151
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Kavamura VN, Esposito E. Biotechnological strategies applied to the decontamination of soils polluted with heavy metals. Biotechnol Adv 2010; 28:61-9. [PMID: 19778598 DOI: 10.1016/j.biotechadv.2009.09.002] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Revised: 09/14/2009] [Accepted: 09/15/2009] [Indexed: 10/20/2022]
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152
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Decorosi F, Tatti E, Mini A, Giovannetti L, Viti C. Characterization of two genes involved in chromate resistance in a Cr(VI)-hyper-resistant bacterium. Extremophiles 2009; 13:917-23. [PMID: 19768364 DOI: 10.1007/s00792-009-0279-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 08/26/2009] [Indexed: 11/30/2022]
Abstract
Mechanisms underlying chromate resistance in Cr(VI)-hyper-resistant Pseudomonas corrugata strain 28, isolated from a highly Cr(VI) polluted soil, were studied by analyzing its two Cr(VI)-sensitive mutants obtained by insertion mutagenesis. The mutants, namely Crg3 and Crg96, were characterized by the identification of disrupted genes, and by the high-throughput approach called Phenotype MicroArray (PM), which permitted the assay of 1,536 phenotypes simultaneously. Crg3 and Crg96 mutants were affected in a malic enzyme family gene and in a gene encoding for a RecG helicase, respectively. The application of PM provided a wealth of new information relating to the disrupted genes and permitted to establish that chromate resistance in P. corrugata strain 28 also depends on supply on NADPH required in repairing damage induced by chromate and on DNA integrity maintenance.
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Affiliation(s)
- Francesca Decorosi
- Dipartimento di Biotecnologie Agrarie, Sez. Microbiologia, Università degli Studi di Firenze, Florence, Italy
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153
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Henne KL, Nakatsu CH, Thompson DK, Konopka AE. High-level chromate resistance in Arthrobacter sp. strain FB24 requires previously uncharacterized accessory genes. BMC Microbiol 2009; 9:199. [PMID: 19758450 PMCID: PMC2751784 DOI: 10.1186/1471-2180-9-199] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Accepted: 09/16/2009] [Indexed: 11/17/2022] Open
Abstract
Background The genome of Arthrobacter sp. strain FB24 contains a chromate resistance determinant (CRD), consisting of a cluster of 8 genes located on a 10.6 kb fragment of a 96 kb plasmid. The CRD includes chrA, which encodes a putative chromate efflux protein, and three genes with amino acid similarities to the amino and carboxy termini of ChrB, a putative regulatory protein. There are also three novel genes that have not been previously associated with chromate resistance in other bacteria; they encode an oxidoreductase (most similar to malate:quinone oxidoreductase), a functionally unknown protein with a WD40 repeat domain and a lipoprotein. To delineate the contribution of the CRD genes to the FB24 chromate [Cr(VI)] response, we evaluated the growth of mutant strains bearing regions of the CRD and transcript expression levels in response to Cr(VI) challenge. Results A chromate-sensitive mutant (strain D11) was generated by curing FB24 of its 96-kb plasmid. Elemental analysis indicated that chromate-exposed cells of strain D11 accumulated three times more chromium than strain FB24. Introduction of the CRD into strain D11 conferred chromate resistance comparable to wild-type levels, whereas deletion of specific regions of the CRD led to decreased resistance. Using real-time reverse transcriptase PCR, we show that expression of each gene within the CRD is specifically induced in response to chromate but not by lead, hydrogen peroxide or arsenate. Higher levels of chrA expression were achieved when the chrB orthologs and the WD40 repeat domain genes were present, suggesting their possible regulatory roles. Conclusion Our findings indicate that chromate resistance in Arthrobacter sp. strain FB24 is due to chromate efflux through the ChrA transport protein. More importantly, new genes have been identified as having significant roles in chromate resistance. Collectively, the functional predictions of these additional genes suggest the involvement of a signal transduction system in the regulation of chromate efflux and warrants further study.
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Affiliation(s)
- Kristene L Henne
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.
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154
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Lourenço RF, Gomes SL. The transcriptional response to cadmium, organic hydroperoxide, singlet oxygen and UV-A mediated by the σE-ChrR system inCaulobacter crescentus. Mol Microbiol 2009; 72:1159-70. [DOI: 10.1111/j.1365-2958.2009.06714.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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155
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Cheng Z, Wei YYC, Sung WWL, Glick BR, McConkey BJ. Proteomic analysis of the response of the plant growth-promoting bacterium Pseudomonas putida UW4 to nickel stress. Proteome Sci 2009; 7:18. [PMID: 19422705 PMCID: PMC2689183 DOI: 10.1186/1477-5956-7-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Accepted: 05/07/2009] [Indexed: 12/03/2022] Open
Abstract
Background Plant growth-promoting bacteria can alleviate the inhibitory effects of various heavy metals on plant growth, via decreasing levels of stress-induced ethylene. However, little has been done to detect any mechanisms specific for heavy metal resistance of this kind of bacteria. Here, we investigate the response of the wild-type plant growth-promoting bacterium Pseudomonas putida UW4 to nickel stress using proteomic approaches. The mutant strain P. putida UW4/AcdS-, lacking a functional 1-aminocyclopropane-1-carboxylic acid deaminase gene, was also assessed for its response to nickel stress. Results Two dimensional difference in-gel electrophoresis (DIGE) was used to detect significantly up- or down- regulated proteins (p < 0.05, | ratio | > 1.5) in P. putida in response to the presence of 2 mM Ni. Out of a total number of 1,702 proteins detected on the analytical gels for P. putida UW4, the expression levels of 82 (4.82%) proteins increased significantly while the expression of 81 (4.76%) proteins decreased significantly. Of 1,575 proteins detected on the analytical gels for P. putida UW4/AcdS-, the expression levels of 74 (4.70%) proteins increased and 51 (3.24%) proteins decreased significantly. Thirty-five proteins whose expression was altered were successfully identified by mass spectrometry and sequence comparisons with related species. Nineteen of the identified proteins were detected as differentially expressed in both wild-type and mutant expression profiles. Conclusion Functional assessment of proteins with significantly altered expression levels revealed several mechanisms thought to be involved in bacterial heavy metal detoxification, including general stress adaptation, anti-oxidative stress and heavy metal efflux proteins. This information may contribute to the development of plant growth-promoting bacteria mediated phytoremediation processes.
