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Phelan J, Maitra A, McNerney R, Nair M, Gupta A, Coll F, Pain A, Bhakta S, Clark TG. The draft genome of Mycobacterium aurum, a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae. Int J Mycobacteriol 2015; 4:207-16. [PMID: 27649868 DOI: 10.1016/j.ijmyco.2015.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 05/03/2015] [Indexed: 10/23/2022] Open
Abstract
Mycobacterium aurum (M. aurum) is an environmental mycobacteria that has previously been used in studies of anti-mycobacterial drugs due to its fast growth rate and low pathogenicity. The M. aurum genome has been sequenced and assembled into 46 contigs, with a total length of 6.02Mb containing 5684 annotated protein-coding genes. A phylogenetic analysis using whole genome alignments positioned M. aurum close to Mycobacterium vaccae and Mycobacterium vanbaalenii, within a clade related to fast-growing mycobacteria. Large-scale genomic rearrangements were identified by comparing the M. aurum genome to those of Mycobacterium tuberculosis and Mycobacterium leprae. M. aurum orthologous genes implicated in resistance to anti-tuberculosis drugs in M. tuberculosis were observed. The sequence identity at the DNA level varied from 68.6% for pncA (pyrazinamide drug-related) to 96.2% for rrs (streptomycin, capreomycin). We observed two homologous genes encoding the catalase-peroxidase enzyme (katG) that is associated with resistance to isoniazid. Similarly, two embB homologues were identified in the M. aurum genome. In addition to describing for the first time the genome of M. aurum, this work provides a resource to aid the use of M. aurum in studies to develop improved drugs for the pathogenic mycobacteria M. tuberculosis and M. leprae.
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Affiliation(s)
- Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom.
| | - Arundhati Maitra
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Mridul Nair
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Antima Gupta
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom
| | - Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Arnab Pain
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
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52
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Ebihara A, Manzoku M, Fukui K, Shimada A, Morita R, Masui R, Kuramitsu S. Roles of Mn-catalase and a possible heme peroxidase homologue in protection from oxidative stress in Thermus thermophilus. Extremophiles 2015; 19:775-85. [PMID: 25997395 DOI: 10.1007/s00792-015-0753-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 04/26/2015] [Indexed: 10/23/2022]
Abstract
Hydrogen peroxide (H2O2) produces hydroxyl radicals that directly attack a variety of biomolecules and cause severe cellular dysfunction. An extremely thermophilic bacterium, Thermus thermophilus HB8, possesses at least three enzymes that can scavenge H2O2: manganese-containing catalase (TTHA0122, MnCAT), a possible peroxiredoxin homologue (TTHA1300), and a possible heme peroxidase (HPX) homologue (TTHA1714). To investigate the roles of these proteins, we attempted to disrupt each of these genes in T. thermophilus HB8. Although we were able to completely disrupt ttha1300, we were unable to completely delete ttha0122 and ttha1714 because of polyploidy. Quantitative real-time PCR showed that, compared to the wild type, 31 % of ttha0122 and 11 % of ttha1714 remained in the ∆ttha0122 and ∆ttha1714 disruption mutants, respectively. Mutants with reduced levels of ttha0122 or ttha1714 exhibited a significant increase in spontaneous mutation frequency. ∆ttha1714 grew slower than the wild type under normal conditions. ∆ttha0122 grew very poorly after exposure to H2O2. Moreover, ∆ttha0122 did not show H2O2-scavenging activity, whereas ∆ttha1300 and ∆ttha1714 scavenged H2O2, a property similar to that exhibited by the wild type. MnCAT purified from T. thermophilus HB8 cells scavenged H2O2 in vitro. The recombinant form of the possible HPX homologue, reconstituted with hemin, showed peroxidase activity with H2O2 as an oxidant substrate. Based on these results, we propose that not only MnCAT but also the possible HPX homologue is involved in protecting the cell from oxidative stress in T. thermophilus.
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Affiliation(s)
- Akio Ebihara
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan,
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53
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Salzer R, Kern T, Joos F, Averhoff B. The Thermus thermophilus comEA/comEC operon is associated with DNA binding and regulation of the DNA translocator and type IV pili. Environ Microbiol 2015; 18:65-74. [PMID: 25727469 DOI: 10.1111/1462-2920.12820] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 02/20/2015] [Indexed: 11/30/2022]
Abstract
Natural transformation systems and type IV pili are linked in many naturally competent bacteria. In the Gram-negative bacterium Thermus thermophilus, a leading model organism for studies of DNA transporters in thermophilic bacteria, seven competence proteins play a dual role in both systems, whereas two competence genes, comEA and comEC, are suggested to represent unique DNA translocator proteins. Here we show that the T. thermophilus ComEA protein binds dsDNA and is anchored in the inner membrane. comEA is co-transcribed with the flanking comEC gene, and transcription of this operon is upregulated by nutrient limitation and low temperature. To our surprise, a comEC mutant was impaired in piliation. We followed this observation and uncovered that the impaired piliation of the comEC mutant is due to a transcriptional downregulation of pilA4 and the pilN both playing a dual role in piliation and natural competence. Moreover, the comEC mutation resulted in a dramatic decrease in mRNA levels of the pseudopilin gene pilA1, which is unique for the DNA transporter. We conclude that ComEC modulates transcriptional regulation of type IV pili and DNA translocator components thereby mediating a response to extracellular parameters.
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Affiliation(s)
- Ralf Salzer
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Timo Kern
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Friederike Joos
- Department of Structural Biology, Max-Planck Institute of Biophysics, Frankfurt am Main, 60438, Germany
| | - Beate Averhoff
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
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54
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Tsai CH, Liao R, Chou B, Contreras LM. Transcriptional analysis of Deinococcus radiodurans reveals novel small RNAs that are differentially expressed under ionizing radiation. Appl Environ Microbiol 2015; 81:1754-64. [PMID: 25548054 PMCID: PMC4325154 DOI: 10.1128/aem.03709-14] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 12/19/2014] [Indexed: 02/08/2023] Open
Abstract
Small noncoding RNAs (sRNAs) are posttranscriptional regulators that have been identified in multiple species and shown to play essential roles in responsive mechanisms to environmental stresses. The natural ability of specific bacteria to resist high levels of radiation has been of high interest to mechanistic studies of DNA repair and biomolecular protection. Deinococcus radiodurans is a model extremophile for radiation studies that can survive doses of ionizing radiation of >12,000 Gy, 3,000 times higher than for most vertebrates. Few studies have investigated posttranscriptional regulatory mechanisms of this organism that could be relevant in its general gene regulatory patterns. In this study, we identified 199 potential sRNA candidates in D. radiodurans by whole-transcriptome deep sequencing analysis and confirmed the expression of 41 sRNAs by Northern blotting and reverse transcriptase PCR (RT-PCR). A total of 8 confirmed sRNAs showed differential expression during recovery after acute ionizing radiation (15 kGy). We have also found and confirmed 7 sRNAs in Deinococcus geothermalis, a closely related radioresistant species. The identification of several novel sRNAs in Deinococcus bacteria raises important questions about the evolution and nature of global gene regulation in radioresistance.
