ISPst9, an ISL3-like insertion sequence from Pseudomonas stutzeri AN 10 involved in catabolic gene inactivation

International Microbiology

Volumn 11, Issue 2, 2008, Pages 101-110

  Christie Oleza, Joseph A ^a   Nogales, Balbina ^a   Martín Cardona, Celia ^a   Lanfranconi, Mariana P ^a   Albertí, Sebastián ^a   Lalucat, Jorge ^a   Bosch, Rafael ^a  

^a UNIVERSITAT DE LES ILLES BALEARS   (Spain)

Author keywords

Catabolic gene inactivation; Insertion sequences; Mobile elements; Pseudomonas stutzeri; Transposition

Indexed keywords

BACTERIA (MICROORGANISMS); PSEUDOMONAS STUTZERI;

EID: 51149122341     PISSN: 11396709     EISSN: 16181905     Source Type: Journal    
DOI: 10.2436/20.1501.01.49     Document Type: Article

References (56)

1. Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, Lipman D (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
2. Aragno M, Schlegel HG (1981) The hydrogen-oxidizing bacteria. In: Starr MP, Stolp H, Trüper HG, Balows A, Schlegel HG (eds) The prokaryotes. A handbook on habitats, isolation, and identification of bacteria. Springer-Verlag, Berlin-Heildelberg, pp 865-893
3. Aramaki H, Sagara Y, Takeuchi K, Koga H, Horiuchi T (1994) Nucleotide sequence of the gene encoding a repressor for the cytochrome P-450 cam hydroxylase operon on the Pseudomonas putida CAM plasmid. Biochimie 76:63-70
4. Baggi G, Barbieri P, Galli E, Tollari S (1987) Isolation of a Pseudomonas stutzeri strain that degrades o-xylene. Appl Environ Microbiol 53:2129-2132
5. Bennasar A, Rosselló-Mora R Lalucat J, Moore ERB (1996) 16S rRNA gene sequence analysis relative to genomovars of Pseudomonas stutzeri and proposal of Pseudomonas balearica sp. nov. Int J Syst Bacteriol 46:200-205
6. Bertoni G, Bolognese F, Galli E, Barbieri P (1996) Cloning of the genes for and characterization of the early stages of toluene and o-xylene catabolism in Pseudomonas stutzeri OX1. Appl Environ Microbiol 62:3704-3711
7. Bolognese F, di Lecce C, Galli E, Barbieri P (1999) Activation and inactivation of Pseudomonas stutzeri methylbenzene catabolism pathways mediated by a transposable element. Appl Environ Microbiol 65:1876-1882
8. Bosch R, García-Valdés E, Moore ERB (1999) Genetic characterization and evolutionary implications of a chromosomally encoded naphthalene-degradation upper pathway from Pseudomonas stutzeri AN10. Gene 236:149-157
9. Bosch R, Moore ERB, García-Valdés E, Pieper DH (1999) NahW, a novel, inducible salicylate hydroxylase involved in mineralization of naphthalene by Pseudomonas stutzeri AN10. J Bacteriol 181:2315-2322
10. Bosch R, García-Valdés E, Moore ERB (2000) Complete nucleotide sequence and evolutionary significance of a chromosomally encoded naphthalene-degradation lower pathway from Pseudomonas stutzeri AN10. Gene 245:65-74
11. Chandler M, Mahillon J (2002) Insertion sequence revisited. In: Craig NL, Craigie R, Gellert M, Lambowitz AM (eds) Mobile DNA II. ASM Press, Washington, DC, pp 305-366
12. Cladera AM, Bennasar A, Barceló M, Lalucat J, García- Valdés E (2004) Comparative genetic diversity of Pseudomonas stutzeri genomovars, clonal structure, and phylogeny of the species. J Bacteriol 186:5239-5248
13. Cladera AM, Sepúlveda-Torres LdC, Valens-Vadell M, Meyer J-M, Lalucat J, García-Valdés E (2006) A detailed phenotypic and genotypic description of Pseudomonas strain 0X1. Syst Appl Microbiol 29:422-430