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Affiliation(s)
- Zhenyu Cheng
- Department of Biology, University of Waterloo, Ontario, Canada.
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156
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Mugerfeld I, Law BA, Wickham GS, Thompson DK. A putative azoreductase gene is involved in the Shewanella oneidensis response to heavy metal stress. Appl Microbiol Biotechnol 2009; 82:1131-41. [PMID: 19238379 DOI: 10.1007/s00253-009-1911-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Revised: 02/03/2009] [Accepted: 02/05/2009] [Indexed: 11/24/2022]
Abstract
The Shewanella oneidensis MR-1 gene SO3585, which is annotated as a putative flavin mononucleotide-dependent azoreductase, shares 28% sequence identity with Bacillus subtilis azoreductase and Pseudomonas putida ChrR, a soluble flavoprotein exhibiting chromate reductase activity. Reverse transcription polymerase chain reaction demonstrated that the SO3585 gene is co-transcribed with two downstream open reading frames: SO3586 (a glyoxalase family protein) and SO3587 (a predicted membrane-associated hypothetical protein). The transcriptional start site of the so3585 transcript was localized using 5' rapid amplification of complementary DNA ends analysis. To investigate the cellular function of SO3585, an in-frame deletion of the so3585 locus was generated in MR-1, and the phenotype of the resulting mutant was characterized. The so3585 deletion mutant was comparable to the parental strain in its ability to decolorize two sulfonated azo dyes (Orange II, Direct Blue 15) under aerobic conditions. By contrast, growth of the so3585 deletion mutant was sensitive to different exogenous transition heavy metals [Cr(VI), Cd(II), Cu(II), and Zn(II)], while the most severe growth deficiencies were observed in the presence of Cd(II) and Cu(II). In addition, the rate of extracellular chromate disappearance by the deletion strain was initially impaired, although both the so3585 mutant and MR-1 wild type reduced Cr(VI) within the same time period.
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Affiliation(s)
- Irina Mugerfeld
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
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157
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Henne KL, Turse JE, Nicora CD, Lipton MS, Tollaksen SL, Lindberg C, Babnigg G, Giometti CS, Nakatsu CH, Thompson DK, Konopka AE. Global Proteomic Analysis of the Chromate Response in Arthrobacter sp. Strain FB24. J Proteome Res 2009; 8:1704-16. [DOI: 10.1021/pr800705f] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Kristene L. Henne
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Joshua E. Turse
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Carrie D. Nicora
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Mary S. Lipton
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Sandra L. Tollaksen
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Carl Lindberg
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Gyorgy Babnigg
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Carol S. Giometti
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Cindy H. Nakatsu
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Dorothea K. Thompson
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Allan E. Konopka
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
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158
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Patel J, Zhang Q, McKay RML, Vincent R, Xu Z. Genetic Engineering of Caulobacter crescentus for Removal of Cadmium from Water. Appl Biochem Biotechnol 2009; 160:232-43. [DOI: 10.1007/s12010-009-8540-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2008] [Accepted: 01/20/2009] [Indexed: 11/28/2022]
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159
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Viti C, Decorosi F, Mini A, Tatti E, Giovannetti L. Involvement of the oscA gene in the sulphur starvation response and in Cr(VI) resistance in Pseudomonas corrugata 28. Microbiology (Reading) 2009; 155:95-105. [DOI: 10.1099/mic.0.021873-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas corrugata28 is a Cr(VI)-hyper-resistant bacterium. A Cr(VI)-sensitive mutant was obtained by insertional mutagenesis using EZ-Tn5<R6Kγori/KAN-2>Tnp. The mutant strain was impaired in a gene, here namedoscA(organosulphurcompounds), which encoded a hypothetical small protein of unknown function. The gene was located upstream of a gene cluster that encodes the components of the sulphate ABC transporter, and it formed a transcriptional unit withsbp, which encoded the periplasmic binding protein of the transporter. TheoscA–sbptranscriptional unit was strongly and quickly overexpressed after chromate exposure, suggesting the involvement ofoscAin chromate resistance, which was further confirmed by means of a complementation experiment. Phenotype MicroArray (PM) analysis made it possible to assay 1536 phenotypes and also indicated that theoscAgene was involved in the utilization of organosulphur compounds as a sole source of sulphur. This is believed to be the first evidence thatoscAplays a role in activating a sulphur starvation response, which is required to cope with oxidative stress induced by chromate.
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Affiliation(s)
- Carlo Viti
- Dipartimento di Biotecnologie Agrarie, Sez. Microbiologia, Università degli Studi di Firenze, Piazzale delle Cascine 24, 50144 Firenze, Italy
| | - Francesca Decorosi
- Dipartimento di Biotecnologie Agrarie, Sez. Microbiologia, Università degli Studi di Firenze, Piazzale delle Cascine 24, 50144 Firenze, Italy
| | - Annalisa Mini
- Dipartimento di Biotecnologie Agrarie, Sez. Microbiologia, Università degli Studi di Firenze, Piazzale delle Cascine 24, 50144 Firenze, Italy
| | - Enrico Tatti
- Dipartimento di Biotecnologie Agrarie, Sez. Microbiologia, Università degli Studi di Firenze, Piazzale delle Cascine 24, 50144 Firenze, Italy
| | - Luciana Giovannetti
- Dipartimento di Biotecnologie Agrarie, Sez. Microbiologia, Università degli Studi di Firenze, Piazzale delle Cascine 24, 50144 Firenze, Italy
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160
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Pisani F, Italiano F, de Leo F, Gallerani R, Rinalducci S, Zolla L, Agostiano A, Ceci L, Trotta M. Soluble proteome investigation of cobalt effect on the carotenoidless mutant ofRhodobacter sphaeroides. J Appl Microbiol 2009; 106:338-49. [DOI: 10.1111/j.1365-2672.2008.04007.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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161
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Complex regulatory pathways coordinate cell-cycle progression and development in Caulobacter crescentus. Adv Microb Physiol 2008; 54:1-101. [PMID: 18929067 DOI: 10.1016/s0065-2911(08)00001-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Caulobacter crescentus has become the predominant bacterial model system to study the regulation of cell-cycle progression. Stage-specific processes such as chromosome replication and segregation, and cell division are coordinated with the development of four polar structures: the flagellum, pili, stalk, and holdfast. The production, activation, localization, and proteolysis of specific regulatory proteins at precise times during the cell cycle culminate in the ability of the cell to produce two physiologically distinct daughter cells. We examine the recent advances that have enhanced our understanding of the mechanisms of temporal and spatial regulation that occur during cell-cycle progression.
