Abstract
Transposition and transcriptional activation by insertion sequences in Burkholderia cepacia AC1100 were investigated. Two closely related new elements, IS1413 and IS1490, were identified and characterized. These elements are not highly related to other insertion sequences identified in AC1100 or other B. cepacia isolates. Based on their structures and the sequences of the inverted terminal repeats and the putative transposase protein, the insertion elements (IS elements) are similar to IST2 of Thiobacillus ferrooxidans and several related elements. All the IS elements that have been identified in this strain are found in multiple copies (10 to 40), and they have high-level promoter activity capable of stimulating transcription from a distance up to 500 bp from a target gene. Strain AC1100 was originally isolated after prolonged selection for the ability to utilize the herbicide 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) as a sole carbon source. Three IS elements are located near the first gene of the 2,4,5-T catabolic pathway, tftA. IS1490 inserted 110 bp upstream of tftA and created a fusion promoter responsible for constitutive transcription of the gene. Our results confirm the hypothesis that IS elements play a central role in transcription of 2,4,5-T genes and likely have stimulated rapid evolution of the metabolic pathway.
Full Text
The Full Text of this article is available as a PDF (409.4 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
- Bagdasarian M. M., Amann E., Lurz R., Rückert B., Bagdasarian M. Activity of the hybrid trp-lac (tac) promoter of Escherichia coli in Pseudomonas putida. Construction of broad-host-range, controlled-expression vectors. Gene. 1983 Dec;26(2-3):273–282. doi: 10.1016/0378-1119(83)90197-x. [DOI] [PubMed] [Google Scholar]
- Barsomian G., Lessie T. G. Replicon fusions promoted by insertion sequences on Pseudomonas cepacia plasmid pTGL6. Mol Gen Genet. 1986 Aug;204(2):273–280. doi: 10.1007/BF00425509. [DOI] [PubMed] [Google Scholar]
- Barth A. L., Pitt T. L. Auxotrophy of Burkholderia (Pseudomonas) cepacia from cystic fibrosis patients. J Clin Microbiol. 1995 Aug;33(8):2192–2194. doi: 10.1128/jcm.33.8.2192-2194.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Butler S. L., Doherty C. J., Hughes J. E., Nelson J. W., Govan J. R. Burkholderia cepacia and cystic fibrosis: do natural environments present a potential hazard? J Clin Microbiol. 1995 Apr;33(4):1001–1004. doi: 10.1128/jcm.33.4.1001-1004.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Byrne A. M., Lessie T. G. Characteristics of IS401, a new member of the IS3 family implicated in plasmid rearrangements in Pseudomonas cepacia. Plasmid. 1994 Mar;31(2):138–147. doi: 10.1006/plas.1994.1015. [DOI] [PubMed] [Google Scholar]
- Byrne M. E., Rouch D. A., Skurray R. A. Nucleotide sequence analysis of IS256 from the Staphylococcus aureus gentamicin-tobramycin-kanamycin-resistance transposon Tn4001. Gene. 1989 Sep 30;81(2):361–367. doi: 10.1016/0378-1119(89)90197-2. [DOI] [PubMed] [Google Scholar]
- Cheng H. P., Lessie T. G. Multiple replicons constituting the genome of Pseudomonas cepacia 17616. J Bacteriol. 1994 Jul;176(13):4034–4042. doi: 10.1128/jb.176.13.4034-4042.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cimolai N., Trombley C., Davidson A. G., Wong L. T. Selective media for isolation of Burkholderia (Pseudomonas) cepacia from the respiratory secretions of patients with cystic fibrosis. J Clin Pathol. 1995 May;48(5):488–490. doi: 10.1136/jcp.48.5.488. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cádiz R., Gaete L., Jedlicki E., Yates J., Holmes D. S., Orellana O. Transposition of IST2 in Thiobacillus ferrooxidans. Mol Microbiol. 1994 Apr;12(1):165–170. doi: 10.1111/j.1365-2958.1994.tb01005.x. [DOI] [PubMed] [Google Scholar]
