Novel polymerase chain reaction primers for the specific detection of bacterial copper P-type ATPases gene sequences in environmental isolates and metagenomic DNA

Letters in Applied Microbiology

Volumn 50, Issue 6, 2010, Pages 552-562

  De La Iglesia, R ^a   Valenzuela Heredia, D ^a   Pavissich, J P ^a   Freyhoffer, S ^a   Andrade, S ^a   Correa, J A ^a   González, Bernardo ^a,b  

^a PONTIFICIA UNIVERSIDAD CATÓLICA DE CHILE   (Chile)

^b UNIVERSIDAD ADOLFO IBÁÑEZ   (Chile)

Author keywords

ATPases; Bacterial communities; Copper resistance; Metagenomic DNA; PCR primer pair

Indexed keywords

BACTERIOLOGY; COPPER; DNA; DNA SEQUENCES; IMPACT RESISTANCE; MARINE POLLUTION; POLYMERASE CHAIN REACTION;

ATPASES; BACTERIAL COMMUNITIES; BACTERIAL COMMUNITY; METAGENOMIC DNA; PCR PRIMERS;

GENES;

ADENOSINE TRIPHOSPHATASE COPPER P TYPE; BACTERIAL DNA; BACTERIAL ENZYME; UNCLASSIFIED DRUG;

BACTERIUM; BIOMARKER; COPPER; DETECTION METHOD; DNA; MARINE POLLUTION; MICROBIAL COMMUNITY; POLLUTION EFFECT; POLLUTION EXPOSURE; POLYMERASE CHAIN REACTION;

ARTICLE; BACTERIUM ISOLATE; CONTROLLED STUDY; DNA SEQUENCE; ENZYME ASSAY; MARINE ENVIRONMENT; METAGENOMICS; MICROBIAL COMMUNITY; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; WATER POLLUTION;

BACTERIA (MICROORGANISMS);

EID: 77952113000     PISSN: 02668254     EISSN: 1472765X     Source Type: Journal    
DOI: 10.1111/j.1472-765X.2010.02832.x     Document Type: Article

References (32)