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162
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Fanous A, Weiss W, Görg A, Jacob F, Parlar H. A proteome analysis of the cadmium and mercury response in Corynebacterium glutamicum. Proteomics 2008; 8:4976-86. [DOI: 10.1002/pmic.200800165] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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163
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Wolfaardt G, Hendry M, Korber D. Microbial distribution and diversity in saturated, high pH, uranium mine tailings, Saskatchewan, Canada. Can J Microbiol 2008; 54:932-40. [DOI: 10.1139/w08-084] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microbiological analyses were conducted on core samples collected along a vertical profile (0–66 m below surface) from the tailings management facility (TMF) at the Rabbit Lake uranium mine in northern Saskatchewan, Canada. Bacterial numbers in the core materials were similar to surrounding soils and surface waters, regardless of the seemingly unfavorable pH (mean = 9.9) and temperature (∼0 °C) in the TMF. The greatest number of viable cells (105CFU/g) was detected at the interface between the tailings and overlying standing water, below which cell counts decreased rapidly with depth. Whole-community metabolic profiles for samples from the different depths grouped into 3 clusters; however, these groups could not be positively correlated with sampling depth, temperature, redox potential, pH, or ore-mill feed. Flow-cell studies demonstrated microbial communities in the tailings surface water could develop biofilms and maintain cell activity at both pH 10 and 7, and altering the pH between these 2 values had little effect on biofilm viability. These results demonstrate the resilience and adaptive nature of naturally occurring microbial communities and signify a potential role of microbial activity in the long-term geochemical evolution of the TMF.
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Affiliation(s)
- G.M. Wolfaardt
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
- Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, SK S7N 5E2, Canada
- Department of Food and Bioproduct Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - M.J. Hendry
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
- Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, SK S7N 5E2, Canada
- Department of Food and Bioproduct Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - D.R. Korber
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
- Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, SK S7N 5E2, Canada
- Department of Food and Bioproduct Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
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164
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Holmes DE, O'Neil RA, Chavan MA, N'Guessan LA, Vrionis HA, Perpetua LA, Larrahondo MJ, DiDonato R, Liu A, Lovley DR. Transcriptome of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments. ISME JOURNAL 2008; 3:216-30. [PMID: 18843300 DOI: 10.1038/ismej.2008.89] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To learn more about the physiological state of Geobacter species living in subsurface sediments, heat-sterilized sediments from a uranium-contaminated aquifer in Rifle, Colorado, were inoculated with Geobacter uraniireducens, a pure culture representative of the Geobacter species that predominates during in situ uranium bioremediation at this site. Whole-genome microarray analysis comparing sediment-grown G. uraniireducens with cells grown in defined culture medium indicated that there were 1084 genes that had higher transcript levels during growth in sediments. Thirty-four c-type cytochrome genes were upregulated in the sediment-grown cells, including several genes that are homologous to cytochromes that are required for optimal Fe(III) and U(VI) reduction by G. sulfurreducens. Sediment-grown cells also had higher levels of transcripts, indicative of such physiological states as nitrogen limitation, phosphate limitation and heavy metal stress. Quantitative reverse transcription PCR showed that many of the metabolic indicator genes that appeared to be upregulated in sediment-grown G. uraniireducens also showed an increase in expression in the natural community of Geobacter species present during an in situ uranium bioremediation field experiment at the Rifle site. These results demonstrate that it is feasible to monitor gene expression of a microorganism growing in sediments on a genome scale and that analysis of the physiological status of a pure culture growing in subsurface sediments can provide insights into the factors controlling the physiology of natural subsurface communities.
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Affiliation(s)
- Dawn E Holmes
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA.
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165
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Scoccianti V, Iacobucci M, Paoletti MF, Fraternale A, Speranza A. Species-dependent chromium accumulation, lipid peroxidation, and glutathione levels in germinating kiwifruit pollen under Cr(III) and Cr(VI) stress. CHEMOSPHERE 2008; 73:1042-1048. [PMID: 18790514 DOI: 10.1016/j.chemosphere.2008.07.083] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Revised: 07/24/2008] [Accepted: 07/31/2008] [Indexed: 05/26/2023]
Abstract
The accumulation of chromium by germinating kiwifruit pollen appears to be significantly affected by Cr species, Cr concentration and calcium availability. Cr(III) accumulation always occurred in a linear manner while Cr(VI) uptake followed a logarithmic model. In the absence of exogenous calcium, Cr(III) accumulation was much higher than that of Cr(VI). It was observed that, as the Cr(III) concentration increased, there was a significant decrease in the endogenous calcium content of pollen, ultimately leading to complete calcium depletion after 90 min of incubation at 150 microM Cr(III). This loss of calcium could be responsible for the strong inhibition of tube emergence and growth following exposure of pollen to Cr(III). Indeed, when exogenous calcium was added to the kiwifruit pollen culture medium, significant growth recovery and reduced Cr(III) uptake occurred; the opposite was true in Cr(VI)-treatments. A significant rise in lipid peroxide production occurs in the presence of both Cr species; the effect was more pronounced following Cr(VI) exposure. Finally, glutathione pool dynamics appears to be differentially affected by chromium species and concentrations. In conclusion, results of the present study have provided important information regarding the different activity profiles of Cr(III) and Cr(VI) in relation to kiwifruit pollen performance, and have also demonstrated differences in some biochemical responses of pollen to metal stress.
