1
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Gómez‐Campo CL, Abdelmoteleb A, Pulido V, Gost M, Sánchez‐Hevia DL, Berenguer J, Mencía M. Differential requirement for RecFOR pathway components in Thermus thermophilus. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13269. [PMID: 38822640 PMCID: PMC11143384 DOI: 10.1111/1758-2229.13269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/06/2024] [Indexed: 06/03/2024]
Abstract
Recombinational repair is an important mechanism that allows DNA replication to overcome damaged templates, so the DNA is duplicated timely and correctly. The RecFOR pathway is one of the common ways to load RecA, while the RuvABC complex operates in the resolution of DNA intermediates. We have generated deletions of recO, recR and ruvB genes in Thermus thermophilus, while a recF null mutant could not be obtained. The recO deletion was in all cases accompanied by spontaneous loss of function mutations in addA or addB genes, which encode a helicase-exonuclease also key for recombination. The mutants were moderately affected in viability and chromosome segregation. When we generated these mutations in a Δppol/addAB strain, we observed that the transformation efficiency was maintained at the typical level of Δppol/addAB, which is 100-fold higher than that of the wild type. Most mutants showed increased filamentation phenotypes, especially ruvB, which also had DNA repair defects. These results suggest that in T. thermophilus (i) the components of the RecFOR pathway have differential roles, (ii) there is an epistatic relationship of the AddAB complex over the RecFOR pathway and (iii) that neither of the two pathways or their combination is strictly required for viability although they are necessary for normal DNA repair and chromosome segregation.
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Affiliation(s)
- Cristina L. Gómez‐Campo
- Center for Plant Biotechnology and Genomics (CBGP)Polytechnic University of MadridMadridSpain
| | - Ali Abdelmoteleb
- Department of Molecular BiologyScience Faculty, Center for Molecular Biology Severo Ochoa (CBM), Autonomous University of Madrid‐Higher Council of Scientific Research (CSIC)MadridSpain
- Department of Botany, Faculty of AgricultureMenoufia UniversityShebin El‐KomEgypt
| | - Verónica Pulido
- Department of Molecular BiologyScience Faculty, Center for Molecular Biology Severo Ochoa (CBM), Autonomous University of Madrid‐Higher Council of Scientific Research (CSIC)MadridSpain
| | - Marc Gost
- Department of Molecular BiologyScience Faculty, Center for Molecular Biology Severo Ochoa (CBM), Autonomous University of Madrid‐Higher Council of Scientific Research (CSIC)MadridSpain
| | | | - José Berenguer
- Department of Molecular BiologyScience Faculty, Center for Molecular Biology Severo Ochoa (CBM), Autonomous University of Madrid‐Higher Council of Scientific Research (CSIC)MadridSpain
| | - Mario Mencía
- Department of Molecular BiologyScience Faculty, Center for Molecular Biology Severo Ochoa (CBM), Autonomous University of Madrid‐Higher Council of Scientific Research (CSIC)MadridSpain
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2
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Belykh E, Maystrenko T, Velegzhaninov I, Tavleeva M, Rasova E, Rybak A. Taxonomic Diversity and Functional Traits of Soil Bacterial Communities under Radioactive Contamination: A Review. Microorganisms 2024; 12:733. [PMID: 38674676 PMCID: PMC11051952 DOI: 10.3390/microorganisms12040733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 04/28/2024] Open
Abstract
Studies investigating the taxonomic diversity and structure of soil bacteria in areas with enhanced radioactive backgrounds have been ongoing for three decades. An analysis of data published from 1996 to 2024 reveals changes in the taxonomic structure of radioactively contaminated soils compared to the reference, showing that these changes are not exclusively dependent on contamination rates or pollutant compositions. High levels of radioactive exposure from external irradiation and a high radionuclide content lead to a decrease in the alpha diversity of soil bacterial communities, both in laboratory settings and environmental conditions. The effects of low or moderate exposure are not consistently pronounced or unidirectional. Functional differences among taxonomic groups that dominate in contaminated soil indicate a variety of adaptation strategies. Bacteria identified as multiple-stress tolerant; exhibiting tolerance to metals and antibiotics; producing antioxidant enzymes, low-molecular antioxidants, and radioprotectors; participating in redox reactions; and possessing thermophilic characteristics play a significant role. Changes in the taxonomic and functional structure, resulting from increased soil radionuclide content, are influenced by the combined effects of ionizing radiation, the chemical toxicity of radionuclides and co-contaminants, as well as the physical and chemical properties of the soil and the initial bacterial community composition. Currently, the quantification of the differential contributions of these factors based on the existing published studies presents a challenge.
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Affiliation(s)
- Elena Belykh
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Tatiana Maystrenko
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Ilya Velegzhaninov
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Marina Tavleeva
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
- Department of Biology, Institute of Natural Sciences, Pitirim Sorokin Syktyvkar State University, 55 Oktyabrsky Prospekt, Syktyvkar 167001, Russia
| | - Elena Rasova
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Anna Rybak
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
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3
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Wang XW, Tan X, Dang CC, Lu Y, Xie GJ, Liu BF. Thermophilic microorganisms involved in the nitrogen cycle in thermal environments: Advances and prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165259. [PMID: 37400035 DOI: 10.1016/j.scitotenv.2023.165259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/05/2023]
Abstract
Thermophilic microorganisms mediated significant element cycles and material conversion in the early Earth as well as mediating current thermal environments. Over the past few years, versatile microbial communities that drive the nitrogen cycle have been identified in thermal environments. Understanding the microbial-mediated nitrogen cycling processes in these thermal environments has important implications for the cultivation and application of thermal environment microorganisms as well as for exploring the global nitrogen cycle. This work provides a comprehensive review of different thermophilic nitrogen-cycling microorganisms and processes, which are described in detail according to several categories, including nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and dissimilatory nitrate reduction to ammonium. In particular, we assess the environmental significance and potential applications of thermophilic nitrogen-cycling microorganisms, and highlight knowledge gaps and future research opportunities.
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Affiliation(s)
- Xiao-Wei Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xin Tan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Cheng-Cheng Dang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yang Lu
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
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4
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Daly MJ. The scientific revolution that unraveled the astonishing DNA repair capacity of the Deinococcaceae: 40 years on. Can J Microbiol 2023; 69:369-386. [PMID: 37267626 DOI: 10.1139/cjm-2023-0059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The family Deinococcaceae exhibits exceptional radiation resistance and possesses all the necessary traits for surviving in radiation-exposed environments. Their survival strategy involves the coupling of metabolic and DNA repair functions, resulting in an extraordinarily efficient homologous repair of DNA double-strand breaks (DSBs) caused by radiation or desiccation. The keys to their survival lie in the hyperaccumulation of manganous (Mn2+)-metabolite antioxidants that protect their DNA repair proteins under extreme oxidative stress and the persistent structural linkage by Holliday junctions of their multiple genome copies per cell that facilitates DSB repair. This coupling of metabolic and DNA repair functions has made polyploid Deinococcus bacteria a useful tool in environmental biotechnology, radiobiology, aging, and planetary protection. The review highlights the groundbreaking contributions of the late Robert G.E. Murray to the field of Deinococcus research and the emergent paradigm-shifting discoveries that revolutionized our understanding of radiation survivability and oxidative stress defense, demonstrating that the proteome, rather than the genome, is the primary target responsible for survivability. These discoveries have led to the commercial development of irradiated vaccines using Deinococcus Mn-peptide antioxidants and have significant implications for various fields.
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Affiliation(s)
- Michael J Daly
- Uniformed Services University of the Health Sciences (USUHS), School of Medicine, Department of Pathology, Bethesda, MD 20814-4799, USA
- Committee on Planetary Protection (CoPP), National Academies of Sciences, Washington, DC 20001, USA
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5
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Sadowska-Bartosz I, Bartosz G. Antioxidant defense of Deinococcus radiodurans: how does it contribute to extreme radiation resistance? Int J Radiat Biol 2023; 99:1803-1829. [PMID: 37498212 DOI: 10.1080/09553002.2023.2241895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 06/28/2023] [Accepted: 07/08/2023] [Indexed: 07/28/2023]
Abstract
PURPOSE Deinococcus radiodurans is an extremely radioresistant bacterium characterized by D10 of 10 kGy, and able to grow luxuriantly under chronic ionizing radiation of 60 Gy/h. The aim of this article is to review the antioxidant system of D. radiodurans and its possible role in the unusual resistance of this bacterium to ionizing radiation. CONCLUSIONS The unusual radiation resistance of D. radiodurans has apparently evolved as a side effect of the adaptation of this extremophile to other damaging environmental factors, especially desiccation. The antioxidant proteins and low-molecular antioxidants (especially low-molecular weight Mn2+ complexes and carotenoids, in particular, deinoxanthin), as well as protein and non-protein regulators, are important for the antioxidant defense of this species. Antioxidant protection of proteins from radiation inactivation enables the repair of DNA damage caused by ionizing radiation.
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Affiliation(s)
- Izabela Sadowska-Bartosz
- Laboratory of Analytical Biochemistry, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
| | - Grzegorz Bartosz
- Department of Bioenergetics, Food Analysis and Microbiology, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
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6
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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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7
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Nguyen K, Kumar P. Morphological Phenotypes, Cell Division, and Gene Expression of Escherichia coli under High Concentration of Sodium Sulfate. Microorganisms 2022; 10:microorganisms10020274. [PMID: 35208727 PMCID: PMC8875244 DOI: 10.3390/microorganisms10020274] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 01/10/2023] Open
Abstract
Sodium and sulfate ions are among the suggested abundant ions on Europa, a moon of Jupiter. In order to investigate the potential habitability of Europa, we study the effects of sodium sulfate (Na2SO4) on a non-halophilic bacterium by subjecting Escherichia coli (E. coli) to a wide range of Na2SO4 concentrations (0–1.0 m). We discover that, as the concentration of sodium sulfate increases, the biomass doubling time increases and the cell growth is completely inhibited at 1.0 m Na2SO4. Furthermore, we find that E. coli exhibits three distinct morphological phenotypes—(i) shortened, (ii) normal, and (iii) elongated/filamented cells at 0.6 m and 0.8 m Na2SO4. We have examined the expression of different genes involved in sodium and sulfate transport (nhaA, nhaB, cysZ, sbp), osmotically driven transport of water (aqpZ), sulfate metabolism (cysN), fatty acid production (fabA), and a global transcriptional regulator (osmZ). Our results suggest that the expression of these genes is not affected significantly at high concentrations of sodium sulfate in the exponential growth phase. Using our experimental data and the existing data in the literature, we show that the osmotic pressure difference may play a major role in determining the growth inhibition of E. coli and B. subtilis at high concentrations of salt.