1. Adaikkalam, V. Swarup, S. (2005) Characterization of copABCD operon from a copper-sensitive Pseudomonas putida strain. Can J Microbiol 51, 209 216.
2. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Millar, W. Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389 3402.
3. Andrade, S., Moffett, J. Correa, J.A. (2006) Distribution of dissolved species and suspended particulate copper in an intertidal ecosystem affected by copper mine tailings in Northern Chile. Mar Chem 101, 203 212.
4. IB-ATPases. Biometals 20, 233 248.
5. Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A. Struhl, K. (1994) Current Protocols in Molecular Biology.
6. Bruins, M.R., Kapil, S. Oehme, F.W. (2000) Microbial resistance to metals in the environment. Ecotoxicol Environ Saf 45, 198 207.
7. Clarke, K.R. (1993) Non-parametric multivariate analyses of changes in community structure. Aust J Ecol 19, 117 143.
8. Correa, J.A., Castilla, J.C., Ramírez, M., Varas, M., Lagos, N., Vergara, S., Moenne, A., Román, A. et al. (1999) Copper, copper mine tailings and their effect on marine algae in Northern Chile. J Appl Phycol 11, 57 67.
9. De la Iglesia, R., Castro, D., Ginocchio, R., van der Lelie, D. González, B. (2006) Factors influencing the composition of bacterial communities found at abandoned copper-tailings dumps. J Appl Microbiol 100, 537 544.
10. Fan, B., Grass, G., Rensing, C. Rosen, B.P. (2001) Escherichia coli CopA N-terminal Cys(X)(2)Cys motifs are not required for copper resistance or transport. Biochem Biophys Res Commun 286, 414 418.
11. Gordon, A.S., Donat, J.R., Kango, R.A., Dyer, B.J. Stuart, L.M. (2000) Dissolved copper-complexing ligands in cultures of marine bacteria and estuarine water. Mar Chem 70, 149 160.
12. Gupta, A., Matsui, K., Lo, J.F. Silver, S. (1999) Molecular basis for resistance to silver cations in Salmonella. Nat Med 5, 183 188.
13. Halliwell, B. Gutteridge, J.M.C. (1984) Oxygen-toxicity, oxygen radicals, transition-metals and disease. Biochem J 219, 1 14.
14. Kemp, P.F. Aller, J.Y. (2004) Bacterial diversity in aquatic and other environments: what 16S rDNA libraries can tell us. FEMS Microbiol Ecol 47, 161 177.
15. Kotrba, P., Dolećková, L., de Lorenzo, V. Ruml, T. (1999) Enhanced bioaccumulation of heavy metal ions by bacterial cells due to surface display of short metal binding peptides. Appl Environ Microbiol 65, 1092 1098.
16. Lane, D.J. (1991) 16S/23S rRNA Sequencing. Nucleic Acids in Bacterial Systematics.
17. Lejon, D.P., Nowak, V., Bouko, S., Pascault, N., Mougel, C., Martins, J.M.F. Ranjard, L. (2007) Fingerprinting and diversity of bacterial copA genes in response to soil types, soil organic status and copper contamination. FEMS Microbiol Ecol 61, 424 437.
18. Moffett, J.W. Brand, R. (1996) Production of strong, extracellular Cu chelators by marine Cyanobacteria in response to Cu stress. Limnol Oceanogr 41, 288 295.
19. Morán, A.C., Hengst, M.B., De la Iglesia, R., Andrade, S., Correa, J.A. González, B. (2008) Changes in bacterial community structure associated with coastal copper enrichment. Environ Toxicol Chem 27, 2239 2245.
20. Nies, D.H. (1999) Microbial heavy-metal resistance. Appl Microbiol Biotechnol 51, 730 750.
21. Nies, D.H. Silver, S. (1995) Ion efflux systems involved in bacterial metal resistances. J Ind Microbiol 14, 186 199.
22. Palmgren, M.G. Axelsen, K.B. (1998) Evolution of P-type ATPases. Biochim Biophys Acta 1365, 37 45.
23. Pavissich, J.P., Silva, M. González, B. (2010) Sulfate reduction, molecular diversity, and copper amendment effects in bacterial communities enriched from sediments exposed to copper mining residues. Environ Toxicol Chem 29, 256 264.
24. Petersen, C. Moller, L.B. (2000) Control of copper homeostasis in Escherichia coli by a P-type ATPase, CopA, and a MerR-like transcriptional activator, CopR. Gene 261, 289 298.
25. Ramírez, M., Massolo, S., Frache, R. Correa, J.A. (2005) Metal speciation and environmental impact on sandy beaches due to El Salvador copper mine, Chile. Mar Pollut Bull 50, 62 72.
26. Rees, G., Baldwin, D., Watson, G., Perryman, S. Nielsen, D. (2004) Ordination and significance testing of microbial community composition derived from terminal restriction fragment length polymorphisms: application of multivariate statistics. Antonie Van Leeuwenhoek 86, 339 447.
27. Reeve, W.G., Tiwari, R.P., Kale, N.B., Dilworth, M.J. Glenn, A.R. (2002) ActP controls copper homeostasis in Rhizobium leguminosarum bv. viciae and Sinorhizobium meliloti preventing low pH-induced copper toxicity. Mol Microbiol 43, 981 991.
28. Silver, S. Phung, L.T. (1996) Bacterial heavy metal resistance: new surprises. Annu Rev Microbiol 50, 753 789.
29. Solioz, M. Stoyanov, J.V. (2003) Copper homeostasis in Enterococcus hirae. FEMS Microbiol Rev 27, 183 195.
30. Tamura, K., Dudley, J., Nei, M. Kumar, S. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version. Mol Biol Evol 24, 1596 1599.
31. Teitzel, G.M. Parsek, M.R. (2003) Heavy metal resistance of biofilm and planktonic Pseudomonas aeruginosa. Appl Environ Microbiol 69, 2313 2320.
32. Thompson, J.D., Higgins, D.G. Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673 4680.