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Affiliation(s)
- Valeria Scoccianti
- Istituto di Botanica, Università di Urbino Carlo Bo, Via Bramante 28, 61029 Urbino, Italy.
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166
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Abstract
Cadmium ions are a potent carcinogen in animals, and cadmium is a toxic metal of significant environmental importance for humans. Response curves were used to investigate the effects of cadmium chloride on the growth of Camplyobacter jejuni. In vitro, the bacterium showed reduced growth in the presence of 0.1 mm cadmium chloride, and the metal ions were lethal at 1 mm concentration. Two-dimensional gel electrophoresis combined with tandem mass spectrometry analysis enabled identification of 67 proteins differentially expressed in cells grown without and with 0.1 mm cadmium chloride. Cellular processes and pathways regulated under cadmium stress included fatty acid biosynthesis, protein biosynthesis, chemotaxis and mobility, the tricarboxylic acid cycle, protein modification, redox processes and the heat-shock response. Disulfide reductases and their substrates play many roles in cellular processes, including protection against reactive oxygen species and detoxification of xenobiotics, such as cadmium. The effects of cadmium on thioredoxin reductase and disulfide reductases using glutathione as a substrate were studied in bacterial lysates by spectrophotometry and nuclear magnetic resonance spectroscopy, respectively. The presence of 0.1 mm cadmium ions modulated the activities of both enzymes. The interactions of cadmium ions with oxidized glutathione and reduced glutathione were investigated using nuclear magnetic resonance spectroscopy. The data suggested that, unlike other organisms, C. jejuni downregulates thioredoxin reductase and upregulates other disulfide reductases involved in metal detoxification in the presence of cadmium.
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Affiliation(s)
- Nadeem O Kaakoush
- School of Medical Sciences, University of New South Wales, Sydney, Australia
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167
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Cloning and overexpression of alkaline phosphatase PhoK from Sphingomonas sp. strain BSAR-1 for bioprecipitation of uranium from alkaline solutions. Appl Environ Microbiol 2008; 74:5516-23. [PMID: 18641147 DOI: 10.1128/aem.00107-08] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cells of Sphingomonas sp. strain BSAR-1 constitutively expressed an alkaline phosphatase, which was also secreted in the extracellular medium. A null mutant lacking this alkaline phosphatase activity was isolated by Tn5 random mutagenesis. The corresponding gene, designated phoK, was cloned and overexpressed in Escherichia coli strain BL21(DE3). The resultant E. coli strain EK4 overexpressed cellular activity 55 times higher and secreted extracellular PhoK activity 13 times higher than did BSAR-1. The recombinant strain very rapidly precipitated >90% of input uranium in less than 2 h from alkaline solutions (pH, 9 +/- 0.2) containing 0.5 to 5 mM of uranyl carbonate, compared to BSAR-1, which precipitated uranium in >7 h. In both strains BSAR-1 and EK4, precipitated uranium remained cell bound. The EK4 cells exhibited a much higher loading capacity of 3.8 g U/g dry weight in <2 h compared to only 1.5 g U/g dry weight in >7 h in BSAR-1. The data demonstrate the potential utility of genetically engineering PhoK for the bioprecipitation of uranium from alkaline solutions.
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168
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Candidate stress genes of Nitrosomonas europaea for monitoring inhibition of nitrification by heavy metals. Appl Environ Microbiol 2008; 74:5475-82. [PMID: 18606795 DOI: 10.1128/aem.00500-08] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Heavy metals have been shown to be strong inhibitors of nitrification in wastewater treatment plants. In this research, the effects of cadmium, copper, and mercury on Nitrosomonas europaea were studied in quasi-steady-state batch reactors. When cells were exposed to 1 microM CdCl2, 6 microM HgCl2, or 8 microM CuCl2, ammonia oxidation rates were decreased by about 90%. Whole-genome transcriptional and proteomic responses of N. europaea to cadmium were used to identify heavy metal stress response genes. When cells were exposed to 1 microM CdCl2 for 1 h, 66 genes (of the total of 2,460 genes) were upregulated, and 50 genes were downregulated more than twofold. Of these, the mercury resistance genes (merTPCADE) averaged 277-fold upregulation under 1 microM CdCl2, with merA (mercuric reductase) showing 297-fold upregulation. In N. europaea cells exposed to 6 microM HgCl2 or to 8 microM CuCl2, merA showed 250-fold and 1.7-fold upregulation, respectively. Cells showed the ability to recover quickly from Hg2+-related toxic effects, apparently associated with upregulation of the mercury resistance genes and amoA, but no such recovery was evident in Cd2+-exposed cells even though merTPCADE were highly upregulated. We suggest that the upregulation of merA in response to CdCl2 and HgCl2 exposure may provide a means to develop an early-warning indicator for inhibition of nitrification by these metals.