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8
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Fasnacht M, Gallo S, Sharma P, Himmelstoß M, Limbach PA, Willi J, Polacek N. Dynamic 23S rRNA modification ho5C2501 benefits Escherichia coli under oxidative stress. Nucleic Acids Res 2021; 50:473-489. [PMID: 34904663 PMCID: PMC8754641 DOI: 10.1093/nar/gkab1224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 11/23/2021] [Accepted: 12/02/2021] [Indexed: 11/30/2022] Open
Abstract
Post-transcriptional modifications are added to ribosomal RNAs (rRNAs) to govern ribosome biogenesis and to fine-tune protein biosynthesis. In Escherichia coli and related bacteria, RlhA uniquely catalyzes formation of a 5-hydroxycytidine (ho5C) at position 2501 of 23S rRNA. However, the molecular and biological functions as well as the regulation of ho5C2501 modification remain unclear. We measured growth curves with the modification-deficient ΔrlhA strain and quantified the extent of the modification during different conditions by mass spectrometry and reverse transcription. The levels of ho5C2501 in E. coli ribosomes turned out to be highly dynamic and growth phase-dependent, with the most effective hydroxylation yields observed in the stationary phase. We demonstrated a direct effect of ho5C2501 on translation efficiencies in vitro and in vivo. High ho5C2501 levels reduced protein biosynthesis which however turned out to be beneficial for E. coli for adapting to oxidative stress. This functional advantage was small under optimal conditions or during heat or cold shock, but becomes pronounced in the presence of hydrogen peroxide. Taken together, these data provided first functional insights into the role of this unique 23S rRNA modification for ribosome functions and bacterial growth under oxidative stress.
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Affiliation(s)
- Michel Fasnacht
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Stefano Gallo
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Puneet Sharma
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Maximilian Himmelstoß
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, OH, USA
| | - Jessica Willi
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland.,Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, OH, USA
| | - Norbert Polacek
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland
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9
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Shen J, Wyness AJ, Claire MW, Zerkle AL. Spatial Variability of Microbial Communities and Salt Distributions Across a Latitudinal Aridity Gradient in the Atacama Desert. MICROBIAL ECOLOGY 2021; 82:442-458. [PMID: 33438074 PMCID: PMC8384830 DOI: 10.1007/s00248-020-01672-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/21/2020] [Indexed: 05/13/2023]
Abstract
Over the past 150 million years, the Chilean Atacama Desert has been transformed into one of the most inhospitable landscapes by geophysical changes, which makes it an ideal Mars analog that has been explored for decades. However, a heavy rainfall that occurred in the Atacama in 2017 provides a unique opportunity to study the response of resident extremophiles to rapid environmental change associated with excessive water and salt shock. Here we combine mineral/salt composition measurements, amendment cell culture experiments, and next-generation sequencing analyses to study the variations in salts and microbial communities along a latitudinal aridity gradient of the Atacama Desert. In addition, we examine the reshuffling of Atacama microbiomes after the rainfall event. Analysis of microbial community composition revealed that soils within the southern arid desert were consistently dominated by Actinobacteria, Chloroflexi, Proteobacteria, Firmicutes, Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Acidobacteria, and Verrucomicrobia. Intriguingly, the hyperarid microbial consortia exhibited a similar pattern to the more southern desert. Salts at the shallow subsurface were dissolved and leached down to a deeper layer, challenging indigenous microorganisms with the increasing osmotic stress. Microbial viability was found to change with aridity and rainfall events. This study sheds light on the structure of xerotolerant, halotolerant, and radioresistant microbiomes from the hyperarid northern desert to the less arid southern transition region, as well as their response to changes in water availability.
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Affiliation(s)
- Jianxun Shen
- School of Earth and Environmental Sciences and Centre for Exoplanet Science, University of St Andrews, St Andrews, KY16 9AL, UK.
| | - Adam J Wyness
- Sediment Ecology Research Group, Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, KY16 8LB, UK
- Coastal Research Group, Department of Zoology and Entomology, Rhodes University, Grahamstown, 6139, South Africa
| | - Mark W Claire
- School of Earth and Environmental Sciences and Centre for Exoplanet Science, University of St Andrews, St Andrews, KY16 9AL, UK
| | - Aubrey L Zerkle
- School of Earth and Environmental Sciences and Centre for Exoplanet Science, University of St Andrews, St Andrews, KY16 9AL, UK
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10
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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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11
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History, evolution and classification of CRISPR-Cas associated systems. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 179:11-76. [PMID: 33785174 DOI: 10.1016/bs.pmbts.2020.12.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This chapter provides a detailed description of the history of CRISPR-Cas and its evolution into one of the most efficient genome-editing strategies. The chapter begins by providing information on early findings that were critical in deciphering the role of CRISPR-Cas associated systems in prokaryotes. It then describes how CRISPR-Cas had been evolved into an efficient genome-editing strategy. In the subsequent section, latest developments in the genome-editing approaches based on CRISPR-Cas are discussed. The chapter ends with the recent classification and possible evolution of CRISPR-Cas systems.
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12
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Jeong SW, Kim MK, Zhao L, Yang SK, Jung JH, Lim HM, Lim S. Effects of Conserved Wedge Domain Residues on DNA Binding Activity of Deinococcus radiodurans RecG Helicase. Front Genet 2021; 12:634615. [PMID: 33613647 PMCID: PMC7889586 DOI: 10.3389/fgene.2021.634615] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 01/18/2021] [Indexed: 11/13/2022] Open
Abstract
Deinococcus radiodurans is extremely resistant to ionizing radiation and has an exceptional ability to repair DNA damage caused by various DNA-damaging agents. D. radiodurans uses the same DNA-repair strategies as other prokaryotes, but certain proteins involved in the classical DNA repair machinery have characteristics different from their counterparts. RecG helicase, which unwinds a variety of branched DNA molecules, such as Holliday junctions (HJ) and D-loops, plays important roles in DNA repair, recombination, and replication. Primary sequence analysis of RecG from a number of bacterial species revealed that three amino acids (QPW) in the DNA-binding wedge domain (WD) are well-conserved across the Deinococcus RecG proteins. Interactions involving these conserved residues and DNA substrates were predicted in modeled domain structures of D. radiodurans RecG (DrRecG). Compared to the WD of Escherichia coli RecG protein (EcRecG) containing FSA amino acids corresponding to QPW in DrRecG, the HJ binding activity of DrRecG-WD was higher than that of EcRecG-WD. Reciprocal substitution of FSA and QPW increased and decreased the HJ binding activity of the mutant WDs, EcRecG-WDQPW, and DrRecG-WDFSA, respectively. Following γ-irradiation treatment, the reduced survival rate of DrRecG mutants (ΔrecG) was fully restored by the expression of DrRecG, but not by that of EcRecG. EcRecGQPW also enhanced γ-radioresistance of ΔrecG, whereas DrRecGFSA did not. ΔrecG cells complemented in trans by DrRecG and EcRecGQPW reconstituted an intact genome within 3 h post-irradiation, as did the wild-type strain, but ΔrecG with EcRecG and DrRecGFSA exhibited a delay in assembly of chromosomal fragments induced by γ-irradiation. These results suggested that the QPW residues facilitate the association of DrRecG with DNA junctions, thereby enhancing the DNA repair efficiency of DrRecG.
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Affiliation(s)
- Sun-Wook Jeong
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea.,Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Min-Kyu Kim
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - Lei Zhao
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - Seul-Ki Yang
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - Jong-Hyun Jung
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea.,Department of Radiation Science and Technology, University of Science and Technology, Daejeon, South Korea
| | - Heon-Man Lim
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Sangyong Lim
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea.,Department of Radiation Science and Technology, University of Science and Technology, Daejeon, South Korea
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13
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Enhanced Symbiotic Characteristics in Bacterial Genomes with the Disruption of rRNA Operon. BIOLOGY 2020; 9:biology9120440. [PMID: 33287185 PMCID: PMC7761764 DOI: 10.3390/biology9120440] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/11/2020] [Accepted: 12/01/2020] [Indexed: 11/18/2022]
Abstract
Simple Summary Exploring the genomic changes that organisms have undergone to adapt to their specific environment is one of the most important processes in ecology and evolutionary biology. Here, we found that almost all rRNA operon-unlinked bacteria are symbiotic bacteria, which could be evidence of specific selective pressures in symbionts like genome reduction. This is meaningful and suggests that not only does the copy number variation of the rRNA operon sensitively respond to the bacterial lifestyle, but structural modification can also strongly reflect adaptation to the surrounding environmental conditions. Abstract Ribosomal RNA is an indispensable molecule in living organisms that plays an essential role in protein synthesis. Especially in bacteria, 16S, 23S, and 5S rRNAs are usually co-transcribed as operons. Despite the positive effects of rRNA co-transcription on growth and reproduction rate, a recent study revealed that bacteria with unlinked rRNA operons are more widespread than expected. However, it is still unclear why the rRNA operon is broken. Here, we explored rRNA operon linkage status in 15,898 bacterial genomes and investigated whether they have common features or lifestyles; 574 genomes were found to have unlinked rRNA operons and tended to be phylogenetically conserved. Most of them were symbionts and showed enhanced symbiotic genomic features such as reduced genome size and high adenine–thymine (AT) content. In an eggNOG-mapper analysis, they were also found to have significantly fewer genes than rRNA operon-linked bacteria in the “transcription” and “energy production and conversion in metabolism” categories. These genomes also tend to decrease RNases related to the synthesis of ribosomes and tRNA processing. Based on these results, the disruption of the rRNA operon seems to be one of the tendencies associated with the characteristics of bacteria requiring a low dynamic range.