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Affiliation(s)
- Chen-Hsun Tsai
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Rick Liao
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Brendan Chou
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas, USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
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55
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Lewis DL, Notey JS, Chandrayan SK, Loder AJ, Lipscomb GL, Adams MWW, Kelly RM. A mutant ('lab strain') of the hyperthermophilic archaeon Pyrococcus furiosus, lacking flagella, has unusual growth physiology. Extremophiles 2014; 19:269-81. [PMID: 25472011 DOI: 10.1007/s00792-014-0712-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 11/16/2014] [Indexed: 10/24/2022]
Abstract
A mutant ('lab strain') of the hyperthermophilic archaeon Pyrococcus furiosus DSM3638 exhibited an extended exponential phase and atypical cell aggregation behavior. Genomic DNA from the mutant culture was sequenced and compared to wild-type (WT) DSM3638, revealing 145 genes with one or more insertions, deletions, or substitutions (12 silent, 33 amino acid substitutions, and 100 frame shifts). Approximately, half of the mutated genes were transposases or hypothetical proteins. The WT transcriptome revealed numerous changes in amino acid and pyrimidine biosynthesis pathways coincidental with growth phase transitions, unlike the mutant whose transcriptome reflected the observed prolonged exponential phase. Targeted gene deletions, based on frame-shifted ORFs in the mutant genome, in a genetically tractable strain of P. furiosus (COM1) could not generate the extended exponential phase behavior observed for the mutant. For example, a putative radical SAM family protein (PF2064) was the most highly up-regulated ORF (>25-fold) in the WT between exponential and stationary phase, although this ORF was unresponsive in the mutant; deletion of this gene in P. furiosus COM1 resulted in no apparent phenotype. On the other hand, frame-shifting mutations in the mutant genome negatively impacted transcription of a flagellar biosynthesis operon (PF0329-PF0338).Consequently, cells in the mutant culture lacked flagella and, unlike the WT, showed minimal evidence of exopolysaccharide-based cell aggregation in post-exponential phase. Electron microscopy of PF0331-PF0337 deletions in P. furiosus COM1 showed that absence of flagella impacted normal cell aggregation behavior and, furthermore, indicated that flagella play a key role, beyond motility, in the growth physiology of P. furiosus.
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Affiliation(s)
- Derrick L Lewis
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, EB-1,911 Partners Way, Raleigh, NC, 27695-7905, US
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56
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Noncanonical cell-to-cell DNA transfer in Thermus spp. is insensitive to argonaute-mediated interference. J Bacteriol 2014; 197:138-46. [PMID: 25331432 DOI: 10.1128/jb.02113-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Horizontal gene transfer drives the rapid evolution of bacterial populations. Classical processes that promote the lateral flow of genetic information are conserved throughout the prokaryotic world. However, some species have nonconserved transfer mechanisms that are not well known. This is the case for the ancient extreme thermophile Thermus thermophilus. In this work, we show that T. thermophilus strains are capable of exchanging large DNA fragments by a novel mechanism that requires cell-to-cell contacts and employs components of the natural transformation machinery. This process facilitates the bidirectional transfer of virtually any DNA locus but favors by 10-fold loci found in the megaplasmid over those in the chromosome. In contrast to naked DNA acquisition by transformation, the system does not activate the recently described DNA-DNA interference mechanism mediated by the prokaryotic Argonaute protein, thus allowing the organism to distinguish between DNA transferred from a mate and exogenous DNA acquired from unknown hosts. This Argonaute-mediated discrimination may be tentatively viewed as a strategy for safe sharing of potentially "useful" traits by the components of a given population of Thermus spp. without increasing the genome sizes of its individuals.
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57
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Borges PT, Frazão C, Miranda CS, Carrondo MA, Romão CV. Structure of the monofunctional heme catalase DR1998 from Deinococcus radiodurans. FEBS J 2014; 281:4138-50. [PMID: 24975828 DOI: 10.1111/febs.12895] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/12/2014] [Accepted: 06/24/2014] [Indexed: 11/30/2022]
Abstract
UNLABELLED Deinococcus radiodurans is an aerobic organism with the ability to survive under conditions of high radiation doses or desiccation. As part of its protection system against oxidative stress, this bacterium encodes three monofunctional catalases. The DR1998 catalase belongs to clade 1, and is present at high levels under normal growth conditions. The crystals of DR1998 diffracted very weakly, and the merged diffraction data showed an R sym of 0.308. Its crystal structure was determined and refined to 2.6 Å. The four molecules present in the asymmetric unit form, by crystallographic symmetry, two homotetramers with 222 point-group symmetry. The overall structure of DR1998 is similar to that of other monofunctional catalases, showing higher structural homology with the catalase structures of clade 1. Each monomer shows the typical catalase fold, and contains one heme b in the active site. The heme is coordinated by the proximal ligand Tyr369, and on the heme distal side the essential His81 and Asn159 are hydrogen-bonded to a water molecule. A 25-Å-long channel is the main channel connecting the active site to the external surface. This channel starts with a hydrophobic region from the catalytic heme site, which is followed by a hydrophilic region that begins on Asp139 and expands up to the protein surface. Apart from this channel, an alternative channel, also near the heme active site, is presented and discussed. DATABASE Coordinates and structure factors have been deposited in the Protein Data Bank in Europe under accession code 4CAB.
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Affiliation(s)
- Patrícia T Borges
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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58
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Panda A, Ghosh TC. Prevalent structural disorder carries signature of prokaryotic adaptation to oxic atmosphere. Gene 2014; 548:134-41. [PMID: 24999584 DOI: 10.1016/j.gene.2014.07.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 06/27/2014] [Accepted: 07/03/2014] [Indexed: 12/12/2022]
Abstract
Microbes have adopted efficient mechanisms to contend with environmental changes. The emergence of oxygen was a major event that led to an abrupt change in Earth's atmosphere. To adjust with this shift in environmental condition ancient microbes must have undergone several modifications. Although some proteomic and genomic attributes were proposed to facilitate survival of microorganisms in the presence of oxygen, the process of adaptation still remains elusive. Recent studies have focused that intrinsically disordered proteins play crucial roles in adaptation to a wide range of ecological conditions. Therefore, it is likely that disordered proteins could also play indispensable roles in microbial adaptation to the aerobic environment. To test this hypothesis we measured the disorder content of 679 prokaryotes from four oxygen requirement groups. Our result revealed that aerobic proteomes are endowed with the highest protein disorder followed by facultative microbes. Minimal disorder was observed in anaerobic and microaerophilic microbes with no significant difference in their disorder content. Considering all the potential confounding factors that can modulate protein disorder, here we established that the high protein disorder in aerobic microbe is not a by-product of adaptation to any other selective pressure. On the functional level, we found that the high disorder in aerobic proteomes has been utilized for processes that are important for their aerobic lifestyle. Moreover, aerobic proteomes were found to be enriched with disordered binding sites and to contain transcription factors with high disorder propensity. Based on our results, here we proposed that the high protein disorder is an adaptive opportunity for aerobic microbes to fit with the genomic and functional complexities of the aerobic lifestyle.
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Affiliation(s)
- Arup Panda
- Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054, India
| | - Tapash Chandra Ghosh
- Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054, India.
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59
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General Characteristics and Important Model Organisms. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014. [DOI: 10.1128/9781555815516.ch2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Braakman R, Smith E. Metabolic evolution of a deep-branching hyperthermophilic chemoautotrophic bacterium. PLoS One 2014; 9:e87950. [PMID: 24516572 PMCID: PMC3917532 DOI: 10.1371/journal.pone.0087950] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 01/05/2014] [Indexed: 11/19/2022] Open
Abstract
Aquifex aeolicus is a deep-branching hyperthermophilic chemoautotrophic bacterium restricted to hydrothermal vents and hot springs. These characteristics make it an excellent model system for studying the early evolution of metabolism. Here we present the whole-genome metabolic network of this organism and examine in detail the driving forces that have shaped it. We make extensive use of phylometabolic analysis, a method we recently introduced that generates trees of metabolic phenotypes by integrating phylogenetic and metabolic constraints. We reconstruct the evolution of a range of metabolic sub-systems, including the reductive citric acid (rTCA) cycle, as well as the biosynthesis and functional roles of several amino acids and cofactors. We show that A. aeolicus uses the reconstructed ancestral pathways within many of these sub-systems, and highlight how the evolutionary interconnections between sub-systems facilitated several key innovations. Our analyses further highlight three general classes of driving forces in metabolic evolution. One is the duplication and divergence of genes for enzymes as these progress from lower to higher substrate specificity, improving the kinetics of certain sub-systems. A second is the kinetic optimization of established pathways through fusion of enzymes, or their organization into larger complexes. The third is the minimization of the ATP unit cost to synthesize biomass, improving thermodynamic efficiency. Quantifying the distribution of these classes of innovations across metabolic sub-systems and across the tree of life will allow us to assess how a tradeoff between maximizing growth rate and growth efficiency has shaped the long-term metabolic evolution of the biosphere.