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169
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Rivera SL, Vargas E, Ramírez-Díaz MI, Campos-García J, Cervantes C. Genes related to chromate resistance by Pseudomonas aeruginosa PAO1. Antonie van Leeuwenhoek 2008; 94:299-305. [DOI: 10.1007/s10482-008-9247-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Accepted: 04/17/2008] [Indexed: 10/22/2022]
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170
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Pagès D, Sanchez L, Conrod S, Gidrol X, Fekete A, Schmitt-Kopplin P, Heulin T, Achouak W. Exploration of intraclonal adaptation mechanisms of Pseudomonas brassicacearum facing cadmium toxicity. Environ Microbiol 2008; 9:2820-35. [PMID: 17922765 PMCID: PMC2121137 DOI: 10.1111/j.1462-2920.2007.01394.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Pseudomonas brassicacearum forms phenotypic variants in vitro as well as in planta during root colonization under natural conditions, leading to subpopulations (phase I and II cells) that differ in colony morphology and production of exoenzymes/secondary metabolites. The maximal concentration of cadmium allowing both variants growth was 25 μM; however, phase II cells accumulated fivefold higher Cd than phase I cells, even though both variants showed the same growth rate and kinetics, comprising a long stasis period (50 h). The whole transcriptome analysis of both variants in response to Cd was investigated using the home-made DNA microarrays. This analysis revealed completely different adaptation mechanisms developed by each variant to withstand and grow in the presence of the toxic. A re-organization of the cell wall to limit Cd entrance was noticed for phase I cells, as genes encoding levan exopolymers were downregulated at the expense of an upregulation of genes encoding alginate, and an upregulation of transporters such as cadA, and a downregulation of copper transporters. Phase II cells were unable to prevent Cd entrance and recruited genes under the control of oxyR and soxR regulation to face osmotic and oxidant stresses generated by Cd. Putrescine and spermidine metabolism appeared to play a central role in Cd tolerance. Microarray data were validated by biological analyses such as motility, oxidative stress assay, metabolite profiling with ICR-FT/MS and UPLC, capillary electrophoresis analysis of biogenic amines.
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Affiliation(s)
- Delphine Pagès
- Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes, CEA, DSV, iBEB, LEMiRE, CNRS, Aix Marseille Universite. CEA Cadarache, F-13108 Saint-Paul-lez-Durance, France
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171
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Landt SG, Abeliuk E, McGrath PT, Lesley JA, McAdams HH, Shapiro L. Small non-coding RNAs in Caulobacter crescentus. Mol Microbiol 2008; 68:600-14. [PMID: 18373523 DOI: 10.1111/j.1365-2958.2008.06172.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Small non-coding RNAs (sRNAs) are active in many bacterial cell functions, including regulation of the cell's response to environmental challenges. We describe the identification of 27 novel Caulobacter crescentus sRNAs by analysis of RNA expression levels assayed using a tiled Caulobacter microarray and a protocol optimized for detection of sRNAs. The principal analysis method involved identification of sets of adjacent probes with unusually high correlation between the individual intergenic probes within the set, suggesting presence of a sRNA. Among the validated sRNAs, two are candidate transposase gene antisense RNAs. The expression of 10 of the sRNAs is regulated by either entry into stationary phase, carbon starvation, or rich versus minimal media. The expression of four of the novel sRNAs changes as the cell cycle progresses. One of these shares a promoter motif with several genes expressed at the swarmer-to-stalked cell transition; while another appears to be controlled by the CtrA global transcriptional regulator. The probe correlation analysis approach reported here is of general use for large-scale sRNA identification for any sequenced microbial genome.
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Affiliation(s)
- Stephen G Landt
- Department of Developmental Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA
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172
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Park S, Ely RL. Genome-wide transcriptional responses of Nitrosomonas europaea to zinc. Arch Microbiol 2007; 189:541-8. [PMID: 18097650 DOI: 10.1007/s00203-007-0341-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Revised: 11/24/2007] [Accepted: 12/04/2007] [Indexed: 11/28/2022]
Abstract
Nitrosomonas europaea, a Gram-negative obligate chemolithoautotroph, participates in global nitrogen cycling by carrying out nitrification and derives energy for growth through oxidation of ammonia. In this work, the physiological, proteomic, and transcriptional responses of N. europaea to zinc stress were studied. The nitrite production rate and ammonia-dependent oxygen uptake rate of the cells exposed to 3.4 microM ZnCl2 decreased about 61 and 69% within 30 min, respectively. Two proteins were notably up regulated in zinc treatment and the mRNA levels of their encoding genes started to increase by 1 h after the addition of zinc. A total of 27 genes were up regulated and 30 genes were down regulated. Up-regulated genes included mercury resistance genes (merTPCAD), inorganic ion transport genes, oxidative stress genes, toxin-antitoxin genes, and two-component signal transduction systems genes. merTPCAD was the highest up-regulated operon (46-fold). Down-regulated genes included the RubisCO operon (cbbO), biosynthesis (mrsA), and amino acid transporter.
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Affiliation(s)
- Sunhwa Park
- Department of Biological and Ecological Engineering, Oregon State University, Corvallis, OR 97331, USA
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173
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Harrison JJ, Ceri H, Turner RJ. Multimetal resistance and tolerance in microbial biofilms. Nat Rev Microbiol 2007; 5:928-38. [PMID: 17940533 DOI: 10.1038/nrmicro1774] [Citation(s) in RCA: 379] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Geochemical cycling and industrial pollution have made toxic metal ions a pervasive environmental pressure throughout the world. Biofilm formation is a strategy that microorganisms might use to survive a toxic flux in these inorganic compounds. Evidence in the literature suggests that biofilm populations are protected from toxic metals by the combined action of chemical, physical and physiological phenomena that are, in some instances, linked to phenotypic variation among the constituent biofilm cells. Here, we propose a multifactorial model by which biofilm populations can withstand metal toxicity by a process of cellular diversification.
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Affiliation(s)
- Joe J Harrison
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, Alberta T2N 1N4, Canada
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174
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PhyR is involved in the general stress response of Methylobacterium extorquens AM1. J Bacteriol 2007; 190:1027-35. [PMID: 18024517 DOI: 10.1128/jb.01483-07] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PhyR represents a novel alphaproteobacterial family of response regulators having a structure consisting of two domains; a predicted amino-terminal extracytoplasmic function (ECF) sigma factor-like domain and a carboxy-terminal receiver domain. PhyR was first described in Methylobacterium extorquens AM1, in which it has been shown to be essential for plant colonization, probably due to its suggested involvement in the regulation of a number of stress proteins. Here we investigated the PhyR regulon using microarray technology. We found that the PhyR regulon is rather large and that most of the 246 targets are under positive control. Mapping of transcriptional start sites revealed candidate promoters for PhyR-mediated regulation. One of these promoters, an ECF-type promoter, was identified upstream of one-third of the target genes by in silico analysis. Among the PhyR targets are genes predicted to be involved in multiple stress responses, including katE, osmC, htrA, dnaK, gloA, dps, and uvrA. The induction of these genes is consistent with our phenotypic analyses which revealed that PhyR is involved in resistance to heat shock and desiccation, as well as oxidative, UV, ethanol, and osmotic stresses, in M. extorquens AM1. The finding that PhyR is involved in the general stress response was further substantiated by the finding that carbon starvation induces protection against heat shock and that this protection is at least in part dependent on PhyR.