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Biomolecules as Flame Retardant Additives for Polymers: A Review. Polymers (Basel) 2020; 12:polym12040849. [PMID: 32272648 PMCID: PMC7240707 DOI: 10.3390/polym12040849] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 12/02/2022] Open
Abstract
Biological molecules can be obtained from natural sources or from commercial waste streams and can serve as effective feedstocks for a wide range of polymer products. From foams to epoxies and composites to bulk plastics, biomolecules show processability, thermal stability, and mechanical adaptations to fulfill current material requirements. This paper summarizes the known bio-sourced (or bio-derived), environmentally safe, thermo-oxidative, and flame retardant (BEST-FR) additives from animal tissues, plant fibers, food waste, and other natural resources. The flammability, flame retardance, and—where available—effects on polymer matrix’s mechanical properties of these materials will be presented. Their method of incorporation into the matrix, and the matrices for which the BEST-FR should be applicable will also be made known if reported. Lastly, a review on terminology and testing methodology is provided with comments on future developments in the field.
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A Novel Noncoding RNA dsr11 Involved in Heat Stress Tolerance in Deinococcus radiodurans. Biomolecules 2019; 10:biom10010022. [PMID: 31877996 PMCID: PMC7022480 DOI: 10.3390/biom10010022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/11/2019] [Accepted: 12/18/2019] [Indexed: 12/30/2022] Open
Abstract
Deinococcus radiodurans is an extremely resistant bacteria that has evolved masterful strategies to enable survival under various environmental stress conditions. Heat stress is a major environmental stress factor that can cause denaturation of proteins, membrane disruption, and oxidative stress. Previous studies have examined the mechanisms of the heat stress response by analyzing changes in protein levels; however, little is known about the role of small noncoding RNAs (ncRNAs), which are known to play important regulatory functions in bacteria during various environmental stress response. The ncRNA dsr11 of D. radiodurans was previously identified by RNA-seq and Northern blot. In this study, we showed that the transcription level of dsr11 was up-regulated 4.2-fold under heat stress by qRT-PCR analysis. Heat tolerance assay showed that deleting dsr11 significantly inhibited the viability under high temperature conditions. To assess the influence of dsr11 on the D. radiodurans transcriptome, 157 genes were found differentially expressed in the knock-out mutant by RNA-seq experiment. Combining RNA-seq and in silico analysis, we found that trmE (tRNA modification GTPase) and dr_0651 (arginase) were likely to be the direct targets of dsr11. Further microscale thermophoresis results demonstrated that dsr11 can directly bind to the mRNA of trmE and dr_0651. Our results indicated that dsr11 can enhance the tolerance to heat stress of D. radiodurans by binding to trmE and dr_0651 mRNA. Overall, these results extend our understanding of ncRNA regulation and provide new insights into the heat stress response in D. radiodurans.
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16
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Shifts in microbial community composition in tannery-contaminated soil in response to increased gamma radiation. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01541-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Abstract
Purpose
Contaminated sites from man-made activities such as old-fashioned tanneries are inhabited by virulent microorganisms that exhibit more resistance against extreme and toxic environmental conditions. We investigated the effect of different Gamma radiation doses on microbial community composition in the sediment of an old-fashioned tannery.
Methods
Seven samples collected from the contaminated sites received different gamma radiation doses (I = 0.0, II = 5, III = 10, VI = 15, V = 20, VI = 25, and VII = 30 kGy) as an acute exposure. The shift in microbial community structure was assessed using the high throughput 454 pyrosequencing. Variations in diversity, richness, and the shift in operational taxonomic units (OTUs) were investigated using statistical analysis.
Result
Our results showed that the control sample (I) had the highest diversity, richness, and OTUs when compared with the irradiated samples. Species of Halocella, Parasporobacterium, and Anaerosporobacter had the highest relative abundance at the highest radiation dose of 30 kGy. Members of the Firmicutes also increased by 20% at the highest radiation dose when compared with the control sample (0.0 kGy). Representatives of Synergistetes decreased by 25% while Bacteroidetes retained a steady distribution across the range of gamma radiation intensities.
Conclusion
This study provides information about potential “radioresistant” and/or “radiotolerant” microbial species that are adapted to elevated level of chemical toxicity such as Cr and Sr in tannery. These species can be of a high biotechnological and environmental importance.
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Khlebodarova TM, Likhoshvai VA. Molecular Mechanisms of Non-Inherited Antibiotic Tolerance in Bacteria and Archaea. Mol Biol 2019. [DOI: 10.1134/s0026893319040058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage. Appl Environ Microbiol 2019; 85:AEM.00988-19. [PMID: 31126947 DOI: 10.1128/aem.00988-19] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 05/19/2019] [Indexed: 01/01/2023] Open
Abstract
Survival and growth of the anaerobic gut fungi (AGF; Neocallimastigomycota) in the herbivorous gut necessitate the possession of multiple abilities absent in other fungal lineages. We hypothesized that horizontal gene transfer (HGT) was instrumental in forging the evolution of AGF into a phylogenetically distinct gut-dwelling fungal lineage. The patterns of HGT were evaluated in the transcriptomes of 27 AGF strains, 22 of which were isolated and sequenced in this study, and 4 AGF genomes broadly covering the breadth of AGF diversity. We identified 277 distinct incidents of HGT in AGF transcriptomes, with subsequent gene duplication resulting in an HGT frequency of 2 to 3.5% in AGF genomes. The majority of HGT events were AGF specific (91.7%) and wide (70.8%), indicating their occurrence at early stages of AGF evolution. The acquired genes allowed AGF to expand their substrate utilization range, provided new venues for electron disposal, augmented their biosynthetic capabilities, and facilitated their adaptation to anaerobiosis. The majority of donors were anaerobic fermentative bacteria prevalent in the herbivorous gut. This study strongly indicates that HGT indispensably forged the evolution of AGF as a distinct fungal phylum and provides a unique example of the role of HGT in shaping the evolution of a high-rank taxonomic eukaryotic lineage.IMPORTANCE The anaerobic gut fungi (AGF) represent a distinct basal phylum lineage (Neocallimastigomycota) commonly encountered in the rumen and alimentary tracts of herbivores. Survival and growth of anaerobic gut fungi in these anaerobic, eutrophic, and prokaryote-dominated habitats necessitates the acquisition of several traits absent in other fungal lineages. We assess here the role of horizontal gene transfer as a relatively fast mechanism for trait acquisition by the Neocallimastigomycota postsequestration in the herbivorous gut. Analysis of 27 transcriptomes that represent the broad diversity of Neocallimastigomycota identified 277 distinct HGT events, with subsequent gene duplication resulting in an HGT frequency of 2 to 3.5% in AGF genomes. These HGT events have allowed AGF to survive in the herbivorous gut by expanding their substrate utilization range, augmenting their biosynthetic pathway, providing new routes for electron disposal by expanding fermentative capacities, and facilitating their adaptation to anaerobiosis. HGT in the AGF is also shown to be mainly a cross-kingdom affair, with the majority of donors belonging to the bacteria. This study represents a unique example of the role of HGT in shaping the evolution of a high-rank taxonomic eukaryotic lineage.
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19
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Farci D, Guadalupi G, Bierła K, Lobinski R, Piano D. The Role of Iron and Copper on the Oligomerization Dynamics of DR_2577, the Main S-Layer Protein of Deinococcus radiodurans. Front Microbiol 2019; 10:1450. [PMID: 31333601 PMCID: PMC6615493 DOI: 10.3389/fmicb.2019.01450] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/11/2019] [Indexed: 01/04/2023] Open
Abstract
Surface (S)-layers are cryptic structures that coat the external surface of the bacterial cell in many species. The paracrystalline regularity of the S-layer is due to the self-assembling of one or more protein units. The property of self-assembling seems to be mediated by specific topologies of the S-layer proteins as well as the presence of specific ions that provide support in building and stabilizing the bi-dimensional S-layer organization. In the present study, we have investigated the self-assembling mechanism of the main S-layer protein of Deinococcus radiodurans (DR_2577) finding an unusual role played by Fe3+ and Cu2+ in the oligomerization of this protein. These findings may trace a structural and functional metallo-mediated convergence between the role of these metals in the assembling of the S-layer and their well-known roles in protecting against oxidative stress in D. radiodurans.
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Affiliation(s)
- Domenica Farci
- Department of Plant Physiology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland.,Laboratory of Photobiology and Plant Physiology, Department of Life and Environmental Sciences University of Cagliari, Cagliari, Italy
| | - Giulia Guadalupi
- Laboratory of Photobiology and Plant Physiology, Department of Life and Environmental Sciences University of Cagliari, Cagliari, Italy
| | - Katarzyna Bierła
- Laboratory of Analitycal and Bioinorganic Chemistry and Environment, UMR5254 Institute of Analytical and Physical Chemistry for the Environment and Materials (IPREM), Pau, France
| | - Ryszard Lobinski
- Laboratory of Analitycal and Bioinorganic Chemistry and Environment, UMR5254 Institute of Analytical and Physical Chemistry for the Environment and Materials (IPREM), Pau, France
| | - Dario Piano
- Department of Plant Physiology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland.,Laboratory of Photobiology and Plant Physiology, Department of Life and Environmental Sciences University of Cagliari, Cagliari, Italy
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20
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Krupovic M, Makarova KS, Wolf YI, Medvedeva S, Prangishvili D, Forterre P, Koonin EV. Integrated mobile genetic elements in Thaumarchaeota. Environ Microbiol 2019; 21:2056-2078. [PMID: 30773816 PMCID: PMC6563490 DOI: 10.1111/1462-2920.14564] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/10/2019] [Accepted: 02/13/2019] [Indexed: 12/20/2022]
Abstract
To explore the diversity of mobile genetic elements (MGE) associated with archaea of the phylum Thaumarchaeota, we exploited the property of most MGE to integrate into the genomes of their hosts. Integrated MGE (iMGE) were identified in 20 thaumarchaeal genomes amounting to 2 Mbp of mobile thaumarchaeal DNA. These iMGE group into five major classes: (i) proviruses, (ii) casposons, (iii) insertion sequence-like transposons, (iv) integrative-conjugative elements and (v) cryptic integrated elements. The majority of the iMGE belong to the latter category and might represent novel families of viruses or plasmids. The identified proviruses are related to tailed viruses of the order Caudovirales and to tailless icosahedral viruses with the double jelly-roll capsid proteins. The thaumarchaeal iMGE are all connected within a gene sharing network, highlighting pervasive gene exchange between MGE occupying the same ecological niche. The thaumarchaeal mobilome carries multiple auxiliary metabolic genes, including multicopper oxidases and ammonia monooxygenase subunit C (AmoC), and stress response genes, such as those for universal stress response proteins (UspA). Thus, iMGE might make important contributions to the fitness and adaptation of their hosts. We identified several iMGE carrying type I-B CRISPR-Cas systems and spacers matching other thaumarchaeal iMGE, suggesting antagonistic interactions between coexisting MGE and symbiotic relationships with the ir archaeal hosts.