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Affiliation(s)
- Rogier Braakman
- Krasnow Institute for Advanced Study, George Mason University, Fairfax, Virginia, United States of America
- * E-mail:
| | - Eric Smith
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Krasnow Institute for Advanced Study, George Mason University, Fairfax, Virginia, United States of America
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Luan H, Meng N, Fu J, Chen X, Xu X, Feng Q, Jiang H, Dai J, Yuan X, Lu Y, Roberts AA, Luo X, Chen M, Xu S, Li J, Hamilton CJ, Fang C, Wang J. Genome-wide transcriptome and antioxidant analyses on gamma-irradiated phases of deinococcus radiodurans R1. PLoS One 2014; 9:e85649. [PMID: 24465634 PMCID: PMC3900439 DOI: 10.1371/journal.pone.0085649] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 11/29/2013] [Indexed: 11/18/2022] Open
Abstract
Adaptation of D. radiodurans cells to extreme irradiation environments requires dynamic interactions between gene expression and metabolic regulatory networks, but studies typically address only a single layer of regulation during the recovery period after irradiation. Dynamic transcriptome analysis of D. radiodurans cells using strand-specific RNA sequencing (ssRNA-seq), combined with LC-MS based metabolite analysis, allowed an estimate of the immediate expression pattern of genes and antioxidants in response to irradiation. Transcriptome dynamics were examined in cells by ssRNA-seq covering its predicted genes. Of the 144 non-coding RNAs that were annotated, 49 of these were transfer RNAs and 95 were putative novel antisense RNAs. Genes differentially expressed during irradiation and recovery included those involved in DNA repair, degradation of damaged proteins and tricarboxylic acid (TCA) cycle metabolism. The knockout mutant crtB (phytoene synthase gene) was unable to produce carotenoids, and exhibited a decreased survival rate after irradiation, suggesting a role for these pigments in radiation resistance. Network components identified in this study, including repair and metabolic genes and antioxidants, provided new insights into the complex mechanism of radiation resistance in D. radiodurans.
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Affiliation(s)
- Hemi Luan
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
- Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Nan Meng
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
| | - Jin Fu
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
| | - Xiaomin Chen
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
| | - Xun Xu
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
| | - Qiang Feng
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
| | - Hui Jiang
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
| | - Jun Dai
- College of Life Sciences, Wuhan University, Wuhan, China
- Key Laboratory of Fermentation Engineering, Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan, China
| | - Xune Yuan
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
| | - Yanping Lu
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
| | - Alexandra A. Roberts
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Xiao Luo
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
| | - Maoshan Chen
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
| | - Shengtao Xu
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
| | - Jun Li
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
| | - Chris J. Hamilton
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Chengxiang Fang
- College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail: (CF); (JW)
| | - Jun Wang
- Department of Science and Technology, BGI-Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail: (CF); (JW)
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62
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Holton TA, Vijayakumar V, Khaldi N. Bioinformatics: Current perspectives and future directions for food and nutritional research facilitated by a Food-Wiki database. Trends Food Sci Technol 2013. [DOI: 10.1016/j.tifs.2013.08.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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63
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Shao H, Xu L, Yan Y. Thermostable lipases from extremely radioresistant bacteriumDeinococcus radiodurans: Cloning, expression, and biochemical characterization. J Basic Microbiol 2013; 54:984-95. [DOI: 10.1002/jobm.201300434] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/21/2013] [Indexed: 11/05/2022]
Affiliation(s)
- Hua Shao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology; Huazhong University of Science and Technology; Wuhan P. R. China
| | - Li Xu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology; Huazhong University of Science and Technology; Wuhan P. R. China
| | - Yunjun Yan
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology; Huazhong University of Science and Technology; Wuhan P. R. China
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64
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Hypothetical Proteins Present During Recovery Phase of Radiation Resistant Bacterium Deinococcus radiodurans are Under Purifying Selection. J Mol Evol 2013; 77:31-42. [DOI: 10.1007/s00239-013-9577-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 07/26/2013] [Indexed: 01/15/2023]
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65
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Wu WL, Liao JH, Lin GH, Lin MH, Chang YC, Liang SY, Yang FL, Khoo KH, Wu SH. Phosphoproteomic analysis reveals the effects of PilF phosphorylation on type IV pilus and biofilm formation in Thermus thermophilus HB27. Mol Cell Proteomics 2013; 12:2701-13. [PMID: 23828892 DOI: 10.1074/mcp.m113.029330] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Thermus thermophilus HB27 is an extremely thermophilic eubacteria with a high frequency of natural competence. This organism is therefore often used as a thermophilic model to investigate the molecular basis of type IV pili-mediated functions, such as the uptake of free DNA, adhesion, twitching motility, and biofilm formation, in hot environments. In this study, the phosphoproteome of T. thermophilus HB27 was analyzed via a shotgun approach and high-accuracy mass spectrometry. Ninety-three unique phosphopeptides, including 67 in vivo phosphorylated sites on 53 phosphoproteins, were identified. The distribution of Ser/Thr/Tyr phosphorylation sites was 57%/36%/7%. The phosphoproteins were mostly involved in central metabolic pathways and protein/cell envelope biosynthesis. According to this analysis, the ATPase motor PilF, a type IV pili-related component, was first found to be phosphorylated on Thr-368 and Ser-372. Through the point mutation of PilF, mimic phosphorylated mutants T368D and S372E resulted in nonpiliated and nontwitching phenotypes, whereas nonphosphorylated mutants T368V and S372A displayed piliation and twitching motility. In addition, mimic phosphorylated mutants showed elevated biofilm-forming abilities with a higher initial attachment rate, caused by increasing exopolysaccharide production. In summary, the phosphorylation of PilF might regulate the pili and biofilm formation associated with exopolysaccharide production.
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Affiliation(s)
- Wan-Ling Wu
- Institute of Biochemical Sciences, College of Life Sciences, National Taiwan University, Taipei 106, Taiwan
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66
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Krisko A, Radman M. Biology of extreme radiation resistance: the way of Deinococcus radiodurans. Cold Spring Harb Perspect Biol 2013; 5:5/7/a012765. [PMID: 23818498 DOI: 10.1101/cshperspect.a012765] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The bacterium Deinococcus radiodurans is a champion of extreme radiation resistance that is accounted for by a highly efficient protection against proteome, but not genome, damage. A well-protected functional proteome ensures cell recovery from extensive radiation damage to other cellular constituents by molecular repair and turnover processes, including an efficient repair of disintegrated DNA. Therefore, cell death correlates with radiation-induced protein damage, rather than DNA damage, in both robust and standard species. From the reviewed biology of resistance to radiation and other sources of oxidative damage, we conclude that the impact of protein damage on the maintenance of life has been largely underestimated in biology and medicine.
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Affiliation(s)
- Anita Krisko
- Mediterranean Institute for Life Sciences, 21000 Split, Croatia
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67
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van Wolferen M, Ajon M, Driessen AJM, Albers SV. How hyperthermophiles adapt to change their lives: DNA exchange in extreme conditions. Extremophiles 2013; 17:545-63. [PMID: 23712907 DOI: 10.1007/s00792-013-0552-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/12/2013] [Indexed: 01/24/2023]
Abstract
Transfer of DNA has been shown to be involved in genome evolution. In particular with respect to the adaptation of bacterial species to high temperatures, DNA transfer between the domains of bacteria and archaea seems to have played a major role. In addition, DNA exchange between similar species likely plays a role in repair of DNA via homologous recombination, a process that is crucial under DNA damaging conditions such as high temperatures. Several mechanisms for the transfer of DNA have been described in prokaryotes, emphasizing its general importance. However, until recently, not much was known about this process in prokaryotes growing in highly thermophilic environments. This review describes the different mechanisms of DNA transfer in hyperthermophiles, and how this may contribute to the survival and adaptation of hyperthermophilic archaea and bacteria to extreme environments.