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175
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Alvarez-Martinez CE, Lourenço RF, Baldini RL, Laub MT, Gomes SL. The ECF sigma factor sigma(T) is involved in osmotic and oxidative stress responses in Caulobacter crescentus. Mol Microbiol 2007; 66:1240-55. [PMID: 17986185 DOI: 10.1111/j.1365-2958.2007.06005.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Sigma factors of the ECF subfamily are important regulators of stress responses in bacteria. Analysis of Caulobacter crescentus genome sequence has indicated the presence of 13 members of the ECF (extracytoplasmic function) subfamily, suggesting that these regulators play an important role in C. crescentus physiology. This work describes the characterization of two highly similar C. crescentus ECF sigma factors, sigma(U) and sigma(T). The corresponding genes are not essential under normal growth conditions and absence of sigma(U) does not impair bacterial resistance to the environmental stresses tested. However, absence of sigma(T) significantly affects the ability of C. crescentus cells to survive osmotic and oxidative stress. Using transcription fusions to sigT and sigU upstream regions we demonstrate that both genes are induced by osmotic stress in a sigma(T)-dependent manner. Determination of sigU and sigT transcription start sites revealed an identical promoter motif, typical of ECF-dependent promoters. Transcriptome analysis revealed 40 putative members of the sigma(T) regulon, including sigU and sigR, encoding another ECF subfamily member, and genes involved in general stress responses and cell envelope functions. Twenty of those genes exhibit the sigT/sigU promoter motif in their upstream regions. Our data indicate a role of sigma(T) in distinct stress responses in C. crescentus.
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176
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Pacheco CC, Passos JF, Castro AR, Moradas-Ferreira P, De Marco P. Role of respiration and glutathione in cadmium-induced oxidative stress in Escherichia coli K-12. Arch Microbiol 2007; 189:271-8. [PMID: 17968530 DOI: 10.1007/s00203-007-0316-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Revised: 10/09/2007] [Accepted: 10/15/2007] [Indexed: 11/26/2022]
Abstract
Cadmium is a widespread pollutant that has been associated with oxidative stress, but the mechanism behind this effect in prokaryotes is still unclear. In this work, we exposed two glutathione deficient mutants (DeltagshA and DeltagshB) and one respiration deficient mutant (DeltaubiE) to a sublethal concentration of cadmium. The glutathione mutants show a similar increase in reactive oxygen species as the wild type. Experiments performed using the DeltaubiE strain showed that this mutant is more resistant to cadmium ions and that Cd-induced reactive oxygen species levels were not altered. In the light of these facts, we conclude that the interference of cadmium with the respiratory chain is the cause of the oxidative stress induced by this metal and that, contrary to previously proposed models, the reactive oxygen species increase is not due to glutathione depletion, although this peptide is crucial for cadmium detoxification.
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Affiliation(s)
- Catarina C Pacheco
- Grupo de Microbiologia Celular e Aplicada (MCA), IBMC, R. Campo Alegre, 823, 4150-180 Porto, Portugal
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177
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Ramírez-Díaz MI, Díaz-Pérez C, Vargas E, Riveros-Rosas H, Campos-García J, Cervantes C. Mechanisms of bacterial resistance to chromium compounds. Biometals 2007; 21:321-32. [PMID: 17934697 DOI: 10.1007/s10534-007-9121-8] [Citation(s) in RCA: 209] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2007] [Accepted: 09/25/2007] [Indexed: 11/27/2022]
Abstract
Chromium is a non-essential and well-known toxic metal for microorganisms and plants. The widespread industrial use of this heavy metal has caused it to be considered as a serious environmental pollutant. Chromium exists in nature as two main species, the trivalent form, Cr(III), which is relatively innocuous, and the hexavalent form, Cr(VI), considered a more toxic species. At the intracellular level, however, Cr(III) seems to be responsible for most toxic effects of chromium. Cr(VI) is usually present as the oxyanion chromate. Inhibition of sulfate membrane transport and oxidative damage to biomolecules are associated with the toxic effects of chromate in bacteria. Several bacterial mechanisms of resistance to chromate have been reported. The best characterized mechanisms comprise efflux of chromate ions from the cell cytoplasm and reduction of Cr(VI) to Cr(III). Chromate efflux by the ChrA transporter has been established in Pseudomonas aeruginosa and Cupriavidus metallidurans (formerly Alcaligenes eutrophus) and consists of an energy-dependent process driven by the membrane potential. The CHR protein family, which includes putative ChrA orthologs, currently contains about 135 sequences from all three domains of life. Chromate reduction is carried out by chromate reductases from diverse bacterial species generating Cr(III) that may be detoxified by other mechanisms. Most characterized enzymes belong to the widespread NAD(P)H-dependent flavoprotein family of reductases. Several examples of bacterial systems protecting from the oxidative stress caused by chromate have been described. Other mechanisms of bacterial resistance to chromate involve the expression of components of the machinery for repair of DNA damage, and systems related to the homeostasis of iron and sulfur.
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Affiliation(s)
- Martha I Ramírez-Díaz
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B-3, Ciudad Universitaria, Morelia, Michoacan 58030, Mexico.