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Affiliation(s)
- Mart Krupovic
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, 75015, Paris, France
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Sofia Medvedeva
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, 75015, Paris, France.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia.,Sorbonne Université, Collège doctoral, 75005, Paris, France
| | - David Prangishvili
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, 75015, Paris, France
| | - Patrick Forterre
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, 75015, Paris, France.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris- Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, Paris, France
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
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21
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Blesa A, Sánchez M, Sacristán-Horcajada E, González-de la Fuente S, Peiró R, Berenguer J. Into the Thermus Mobilome: Presence, Diversity and Recent Activities of Insertion Sequences Across Thermus spp. Microorganisms 2019; 7:microorganisms7010025. [PMID: 30669685 PMCID: PMC6352166 DOI: 10.3390/microorganisms7010025] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/09/2019] [Accepted: 01/17/2019] [Indexed: 11/28/2022] Open
Abstract
A high level of transposon-mediated genome rearrangement is a common trait among microorganisms isolated from thermal environments, probably contributing to the extraordinary genomic plasticity and horizontal gene transfer (HGT) observed in these habitats. In this work, active and inactive insertion sequences (ISs) spanning the sequenced members of the genus Thermus were characterized, with special emphasis on three T. thermophilus strains: HB27, HB8, and NAR1. A large number of full ISs and fragments derived from different IS families were found, concentrating within megaplasmids present in most isolates. Potentially active ISs were identified through analysis of transposase integrity, and domestication-related transposition events of ISTth7 were identified in laboratory-adapted HB27 derivatives. Many partial copies of ISs appeared throughout the genome, which may serve as specific targets for homologous recombination contributing to genome rearrangement. Moreover, recruitment of IS1000 32 bp segments as spacers for CRISPR sequence was identified, pointing to the adaptability of these elements in the biology of these thermophiles. Further knowledge about the activity and functional diversity of ISs in this genus may contribute to the generation of engineered transposons as new genetic tools, and enrich our understanding of the outstanding plasticity shown by these thermophiles.
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Affiliation(s)
- Alba Blesa
- Department of Biotechnology, Faculty of Experimental Sciences, Universidad Francisco de Vitoria, Madrid 28223, Spain.
| | - Mercedes Sánchez
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
| | - Eva Sacristán-Horcajada
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
| | - Sandra González-de la Fuente
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
| | - Ramón Peiró
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
| | - José Berenguer
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
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22
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Kerfahi D, Tripathi BM, Dong K, Kim M, Kim H, Ferry Slik JW, Go R, Adams JM. From the High Arctic to the Equator: Do Soil Metagenomes Differ According to Our Expectations? MICROBIAL ECOLOGY 2019; 77:168-185. [PMID: 29882154 DOI: 10.1007/s00248-018-1215-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 05/28/2018] [Indexed: 06/08/2023]
Abstract
Comparing the functional gene composition of soils at opposite extremes of environmental gradients may allow testing of hypotheses about community and ecosystem function. Here, we were interested in comparing how tropical microbial ecosystems differ from those of polar climates. We sampled several sites in the equatorial rainforest of Malaysia and Brunei, and the high Arctic of Svalbard, Canada, and Greenland, comparing the composition and the functional attributes of soil biota between the two extremes of latitude, using shotgun metagenomic Illumina HiSeq2000 sequencing. Based upon "classical" views of how tropical and higher latitude ecosystems differ, we made a series of predictions as to how various gene function categories would differ in relative abundance between tropical and polar environments. Results showed that in some respects our predictions were correct: the polar samples had higher relative abundance of dormancy related genes, and lower relative abundance of genes associated with respiration, and with metabolism of aromatic compounds. The network complexity of the Arctic was also lower than the tropics. However, in various other respects, the pattern was not as predicted; there were no differences in relative abundance of stress response genes or in genes associated with secondary metabolism. Conversely, CRISPR genes, phage-related genes, and virulence disease and defense genes, were unexpectedly more abundant in the Arctic, suggesting more intense biotic interaction. Also, eukaryote diversity and bacterial diversity were higher in the Arctic of Svalbard compared to tropical Brunei, which is consistent with what may expected from amplicon studies in terms of the higher pH of the Svalbard soil. Our results in some respects confirm expectations of how tropical versus polar nature may differ, and in other respects challenge them.
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Affiliation(s)
- Dorsaf Kerfahi
- Department of Biological Sciences, Seoul National University, Gwanak-Gu, Seoul, 151-747, Republic of Korea
| | - Binu M Tripathi
- Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - Ke Dong
- Department of Biological Sciences, Seoul National University, Gwanak-Gu, Seoul, 151-747, Republic of Korea
| | - Mincheol Kim
- Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - Hyoki Kim
- Celemics Inc., 19F, Bldg. A, BYC High City, 131, Gasandigital 1-ro, Geumcheon-gu, Seoul, 153-718, Republic of Korea
| | - J W Ferry Slik
- Faculty of Science, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Rusea Go
- Department of Biology, Faculty of Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Jonathan M Adams
- Division of Agrifood and Environment, School of Water, Energy and Environment, Cranfield University, Bedfordshire, MK43 0AL, UK.
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23
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Ding Y, Fleming AM, Burrows CJ. Case studies on potential G-quadruplex-forming sequences from the bacterial orders Deinococcales and Thermales derived from a survey of published genomes. Sci Rep 2018; 8:15679. [PMID: 30356061 PMCID: PMC6200779 DOI: 10.1038/s41598-018-33944-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/06/2018] [Indexed: 12/13/2022] Open
Abstract
Genomes provide a platform for storage of chemical information that must be stable under the context in which an organism thrives. The 2'-deoxyguanosine (G) nucleotide has the potential to provide additional chemical information beyond its Watson-Crick base-pairing capacity. Sequences with four or more runs of three G nucleotides each are potential G-quadruplex forming sequences (PQSs) that can adopt G-quadruplex folds. Herein, we analyzed sequenced genomes from the NCBI database to determine the PQS densities of the genome sequences. First, we found organisms with large genomes, including humans, alligators, and maize, have similar densities of PQSs (~300 PQSs/Mbp), and the genomes are significantly enriched in PQSs with more than four G tracks. Analysis of microorganism genomes found a greater diversity of PQS densities. In general, PQS densities positively tracked with the GC% of the genome. Exceptions to this observation were the genomes from thermophiles that had many more PQSs than expected by random chance. Analysis of the location of these PQSs in annotated genomes from the order Thermales showed these G-rich sequences to be randomly distributed; in contrast, in the order Deinococcales the PQSs were enriched and biased around transcription start sites of genes. Four representative PQSs, two each from the Thermales and Deinococcales, were studied by biophysical methods to establish the ability of them to fold to G-quadruplexes. The experiments found the two PQSs in the Thermales did not adopt G-quadruplex folds, while the two most common in the Deinococcales adopted stable parallel-stranded G-quadruplexes. The findings lead to a hypothesis that thermophilic organisms are enriched with PQSs as an unavoidable consequence to stabilize thermally their genomes to live at high temperature; in contrast, the genomes from stress-resistant bacteria found in the Deinococcales may utilize PQSs for gene regulatory purposes.
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Affiliation(s)
- Yun Ding
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112-0850, United States.
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112-0850, United States.
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24
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Farci D, Farci SF, Esposito F, Tramontano E, Kirkpatrick J, Piano D. On the S-layer of Thermus thermophilus and the assembling of its main protein SlpA. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1554-1562. [PMID: 29803693 DOI: 10.1016/j.bbamem.2018.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 05/21/2018] [Accepted: 05/23/2018] [Indexed: 02/07/2023]
Abstract
We have isolated and analysed the cell envelope of the thermophilic bacterium Thermus thermophilus HB8. Isolated cell walls, characterized by the dominance of the S-layer protein SlpA, are found to be constituted by several protein complexes of high molecular weights. Further isolation steps, starting from the cell wall samples, led to the selective release of the S-layer protein SlpA in solution as confirmed by mass spectrometry. Blue Native gel electrophoresis on these samples showed that SlpA is organized into a specific hierarchical order of oligomeric states that are consistent with the complexes at high molecular weight identified on the total cell wall fraction. The analysis showed that SlpA bases this peculiar organization on monomers and exceptionally stable dimers, leading to the formation of tetramers, heptamers, and decamers. Furthermore, the two elementary units of SlpA, monomers and dimers, are regulated by the presence of calcium not only for the assembling of monomers into dimers, but also for the splitting of dimers into monomers. Finally, the SlpA protein was found to be subjected to specific proteolysis leading to characteristic degradation products. Findings are discussed in terms of S-layer assembling properties as bases for understanding its structure, turn-over and organization.
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Affiliation(s)
- Domenica Farci
- Department of Life and Environmental Sciences, Laboratory of Photobiology and Plant Physiology, University of Cagliari, V.le S. Ingnazio da Laconi 13, 09123 Cagliari, Italy.
| | - Stefano Francesco Farci
- Department of Life and Environmental Sciences, Laboratory of Photobiology and Plant Physiology, University of Cagliari, V.le S. Ingnazio da Laconi 13, 09123 Cagliari, Italy
| | - Francesca Esposito
- Department of Life and Environmental Sciences, Laboratory of Molecular Virology, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, 09042 Monserrato, Cagliari, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, Laboratory of Molecular Virology, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, 09042 Monserrato, Cagliari, Italy
| | - Joanna Kirkpatrick
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutebergstraβe 11, 07745 Jena, Germany
| | - Dario Piano
- Department of Life and Environmental Sciences, Laboratory of Photobiology and Plant Physiology, University of Cagliari, V.le S. Ingnazio da Laconi 13, 09123 Cagliari, Italy.
