Phylogenetic analysis of tnpR genes in mercury resistant soil bacteria: The relationship between DNA sequencing and RFLP typing approaches

FEMS Microbiology Letters

Volumn 144, Issue 1, 1996, Pages 95-102

  Holt, Robert J ^a   Strike, Peter ^a   Bruce, Kenneth D ^a  

^a UNIVERSITY OF LIVERPOOL   (United Kingdom)

Author keywords

DNA sequencing; phylogeny; resolvase; restriction fragment length polymorphism; soil bacteria

Indexed keywords

ENZYME; MERCURY; RESOLVASE;

ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; EVOLUTION; GENETIC ANALYSIS; GENETIC VARIABILITY; MERCURIALISM; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SOIL MICROFLORA;

BACTERIA (MICROORGANISMS);

EID: 0030588106     PISSN: 03781097     EISSN: None     Source Type: Journal    
DOI: 10.1016/0378-1097(96)00345-X     Document Type: Article

References (32)

1. [1] Osborn, A.M., Bruce, K.D., Strike, P. and Ritchie, D.A. (1993) Polymerase chain reaction - Restriction fragment length polymorphism analysis shows divergence among mer determinants from Gram-negative bacteria indistinguishable by DNA-DNA hybridisation. Appl. Environ. Microbiol. 59, 4024-4030.
2. [2] Bennett, P.M., Grinstedt, J., Choi, C.L and Richmond, M.H. (1978) Characterisation of Tn501, a transposon determining resistance to mercuric ions. Mol. Gen. Genet. 159, 101-106.
3. [3] Brown, N.L., Winnie, J.N., Fritzinger, D and Pridmore, R.D. (1985) The nucleotide sequence of the tnpA. gene completes the sequence of the Pseudomonas transposon Tn501. Nucleic Acids Res. 13, 5657-5669.
4. [4] De la Cruz, F. and Grinsted, J.(1982) Genetic and molecular characterisation of Tn21, a multiple resistance transposon from R100.1. J. Bacteriol. 151, 222-228.
5. [5] Kholodii, G.Ya., Yurieva, O.V., Lomovskaya, O.L., Gorlenko, Zh.M., Mindlin, S.Z. and Nikiforov, V.G. (1993) Tn5053, a mercury resistance transposon with integrons ends. J. Mol. Biol. 230, 1103-1107.
6. [6] Ippen-Ihler, K. Bacterial conjugation. In: Gene Transfer in the Environment (Levy, S.B. and Miller, R.V., Eds.), pp. 33-72, McGraw Hill, New York.
7. [7] Trevors, J.T., Barkay, T. and Bourquin, A.W. (1987) Gene transfer among bacteria in soil and aquatic environments -a review. Can. J. Microbiol. 33, 191-198.
8. [8] Grinstead, J., De la Cruz, F., Altenbuchner J. and Schmitt, R. (1982) Complementation of transposition of tnpA mutants of Tn3, Tn21, Tn 501 and Tn1721. Plasmid 8, 276-286.
9. [9] Diver, W.P., Grinstead, J., Fritzinger, D.C., Brown, N.L., Altenbuchner, J., Rogowsky, P. and Schmitt, R. (1983) DNA sequences of and complementation by the tnpR genes of Tn21, Tn501 and Tn1721. Mol. Gen. Genet. 191, 189-193.
10. [10] Osborn, A.M., Bruce, K.D., Strike, P. and Ritchie, D.A. (1995) Sequence conservation between regulatory mercury resistance genes in bacteria from mercury polluted and pristine environments. Syst. Appl. Microbiol. 18, 1-6.
11. [11] Bruce, K.D., Osborn, A.M., Pearson, A.J., Strike, P and Ritchie, D.A. (1995) Genetic diversity within mer genes directly amplified from communities of non-cultivated soil bacteria. Mol. Ecol. 4, 605-612.
12. [12] Pearson, A.J., Bruce, K.D., Osborn, A.M., Ritchie, D.A. and Strike, P. (1996) The distribution and association of class II transposase and resolvase genes with mer genes in soil bacteria. In press.