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178
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Hillson NJ, Hu P, Andersen GL, Shapiro L. Caulobacter crescentus as a whole-cell uranium biosensor. Appl Environ Microbiol 2007; 73:7615-21. [PMID: 17905881 PMCID: PMC2168040 DOI: 10.1128/aem.01566-07] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We engineered a strain of the bacterium Caulobacter crescentus to fluoresce in the presence of micromolar levels of uranium at ambient temperatures when it is exposed to a hand-held UV lamp. Previous microarray experiments revealed that several Caulobacter genes are significantly upregulated in response to uranium but not in response to other heavy metals. We designated one of these genes urcA (for uranium response in caulobacter). We constructed a reporter that utilizes the urcA promoter to produce a UV-excitable green fluorescent protein in the presence of the uranyl cation, a soluble form of uranium. This reporter is specific for uranium and has little cross specificity for nitrate (<400 microM), lead (<150 microM), cadmium (<48 microM), or chromium (<41.6 microM). The uranium reporter construct was effective for discriminating contaminated groundwater samples (4.2 microM uranium) from uncontaminated groundwater samples (<0.1 microM uranium) collected at the Oak Ridge Field Research Center. In contrast to other uranium detection methodologies, the Caulobacter reporter strain can provide on-demand usability in the field; it requires minimal sample processing and no equipment other than a hand-held UV lamp, and it may be sprayed directly on soil, groundwater, or industrial surfaces.
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Affiliation(s)
- Nathan J Hillson
- Department of Developmental Biology, Beckman Center, Stanford University School of Medicine, Stanford, California 94305, USA
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179
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Fanous A, Weiland F, Lück C, Görg A, Friess A, Parlar H. A proteome analysis of Corynebacterium glutamicum after exposure to the herbicide 2,4-dichlorophenoxy acetic acid (2,4-D). CHEMOSPHERE 2007; 69:25-31. [PMID: 17568655 DOI: 10.1016/j.chemosphere.2007.04.075] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Revised: 04/18/2007] [Accepted: 04/29/2007] [Indexed: 05/15/2023]
Abstract
The herbicide 2,4-dichlorophenoxy acetic acid (2,4-D) induces a wide spectrum of toxic responses in living organisms. In this study, we analyzed the stress-induced responses of Corynebacterium glutamicum cells on protein level upon treatment with 2,4-D. For this, growing C. glutamicum cells were exposed to sublethal concentrations of 2,4-D, and changes of the gene expression profiles in comparison to non-exposed organisms were analyzed by two-dimensional gel electrophoresis and mass spectrometry. 2,4-D induced the over-expression of at least six C. glutamicum proteins, four of which could be identified by MALDI-TOF-MS. One protein (Cg2521; long-chain acyl-CoA synthetase) was related to the energy metabolism, and two proteins were involved in cell envelope synthesis (Cg2410; glutamine-dependent amidotransferase, and Cg1672; glycosyltransferase). The last induced protein was the ABC type transport system (Cg2695, ATPase component). The newly observed proteins, except for the ABC transport system, were not in general stress-related proteins, but were specifically expressed upon 2,4-D exposure and, therefore, can be used as respective biomarkers. Moreover, since these proteins seem to play a pivotal role in the adaptation of the cell to 2,4-D, they may help to gain deeper insight into the damage mechanisms of 2,4-D induced in the living cell.
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Affiliation(s)
- Ali Fanous
- Technical University of Munich, Department for Chemical-Technical Analysis, Research Center for Brewing and Food Quality, Weihenstephaner Steig 23, D-85354 Freising-Weihenstephan, Germany
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180
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Hendrischk AK, Braatsch S, Glaeser J, Klug G. The phrA gene of Rhodobacter sphaeroides encodes a photolyase and is regulated by singlet oxygen and peroxide in a σ E-dependent manner. Microbiology (Reading) 2007; 153:1842-1851. [PMID: 17526841 DOI: 10.1099/mic.0.2006/004390-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genome of the facultatively photosynthetic bacterium Rhodobacter sphaeroides encodes three proteins of the photolyase/cryptochrome family. This paper shows that phrA (RSP2143) encodes a functional photolyase, which is an enzyme that repairs UV radiation-induced DNA damage in a blue light dependent manner. Expression of phrA is upregulated in response to light, with no photoreceptor or the photosynthetic electron transport being involved. The results reveal that singlet oxygen and hydrogen peroxide dependent signals are transmitted by the sigma(E) factor and the anti-sigma(E) factor ChrR affecting phrA expression, while superoxide anions do not stimulate phrA expression. Thus, the sigma(E) regulon is involved not only in the response to singlet oxygen but also in the hydrogen peroxide response.
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Affiliation(s)
- Anne-Kathrin Hendrischk
- Institut für Mikrobiologie und Molekularbiologie, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Stephan Braatsch
- Institut für Mikrobiologie und Molekularbiologie, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Jens Glaeser
- Institut für Mikrobiologie und Molekularbiologie, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Gabriele Klug
- Institut für Mikrobiologie und Molekularbiologie, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
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181
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McGrath PT, Lee H, Zhang L, Iniesta AA, Hottes AK, Tan MH, Hillson NJ, Hu P, Shapiro L, McAdams HH. High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons. Nat Biotechnol 2007; 25:584-92. [PMID: 17401361 DOI: 10.1038/nbt1294] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Accepted: 03/01/2007] [Indexed: 11/08/2022]
Abstract
Using 62 probe-level datasets obtained with a custom-designed Caulobacter crescentus microarray chip, we identify transcriptional start sites of 769 genes, 53 of which are transcribed from multiple start sites. Transcriptional start sites are identified by analyzing probe signal cross-correlation matrices created from probe pairs tiled every 5 bp upstream of the genes. Signals from probes binding the same message are correlated. The contribution of each promoter for genes transcribed from multiple promoters is identified. Knowing the transcription start site enables targeted searching for regulatory-protein binding motifs in the promoter regions of genes with similar expression patterns. We identified 27 motifs, 17 of which share no similarity to the characterized motifs of other C. crescentus transcriptional regulators. Using these motifs, we predict coregulated genes. We verified novel promoter motifs that regulate stress-response genes, including those responding to uranium challenge, a stress-response sigma factor and a stress-response noncoding RNA.