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25
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Rastogi A, Maheswari U, Dorrell RG, Vieira FRJ, Maumus F, Kustka A, McCarthy J, Allen AE, Kersey P, Bowler C, Tirichine L. Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms. Sci Rep 2018; 8:4834. [PMID: 29556065 PMCID: PMC5859163 DOI: 10.1038/s41598-018-23106-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 03/02/2018] [Indexed: 11/13/2022] Open
Abstract
Diatoms are one of the most successful and ecologically important groups of eukaryotic phytoplankton in the modern ocean. Deciphering their genomes is a key step towards better understanding of their biological innovations, evolutionary origins, and ecological underpinnings. Here, we have used 90 RNA-Seq datasets from different growth conditions combined with published expressed sequence tags and protein sequences from multiple taxa to explore the genome of the model diatom Phaeodactylum tricornutum, and introduce 1,489 novel genes. The new annotation additionally permitted the discovery of extensive alternative splicing in diatoms, including intron retention and exon skipping, which increase the diversity of transcripts generated in changing environments. In addition, we have used up-to-date reference sequence libraries to dissect the taxonomic origins of diatom genes. We show that the P. tricornutum genome is enriched in lineage-specific genes, with up to 47% of the gene models present only possessing orthologues in other stramenopile groups. Finally, we have performed a comprehensive de novo annotation of repetitive elements showing novel classes of transposable elements such as SINE, MITE and TRIM/LARD. This work provides a solid foundation for future studies of diatom gene function, evolution and ecology.
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Affiliation(s)
- Achal Rastogi
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université, 75005, Paris, France
| | - Uma Maheswari
- EMBL-EBI, Wellcome Trust Genome Campus, Cambridge, CB10 1 SD, United Kingdom
| | - Richard G Dorrell
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université, 75005, Paris, France
| | - Fabio Rocha Jimenez Vieira
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université, 75005, Paris, France
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, Versailles, 78026, France
| | - Adam Kustka
- Earth and Environmental Sciences, Rutgers University, 101 Warren Street, 07102, Newark, New Jersey, USA
| | - James McCarthy
- J. Craig Venter Institute, 10355 Science Center Drive, 92121, San Diego, California, USA
| | - Andy E Allen
- J. Craig Venter Institute, 10355 Science Center Drive, 92121, San Diego, California, USA
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Paul Kersey
- EMBL-EBI, Wellcome Trust Genome Campus, Cambridge, CB10 1 SD, United Kingdom
| | - Chris Bowler
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université, 75005, Paris, France.
| | - Leila Tirichine
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université, 75005, Paris, France.
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Gostinčar C, Gunde-Cimerman N. Overview of Oxidative Stress Response Genes in Selected Halophilic Fungi. Genes (Basel) 2018; 9:E143. [PMID: 29509668 PMCID: PMC5867864 DOI: 10.3390/genes9030143] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/22/2018] [Accepted: 02/27/2018] [Indexed: 11/17/2022] Open
Abstract
Exposure of microorganisms to stress, including to high concentrations of salt, can lead to increased production of reactive oxygen species in the cell. To limit the resulting damage, cells have evolved a variety of antioxidant defenses. The role of these defenses in halotolerance has been proposed before. Whole genome sequencing for some of the most halotolerant and halophilic fungal species has enabled us to investigate the possible links between oxidative and salt stress tolerance on the genomic level. We identified genes involved in oxidative stress response in the halophilic basidiomycete Wallemia ichthyophaga, and halotolerant ascomycetous black yeasts Hortaea werneckii and Aureobasidium pullulans, and compared them to genes from 16 other fungi, both asco- and basidiomycetes. According to our results, W. ichthyophaga can survive salinities detrimental to most other organisms with only a moderate number of oxidative stress response genes. In other investigated species, however, the maximum tolerated salinity correlated with the number of genes encoding three major enzymes of the cellular oxidative stress response: superoxide dismutases, catalases, and peroxiredoxins. This observation supports the hypothetical link between the antioxidant capacity of cells and their halotolerance.
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Affiliation(s)
- Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.
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27
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Functional dissection of the three N-terminal general secretory pathway domains and the Walker motifs of the traffic ATPase PilF from Thermus thermophilus. Extremophiles 2018; 22:461-471. [PMID: 29464394 DOI: 10.1007/s00792-018-1008-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/05/2018] [Indexed: 01/25/2023]
Abstract
The traffic ATPase PilF of Thermus thermophilus powers pilus assembly as well as uptake of DNA. PilF differs from other traffic ATPases by a triplicated general secretory pathway II, protein E, N-terminal domain (GSPIIABC). We investigated the in vivo and in vitro roles of the GSPII domains, the Walker A motif and a catalytic glutamate by analyzing a set of PilF deletion derivatives and pilF mutants. Here, we report that PilF variants devoid of the first two or all three GSPII domains do not form stable hexamers indicating a role of the triplicated GSPII domain in complex formation and/or stability. A pilFΔGSPIIC mutant was significantly impaired in piliation which leads to the conclusion that the GSPIIC domain plays a vital role in pilus assembly. Interestingly, the pilFΔGSPIIC mutant was hypertransformable. This suggests that GSPIIC strongly affects transformation efficiency. A pilF∆GSPIIA mutant exhibited wild-type piliation but reduced pilus-mediated twitching motility, suggesting that GSPIIA plays a role in pilus dynamics. Furthermore, we report that pilF mutants with a defect in the ATP binding Walker A motif or in the catalytic glutamate residue are defective in piliation and natural transformation. These findings show that both, ATP binding and hydrolysis, are essential for the dual function of PilF in natural transformation and pilus assembly.
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28
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Ott E, Kawaguchi Y, Kölbl D, Chaturvedi P, Nakagawa K, Yamagishi A, Weckwerth W, Milojevic T. Proteometabolomic response of Deinococcus radiodurans exposed to UVC and vacuum conditions: Initial studies prior to the Tanpopo space mission. PLoS One 2017; 12:e0189381. [PMID: 29244852 PMCID: PMC5731708 DOI: 10.1371/journal.pone.0189381] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/24/2017] [Indexed: 11/18/2022] Open
Abstract
The multiple extremes resistant bacterium Deinococcus radiodurans is able to withstand harsh conditions of simulated outer space environment. The Tanpopo orbital mission performs a long-term space exposure of D. radiodurans aiming to investigate the possibility of interplanetary transfer of life. The revealing of molecular machinery responsible for survivability of D. radiodurans in the outer space environment can improve our understanding of underlying stress response mechanisms. In this paper, we have evaluated the molecular response of D. radiodurans after the exposure to space-related conditions of UVC irradiation and vacuum. Notably, scanning electron microscopy investigations showed that neither morphology nor cellular integrity of irradiated cells was affected, while integrated proteomic and metabolomic analysis revealed numerous molecular alterations in metabolic and stress response pathways. Several molecular key mechanisms of D. radiodurans, including the tricarboxylic acid cycle, the DNA damage response systems, ROS scavenging systems and transcriptional regulators responded in order to cope with the stressful situation caused by UVC irradiation under vacuum conditions. These results reveal the effectiveness of the integrative proteometabolomic approach as a tool in molecular analysis of microbial stress response caused by space-related factors.
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Affiliation(s)
- Emanuel Ott
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Yuko Kawaguchi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Denise Kölbl
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Palak Chaturvedi
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Kazumichi Nakagawa
- Graduate School of Human Development and Environment, Kobe University, Kobe, Japan
| | - Akihiko Yamagishi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
- * E-mail: (TM); (WW)
| | - Tetyana Milojevic
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
- * E-mail: (TM); (WW)
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29
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Thavamani P, Samkumar RA, Satheesh V, Subashchandrabose SR, Ramadass K, Naidu R, Venkateswarlu K, Megharaj M. Microbes from mined sites: Harnessing their potential for reclamation of derelict mine sites. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 230:495-505. [PMID: 28688926 DOI: 10.1016/j.envpol.2017.06.056] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 05/12/2017] [Accepted: 06/17/2017] [Indexed: 05/11/2023]
Abstract
Derelict mines pose potential risks to environmental health. Several factors such as soil structure, organic matter, and nutrient content are the greatly affected qualities in mined soils. Soil microbial communities are an important element for successful reclamation because of their major role in nutrient cycling, plant establishment, geochemical transformations, and soil formation. Yet, microorganisms generally remain an undervalued asset in mined sites. The microbial diversity in derelict mine sites consists of diverse species belonging to four key phyla: Proteobacteria, Acidobacteria, Firmicutes, and Bacteroidetes. The activity of plant symbiotic microorganisms including root-colonizing rhizobacteria and ectomycorrhizal fungi of existing vegetation in the mined sites is very high since most of these microbes are extremophiles. This review outlines the importance of microorganisms to soil health and the rehabilitation of derelict mines and how microbial activity and diversity can be exploited to better plan the soil rehabilitation. Besides highlighting the major breakthroughs in the application of microorganisms for mined site reclamation, we provide a critical view on plant-microbiome interactions to improve revegetation at the mined sites. Also, the need has been emphasized for deciphering the molecular mechanisms of adaptation and resistance of rhizosphere and non-rhizosphere microbes in abandoned mine sites, understanding their role in remediation, and subsequent harnessing of their potential to pave the way in future rehabilitation strategies for mined sites.
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Affiliation(s)
- Palanisami Thavamani
- Global Centre for Environmental Remediation, University of Newcastle, Australia.
| | - R Amos Samkumar
- ICAR- National Research Centre on Plant Biotechnology, Pusa, New Delhi 110012, India
| | - Viswanathan Satheesh
- ICAR- National Research Centre on Plant Biotechnology, Pusa, New Delhi 110012, India
| | | | - Kavitha Ramadass
- Future Industries Institute, University of South Australia, Australia
| | - Ravi Naidu
- Global Centre for Environmental Remediation, University of Newcastle, Australia
| | - Kadiyala Venkateswarlu
- Formerly Department of Microbiology, Sri Krishnadevaraya University, Anantapur 515055, India
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30
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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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31
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Devlin R, Marques CA, McCulloch R. Does DNA replication direct locus-specific recombination during host immune evasion by antigenic variation in the African trypanosome? Curr Genet 2017; 63:441-449. [PMID: 27822899 PMCID: PMC5422504 DOI: 10.1007/s00294-016-0662-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 12/14/2022]
Abstract
All pathogens must survive host immune attack and, amongst the survival strategies that have evolved, antigenic variation is a particularly widespread reaction to thwart adaptive immunity. Though the reactions that underlie antigenic variation are highly varied, recombination by gene conversion is a widespread approach to immune survival in bacterial and eukaryotic pathogens. In the African trypanosome, antigenic variation involves gene conversion-catalysed movement of a huge number of variant surface glycoprotein (VSG) genes into a few telomeric sites for VSG expression, amongst which only a single site is actively transcribed at one time. Genetic evidence indicates VSG gene conversion has co-opted the general genome maintenance reaction of homologous recombination, aligning the reaction strategy with targeted rearrangements found in many organisms. What is less clear is how gene conversion might be initiated within the locality of the VSG expression sites. Here, we discuss three emerging models for VSG switching initiation and ask how these compare with processes for adaptive genome change found in other organisms.