13. [13] Barkay, T., Fouts, D.L. and Olson, B.H. (1985) Preparation of a DNA gene probe for detection of mercury resistance genes in Gram-negative bacterial communities. Appl. Environ. Microbiol. 49, 686-692.
14. [14] Olson, B.H., Lester, J.N., Cayless, S.M. and Ford, S. (1989) Distribution of mercury resistance determinants in bacterial communities of river sediments. Water. Res. 23, 1209-1217.
15. [15] Olson, B.H., Cayless, S.M., Ford, S. and Lester, J.N. (1991) Toxic element contamination and the occurrence of mercury resistant bacteria in Hg-contaminated soil, sediments and sludges. Arch. Environ. Contain. Toxicol. 20, 226-233.
16. [16] Rochelle, P.A., Wetherbee, M.K. and Olson, B.H. (1991) Distribution of DNA sequences encoding narrow spectrum and broad spectrum mercury resistance. Appl. Environ. Microbiol. 57, 1581-1589.
17. [17] Felsenstein, J. (1993) PHYLIP (Phylogeny Inference Package) version 3.5C, Department of Genetics, University of Washington, Seattle.
18. [18] Felsenstein, J. (1981) Evolutionary trees from DNA sequence: A maximum likelihood approach. J. Mol. Evol. 17, 368-376.
19. [19] Fitch, W.M. (1971) Toward defining the course of evolution: minimum change needed for a specific tree topology. Syst. Zool. 20, 406-416.
20. [20] Olsen, J.E. (1990) An improved method for rapid isolation of plasmid DNA from wild type Gram-negative bacteria for plasmid restriction profile analysis. Lett. Appl. Microbiol. 10, 209-212.
21. [21] Kado, C.I. and Liu, S.T. (1981) Rapid procedure for detection and isolation of large and small plasmids. J. Bacteriol. 145, 1365-1373.
22. [22] Birnbiom, H.C and Doly, J. (1979) A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 7, 1513-1523.
23. [23] Pitcher, D.G., Saunders, N.A. and Owen, R.J. (1989) Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett. Appl. Microbiol. 8, 151-156.
24. [24] Genetics Computer Group. Program for the Wisconsin Package. Version 8, Sept. 1994, Genetics Computer Group, Madison, WI.
25. [25] Hills, D.M., Huelsenbeck, J.P. and Cunningham, C.W. (1994) Application and accuracy of molecular phylogenies. Science 264, 671-677.
26. [26] Fukami, K. and Tateno, Y. (1991) Robustness of maximum likelihood tree estimation against different patterns of base substitutions. J. Mol. Evol. 32, 79-91.
27. [27] Tateno, Y., Takezaki, N. and Nei, M. (1994) Relative efficiencies of the maximum likelihood, neighbor-joining, and maximum parsimony methods when substitution rate varies with site. Mol. Biol. Evol. 11, 261-277.
28. [28] Tillier, E.R.M. and Collins, R.A. (1995) Neighbor joining and maximum likelihood with RNA sequence: Addressing the interdependence of sites. Mol. Biol. Evol. 12, 7-15.
29. [29] DeBry, R.W. and Abele, L.G. (1995) The relationship betwen parsimony and maximum likelihood analyses: Tree scores and confidence estimates for three data sets. Mol. Biol. Evol. 12, 291-297.
30. [30] Huelsenbeck, J.P. (1995) The robustness of two phylogenetic methods: Four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining. Mol. Biol. Evol. 12, 843-849.
31. [31] Hall, L.M.C. (1994) Are point mutations or DNA rearrangements responsible for the restriction fragment length polymorphisms that are used to type bacteria? Microbiology. 140, 197-204.
32. [32] Ogram, A., Sayler, G.S. and Barkay, T. (1987) The extraction and purification of microbial DNA from sediments. J. Microbiol. Methods 7, 57-66.