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Affiliation(s)
- Marleen van Wolferen
- Molecular Biology of Archaea, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
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68
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There are more small amino acids and fewer aromatic rings in proteins of ionizing radiation-resistant bacteria. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0612-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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69
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Radiation Resistance in Extremophiles: Fending Off Multiple Attacks. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2013. [DOI: 10.1007/978-94-007-6488-0_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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70
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Wolf YI, Makarova KS, Yutin N, Koonin EV. Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer. Biol Direct 2012; 7:46. [PMID: 23241446 PMCID: PMC3534625 DOI: 10.1186/1745-6150-7-46] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 12/11/2012] [Indexed: 12/17/2022] Open
Abstract
Background Collections of Clusters of Orthologous Genes (COGs) provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made for all complete genomes of cellular life forms that were available at the time. However, with the accumulation of thousands of complete genomes, construction of a comprehensive COG set has become extremely computationally demanding and prone to error propagation, necessitating the switch to taxon-specific COG collections. Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs). Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea. Results The updated version of the arCOG database incorporates 91% of the pangenome of 120 archaea (251,032 protein-coding genes altogether) into 10,335 arCOGs. Using this new set of arCOGs, we performed maximum likelihood reconstruction of the genome content of archaeal ancestral forms and gene gain and loss events in archaeal evolution. This reconstruction shows that the last Common Ancestor of the extant Archaea was an organism of greater complexity than most of the extant archaea, probably with over 2,500 protein-coding genes. The subsequent evolution of almost all archaeal lineages was apparently dominated by gene loss resulting in genome streamlining. Overall, in the evolution of Archaea as well as a representative set of bacteria that was similarly analyzed for comparison, gene losses are estimated to outnumber gene gains at least 4 to 1. Analysis of specific patterns of gene gain in Archaea shows that, although some groups, in particular Halobacteria, acquire substantially more genes than others, on the whole, gene exchange between major groups of Archaea appears to be largely random, with no major ‘highways’ of horizontal gene transfer. Conclusions The updated collection of arCOGs is expected to become a key resource for comparative genomics, evolutionary reconstruction and functional annotation of new archaeal genomes. Given that, in spite of the major increase in the number of genomes, the conserved core of archaeal genes appears to be stabilizing, the major evolutionary trends revealed here have a chance to stand the test of time. Reviewers This article was reviewed by (for complete reviews see the Reviewers’ Reports section): Dr. PLG, Prof. PF, Dr. PL (nominated by Prof. JPG).
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Affiliation(s)
- Yuri I Wolf
- National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA.
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71
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Møller AP, Mousseau TA. The effects of natural variation in background radioactivity on humans, animals and other organisms. Biol Rev Camb Philos Soc 2012; 88:226-54. [DOI: 10.1111/j.1469-185x.2012.00249.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 09/26/2012] [Accepted: 10/05/2012] [Indexed: 01/23/2023]
Affiliation(s)
- Anders P. Møller
- Laboratoire d'Ecologie; Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud; Bâtiment 362; F-91405; Orsay Cedex; France
| | - Timothy A. Mousseau
- Department of Biological Sciences; University of South Carolina; Columbia; SC; 29208; USA
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Seitz P, Blokesch M. Cues and regulatory pathways involved in natural competence and transformation in pathogenic and environmental Gram-negative bacteria. FEMS Microbiol Rev 2012; 37:336-63. [PMID: 22928673 DOI: 10.1111/j.1574-6976.2012.00353.x] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 07/27/2012] [Accepted: 08/21/2012] [Indexed: 12/23/2022] Open
Abstract
Bacterial genomics is flourishing, as whole-genome sequencing has become affordable, readily available and rapid. As a result, it has become clear how frequently horizontal gene transfer (HGT) occurs in bacteria. The potential implications are highly significant because HGT contributes to several processes, including the spread of antibiotic-resistance cassettes, the distribution of toxin-encoding phages and the transfer of pathogenicity islands. Three modes of HGT are recognized in bacteria: conjugation, transduction and natural transformation. In contrast to the first two mechanisms, natural competence for transformation does not rely on mobile genetic elements but is driven solely by a developmental programme in the acceptor bacterium. Once the bacterium becomes competent, it is able to take up DNA from the environment and to incorporate the newly acquired DNA into its own chromosome. The initiation and duration of competence differ significantly among bacteria. In this review, we outline the latest data on representative naturally transformable Gram-negative bacteria and how their competence windows differ. We also summarize how environmental cues contribute to the initiation of competence in a subset of naturally transformable Gram-negative bacteria and how the complexity of the niche might dictate the fine-tuning of the competence window.
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Affiliation(s)
- Patrick Seitz
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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73
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Evolution of lysine biosynthesis in the phylum deinococcus-thermus. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2012; 2012:745931. [PMID: 22645699 PMCID: PMC3356886 DOI: 10.1155/2012/745931] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Accepted: 02/17/2012] [Indexed: 12/04/2022]
Abstract
Thermus thermophilus biosynthesizes lysine through the α-aminoadipate (AAA) pathway: this observation was the first discovery of lysine biosynthesis through the AAA pathway in archaea and bacteria. Genes homologous to the T. thermophilus lysine biosynthetic genes are widely distributed in bacteria of the Deinococcus-Thermus phylum. Our phylogenetic analyses strongly suggest that a common ancestor of the Deinococcus-Thermus phylum had the ancestral genes for bacterial lysine biosynthesis through the AAA pathway. In addition, our findings suggest that the ancestor lacked genes for lysine biosynthesis through the diaminopimelate (DAP) pathway. Interestingly, Deinococcus proteolyticus does not have the genes for lysine biosynthesis through the AAA pathway but does have the genes for lysine biosynthesis through the DAP pathway. Phylogenetic analyses of D. proteolyticus lysine biosynthetic genes showed that the key gene cluster for the DAP pathway was transferred horizontally from a phylogenetically distant organism.
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Trost B, Pajon R, Jayaprakash T, Kusalik A. Comparing the similarity of different groups of bacteria to the human proteome. PLoS One 2012; 7:e34007. [PMID: 22558081 PMCID: PMC3338800 DOI: 10.1371/journal.pone.0034007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 02/20/2012] [Indexed: 11/19/2022] Open
Abstract
Numerous aspects of the relationship between bacteria and human have been investigated. One aspect that has recently received attention is sequence overlap at the proteomic level. However, there has not yet been a study that comprehensively characterizes the level of sequence overlap between bacteria and human, especially as it relates to bacterial characteristics like pathogenicity, G-C content, and proteome size. In this study, we began by performing a general characterization of the range of bacteria-human similarity at the proteomic level, and identified characteristics of the most- and least-similar bacterial species. We then examined the relationship between proteomic similarity and numerous other variables. While pathogens and nonpathogens had comparable similarity to the human proteome, pathogens causing chronic infections were found to be more similar to the human proteome than those causing acute infections. Although no general correspondence between a bacterium’s proteome size and its similarity to the human proteome was noted, no bacteria with small proteomes had high similarity to the human proteome. Finally, we discovered an interesting relationship between similarity and a bacterium’s G-C content. While the relationship between bacteria and human has been studied from many angles, their proteomic similarity still needs to be examined in more detail. This paper sheds further light on this relationship, particularly with respect to immunity and pathogenicity.
