Structural and functional genomics of plasmid pSinA of Sinorhizobium sp. M14 encoding genes for the arsenite oxidation and arsenic resistance

Journal of Biotechnology

Volumn 164, Issue 4, 2013, Pages 479-488

  Drewniak, Lukasz ^a   Dziewit, Lukasz ^a   Ciezkowska, Martyna ^a   Gawor, Jan ^b   Gromadka, Robert ^b   Sklodowska, Aleksandra ^a  

^a UNIVERSITY OF WARSAW   (Poland)

^b INSTITUTE OF BIOCHEMISTRY AND BIOPHYSICS   (Poland)

Author keywords

Arsenic resistance; Arsenite oxidation; Horizontal gene transfer; Plasmid pSinA

Indexed keywords

ARSENIC RESISTANCE; ARSENITE OXIDATION; FUNCTIONAL GENOMICS; GAMMAPROTEOBACTERIA; HORIZONTAL GENE TRANSFER; MICROBIAL COMMUNITIES; MICROCOSM EXPERIMENTS; PLASMID PSINA;

ARSENIC; GENE TRANSFER; GENES; HEAVY METALS; OXIDATION; SALT REMOVAL; SOIL POLLUTION;

DNA;

ARSENIC; ARSENIC TRIOXIDE; ARSENITE OXIDASE; CADMIUM; COBALT; HEAVY METAL; MERCURY; OXIDOREDUCTASE; UNCLASSIFIED DRUG; ZINC;

ALPHAPROTEOBACTERIA; ANIMAL CELL; ARTICLE; BACTERIAL GENE; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM CONJUGATION; BIOREMEDIATION; CONTROLLED STUDY; FUNCTIONAL GENOMICS; GENE EXPRESSION; HOST PATHOGEN INTERACTION; MICROBIAL COMMUNITY; MICROCOSM; NONHUMAN; OXIDATION; PLASMID; PLASMID PSINA; PRIORITY JOURNAL; PROTEIN STABILITY; SINORHIZOBIUM; SOIL POLLUTION; STRUCTURAL GENOMICS;

ARSENIC; ARSENITES; BACTERIA; DRUG RESISTANCE, BACTERIAL; GENE TRANSFER, HORIZONTAL; GENES, BACTERIAL; MODELS, GENETIC; OXIDATION-REDUCTION; PLASMIDS; SINORHIZOBIUM;

ALPHAPROTEOBACTERIA; GAMMAPROTEOBACTERIA; SINORHIZOBIUM SP.;

EID: 84875622311     PISSN: 01681656     EISSN: 18734863     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2013.01.017     Document Type: Article

References (52)