14. Dhaese P, de Greve H, Decraemer H, Schell J, van Montagu M (1979) Rapid mapping of transposon insertion and deletion mutations in the large Ti-plasmids of Agrobacterium tumefaciens. Nucleic Acids Res 7:1837-1849
15. Diaz E (2004) Bacterial degradation of aromatic pollutants: a paradigm of metabolic versatility. Int Microbiol 7:173-180
16. di Lecce C, Accarino M, Bolognese F, Galli E, Barbieri P (1997) Isolation and metabolic characterization of a Pseudomonas stutzeri mutant able to grow on the three isomers of xylene. Appl Environ Microbiol 63:3279-3281
17. Elhai J, Wolk CP (1988) A versatile class of positive-selection vectors based on the non-viability of palindrome-containing plasmids that allows cloning into long polylinkers. Gene 68:119-138
18. Felsenstein J (1989) PHYLIP-phylogeny inference package. Cladistics 5:164-166
19. Ferrero M, Llobet-Brossa E, Lalucat J, García-Valdés E, Rosselló-Mora R, Bosch R (2002) Coexistence of two distinct copies of naphthalene degradation genes in Pseudomonas strains isolated from the western Mediterranean region. Appl Environ Microbiol 68:957-962
20. García-Valdés E, Castillo MM, Bennasar A, Guasp C, Cladera AM, Bosch R, Engesser KH, Lalucat J (2003) Polyphasic characterization of Pseudomonas stutzeri CLN100 which simultaneously degrades chloro-and methylaromatics: A new genomovar within the species. Syst Appl Microbiol 26:390-403
21. Ginard M, Lalucat J, Tummler B, Romling U (1997) Genome organization of Pseudomonas stutzeri and resulting taxonomic and evolutionary considerations. Int J Syst Bacteriol 47:132-143
22. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704
23. Habe H, Omori T (2003) Genetics of polycyclic aromatic hydrocarbon metabolism in diverse aerobic bacteria. Biosci Biotechnol Biochem 67:225-243
24. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95-98
25. Hanahan D (1983) Studies on transformation of Escherichia coli with plasmids. J Mol Biol 166:557-580
26. Herrero M, de Lorenzo V Timmis KN (1990) Transposon vectors containing non-antibiotic resistance selection markers for cloning and stable chromosomal insertion of foreign genes in gram-negative bacteria. J Bacteriol 172:6557-6567
27. Hou S, Saw JH, Lee KS, et al. (2004) Genome sequence of the deep-sea y-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy. Proc Natl Acad Sci USA 101:18036-18041
28. Kallastu A, Horak R, Kivisaar M (1998) Identification and characterization of IS1411, a new insertion sequence which causes transcriptional activation of the phenol degradation genes in Pseudomonas putida. J Bacteriol 180:5306-5312
29. Kasai Y, Harayama S (2004) Catabolism of PAHs. In: Ramos JL (ed) Pseudomonas, vol. 3. Kluwer Academic/Plenum Publishers, New York, pp 463-490
30. Lalucat J, Bennasar A, Bosch R, García-Valdés E, Palleroni NJ (2006) Biology of Pseudomonas stutzeri. Microbiol Mol Biol Rev 70:510-547
31. Lane D (1991) 16S/23S sequencing. In: Stackebrandt EG, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. John Wiley, Chichester, pp 115-175
32. Mahillon J, Chandler M (1998) Insertion sequences. Microbiol Mol Biol Rev 62:725-774
33. Miller VL, Mekalanos JJ (1988) A novel suicide vector and its use in construction of insertion mutations: osmoregulation of outer membrane proteins and virulence determinants in Vibrio cholerae requires toxR. J Bacteriol 170:2575-2583
34. Navarro F (2006) Acquisition and horizontal diffusion of β-lactam resistance among clinically relevant microorganisms. Int Microbiol 9:79-81