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Affiliation(s)
- Brett Trost
- Department of Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- * E-mail:
| | - Rolando Pajon
- Center for Immunobiology and Vaccine Development, Children’s Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Teenus Jayaprakash
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Genome Signature Difference between Deinococcus radiodurans and Thermus thermophilus. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2012; 2012:205274. [PMID: 22500246 PMCID: PMC3303625 DOI: 10.1155/2012/205274] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 12/08/2011] [Indexed: 01/13/2023]
Abstract
The extremely radioresistant bacteria of the genus Deinococcus and the extremely thermophilic bacteria of the genus Thermus belong to a common taxonomic group. Considering the distinct living environments of Deinococcus and Thermus, different genes would have been acquired through horizontal gene transfer after their divergence from a common ancestor. Their guanine-cytosine (GC) contents are similar; however, we hypothesized that their genomic signatures would be different. Our findings indicated that the genomes of Deinococcus radiodurans and Thermus thermophilus have different tetranucleotide frequencies. This analysis showed that the genome signature of D. radiodurans is most similar to that of Pseudomonas aeruginosa, whereas the genome signature of T. thermophilus is most similar to that of Thermanaerovibrio acidaminovorans. This difference in genome signatures may be related to the different evolutionary backgrounds of the 2 genera after their divergence from a common ancestor.
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76
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Gtari M, Essoussi I, Maaoui R, Sghaier H, Boujmil R, Gury J, Pujic P, Brusetti L, Chouaia B, Crotti E, Daffonchio D, Boudabous A, Normand P. Contrasted resistance of stone-dwelling Geodermatophilaceae species to stresses known to give rise to reactive oxygen species. FEMS Microbiol Ecol 2012; 80:566-77. [DOI: 10.1111/j.1574-6941.2012.01320.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 01/24/2012] [Accepted: 01/25/2012] [Indexed: 11/30/2022] Open
Affiliation(s)
- Maher Gtari
- Laboratoire Microorganismes et Biomolécules Actives; Université de Tunis Elmanar (FST) et Université de Carthage (ISSTE); Tunis; Tunisia
| | - Imen Essoussi
- Laboratoire Microorganismes et Biomolécules Actives; Université de Tunis Elmanar (FST) et Université de Carthage (ISSTE); Tunis; Tunisia
| | - Radhi Maaoui
- Laboratoire Microorganismes et Biomolécules Actives; Université de Tunis Elmanar (FST) et Université de Carthage (ISSTE); Tunis; Tunisia
| | - Haïtham Sghaier
- Unité de Microbiologie et de Biologie Moléculaire; Centre National des Sciences et Technologies Nucléaires (CNSTN); Sidi Thabet; Tunisia
| | - Rabeb Boujmil
- Laboratoire Microorganismes et Biomolécules Actives; Université de Tunis Elmanar (FST) et Université de Carthage (ISSTE); Tunis; Tunisia
| | - Jérôme Gury
- IPREM UMR CNRS 5254; IBEAS - UFR Sciences et Techniques; Université de Pau et des Pays de l'Adour; Pau; France
| | - Petar Pujic
- Ecologie Microbienne; Centre National de la Recherche Scientifique UMR 5557; Université Lyon I; Université Lyon; Villeurbanne; France
| | - Lorenzo Brusetti
- Faculty of Science and Technology; Free University of Bozen/Bolzano; Bolzano; Italy
| | - Bessem Chouaia
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche (DiSTAM); Università degli Studi di Milano; Milan; Italy
| | - Elena Crotti
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche (DiSTAM); Università degli Studi di Milano; Milan; Italy
| | - Daniele Daffonchio
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche (DiSTAM); Università degli Studi di Milano; Milan; Italy
| | - Abdellatif Boudabous
- Laboratoire Microorganismes et Biomolécules Actives; Université de Tunis Elmanar (FST) et Université de Carthage (ISSTE); Tunis; Tunisia
| | - Philippe Normand
- Ecologie Microbienne; Centre National de la Recherche Scientifique UMR 5557; Université Lyon I; Université Lyon; Villeurbanne; France
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Wang L, Yin L, Xu G, Li M, Zhang H, Tian B, Hua Y. Cooperation of PprI and DrRRA in response to extreme ionizing radiation in Deinococcus radiodurans. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s11434-011-4790-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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78
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Death by protein damage in irradiated cells. DNA Repair (Amst) 2012; 11:12-21. [DOI: 10.1016/j.dnarep.2011.10.024] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 10/19/2011] [Indexed: 12/12/2022]
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79
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Gounder K, Brzuszkiewicz E, Liesegang H, Wollherr A, Daniel R, Gottschalk G, Reva O, Kumwenda B, Srivastava M, Bricio C, Berenguer J, van Heerden E, Litthauer D. Sequence of the hyperplastic genome of the naturally competent Thermus scotoductus SA-01. BMC Genomics 2011; 12:577. [PMID: 22115438 PMCID: PMC3235269 DOI: 10.1186/1471-2164-12-577] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 11/24/2011] [Indexed: 11/13/2022] Open
Abstract
Background Many strains of Thermus have been isolated from hot environments around the world. Thermus scotoductus SA-01 was isolated from fissure water collected 3.2 km below surface in a South African gold mine. The isolate is capable of dissimilatory iron reduction, growth with oxygen and nitrate as terminal electron acceptors and the ability to reduce a variety of metal ions, including gold, chromate and uranium, was demonstrated. The genomes from two different Thermus thermophilus strains have been completed. This paper represents the completed genome from a second Thermus species - T. scotoductus. Results The genome of Thermus scotoductus SA-01 consists of a chromosome of 2,346,803 bp and a small plasmid which, together are about 11% larger than the Thermus thermophilus genomes. The T. thermophilus megaplasmid genes are part of the T. scotoductus chromosome and extensive rearrangement, deletion of nonessential genes and acquisition of gene islands have occurred, leading to a loss of synteny between the chromosomes of T. scotoductus and T. thermophilus. At least nine large inserts of which seven were identified as alien, were found, the most remarkable being a denitrification cluster and two operons relating to the metabolism of phenolics which appear to have been acquired from Meiothermus ruber. The majority of acquired genes are from closely related species of the Deinococcus-Thermus group, and many of the remaining genes are from microorganisms with a thermophilic or hyperthermophilic lifestyle. The natural competence of Thermus scotoductus was confirmed experimentally as expected as most of the proteins of the natural transformation system of Thermus thermophilus are present. Analysis of the metabolic capabilities revealed an extensive energy metabolism with many aerobic and anaerobic respiratory options. An abundance of sensor histidine kinases, response regulators and transporters for a wide variety of compounds are indicative of an oligotrophic lifestyle. Conclusions The genome of Thermus scotoductus SA-01 shows remarkable plasticity with the loss, acquisition and rearrangement of large portions of its genome compared to Thermus thermophilus. Its ability to naturally take up foreign DNA has helped it adapt rapidly to a subsurface lifestyle in the presence of a dense and diverse population which acted as source of nutrients. The genome of Thermus scotoductus illustrates how rapid adaptation can be achieved by a highly dynamic and plastic genome.
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Affiliation(s)
- Kamini Gounder
- BioPAD Metagenomics Platform, Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
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A close relationship between primary nucleotides sequence structure and the composition of functional genes in the genome of prokaryotes. Mol Phylogenet Evol 2011; 61:650-8. [PMID: 21864693 DOI: 10.1016/j.ympev.2011.08.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 05/31/2011] [Accepted: 08/05/2011] [Indexed: 11/21/2022]
Abstract
Comparative genomics is an essential tool to unravel how genomes change over evolutionary time and to gain clues on the links between functional genomics and evolution. In prokaryotes, the large, good quality, genome sequences available in public databases and the recently developed large-scale computational methods, offer an unprecedent view on the ecology and evolution of microorganisms through comparative genomics. In this work, we examined the links among genome structure (i.e., the sequential distribution of nucleotides itself by detrended fluctuation analysis, DFA) and genomic diversity (i.e., gene functionality by Clusters of Orthologous Genes, COGs) in 828 full sequenced prokaryotic genomes from 548 different bacteria and archaea species. DFA scaling exponent α indicated persistent long-range correlations (fractality) in each genome analyzed. Higher resolution power was found when considering the sequential succession of purine (AG) vs. pyrimidine (CT) bases than either keto (GT) to amino (AC) forms or strongly (GC) vs. weakly (AT) bonded nucleotides. Interestingly, the phyla Aquificae, Fusobacteria, Dictyoglomi, Nitrospirae, and Thermotogae were closer to archaea than to their bacterial counterparts. A strong significant correlation was found between scaling exponent α and COGs distribution, and we consistently observed that the larger α the more heterogeneous was the gene distribution within each functional category, suggesting a close relationship between primary nucleotides sequence structure and functional genes composition.