1. Bartosik D., Bialkowska A., Baj J., Wlodarczyk M. Construction of mobilizable cloning vectors derived from pBGS18 and their application for analysis of replicator region of a pTAV202 mini-derivative of Paracoccus versutus pTAV1 plasmid. Acta Microbiologica Polonica 1997, 46:387-392.
2. Bartosik D., Baj J., Wlodarczyk M. Molecular and functional analysis of pTAV320, a repABC-type replicon of the Paracoccus versutus composite plasmid pTAV1. Microbiology 1998, 144:3149-3157.
3. Bartosik D., Baj J., Piechucka E., Waker E., Wlodarczyk M. Comparative characterization of repABC-type replicons of Paracoccus pantotrophus composite plasmids. Plasmid 2002, 48:130-141.
4. Bartosik D., Szymanik M., Wysocka E. Identification of the partitioning site within the repABC-type replicon of the composite Paracoccus versutus plasmid pTAV1. Journal of Bacteriology 2001, 183:6234-6243.
5. Bathe S., Hausner M. Plasmid-mediated bioaugmentation of wastewater microbial communities in a laboratory-scale bioreactor. Methods in Molecular Biology 2010, 599:185-200.
6. Battaglia-Brunet F., Dictor M.C., Garrido F., Crouzet C., Morin D., Dekeyser K., Clarens M., Baranger P. An arsenic (III)-oxidizing bacterial population: selection, characterization, and performance in reactors. Journal of Applied Microbiology 2002, 93:1-12.
7. Birnboim H.C., Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Research 1979, 7:1513-1523.
8. Branco R., Francisco R., Chung A.P., Morais P.V. Identification of an aox system that requires cytochrome c in the highly arsenic-resistant bacterium Ochrobactrum tritici SCII24. Applied and Environmental Microbiology 2009, 75:5141-5147.
9. Burgos P.A., Velázquez E., Toro N. Identification and distribution of plasmid-type A replicator region in rhizobia. Molecular Plant-Microbe Interactions 1996, 9:843-849.
10. Cai L., Liu G., Rensing C., Wang G. Genes involved in arsenic transformation and resistance associated with different levels of arsenic-contaminated soils. BMC Microbiology 2009, 9:4.
11. Carver T., Thomson N., Bleasby A., Berriman M., Parkhill J. DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 2009, 25:119-120.
12. Connon S.A., Koski A.K., Neal A.L., Wood S.A., Magnuson T.S. Ecophysiology and geochemistry of microbial arsenic oxidation within a high arsenic circumneutral hot spring system of the Alvord Desert. FEMS Microbiology Ecology 2008, 64:117-128.
13. Drewniak L., Matlakowska R., Sklodowska A. Arsenite and arsenate metabolism of Sinorhizobium sp. M14 living in the extreme environment of the Zloty Stok gold mine. Geomicrobiology Journal 2008, 25:363-370.
14. Drewniak, L., 2009. Characterization of arsenic bacteria isolated from Zloty Stok gold mine. Ph.D. Thesis. University of Warsaw. Laboratory of Environmental Pollution Analysis, Warsaw.
15. Drewniak L., Matlakowska R., Rewerski B., Sklodowska A. Arsenic release from gold mine rocks mediated by the activity of indigenous bacteria. Hydrometallurgy 2010, 104:437-442.
16. Drewniak L., Maryan N., Lewandowski W., Sklodowska A. The contribution of microbial mats to the arsenic geochemistry of an ancient gold mine. Environmental Pollution 2012, 162:190-201.
17. Duquesne K., Lebrun S., Casiot C., Bruneel O., Personne J.C., Leblanc M., Elbaz-Poulichet F., Morin G., Bonnefoy V. Immobilization of arsenite and ferric iron by Acidithiobacillus ferrooxidans and its relevance to acid mine drainage. Applied and Environmental Microbiology 2003, 69:6165-6173.
18. Ellis P.J., Conrads T., Hille R., Kuhn P. Crystal structure of the 100kDa arsenite oxidase from Alcaligenes faecalis in two crystal forms at 1.64Å and 2.03Å. Structure 2001, 9:125-132.
19. El Fantroussi S., Agathos S.N. Is bioaugmentation a feasible strategy for pollutant removal and site remediation?. Current Opinion in Microbiology 2005, 8:268-275.
20. Garcillán-Barcia M.P., Francia M.V., de la Cruz F. The diversity of conjugative relaxases and its application in plasmid classification. FEMS Microbiology Reviews 2009, 33:657-687.
21. Hooykaas P.J.J., Den Dulk-Ras H., Schilperoort R.A. Molecular mechanism of Ti plasmid mobilization by R plasmids: isolation of Ti plasmids with transposon-insertions in Agrobacterium tumefaciens. Plasmid 1980, 4:64-75.
22. Hynes M.F., McGregor N.F. Two plasmids other than the nodulation plasmid are necessary for formation of nitrogen-fixing nodules by Rhizobium leguminosarum. Molecular Microbiology 1990, 4:567-574.
23. Kashyap D.R., Botero L.M., Franck W.L., Hassett D.J., McDermott T.R. Complex regulation of arsenite oxidation in Agrobacterium tumefaciens. Journal of Bacteriology 2006, 188:1081-1088.
24. Kononova S.V., Nesmeyanova M.A. Phosphonates and their degradation by microorganisms. Biochemistry 2002, 67:184-195.
25. Kushner S.R. An improved method for transformation of E. coli with ColE1 derived plasmids. Genetic Engineering 1978, 17-23. Elsevier, North-Holland, Amsterdam, Netherlands. H.B. Boyer, S. Nicosia (Eds.).
26. Lane D.J. 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics 1991, 115-175. Wiley, New York. E. Stackebrandt, M. Goodfellow (Eds.).