35. Nojiri H, Shintani M, Omori T (2004) Divergence of mobile genetic elements involved in the distribution of xenobiotic-catabolic capacity. Appl Microbiol Biotech 64:154-174
36. Osborn AM, Moore ERB, Timmis KN (2000) An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. Environ Microbiol 2:39-50
37. Page RDM (1996) TREEVIEW: An application to display phylogenetic trees on personal computers. Comp Appl Biosc 12:357-358
38. Pearson WR (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol 183:63-98
39. Radice F, Orlandi V, Massa V, Cavalca L, Demarta A, Wood T, Barbieri P (2006) Genotypic characterization and phylogenetic relations of Pseudomonas sp. (formerly P. stutzeri) OX1. Curr Microbiol 52:395-399
40. Ravatn R, Studer S, Zehnder AJB, van der Meer JR (1998) Int-B13, an unusual site-specific recombinase of the bacteriophage P4 integrase family, is responsible for chromosomal insertion of the 105-kilobase clc element of Pseudomonas sp. strain B13. J Bacteriol 180:5505-5514
41. Reineke W, Jeenes DJ, Williams PA, Knackmuss H-J (1982) TOL plasmid pWW0 in constructed halobenzoate-degrading Pseudomonas strains: prevention of meta pathway. J Bacteriol 150:195-201
42. Rice P, Longden I, Bleasby A (2000) EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet 16:276-277
43. Rosselló R, García-Valdés E, Lalucat J, Ursing J (1991) Genotypic and phenotypic diversity of Pseudomonas stutzeri. System Appl Microbiol 14:150-157
44. Rosselló-Mora RA, Lalucat J, García-Valdés E (1994) Comparative biochemical and genetic analysis of naphthalene degradation among Pseudomonas stutzeri strains. Appl Environ Microbiol 60:966-972
45. Sambrook J, Russell DW (2001) Molecular cloning, a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
46. Stanier RY, Palleroni NJ, Doudoroff M (1966) The aerobic Pseudomonas: a taxonomic study. J Gen Microbiol 43:159-271
47. Tan H-M (1999) Bacterial catabolic transposons. Appl Microbiol Biotechnol 51:1-12
48. Thompson J, Gibson T, Plewniak F, Jeanmougin F, Higgins D (1997) The CLUSTALX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882
49. Timmis KN, Steffan RJ, Unterman R (1994) Designing microorganisms for the treatment of toxic wastes. Annu Rev Microbiol 48:525-557
50. Top EM, Springael D (2003) The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds. Curr Op Biotechnol 14:262-269
51. van de Klundert JA, van Gestel MH, Meerdink G, de Marie S (1988) Emergence of bacterial resistance to cefamandole in vivo due to outer membrane protein deficiency. Eur J Clin Microbiol Infect Dis 7:776-778
52. van der Meer JR (2006) Evolution of catabolic pathways in Pseudomonas through gene transfer. In: Ramos JL, Levesque RC (eds) Pseudomonas, vol. 4. Springer, pp 189-236
53. Weightman AJ, Topping AW, Hill KE, Lee LL, Sakai K, Slater JH, Thomas AW (2002) Transposition of DEH, a broad-host-range transposon flanked by ISPpu12, in Pseudomonas putida is associated with genomic rearrangements and dehalogenase gene silencing. J Bacteriol 184:6581-6591
54. Wilson K (1987) Preparation of genomic DNA from bacteria. In: Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (ed) Current protocols in molecular biology. John Wiley, New York, pp 2.4.1-2.4.5
55. Williams PA, Sayers JR (1994) The evolution of pathways for aromatic hydrocarbon oxidation in Pseudomonas. Biodegradation 5:195-217
56. Williams PA, Jones RM, Shaw LE (2002) A third transposable element, ISPpu12, from the toluene-xylene catabolic plasmid pWW0 of Pseudomonas putida mt-2. J Bacteriol 184:6572-6580