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Abstract
Deinococcus radiodurans is a robust bacterium best known for its capacity to repair massive DNA damage efficiently and accurately. It is extremely resistant to many DNA-damaging agents, including ionizing radiation and UV radiation (100 to 295 nm), desiccation, and mitomycin C, which induce oxidative damage not only to DNA but also to all cellular macromolecules via the production of reactive oxygen species. The extreme resilience of D. radiodurans to oxidative stress is imparted synergistically by an efficient protection of proteins against oxidative stress and an efficient DNA repair mechanism, enhanced by functional redundancies in both systems. D. radiodurans assets for the prevention of and recovery from oxidative stress are extensively reviewed here. Radiation- and desiccation-resistant bacteria such as D. radiodurans have substantially lower protein oxidation levels than do sensitive bacteria but have similar yields of DNA double-strand breaks. These findings challenge the concept of DNA as the primary target of radiation toxicity while advancing protein damage, and the protection of proteins against oxidative damage, as a new paradigm of radiation toxicity and survival. The protection of DNA repair and other proteins against oxidative damage is imparted by enzymatic and nonenzymatic antioxidant defense systems dominated by divalent manganese complexes. Given that oxidative stress caused by the accumulation of reactive oxygen species is associated with aging and cancer, a comprehensive outlook on D. radiodurans strategies of combating oxidative stress may open new avenues for antiaging and anticancer treatments. The study of the antioxidation protection in D. radiodurans is therefore of considerable potential interest for medicine and public health.
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Havelund JF, Giessing AMB, Hansen T, Rasmussen A, Scott LG, Kirpekar F. Identification of 5-hydroxycytidine at position 2501 concludes characterization of modified nucleotides in E. coli 23S rRNA. J Mol Biol 2011; 411:529-36. [PMID: 21723290 DOI: 10.1016/j.jmb.2011.06.036] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 06/17/2011] [Accepted: 06/20/2011] [Indexed: 10/18/2022]
Abstract
Complete characterization of a biomolecule's chemical structure is crucial in the full understanding of the relations between their structure and function. The dominating components in ribosomes are ribosomal RNAs (rRNAs), and the entire rRNA-but a single modified nucleoside at position 2501 in 23S rRNA-has previously been characterized in the bacterium Escherichia coli. Despite a first report nearly 20 years ago, the chemical nature of the modification at position 2501 has remained elusive, and attempts to isolate it have so far been unsuccessful. We unambiguously identify this last unknown modification as 5-hydroxycytidine-a novel modification in RNA. Identification of 5-hydroxycytidine was completed by liquid chromatography under nonoxidizing conditions using a graphitized carbon stationary phase in combination with ion trap tandem mass spectrometry and by comparing the fragmentation behavior of the natural nucleoside with that of a chemically synthesized ditto. Furthermore, we show that 5-hydroxycytidine is also present in the equivalent position of 23S rRNA from the bacterium Deinococcus radiodurans. Given the unstable nature of 5-hydroxycytidine, this modification might be found in other RNAs when applying the proper analytical conditions as described here.
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Affiliation(s)
- Jesper Foged Havelund
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
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83
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Partial and complete denitrification in Thermus thermophilus: lessons from genome drafts. Biochem Soc Trans 2011; 39:249-53. [PMID: 21265782 DOI: 10.1042/bst0390249] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We have obtained draft genomic sequences of PD (partial denitrificant) and CD (complete denitrificant) strains of Thermus thermophilus. Their genomes are similar in size to that of the aerobic strains sequenced to date and probably contain a similar megaplasmid. In the CD strain, the genes encoding a putative cytochrome cd1 Nir (nitrite reductase) and ancillary proteins were clustered with a cytochrome c-dependent Nor (nitric oxide reductase), and with genes that are probably implicated in their regulation. The Nar (nitrate reductase) and associated genes were also clustered and located 7 kb downstream of the genes coding for the Nir. The whole nar-nir-nor denitrification supercluster was identified as part of a variable region of a megaplasmid. No homologues of NosZ were found despite nitrogen balance supports the idea that such activity actually exists.
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Abstract
Phylogenetic trees of individual genes of prokaryotes (archaea and bacteria) generally have different topologies, largely owing to extensive horizontal gene transfer (HGT), suggesting that the Tree of Life (TOL) should be replaced by a "net of life" as the paradigm of prokaryote evolution. However, trees remain the natural representation of the histories of individual genes given the fundamentally bifurcating process of gene replication. Therefore, although no single tree can fully represent the evolution of prokaryote genomes, the complete picture of evolution will necessarily combine trees and nets. A quantitative measure of the signals of tree and net evolution is derived from an analysis of all quartets of species in all trees of the "Forest of Life" (FOL), which consists of approximately 7,000 phylogenetic trees for prokaryote genes including approximately 100 nearly universal trees (NUTs). Although diverse routes of net-like evolution collectively dominate the FOL, the pattern of tree-like evolution that reflects the consistent topologies of the NUTs is the most prominent coherent trend. We show that the contributions of tree-like and net-like evolutionary processes substantially differ across bacterial and archaeal lineages and between functional classes of genes. Evolutionary simulations indicate that the central tree-like signal cannot be realistically explained by a self-reinforcing pattern of biased HGT.
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Affiliation(s)
- Pere Puigbò
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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86
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Daly MJ, Gaidamakova EK, Matrosova VY, Kiang JG, Fukumoto R, Lee DY, Wehr NB, Viteri GA, Berlett BS, Levine RL. Small-molecule antioxidant proteome-shields in Deinococcus radiodurans. PLoS One 2010; 5:e12570. [PMID: 20838443 PMCID: PMC2933237 DOI: 10.1371/journal.pone.0012570] [Citation(s) in RCA: 224] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Accepted: 08/09/2010] [Indexed: 01/28/2023] Open
Abstract
For Deinococcus radiodurans and other bacteria which are extremely resistant to ionizing radiation, ultraviolet radiation, and desiccation, a mechanistic link exists between resistance, manganese accumulation, and protein protection. We show that ultrafiltered, protein-free preparations of D. radiodurans cell extracts prevent protein oxidation at massive doses of ionizing radiation. In contrast, ultrafiltrates from ionizing radiation-sensitive bacteria were not protective. The D. radiodurans ultrafiltrate was enriched in Mn, phosphate, nucleosides and bases, and peptides. When reconstituted in vitro at concentrations approximating those in the D. radiodurans cytosol, peptides interacted synergistically with Mn2+ and orthophosphate, and preserved the activity of large, multimeric enzymes exposed to 50,000 Gy, conditions which obliterated DNA. When applied ex vivo, the D. radiodurans ultrafiltrate protected Escherichia coli cells and human Jurkat T cells from extreme cellular insults caused by ionizing radiation. By establishing that Mn2+-metabolite complexes of D. radiodurans specifically protect proteins against indirect damage caused by gamma-rays delivered in vast doses, our findings provide the basis for a new approach to radioprotection and insight into how surplus Mn budgets in cells combat reactive oxygen species.