27. Lett M.C., Muller D., Lièvremont D., Silver S., Santini J. Unified nomenclature for genes involved in prokaryotic aerobic arsenite oxidation. Journal of Bacteriology 2012, 194:207-208.
28. Mankin S.L., Hill D.S., Olhoft P.M., Toren E., Wenck A.R., Nea L., et al. Disarming and sequencing of Agrobacterium rhizogenes strain K599 (NCPPB2659) plasmid pRi2659. In Vitro Cellular & Developmental Biology - Plant 2007, 43:521-535.
29. Mukhopadhyay R., Rosen B.P., Phung L.T., Silver S. Microbial arsenic: from geocycles to genes and enzymes. FEMS Microbiology Reviews 2002, 26:311-325.
30. Muller D., Medigue C., Koechler S., Barbe V., Barakat M., Talla E., et al. A tale of two oxidation states: bacterial colonization of arsenic-rich environments. PLoS Genetics 2007, 3:E53.
31. Nies D.H. Efflux-mediated heavy metal resistance in prokaryotes. FEMS Microbiology Reviews 2003, 27:313-339.
32. Osborne T.H., Jamieson H.E., Hudson-Edwards K.A., Nordstrom D.K., Walker S.R., Ward S.A., Santini J.M. Microbial oxidation of arsenite in a subarctic environment: diversity of arsenite oxidase genes and identification of a psychrotolerant arsenite oxidiser. BMC Microbiology 2010, 10:205.
33. + antiporter. Biochimica et Biophysica Acta 2004, 1658:2-13.
34. Paez-Espino D., Tamames J., de Lorenzo V., Canovas D. Microbial responses to environmental arsenic. Biometals 2009, 22:117-130.
35. Quan X.C., Tang H., Xiong W.C., Yang Z.F. Bioaugmentation of aerobic sludge granules with a plasmid donor strain for enhanced degradation of 2,4-dichlorophenoxyacetic acid. J Hazard Mater 2010, 179:1136-1142.
36. Quemeneur M., Cébron A., Billard P., Battaglia-Brunet F., Garrido F., Leyval C., Joulian C. Population structure and abundance of arsenite-oxidizing bacteria along an arsenic pollution gradient in waters of the upper isle River Basin, France. Applied and Environmental Microbiology 2010, 76:4566-4570.
37. Rawlings D.E., Pretorius I.M., Woods D.R. Construction of arsenic-resistant Thiobacillus ferrooxidans recombinant plasmids and the expression of autotrophic plasmid genes in a heterotrophic cell-free system. Journal of Bacteriology 1984, 1:129-133.
38. Remenant B., Coupat-Goutaland B., Guidot A., Cellier G., Wicker E., Allen C., et al. Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence. BMC Genomics 2010, 11:379.
39. Rhine E.D., Onesios K.M., Serfes M.E., Reinfelder J.R., Young L.Y. Arsenic transformation and mobilization from minerals by the arsenite oxidizing strain WAO. Environmental Science & Technology 2008, 42:1423-1429.
40. Rhine E.D., Phelps C.D., Young L.Y. Anaerobic arsenite oxidation by novel denitrifying isolates. Environmental Microbiology 2006, 8:899-908.
41. Sambrook J., Russell D.W. Molecular Cloning: A Laboratory Manual 2001, Cold Spring Harbor Laboratory Press, New York.
42. Santini J.M., van Den Hoven R.N. Molybdenum-containing arsenite oxidase of the chemolithoautotrophic arsenite oxidizer NT-26. Journal of Bacteriology 2004, 186:1614-1619.
43. Silver S., Phung L.T. Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Applied and Environmental Microbiology 2005, 71:599-608.
44. Silver S., Phung L.T. A bacterial view of the periodic table: genes and proteins for toxic inorganic ions. Journal of Industrial Microbiology and Biotechnology 2005, 32:587-605.
45. Simeonova D.D., Micheva K., Muller D.A., Lagarde F., Lett M.C., Groudeva V.I., Lièvremont D. Arsenite oxidation in batch reactors with alginate-immobilized ULPAs1 strain. Biotechnology and Bioengineering 2005, 91:441-446.
46. Starkenburg S.R., Larimer F.W., Stein L.Y., Klotz M.G., Chain P.S., Sayavedra-Soto L.A., et al. Complete genome sequence of Nitrobacter hamburgensis X14 and comparative genomic analysis of species within the genus Nitrobacter. Applied and Environmental Microbiology 2008, 74:2852-2863.
47. Stiens M., Schneiker S., Keller M., Kuhn S., Pühler A., Schlüter A. Sequence analysis of the 144-kilobase accessory plasmid pSmeSM11a isolated from a dominant Sinorhizobium meliloti strain identified during a long-term field release experiment. Applied and Environmental Microbiology 2006, 72:3662-3672.
48. Stiens M., Schneiker S., Keller M., Pühler A., Schlüter A. Sequence analysis of the 181-kb accessory plasmid pSmeSM11b isolated from a dominant Sinorhizobium meliloti strain identified during a long-term field release experiment. FEMS Microbiology Letters 2007, 271:297-309.
49. Top E.M., Van Daele P., De Saeyer N., Forney L.J. Enhancement of 2,4-dichlorophenoxyacetic acid (2,4-D) degradation in soil by dissemination of catabolic plasmids. Antonie Leeuwenhoek 1998, 73:87-94.
50. World Health Organization, 2003. Arsenic in drinking water. http://www.who.int/mediacentre/factsheets/fs210/en/index.html.
51. Yang C., Xu L., Yan L., Xu Y. Construction of a genetically engineered microorganism with high tolerance to arsenite and strong arsenite oxidative ability. Journal of Environmental Science and Health, Part A. Toxic/Hazardous Substances and Environmental Engineering 2010, 45:732-737.
52. Young J.P., Crossman L.C., Johnston A.W., Thomson N.R., Ghazoui Z.F., Hull K.H., et al. The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biology 2006, 7:R34.