprecedented era of discovery, catalyzed in large part by the development of technologies that provide information about genome sequence and function. An important benefit is the ability to move beyond a handful of model organisms in lab settings to identify the genetic basis for evolutionarily interesting traits in many organisms in natural settings. Other benefits are the abilities to identify causal mutations and validate their phenotypic consequences more readily and in many more species. Genomic technologies have reinvigorated interest in some of the most fundamental and persistent questions in evolutionary genetics, revealed previously unsuspected evolutionary phenomena, and opened the door to a wide range of new questions.
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Affiliation(s)
- Gregory A. Wray
- Department of Biology and Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina 27701
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34
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Impact of Solar Radiation on Gene Expression in Bacteria. Proteomes 2013; 1:70-86. [PMID: 28250399 PMCID: PMC5302746 DOI: 10.3390/proteomes1020070] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 06/21/2013] [Accepted: 07/02/2013] [Indexed: 11/17/2022] Open
Abstract
Microorganisms often regulate their gene expression at the level of transcription and/or translation in response to solar radiation. In this review, we present the use of both transcriptomics and proteomics to advance knowledge in the field of bacterial response to damaging radiation. Those studies pertain to diverse application areas such as fundamental microbiology, water treatment, microbial ecology and astrobiology. Even though it has been demonstrated that mRNA abundance is not always consistent with the protein regulation, we present here an exhaustive review on how bacteria regulate their gene expression at both transcription and translation levels to enable biomarkers identification and comparison of gene regulation from one bacterial species to another.
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Santos AL, Gomes NC, Henriques I, Almeida A, Correia A, Cunha A. Role of Transition Metals in UV-B-Induced Damage to Bacteria. Photochem Photobiol 2013; 89:640-8. [DOI: 10.1111/php.12049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 01/16/2013] [Indexed: 12/01/2022]
Affiliation(s)
- Ana L. Santos
- Dapartment of Biology & CESAM; University of Aveiro; Campus Universitário de Santiago; 3810-193; Aveiro; Portugal
| | - Newton C.M. Gomes
- Dapartment of Biology & CESAM; University of Aveiro; Campus Universitário de Santiago; 3810-193; Aveiro; Portugal
| | - Isabel Henriques
- Dapartment of Biology & CESAM; University of Aveiro; Campus Universitário de Santiago; 3810-193; Aveiro; Portugal
| | - Adelaide Almeida
- Dapartment of Biology & CESAM; University of Aveiro; Campus Universitário de Santiago; 3810-193; Aveiro; Portugal
| | - António Correia
- Dapartment of Biology & CESAM; University of Aveiro; Campus Universitário de Santiago; 3810-193; Aveiro; Portugal
| | - Angela Cunha
- Dapartment of Biology & CESAM; University of Aveiro; Campus Universitário de Santiago; 3810-193; Aveiro; Portugal
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36
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Montgomery K, Charlesworth JC, LeBard R, Visscher PT, Burns BP. Quorum sensing in extreme environments. Life (Basel) 2013; 3:131-48. [PMID: 25371335 PMCID: PMC4187201 DOI: 10.3390/life3010131] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 01/21/2013] [Accepted: 01/22/2013] [Indexed: 11/29/2022] Open
Abstract
Microbial communication, particularly that of quorum sensing, plays an important role in regulating gene expression in a range of organisms. Although this phenomenon has been well studied in relation to, for example, virulence gene regulation, the focus of this article is to review our understanding of the role of microbial communication in extreme environments. Cell signaling regulates many important microbial processes and may play a pivotal role in driving microbial functional diversity and ultimately ecosystem function in extreme environments. Several recent studies have characterized cell signaling in modern analogs to early Earth communities (microbial mats), and characterization of cell signaling systems in these communities may provide unique insights in understanding the microbial interactions involved in function and survival in extreme environments. Cell signaling is a fundamental process that may have co-evolved with communities and environmental conditions on the early Earth. Without cell signaling, evolutionary pressures may have even resulted in the extinction rather than evolution of certain microbial groups. One of the biggest challenges in extremophile biology is understanding how and why some microbial functional groups are located where logically they would not be expected to survive, and tightly regulated communication may be key. Finally, quorum sensing has been recently identified for the first time in archaea, and thus communication at multiple levels (potentially even inter-domain) may be fundamental in extreme environments.
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Affiliation(s)
- Kate Montgomery
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - James C Charlesworth
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Rebecca LeBard
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Pieter T Visscher
- Center for Integrative Geosciences, University of Connecticut 354 Mansfield Road, Storrs, CT 06269-2045, USA.
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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Forde BM, O'Toole PW. Next-generation sequencing technologies and their impact on microbial genomics. Brief Funct Genomics 2013; 12:440-53. [PMID: 23314033 DOI: 10.1093/bfgp/els062] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Next-generation sequencing technologies have had a dramatic impact in the field of genomic research through the provision of a low cost, high-throughput alternative to traditional capillary sequencers. These new sequencing methods have surpassed their original scope and now provide a range of utility-based applications, which allow for a more comprehensive analysis of the structure and content of microbial genomes than was previously possible. With the commercialization of a third generation of sequencing technologies imminent, we discuss the applications of current next-generation sequencing methods and explore their impact on and contribution to microbial genome research.
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Affiliation(s)
- Brian M Forde
- Department of Microbiology, University College Cork, Cork, Ireland.
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38
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Beaume N, Pathak R, Yadav VK, Kota S, Misra HS, Gautam HK, Chowdhury S. Genome-wide study predicts promoter-G4 DNA motifs regulate selective functions in bacteria: radioresistance of D. radiodurans involves G4 DNA-mediated regulation. Nucleic Acids Res 2012; 41:76-89. [PMID: 23161683 PMCID: PMC3592403 DOI: 10.1093/nar/gks1071] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
A remarkable number of guanine-rich sequences with potential to adopt non-canonical secondary structures called G-quadruplexes (or G4 DNA) are found within gene promoters. Despite growing interest, regulatory role of quadruplex DNA motifs in intrinsic cellular function remains poorly understood. Herein, we asked whether occurrence of potential G4 (PG4) DNA in promoters is associated with specific function(s) in bacteria. Using a normalized promoter-PG4-content (PG4P) index we analysed >60 000 promoters in 19 well-annotated species for (a) function class(es) and (b) gene(s) with enriched PG4P. Unexpectedly, PG4-associated functional classes were organism specific, suggesting that PG4 motifs may impart specific function to organisms. As a case study, we analysed radioresistance. Interestingly, unsupervised clustering using PG4P of 21 genes, crucial for radioresistance, grouped three radioresistant microorganisms including Deinococcus radiodurans. Based on these predictions we tested and found that in presence of nanomolar amounts of the intracellular quadruplex-binding ligand N-methyl mesoporphyrin (NMM), radioresistance of D. radiodurans was attenuated by ∼60%. In addition, important components of the RecF recombinational repair pathway recA, recF, recO, recR and recQ genes were found to harbour promoter-PG4 motifs and were also down-regulated in presence of NMM. Together these results provide first evidence that radioresistance may involve G4 DNA-mediated regulation and support the rationale that promoter-PG4s influence selective functions.
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Affiliation(s)
- Nicolas Beaume
- GNR Knowledge Centre for Genome Informatics, Division of Comparative Genomics, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
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39
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Nelson OW, Garrity GM. Genome sequences published outside of Standards in Genomic Sciences, March-April 2012. Stand Genomic Sci 2012. [PMCID: PMC3387800 DOI: 10.4056/sigs.2836114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.
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Affiliation(s)
- Oranmiyan W. Nelson
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
| | - George M. Garrity
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
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