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Affiliation(s)
- Michael J. Daly
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
- * E-mail: (MJD); (RLL)
| | - Elena K. Gaidamakova
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Vera Y. Matrosova
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Juliann G. Kiang
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Risaku Fukumoto
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Duck-Yeon Lee
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nancy B. Wehr
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Gabriela A. Viteri
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Barbara S. Berlett
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Rodney L. Levine
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (MJD); (RLL)
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87
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Dartnell LR, Hunter SJ, Lovell KV, Coates AJ, Ward JM. Low-temperature ionizing radiation resistance of Deinococcus radiodurans and Antarctic Dry Valley bacteria. ASTROBIOLOGY 2010; 10:717-732. [PMID: 20950171 DOI: 10.1089/ast.2009.0439] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The high flux of cosmic rays onto the unshielded surface of Mars poses a significant hazard to the survival of martian microbial life. Here, we determined the survival responses of several bacterial strains to ionizing radiation exposure while frozen at a low temperature characteristic of the martian near-subsurface. Novel psychrotolerant bacterial strains were isolated from the Antarctic Dry Valleys, an environmental analogue of the martian surface, and identified by 16S rRNA gene phylogeny as representatives of Brevundimonas, Rhodococcus, and Pseudomonas genera. These isolates, in addition to the known radioresistant extremophile Deinococcus radiodurans, were exposed to gamma rays while frozen on dry ice (-79°C). We found D. radiodurans to exhibit far greater radiation resistance when irradiated at -79°C than was observed in similar studies performed at higher temperatures. This greater radiation resistance has important implications for the estimation of potential survival times of microorganisms near the martian surface. Furthermore, the most radiation resistant of these Dry Valley isolates, Brevundimonas sp. MV.7, was found to show 99% 16S rRNA gene similarity to contaminant bacteria discovered in clean rooms at both Kennedy and Johnson Space Centers and so is of prime concern to efforts in the planetary protection of Mars from our lander probes. Results from this experimental irradiation, combined with previous radiation modeling, indicate that Brevundimonas sp. MV.7 emplaced only 30 cm deep in martian dust could survive the cosmic radiation for up to 100,000 years before suffering 10⁶ population reduction.
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Affiliation(s)
- Lewis R Dartnell
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, UK
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88
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Abstract
An extremely thermophilic bacterium, Thermus thermophilus HB8, is one of the model organisms for systems biology. Its genome consists of a chromosome (1.85 Mb), a megaplasmid (0.26 Mb) designated pTT27, and a plasmid (9.3 kb) designated pTT8, and the complete sequence is available. We show here that T. thermophilus is a polyploid organism, harboring multiple genomic copies in a cell. In the case of the HB8 strain, the copy number of the chromosome was estimated to be four or five, and the copy number of the pTT27 megaplasmid seemed to be equal to that of the chromosome. It has never been discussed whether T. thermophilus is haploid or polyploid. However, the finding that it is polyploid is not surprising, as Deinococcus radiodurans, an extremely radioresistant bacterium closely related to Thermus, is well known to be a polyploid organism. As is the case for D. radiodurans in the radiation environment, the polyploidy of T. thermophilus might allow for genomic DNA protection, maintenance, and repair at elevated growth temperatures. Polyploidy often complicates the recognition of an essential gene in T. thermophilus as a model organism for systems biology.
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89
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Averhoff B, Müller V. Exploring research frontiers in microbiology: recent advances in halophilic and thermophilic extremophiles. Res Microbiol 2010; 161:506-14. [DOI: 10.1016/j.resmic.2010.05.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 05/05/2010] [Accepted: 05/11/2010] [Indexed: 11/16/2022]
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90
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Li H, Ji X, Zhou Z, Wang Y, Zhang X. Thermus thermophilus proteins that are differentially expressed in response to growth temperature and their implication in thermoadaptation. J Proteome Res 2010; 9:855-64. [PMID: 20017569 DOI: 10.1021/pr900754y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
As a kind of important extremophiles to realize the adaptation of life at high temperatures, thermophiles have attracted extensive studies. However, the pathways of thermophile proteins related to thermoadaptation remain to be addressed. Our study showed that there existed two types of protein profiles for the thermophile Thermus thermophilus wl in response to temperature change. One of them came from cultures growing below 65 degrees C, which was close to the optimal growth temperature, and another from cultures at or above 65 degrees C. These protein profiles were confirmed by Northern blots. On the basis of the proteomic and computational analyses, it was found that the thermophile proteins related to thermoadaptation might be involved in metabolic pathways as well as the stabilities and modifications of DNA and proteins. Interestingly, for the basic metabolism glycolysis, the phosphoglucomutase was up-regulated at below-optimum temperature, while the glyceraldehyde-3-phosphate dehydrogenase was up-regulated at above-optimum temperature, suggesting that different regulations might be used for basic metabolism at different temperatures. To characterize the proteins in response to high temperatures, superoxide dismutase (SOD), an important enzyme in organism to remove free radical produced in stress environment such as high temperature, was selected as a target protein for this investigation. SOD was inactivated to construct a SOD mutant. The results showed that the SOD protein was essential in thermoadaptation of T. thermophilus. Our study, therefore, presented the thermophile proteins required for thermoadaptation and their possible pathways in thermoadaptation.
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Affiliation(s)
- Hebin Li
- Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, The People's Republic of China
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91
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Ekman JV, Raulio M, Busse HJ, Fewer DP, Salkinoja-Salonen M. Deinobacterium chartae gen. nov., sp. nov., an extremely radiation-resistant, biofilm-forming bacterium isolated from a Finnish paper mill. Int J Syst Evol Microbiol 2010; 61:540-548. [PMID: 20382794 DOI: 10.1099/ijs.0.017970-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A rod-shaped, non-spore-forming, non-motile, aerobic, oxidase and catalase-positive and radiation-resistant bacterium (designated strain K4.1(T)) was isolated from biofilm collected from a Finnish paper mill. The bacterium grew as pale pink colonies on oligotrophic medium at 12 to 50 °C (optimum 37 to 45 °C) and at pH 6 to 10.3. The DNA G+C content of the strain was 66.8 l%. According to 16S rRNA gene sequence analysis, strain K4.1(T) was distantly related to the genus Deinococcus, sharing highest similarity with Deinococcus pimensis (90.0 %). In the phylogenetic tree, strain K4.1(T) formed a separate branch in the vicinity of the genus Deinococcus. The peptidoglycan type was A3β with L-Orn-Gly-Gly and the quinone system was determined to be MK-8. The polar lipid profile of strain K4.1(T) differed markedly from that of the genus Deinococcus. The predominant lipid of strain K4.1(T) was an unknown aminophospholipid and it did not contain the unknown phosphoglycolipid predominant in the polar lipid profiles of deinococci analysed to date. Two of the predominant fatty acids of the strain, 15 : 0 anteiso and 17 : 0 anteiso, were lacking or present in small amounts in species of the genus Deinococcus. Phylogenetic distinctness and significant differences in the polar lipid and fatty acid profiles suggest classification of strain K4.1(T) as a novel genus and species in the family Deinococcaceae, for which we propose the name Deinobacterium chartae gen. nov., sp. nov. The type strain is K4.1(T) (=DSM 21458(T) =HAMBI 2721(T)).