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Affiliation(s)
- Rebecca Devlin
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Catarina A Marques
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, UK
| | - Richard McCulloch
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK.
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32
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Vishambra D, Srivastava M, Dev K, Jaiswal V. Subcellular localization based comparative study on radioresistant bacteria: A novel approach to mine proteins involve in radioresistance. Comput Biol Chem 2017; 69:1-9. [PMID: 28527408 DOI: 10.1016/j.compbiolchem.2017.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 03/25/2017] [Accepted: 05/05/2017] [Indexed: 11/16/2022]
Abstract
Radioresistant bacteria (RRB) are among the most radioresistant organisms and has a unique role in evolution. Along with the evolutionary role, radioresistant organisms play important role in paper industries, bioremediation, vaccine development and possibility in anti-aging and anti-cancer treatment. The study of radiation resistance in RRB was mainly focused on cytosolic mechanisms such as DNA repair mechanism, cell cleansing activity and high antioxidant activity. Although it was known that protein localized on outer areas of cell play role in resistance towards extreme condition but the mechanisms/proteins localized on the outer area of cells are not studied for radioresistance. Considering the fact that outer part of cell is more exposed to radiations and proteins present in outer area of the cell may have role in radioresistance. Localization based comparative study of proteome from RRB and non-radio resistant bacteria was carried out. In RRB 20 unique proteins have been identified. Further domain, structural, and pathway analysis of selected proteins were carried out. Out of 20 proteins, 8 proteins were direct involvement in radioresistance and literature study strengthens this, however, 1 proteins had assumed relation in radioresistance. Selected radioresistant proteins may be helpful for optimal use of RRB in industry and health care.
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Affiliation(s)
- Divya Vishambra
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Malay Srivastava
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Kamal Dev
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Varun Jaiswal
- School of Electrical and Computer Science Engineering, Shoolini University, Solan, Himachal Pradesh, India.
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33
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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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34
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Han W, Cheng J, Zhou C, Hua Y, Zhao Y. Crystal structure of the RNA 2',3'-cyclic phosphodiesterase from Deinococcus radiodurans. Acta Crystallogr F Struct Biol Commun 2017; 73:276-280. [PMID: 28471359 PMCID: PMC5417317 DOI: 10.1107/s2053230x17004964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/30/2017] [Indexed: 01/11/2023] Open
Abstract
2',3'-Cyclic phosphodiesterase (CPDase) homologues have been found in all domains of life and are involved in diverse RNA and nucleotide metabolisms. The CPDase from Deinococcus radiodurans was crystallized and the crystals diffracted to 1.6 Å resolution, which is the highest resolution currently known for a CPDase structure. Structural comparisons revealed that the enzyme is in an open conformation in the absence of substrate. Nevertheless, the active site is well formed, and the representative motifs interact with sulfate ion, which suggests a conserved catalytic mechanism.
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Affiliation(s)
- Wanchun Han
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, People’s Republic of China
| | - Jiahui Cheng
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, People’s Republic of China
| | - Congli Zhou
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, People’s Republic of China
| | - Yuejin Hua
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, People’s Republic of China
| | - Ye Zhao
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, People’s Republic of China
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35
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Blesa A, Quintans NG, Baquedano I, Mata CP, Castón JR, Berenguer J. Role of Archaeal HerA Protein in the Biology of the Bacterium Thermus thermophilus. Genes (Basel) 2017; 8:genes8050130. [PMID: 28448436 PMCID: PMC5448004 DOI: 10.3390/genes8050130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/21/2017] [Accepted: 04/24/2017] [Indexed: 11/16/2022] Open
Abstract
Intense gene flux between prokaryotes result in high percentage of archaeal genes in the genome of the thermophilic bacteria Thermus spp. Among these archaeal genes a homolog to the Sulfolobus spp. HerA protein appears in all of the Thermus spp. strains so far sequenced (HepA). The role of HepA in Thermus thermophilus HB27 has been analyzed using deletion mutants, and its structure resolved at low resolution by electron microscopy. Recombinant HepA shows DNA-dependent ATPase activity and its structure revealed a double ring, conically-shaped hexamer with an upper diameter of 150 Å and a bottom module of 95 Å. A central pore was detected in the structure that ranges from 13 Å at one extreme, to 30 Å at the other. Mutants lacking HepA show defective natural competence and DNA donation capability in a conjugation-like process termed "transjugation", and also high sensitivity to UV and dramatic sensitivity to high temperatures. These data support that acquisition of an ancestral archaeal HerA has been fundamental for the adaptation of Thermus spp. to high temperatures.
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Affiliation(s)
- Alba Blesa
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Calle Nicolás Cabrera 1, Madrid 28049, Spain.
| | - Nieves G Quintans
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Calle Nicolás Cabrera 1, Madrid 28049, Spain.
| | - Ignacio Baquedano
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Calle Nicolás Cabrera 1, Madrid 28049, Spain.
| | - Carlos P Mata
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Cantoblanco, Madrid 28049, Spain.
| | - José R Castón
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Cantoblanco, Madrid 28049, Spain.
| | - José Berenguer
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Calle Nicolás Cabrera 1, Madrid 28049, Spain.
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36
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Bentkowski P, van Oosterhout C, Ashby B, Mock T. The effect of extrinsic mortality on genome size evolution in prokaryotes. THE ISME JOURNAL 2017; 11:1011-1018. [PMID: 27922601 PMCID: PMC5364348 DOI: 10.1038/ismej.2016.165] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 10/06/2016] [Accepted: 10/20/2016] [Indexed: 01/13/2023]
Abstract
Mortality has a significant role in prokaryotic ecology and evolution, yet the impact of variations in extrinsic mortality on prokaryotic genome evolution has received little attention. We used both mathematical and agent-based models to reveal how variations in extrinsic mortality affect prokaryotic genome evolution. Our results suggest that the genome size of bacteria increases with increased mortality. A high extrinsic mortality increases the pool of free resources and shortens life expectancy, which selects for faster reproduction, a phenotype we called 'scramblers'. This phenotype is realised by the expansion of gene families involved in nutrient acquisition and metabolism. In contrast, a low mortality rate increases an individual's life expectancy, which results in natural selection favouring tolerance to starvation when conditions are unfavourable. This leads to the evolution of small, streamlined genomes ('stayers'). Our models predict that large genomes, gene family expansion and horizontal gene transfer should be observed in prokaryotes occupying ecosystems exposed to high abiotic stress, as well as those under strong predator- and/or pathogen-mediated selection. A comparison of genome size of cyanobacteria in relatively stable marine versus more turbulent freshwater environments corroborates our predictions, although other factors between these environments could also be responsible.
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Affiliation(s)
- Piotr Bentkowski
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Ben Ashby
- Department of Mathematical Sciences, University of Bath, Bath, UK
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
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37
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Patil NA, Basu B, Deobagkar DD, Apte SK, Deobagkar DN. Putative DNA modification methylase DR_C0020 of Deinococcus radiodurans is an atypical SAM dependent C-5 cytosine DNA methylase. Biochim Biophys Acta Gen Subj 2016; 1861:593-602. [PMID: 28038990 DOI: 10.1016/j.bbagen.2016.12.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 11/17/2016] [Accepted: 12/24/2016] [Indexed: 11/30/2022]
Abstract
BACKGROUND Control of cellular processes by epigenetic modification of cytosine in DNA is widespread among living organisms, but, is hitherto unknown in the extremely radioresistant microbe D. radiodurans. METHODS C-5 methyl cytosines (m5C) were detected by immuno-blotting with m5C-specific antibody. Site of cytosine methylation by DR_C0020 encoded protein was investigated by bisulfite sequencing. The DR_C0020 knockout mutant (Δdcm), constructed by site directed mutagenesis, was assessed for effect on growth, radiation resistance and proteome. Proteins were identified by mass spectrometry. RESULTS Methylated cytosines were detected in the D. radiodurans genome. The DR_C0020 encoded protein (Dcm, NCBI accession: WP_034351354.1), whose amino acid sequence resembles m4C methylases, was shown to be the lone SAM-dependent C-5 cytosine methyltransferase. Purified Dcm protein was found to methylate CpN sequence with a preference for methylation of two consecutive cytosines. The Δdcm strain completely lost m5C modification from its genome, had no effect on growth but became radiation sensitive. The Δdcm cells exhibited minor alterations in the abundance of several proteins involved primarily in protein homeostasis, oxidative stress defense, metabolism, etc. CONCLUSION DR_C0020 encoded SAM-dependent methyltransferase Dcm is solely responsible for C-5cytosine methylation at CpN sites in the genome of D. radiodurans and regulates protein homeostasis under normal growth conditions. The protein is an unusual case of an amino methyltransferase that has evolved to producing m5C. GENERAL SIGNIFICANCE Although, dispensable under optimal growth conditions, the presence of m5C may be important for recognition of parent strand and, thus, could contribute to the extraordinary DNA repair in D. radiodurans.
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Affiliation(s)
- Nayana A Patil
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400 085, India; Department of Zoology, Centre for Advanced Studies, Savitribai Phule Pune University, Pune 411007, India
| | - Bhakti Basu
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Deepti D Deobagkar
- Department of Zoology, Centre for Advanced Studies, Savitribai Phule Pune University, Pune 411007, India
| | - Shree K Apte
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400 085, India.
| | - Dileep N Deobagkar
- Department of Zoology, Centre for Advanced Studies, Savitribai Phule Pune University, Pune 411007, India.