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Affiliation(s)
- Patrick T McGrath
- Department of Physics, Stanford University, Varian Physics, 382 Via Pueblo Mall, Stanford, California 94305, USA
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182
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Bouskill NJ, Barnhart EP, Galloway TS, Handy RD, Ford TE. Quantification of changing Pseudomonas aeruginosa sodA, htpX and mt gene abundance in response to trace metal toxicity: a potential in situ biomarker of environmental health. FEMS Microbiol Ecol 2007; 60:276-86. [PMID: 17374126 DOI: 10.1111/j.1574-6941.2007.00296.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Sediment-dwelling prokaryotes play a vital role in determining the fate and speciation of metals, yet are also susceptible to the biological effects of trace metals. In this article, optimized DNA extraction and purification techniques and species-specific primers are used to assess the genetic incidence and abundance of metal detoxification and general stress genes of Pseudomonas aeruginosa to complement chemical analysis in inferring the severity of metal-contaminated sites along the Clark Fork River, Montana. Results show the highest incidence of candidate genes related to bacterial stress at the most polluted site, while multiple regression analysis demonstrated significant correlations (P<0.05, r(2)=0.9) between in situ metal concentrations (As, Cu and Zn), total gene incidence, and the incidence of metal detoxification genes. Furthermore, principal components plotting the incidence of genes related to metal resistance show clear separation of sites giving clear clusters on the basis of contamination. Quantification of three genes (sodA, htpX and mt) from surveyed sites found significantly higher (anova, P<0.05) copy numbers at the more contaminated sites compared with reference sites. The development of rapid microbial biomarker tools represents a significant advance in the field of environmental biomonitoring and the prediction of metal bioavailability.
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Affiliation(s)
- Nicolas J Bouskill
- Department of Microbiology, Montana State University, Bozeman, MT 59717, USA.
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183
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Martins-Pinheiro M, Marques RCP, Menck CFM. Genome analysis of DNA repair genes in the alpha proteobacterium Caulobacter crescentus. BMC Microbiol 2007; 7:17. [PMID: 17352799 PMCID: PMC1839093 DOI: 10.1186/1471-2180-7-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2006] [Accepted: 03/12/2007] [Indexed: 11/10/2022] Open
Abstract
Background The integrity of DNA molecules is fundamental for maintaining life. The DNA repair proteins protect organisms against genetic damage, by removal of DNA lesions or helping to tolerate them. DNA repair genes are best known from the gamma-proteobacterium Escherichia coli, which is the most understood bacterial model. However, genome sequencing raises questions regarding uniformity and ubiquity of these DNA repair genes and pathways, reinforcing the need for identifying genes and proteins, which may respond to DNA damage in other bacteria. Results In this study, we employed a bioinformatic approach, to analyse and describe the open reading frames potentially related to DNA repair from the genome of the alpha-proteobacterium Caulobacter crescentus. This was performed by comparison with known DNA repair related genes found in public databases. As expected, although C. crescentus and E. coli bacteria belong to separate phylogenetic groups, many of their DNA repair genes are very similar. However, some important DNA repair genes are absent in the C. crescentus genome and other interesting functionally related gene duplications are present, which do not occur in E. coli. These include DNA ligases, exonuclease III (xthA), endonuclease III (nth), O6-methylguanine-DNA methyltransferase (ada gene), photolyase-like genes, and uracil-DNA-glycosylases. On the other hand, the genes imuA and imuB, which are involved in DNA damage induced mutagenesis, have recently been described in C. crescentus, but are absent in E. coli. Particularly interesting are the potential atypical phylogeny of one of the photolyase genes in alpha-proteobacteria, indicating an origin by horizontal transfer, and the duplication of the Ada orthologs, which have diverse structural configurations, including one that is still unique for C. crescentus. Conclusion The absence and the presence of certain genes are discussed and predictions are made considering the particular aspects of the C. crescentus among other known DNA repair pathways. The observed differences enlarge what is known for DNA repair in the Bacterial world, and provide a useful framework for further experimental studies in this organism.
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Affiliation(s)
- Marinalva Martins-Pinheiro
- Department of Microbiology, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes 1374, São Paulo, 05508-900, SP, Brazil
| | - Regina CP Marques
- Department of Microbiology, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes 1374, São Paulo, 05508-900, SP, Brazil
| | - Carlos FM Menck
- Department of Microbiology, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes 1374, São Paulo, 05508-900, SP, Brazil
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184
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Chourey K, Thompson MR, Morrell-Falvey J, Verberkmoes NC, Brown SD, Shah M, Zhou J, Doktycz M, Hettich RL, Thompson DK. Global molecular and morphological effects of 24-hour chromium(VI) exposure on Shewanella oneidensis MR-1. Appl Environ Microbiol 2006; 72:6331-44. [PMID: 16957260 PMCID: PMC1563591 DOI: 10.1128/aem.00813-06] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The biological impact of 24-h ("chronic") chromium(VI) [Cr(VI) or chromate] exposure on Shewanella oneidensis MR-1 was assessed by analyzing cellular morphology as well as genome-wide differential gene and protein expression profiles. Cells challenged aerobically with an initial chromate concentration of 0.3 mM in complex growth medium were compared to untreated control cells grown in the absence of chromate. At the 24-h time point at which cells were harvested for transcriptome and proteome analyses, no residual Cr(VI) was detected in the culture supernatant, thus suggesting the complete uptake and/or reduction of this metal by cells. In contrast to the untreated control cells, Cr(VI)-exposed cells formed apparently aseptate, nonmotile filaments that tended to aggregate. Transcriptome profiling and mass spectrometry-based proteomic characterization revealed that the principal molecular response to 24-h Cr(VI) exposure was the induction of prophage-related genes and their encoded products as well as a number of functionally undefined hypothetical genes that were located within the integrated phage regions of the MR-1 genome. In addition, genes with annotated functions in DNA metabolism, cell division, biosynthesis and degradation of the murein (peptidoglycan) sacculus, membrane response, and general environmental stress protection were upregulated, while genes encoding chemotaxis, motility, and transport/binding proteins were largely repressed under conditions of 24-h chromate treatment.
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Affiliation(s)
- Karuna Chourey
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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