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Affiliation(s)
- Jaakko V Ekman
- Department of Food and Environmental Sciences, P.O. Box 56, FIN 00014 University of Helsinki, Finland
| | - Mari Raulio
- Department of Food and Environmental Sciences, P.O. Box 56, FIN 00014 University of Helsinki, Finland
| | - Hans-Jürgen Busse
- Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität, A-1210 Wien, Austria
| | - David P Fewer
- Department of Food and Environmental Sciences, P.O. Box 56, FIN 00014 University of Helsinki, Finland
| | - Mirja Salkinoja-Salonen
- Department of Food and Environmental Sciences, P.O. Box 56, FIN 00014 University of Helsinki, Finland
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92
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Gonçalves AMD, Fioravanti E, Stelter M, McSweeney S. Structure of an N-terminally truncated Nudix hydrolase DR2204 from Deinococcus radiodurans. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:1083-7. [PMID: 19923723 PMCID: PMC2777031 DOI: 10.1107/s1744309109037191] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2009] [Accepted: 09/14/2009] [Indexed: 01/02/2023]
Abstract
Nudix pyrophosphatases are a well represented protein family in the Deinococcus radiodurans genome. These hydrolases, which are known to be enzymatically active towards nucleoside diphosphate derivatives, play a role in cleansing the cell pool of potentially deleterious damage products. Here, the structure of DR2204, the only ADP-ribose pyrophosphatase in the D. radiodurans genome that is known to be active towards flavin adenosine dinucleotide (FAD), is presented at 2.0 angstrom resolution.
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Affiliation(s)
- A. M. D. Gonçalves
- Macromolecular Crystallography Group, European Synchrotron Radiation Facility, BP 220, 6 Rue Jules Horowitz, F-38043 Grenoble, France
| | - E. Fioravanti
- Macromolecular Crystallography Group, European Synchrotron Radiation Facility, BP 220, 6 Rue Jules Horowitz, F-38043 Grenoble, France
| | - M. Stelter
- Macromolecular Crystallography Group, European Synchrotron Radiation Facility, BP 220, 6 Rue Jules Horowitz, F-38043 Grenoble, France
| | - S. McSweeney
- Macromolecular Crystallography Group, European Synchrotron Radiation Facility, BP 220, 6 Rue Jules Horowitz, F-38043 Grenoble, France
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93
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Nguyen HH, de la Tour CB, Toueille M, Vannier F, Sommer S, Servant P. The essential histone-like protein HU plays a major role inDeinococcus radioduransnucleoid compaction. Mol Microbiol 2009; 73:240-52. [DOI: 10.1111/j.1365-2958.2009.06766.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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94
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The linkage between reverse gyrase and hyperthermophiles: A review of their invariable association. J Microbiol 2009; 47:229-34. [DOI: 10.1007/s12275-009-0019-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Accepted: 04/20/2009] [Indexed: 11/26/2022]
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95
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Averhoff B. Shuffling genes around in hot environments: the unique DNA transporter ofThermus thermophilus. FEMS Microbiol Rev 2009; 33:611-26. [DOI: 10.1111/j.1574-6976.2008.00160.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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96
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Angelov A, Mientus M, Liebl S, Liebl W. A two-host fosmid system for functional screening of (meta)genomic libraries from extreme thermophiles. Syst Appl Microbiol 2009; 32:177-85. [PMID: 19285378 DOI: 10.1016/j.syapm.2008.01.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2007] [Revised: 01/24/2008] [Accepted: 01/27/2008] [Indexed: 11/24/2022]
Abstract
A new cloning system is described, which allows the construction of large-insert fosmid libraries in Escherichia coli and the transfer of the recombinant libraries to the extreme thermophile Thermus thermophilus via natural transformation. Libraries are established in the thermophilic host by site-specific chromosomal insertion of the recombinant fosmids via single crossover or double crossover recombination at the T. thermophilus pyr locus. Comparative screening of a fosmid library constructed from genomic DNA from the thermophilic spirochaete, Spirochaeta thermophila, for clones expressing thermoactive xylanase activity revealed that 50% of the fosmids that conferred xylanase activity upon the corresponding T. thermophilus transformants did not give rise to xylanase-positive E. coli clones, indicating that significantly more S. thermophila genes are functionally expressed in T. thermophilus than in E. coli. The novel T. thermophilus host/vector system may be of value for the construction and functional screening of recombinant DNA libraries from individual thermophilic or extremely thermophilic organisms as well as from complex metagenomes isolated from thermophilic microbial communities.
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Affiliation(s)
- Angel Angelov
- Institut f. Mikrobiologie und Genetik, Georg-August-Universität, Grisebachstr. 8, D-37077 Goettingen, Germany
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97
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Thermus thermophilus as biological model. Extremophiles 2009; 13:213-31. [DOI: 10.1007/s00792-009-0226-6] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Accepted: 12/31/2008] [Indexed: 10/21/2022]
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98
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The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea. J Bacteriol 2009; 191:1974-8. [PMID: 19124572 DOI: 10.1128/jb.01448-08] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lateral gene transfers (LGT) (also called horizontal gene transfers) have been a major force shaping the Thermosipho africanus TCF52B genome, whose sequence we describe here. Firmicutes emerge as the principal LGT partner. Twenty-six percent of phylogenetic trees suggest LGT with this group, while 13% of the open reading frames indicate LGT with Archaea.
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99
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Koonin EV, Wolf YI. Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res 2008; 36:6688-719. [PMID: 18948295 PMCID: PMC2588523 DOI: 10.1093/nar/gkn668] [Citation(s) in RCA: 534] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The first bacterial genome was sequenced in 1995, and the first archaeal genome in 1996. Soon after these breakthroughs, an exponential rate of genome sequencing was established, with a doubling time of approximately 20 months for bacteria and approximately 34 months for archaea. Comparative analysis of the hundreds of sequenced bacterial and dozens of archaeal genomes leads to several generalizations on the principles of genome organization and evolution. A crucial finding that enables functional characterization of the sequenced genomes and evolutionary reconstruction is that the majority of archaeal and bacterial genes have conserved orthologs in other, often, distant organisms. However, comparative genomics also shows that horizontal gene transfer (HGT) is a dominant force of prokaryotic evolution, along with the loss of genetic material resulting in genome contraction. A crucial component of the prokaryotic world is the mobilome, the enormous collection of viruses, plasmids and other selfish elements, which are in constant exchange with more stable chromosomes and serve as HGT vehicles. Thus, the prokaryotic genome space is a tightly connected, although compartmentalized, network, a novel notion that undermines the ‘Tree of Life’ model of evolution and requires a new conceptual framework and tools for the study of prokaryotic evolution.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
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100
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Cutler RW, Chantawannakul P. Synonymous codon usage bias dependent on local nucleotide context in the class Deinococci. J Mol Evol 2008; 67:301-14. [PMID: 18696025 DOI: 10.1007/s00239-008-9152-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2008] [Accepted: 07/14/2008] [Indexed: 11/25/2022]
Abstract
To study the evolution of mutation biased synonymous codon usage, we examined nucleotide co-occurrence patterns in the Deinococcus radiodurans, D. geothermalis, and Thermus thermophilus genomes for nucleotide replacement dependent on the surrounding nucleotide context. Nucleotides on the third codon site were found to be strongly correlated with nucleotide sites at most six nucleotides away in all three species, where abundance patterns were dependent on whether two nucleotides share the same purine(R)/pyrimidine(Y) status. In the class Deinococci adjacent third site nucleotides were strongly correlated, where NNR|NNR and NNY|NNY codon pairs were overabundant while NNR|NNY and NNY|NNR codon pairs were underabundant. By far the largest deviations in all three species occur for NN(YR)|(YR)NN codon pairs. In the Thermus species, the NNY|YNN and NNR|RNN codon pairs were overabundant versus the underabundant NNY|RNN and NNR|YNN codon pairs, whereas in the Deinococcus species the opposite over-/underabundance relationship held for adjacent (GC) bases. We also observed a weaker overabundance of NNR|NRN and NNY|NYN codon pairs versus the underabundant NNR|NYN and NNY|NRN codon pairs. The perfect purine/pyrimidine symmetry of each of these cases, plus the lack of significant deviations for nucleotide pairs on other length scales up to 20 codons apart demonstrates that a pervasive pattern of nucleotide replacement dependent on local nucleotide context, and not codon bias, has occurred in these species. This nucleotide replacement has led to modified synonymous codon usage within the class Deinococci that affects which codons are positioned at particular codon sites dependent on the local nucleotide context.
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