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Fan Y, Hoshino T, Nakamura A. Identification of a VapBC toxin-antitoxin system in a thermophilic bacterium Thermus thermophilus HB27. Extremophiles 2016; 21:153-161. [PMID: 27853887 DOI: 10.1007/s00792-016-0891-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 11/07/2016] [Indexed: 11/30/2022]
Abstract
There are 12 putative toxin-antitoxin (TA) loci in the Thermus thermophilus HB27 genome, including four VapBC and three HicBA families. Expression of these seven putative toxin genes in Escherichia coli demonstrated that one putative VapC toxin TTC0125 and two putative HicA toxins, TTC1395 and TTC1705, inhibited cell growth, and co-expression with cognate antitoxin genes rescued growth, indicating that these genes function as TA loci. In vitro analysis with the purified TTC0125 and total RNA/mRNA from E. coli and T. thermophilus showed that TTC0125 has RNase activity to rRNA and mRNA; this activity was inhibited by the addition of the purified TTC0126. Translation inhibition assays showed that TTC0125 inhibited protein synthesis by degrading mRNA but not by inactivating ribosomes. Amino acid substitutions of 14 predicted catalytic and conserved residues in VapC toxins to Ala or Asp in TTC0125 indicated that nine residues are important for its in vivo toxin activity and in vitro RNase activity. These data demonstrate that TTC0125-TTC0126 functions as a VapBC TA module and causes growth inhibition by degrading free RNA. This is the first study to identify the function of TA systems in T. thermophilus.
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Affiliation(s)
- Yuqi Fan
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Takayuki Hoshino
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Akira Nakamura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan.
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Agapov AA, Kulbachinskiy AV. Mechanisms of Stress Resistance and Gene Regulation in the Radioresistant Bacterium Deinococcus radiodurans. BIOCHEMISTRY (MOSCOW) 2016; 80:1201-16. [PMID: 26567564 DOI: 10.1134/s0006297915100016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The bacterium Deinococcus radiodurans reveals extraordinary resistance to ionizing radiation, oxidative stress, desiccation, and other damaging conditions. In this review, we consider the main molecular mechanisms underlying such resistance, including the action of specific DNA repair and antioxidation systems, and transcription regulation during the anti-stress response.
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Affiliation(s)
- A A Agapov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
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40
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Ho J, Adeolu M, Khadka B, Gupta RS. Identification of distinctive molecular traits that are characteristic of the phylum "Deinococcus-Thermus" and distinguish its main constituent groups. Syst Appl Microbiol 2016; 39:453-463. [PMID: 27506333 DOI: 10.1016/j.syapm.2016.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 07/14/2016] [Accepted: 07/21/2016] [Indexed: 12/30/2022]
Abstract
The phylum "Deinococcus-Thermus" contains two heavily researched groups of extremophilic bacteria: the highly radioresistant order Deinococcales and the thermophilic order Thermales. Very few characteristics are known that are uniquely shared by members of the phylum "Deinococcus-Thermus". Comprehensive phylogenetic and comparative analyses of >65 "Deinococcus-Thermus" genomes reported here have identified numerous molecular signatures in the forms of conserved signature insertions/deletions (CSIs) and conserved signature proteins (CSPs), which provide distinguishing characteristics of the phylum "Deinococcus-Thermus" and its main groups. We have identified 58 unique CSIs and 155 unique CSPs that delineate different phylogenetic groups within the phylum. Of these identified traits, 24 CSIs and 29 CSPs are characteristic of the phylum "Deinococcus-Thermus" and they provide novel and reliable means to circumscribe/describe this phylum. An additional 3 CSIs and 3 CSPs are characteristic of the order Deinococcales, and 6 CSIs and 51 CSPs are characteristic of the order Thermales. The remaining 25 CSIs and 72 CSPs identified in this study are distinctive traits of genus level groups within the phylum "Deinococcus-Thermus". The molecular characteristics identified in this work provide novel and independent support for the common ancestry of the members of the phylum "Deinococcus-Thermus" and provide a new means to distinguish the main constituent clades of the phylum. Additionally, the CSIs and CSPs identified in this work may play a role in the unique extremophilic adaptations of the members of this phylum and further functional analyses of these characteristics could provide novel biochemical insights into the unique adaptations found within the phylum "Deinococcus-Thermus".
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Affiliation(s)
- Jonathan Ho
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z, Canada
| | - Mobolaji Adeolu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z, Canada
| | - Bijendra Khadka
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z, Canada.
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41
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Aridhi S, Sghaier H, Zoghlami M, Maddouri M, Nguifo EM. Prediction of Ionizing Radiation Resistance in Bacteria Using a Multiple Instance Learning Model. J Comput Biol 2016; 23:10-20. [DOI: 10.1089/cmb.2015.0134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Sabeur Aridhi
- Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes (LIMOS)–Université Blaise Pascal (UBP), Clermont Ferrand, France
- Centre National de Recherche Scientifique (CNRS), UMR 6158, LIMOS, Aubière, France
- University of Tunis El Manar, Faculty of Sciences of Tunis, LIPAH, Tunis, Tunisia
| | - Haïtham Sghaier
- National Center for Nuclear Sciences and Technology (CNSTN), Sidi Thabet Technopark, Ariana, Tunisia
- Laboratory BVBGR, ISBST, University of Manouba, La Manouba, Tunisia
| | - Manel Zoghlami
- Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes (LIMOS)–Université Blaise Pascal (UBP), Clermont Ferrand, France
- Centre National de Recherche Scientifique (CNRS), UMR 6158, LIMOS, Aubière, France
- University of Tunis El Manar, Faculty of Sciences of Tunis, LIPAH, Tunis, Tunisia
| | - Mondher Maddouri
- University of Tunis El Manar, Faculty of Sciences of Tunis, LIPAH, Tunis, Tunisia
- Taibah University, Medinah, Saudi Arabia
| | - Engelbert Mephu Nguifo
- Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes (LIMOS)–Université Blaise Pascal (UBP), Clermont Ferrand, France
- Centre National de Recherche Scientifique (CNRS), UMR 6158, LIMOS, Aubière, France
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42
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Bacosa HP, Liu Z, Erdner DL. Natural Sunlight Shapes Crude Oil-Degrading Bacterial Communities in Northern Gulf of Mexico Surface Waters. Front Microbiol 2015; 6:1325. [PMID: 26648916 PMCID: PMC4664628 DOI: 10.3389/fmicb.2015.01325] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 11/11/2015] [Indexed: 01/06/2023] Open
Abstract
Following the Deepwater Horizon (DWH) spill in 2010, an enormous amount of oil was observed in the deep and surface waters of the northern Gulf of Mexico. Surface waters are characterized by intense sunlight and high temperature during summer. While the oil-degrading bacterial communities in the deep-sea plume have been widely investigated, the effect of natural sunlight on those in oil polluted surface waters remains unexplored to date. In this study, we incubated surface water from the DWH site with amendments of crude oil, Corexit dispersant, or both for 36 days under natural sunlight in the northern Gulf of Mexico. The bacterial community was analyzed over time for total abundance, density of alkane and polycyclic aromatic hydrocarbon degraders, and community composition via pyrosequencing. Our results showed that, for treatments with oil and/or Corexit, sunlight significantly reduced bacterial diversity and evenness and was a key driver of shifts in bacterial community structure. In samples containing oil or dispersant, sunlight greatly reduced abundance of the Cyanobacterium Synechococcus but increased the relative abundances of Alteromonas, Marinobacter, Labrenzia, Sandarakinotalea, Bartonella, and Halomonas. Dark samples with oil were represented by members of Thalassobius, Winogradskyella, Alcanivorax, Formosa, Pseudomonas, Eubacterium, Erythrobacter, Natronocella, and Coxiella. Both oil and Corexit inhibited the Candidatus Pelagibacter with or without sunlight exposure. For the first time, we demonstrated the effects of light in structuring microbial communities in water with oil and/or Corexit. Overall, our findings improve understanding of oil pollution in surface water, and provide unequivocal evidence that sunlight is a key factor in determining bacterial community composition and dynamics in oil polluted marine waters.
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Affiliation(s)
- Hernando P Bacosa
- Marine Science Institute, The University of Texas at Austin Port Aransas, TX, USA
| | - Zhanfei Liu
- Marine Science Institute, The University of Texas at Austin Port Aransas, TX, USA
| | - Deana L Erdner
- Marine Science Institute, The University of Texas at Austin Port Aransas, TX, USA
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43
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Hansler A, Chen Q, Ma Y, Gross SS. Untargeted metabolite profiling reveals that nitric oxide bioynthesis is an endogenous modulator of carotenoid biosynthesis in Deinococcus radiodurans and is required for extreme ionizing radiation resistance. Arch Biochem Biophys 2015; 589:38-52. [PMID: 26550929 DOI: 10.1016/j.abb.2015.10.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/12/2015] [Accepted: 10/12/2015] [Indexed: 10/22/2022]
Abstract
Deinococcus radiodurans (Drad) is the most radioresistant organism known. Although mechanisms that underlie the extreme radioresistance of Drad are incompletely defined, resistance to UV irradiation-induced killing was found to be greatly attenuated in an NO synthase (NOS) knockout strain of Drad (Δnos). We now show that endogenous NO production is also critical for protection of Drad against γ-irradiation (3000 Gy), a result of accelerated growth recovery, not protection against killing. NO-donor treatment rescued radiosensitization in Δnos Drad but did not influence radiosensitivity in wild type Drad. To discover molecular mechanisms by which endogenous NO confers radioresistance, metabolite profiling studies were performed. Untargeted LC-MS-based metabolite profiling in Drad quantified relative abundances of 1425 molecules and levels of 294 of these were altered by >5-fold (p < 0.01). Unexpectedly, these studies identified a dramatic perturbation in carotenoid biosynthetic intermediates in Δnos Drad, including a reciprocal switch in the pathway end-products from deoxydeinoxanthin to deinoxanthin. NO supplementation rescued these nos deletion-associated changes in carotenoid biosynthesis, and fully-restored radioresistance to wildtype levels. Because carotenoids were shown to be important contributors to radioprotection in Drad, our findings suggest that endogenously-produced NO serves to maintain a spectrum of carotenoids critical for Drad's ability to withstand radiation insult.
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Affiliation(s)
- Alex Hansler
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA
| | - Qiuying Chen
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA
| | - Yuliang Ma
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA
| | - Steven S Gross
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA.
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44
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Badhai J, Ghosh TS, Das SK. Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India. Front Microbiol 2015; 6:1166. [PMID: 26579081 PMCID: PMC4620158 DOI: 10.3389/fmicb.2015.01166] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/08/2015] [Indexed: 12/31/2022] Open
Abstract
This study describes microbial diversity in four tropical hot springs representing moderately thermophilic environments (temperature range: 40–58°C; pH: 7.2–7.4) with discrete geochemistry. Metagenome sequence data showed a dominance of Bacteria over Archaea; the most abundant phyla were Chloroflexi and Proteobacteria, although other phyla were also present, such as Acetothermia, Nitrospirae, Acidobacteria, Firmicutes, Deinococcus-Thermus, Bacteroidetes, Thermotogae, Euryarchaeota, Verrucomicrobia, Ignavibacteriae, Cyanobacteria, Actinobacteria, Planctomycetes, Spirochaetes, Armatimonadetes, Crenarchaeota, and Aquificae. The distribution of major genera and their statistical correlation analyses with the physicochemical parameters predicted that the temperature, aqueous concentrations of ions (such as sodium, chloride, sulfate, and bicarbonate), total hardness, dissolved solids and conductivity were the main environmental variables influencing microbial community composition and diversity. Despite the observed high taxonomic diversity, there were only little variations in the overall functional profiles of the microbial communities in the four springs. Genes involved in the metabolism of carbohydrates and carbon fixation were the most abundant functional class of genes present in these hot springs. The distribution of genes involved in carbon fixation predicted the presence of all the six known autotrophic pathways in the metagenomes. A high prevalence of genes involved in membrane transport, signal transduction, stress response, bacterial chemotaxis, and flagellar assembly were observed along with genes involved in the pathways of xenobiotic degradation and metabolism. The analysis of the metagenomic sequences affiliated to the candidate phylum Acetothermia from spring TB-3 provided new insight into the metabolism and physiology of yet-unknown members of this lineage of bacteria.
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Affiliation(s)
- Jhasketan Badhai
- Department of Biotechnology, Institute of Life Sciences Bhubaneswar, India
| | | | - Subrata K Das
- Department of Biotechnology, Institute of Life Sciences Bhubaneswar, India
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45
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Teh BS, Lau NS, Ng FL, Abdul Rahman AY, Wan X, Saito JA, Hou S, Teh AH, Najimudin N, Alam M. Complete genome sequence of the thermophilic Thermus sp. CCB_US3_UF1 from a hot spring in Malaysia. Stand Genomic Sci 2015; 10:76. [PMID: 26457128 PMCID: PMC4599208 DOI: 10.1186/s40793-015-0053-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 07/28/2015] [Indexed: 02/08/2023] Open
Abstract
Thermus sp. strain CCB_US3_UF1 is a thermophilic bacterium of the genus Thermus, a member of the family Thermaceae. Members of the genus Thermus have been widely used as a biological model for structural biology studies and to understand the mechanism of microbial adaptation under thermal environments. Here, we present the complete genome sequence of Thermus sp. CCB_US3_UF1 isolated from a hot spring in Malaysia, which is the fifth member of the genus Thermus with a completely sequenced and publicly available genome (Genbank date of release: December 2, 2011). Thermus sp. CCB_US3_UF1 has the third largest genome within the genus. The complete genome comprises of a chromosome of 2.26 Mb and a plasmid of 19.7 kb. The genome contains 2279 protein-coding and 54 RNA genes. In addition, its genome revealed potential pathways for the synthesis of secondary metabolites (isoprenoid) and pigments (carotenoid).
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Affiliation(s)
- Beng Soon Teh
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia ; Present address: Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Nyok-Sean Lau
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia
| | - Fui Ling Ng
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | | | - Xuehua Wan
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii USA
| | - Jennifer A Saito
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii USA
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii USA
| | - Aik-Hong Teh
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia
| | - Nazalan Najimudin
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Maqsudul Alam
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii USA ; Department of Microbiology, University of Hawaii, Honolulu, Hawaii USA
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46
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Wang Q, Cen Z, Zhao J. The survival mechanisms of thermophiles at high temperatures: an angle of omics. Physiology (Bethesda) 2015; 30:97-106. [PMID: 25729055 DOI: 10.1152/physiol.00066.2013] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Thermophiles are referred to as microorganisms with optimal growth temperatures of >60 °C. Over the past few years, a number of studies have been conducted regarding thermophiles, especially using the omics strategies. This review provides a systematic view of the survival physiology of thermophiles from an "omics" perspective, which suggests that the adaptive ability of thermophiles is based on a cooperative mode with multi-dimensional regulations integrating genomics, transcriptomics, and proteomics.
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Affiliation(s)
- Quanhui Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; and BGI-Shenzhen, Shenzhen, China
| | - Zhen Cen
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; and
| | - Jingjing Zhao
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; and
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47
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Williams TA, Heaps SE, Cherlin S, Nye TMW, Boys RJ, Embley TM. New substitution models for rooting phylogenetic trees. Philos Trans R Soc Lond B Biol Sci 2015; 370:20140336. [PMID: 26323766 PMCID: PMC4571574 DOI: 10.1098/rstb.2014.0336] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2015] [Indexed: 12/23/2022] Open
Abstract
The root of a phylogenetic tree is fundamental to its biological interpretation, but standard substitution models do not provide any information on its position. Here, we describe two recently developed models that relax the usual assumptions of stationarity and reversibility, thereby facilitating root inference without the need for an outgroup. We compare the performance of these models on a classic test case for phylogenetic methods, before considering two highly topical questions in evolutionary biology: the deep structure of the tree of life and the root of the archaeal radiation. We show that all three alignments contain meaningful rooting information that can be harnessed by these new models, thus complementing and extending previous work based on outgroup rooting. In particular, our analyses exclude the root of the tree of life from the eukaryotes or Archaea, placing it on the bacterial stem or within the Bacteria. They also exclude the root of the archaeal radiation from several major clades, consistent with analyses using other rooting methods. Overall, our results demonstrate the utility of non-reversible and non-stationary models for rooting phylogenetic trees, and identify areas where further progress can be made.
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Affiliation(s)
- Tom A Williams
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Sarah E Heaps
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK School of Mathematics and Statistics, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Svetlana Cherlin
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK School of Mathematics and Statistics, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Tom M W Nye
- School of Mathematics and Statistics, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Richard J Boys
- School of Mathematics and Statistics, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - T Martin Embley
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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48
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Pollo SM, Zhaxybayeva O, Nesbø CL. Insights into thermoadaptation and the evolution of mesophily from the bacterial phylum Thermotogae. Can J Microbiol 2015. [DOI: 10.1139/cjm-2015-0073] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Thermophiles are extremophiles that grow optimally at temperatures >45 °C. To survive and maintain function of their biological molecules, they have a suite of characteristics not found in organisms that grow at moderate temperature (mesophiles). At the cellular level, thermophiles have mechanisms for maintaining their membranes, nucleic acids, and other cellular structures. At the protein level, each of their proteins remains stable and retains activity at temperatures that would denature their mesophilic homologs. Conversely, cellular structures and proteins from thermophiles may not function optimally at moderate temperatures. These differences between thermophiles and mesophiles presumably present a barrier for evolutionary transitioning between the 2 lifestyles. Therefore, studying closely related thermophiles and mesophiles can help us determine how such lifestyle transitions may happen. The bacterial phylum Thermotogae contains hyperthermophiles, thermophiles, mesophiles, and organisms with temperature ranges wide enough to span both thermophilic and mesophilic temperatures. Genomic, proteomic, and physiological differences noted between other bacterial thermophiles and mesophiles are evident within the Thermotogae. We argue that the Thermotogae is an ideal group of organisms for understanding of the response to fluctuating temperature and of long-term evolutionary adaptation to a different growth temperature range.
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Affiliation(s)
- Stephen M.J. Pollo
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
| | - Olga Zhaxybayeva
- Department of Biological Sciences and Department of Computer Science, Dartmouth College, 78 College Street, Hanover, NH 03755, USA
| | - Camilla L. Nesbø
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway
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49
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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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Dai J, Dai W, Qiu C, Yang Z, Zhang Y, Zhou M, Zhang L, Fang C, Gao Q, Yang Q, Li X, Wang Z, Wang Z, Jia Z, Chen X. Unraveling adaptation of Pontibacter korlensis to radiation and infertility in desert through complete genome and comparative transcriptomic analysis. Sci Rep 2015; 5:10929. [PMID: 26057562 PMCID: PMC4460873 DOI: 10.1038/srep10929] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 04/27/2015] [Indexed: 11/10/2022] Open
Abstract
The desert is a harsh habitat for flora and microbial life due to its aridness and strong radiation. In this study, we constructed the first complete and deeply annotated genome of the genus Pontibacter (Pontibacter korlensis X14-1T = CCTCC AB 206081T, X14-1). Reconstruction of the sugar metabolism process indicated that strain X14-1 can utilize diverse sugars, including cellulose, starch and sucrose; this result is consistent with previous experiments. Strain X14-1 is also able to resist desiccation and radiation in the desert through well-armed systems related to DNA repair, radical oxygen species (ROS) detoxification and the OstAB and TreYZ pathways for trehalose synthesis. A comparative transcriptomic analysis under gamma radiation revealed that strain X14-1 presents high-efficacy operating responses to radiation, including the robust expression of catalase and the manganese transport protein. Evaluation of 73 novel genes that are differentially expressed showed that some of these genes may contribute to the strain’s adaptation to radiation and desiccation through ferric transport and preservation.
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Affiliation(s)
- Jun Dai
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan 430068, China
| | | | | | | | - Yi Zhang
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan 430068, China
| | - Mengzhou Zhou
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan 430068, China
| | - Lei Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chengxiang Fang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Qiang Gao
- BGI Shenzhen, Shenzhen 518083, China
| | - Qiao Yang
- East China Sea fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China
| | - Xin Li
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan 430068, China
| | - Zhi Wang
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan 430068, China
| | | | - Zhenhua Jia
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan 430068, China
| | - Xiong Chen
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan 430068, China
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