- Danganan C. E., Shankar S., Ye R. W., Chakrabarty A. M. Substrate diversity and expression of the 2,4,5-trichlorophenoxyacetic acid oxygenase from Burkholderia cepacia AC1100. Appl Environ Microbiol. 1995 Dec;61(12):4500–4504. doi: 10.1128/aem.61.12.4500-4504.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Danganan C. E., Ye R. W., Daubaras D. L., Xun L., Chakrabarty A. M. Nucleotide sequence and functional analysis of the genes encoding 2,4,5-trichlorophenoxyacetic acid oxygenase in Pseudomonas cepacia AC1100. Appl Environ Microbiol. 1994 Nov;60(11):4100–4106. doi: 10.1128/aem.60.11.4100-4106.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Daubaras D. L., Hershberger C. D., Kitano K., Chakrabarty A. M. Sequence analysis of a gene cluster involved in metabolism of 2,4,5-trichlorophenoxyacetic acid by Burkholderia cepacia AC1100. Appl Environ Microbiol. 1995 Apr;61(4):1279–1289. doi: 10.1128/aem.61.4.1279-1289.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Del Sal G., Manfioletti G., Schneider C. The CTAB-DNA precipitation method: a common mini-scale preparation of template DNA from phagemids, phages or plasmids suitable for sequencing. Biotechniques. 1989 May;7(5):514–520. [PubMed] [Google Scholar]
- Denome S. A., Young K. D. Identification and activity of two insertion sequence elements in Rhodococcus sp. strain IGTS8. Gene. 1995 Aug 8;161(1):33–38. doi: 10.1016/0378-1119(95)00241-w. [DOI] [PubMed] [Google Scholar]
- Feinberg A. P., Vogelstein B. "A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity". Addendum. Anal Biochem. 1984 Feb;137(1):266–267. doi: 10.1016/0003-2697(84)90381-6. [DOI] [PubMed] [Google Scholar]
- Ferrante A. A., Lessie T. G. Nucleotide sequence of IS402 from Pseudomonas cepacia. Gene. 1991 Jun 15;102(1):143–144. doi: 10.1016/0378-1119(91)90555-p. [DOI] [PubMed] [Google Scholar]
- Gaffney T. D., Lessie T. G. Insertion-sequence-dependent rearrangements of Pseudomonas cepacia plasmid pTGL1. J Bacteriol. 1987 Jan;169(1):224–230. doi: 10.1128/jb.169.1.224-230.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gay P., Le Coq D., Steinmetz M., Berkelman T., Kado C. I. Positive selection procedure for entrapment of insertion sequence elements in gram-negative bacteria. J Bacteriol. 1985 Nov;164(2):918–921. doi: 10.1128/jb.164.2.918-921.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Guerrero C., Bernasconi C., Burki D., Bodmer T., Telenti A. A novel insertion element from Mycobacterium avium, IS1245, is a specific target for analysis of strain relatedness. J Clin Microbiol. 1995 Feb;33(2):304–307. doi: 10.1128/jcm.33.2.304-307.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Guilhot C., Gicquel B., Davies J., Martín C. Isolation and analysis of IS6120, a new insertion sequence from Mycobacterium smegmatis. Mol Microbiol. 1992 Jan;6(1):107–113. doi: 10.1111/j.1365-2958.1992.tb00842.x. [DOI] [PubMed] [Google Scholar]
- Haugland R. A., Sangodkar U. M., Chakrabarty A. M. Repeated sequences including RS1100 from Pseudomonas cepacia AC1100 function as IS elements. Mol Gen Genet. 1990 Jan;220(2):222–228. doi: 10.1007/BF00260485. [DOI] [PubMed] [Google Scholar]
- Haugland R. A., Sangodkar U. M., Sferra P. R., Chakrabarty A. M. Cloning and characterization of a chromosomal DNA region required for growth on 2,4,5-T by Pseudomonas cepacia AC1100. Gene. 1991 Apr;100:65–73. doi: 10.1016/0378-1119(91)90351-b. [DOI] [PubMed] [Google Scholar]
- Hawley D. K., McClure W. R. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 1983 Apr 25;11(8):2237–2255. doi: 10.1093/nar/11.8.2237. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hsieh M., Tintut Y., Gralla J. D. Functional roles for the glutamines within the glutamine-rich region of the transcription factor sigma 54. J Biol Chem. 1994 Jan 7;269(1):373–378. [PubMed] [Google Scholar]
- Kellogg S. T., Chatterjee D. K., Chakrabarty A. M. Plasmid-assisted molecular breeding: new technique for enhanced biodegradation of persistent toxic chemicals. Science. 1981 Dec 4;214(4525):1133–1135. doi: 10.1126/science.7302584. [DOI] [PubMed] [Google Scholar]
- Kilger C., Schmid K. Rapid characterization of bacterial clones by microwave treatment and PCR. Trends Genet. 1994 May;10(5):149–149. doi: 10.1016/0168-9525(94)90082-5. [DOI] [PubMed] [Google Scholar]
- Lessie T. G., Phibbs P. V., Jr Alternative pathways of carbohydrate utilization in pseudomonads. Annu Rev Microbiol. 1984;38:359–388. doi: 10.1146/annurev.mi.38.100184.002043. [DOI] [PubMed] [Google Scholar]
- Nurk A., Tamm A., Hôrak R., Kivisaar M. In-vivo-generated fusion promoters in Pseudomonas putida. Gene. 1993 May 15;127(1):23–29. doi: 10.1016/0378-1119(93)90612-7. [DOI] [PubMed] [Google Scholar]
- Podglajen I., Breuil J., Collatz E. Insertion of a novel DNA sequence, 1S1186, upstream of the silent carbapenemase gene cfiA, promotes expression of carbapenem resistance in clinical isolates of Bacteroides fragilis. Mol Microbiol. 1994 Apr;12(1):105–114. doi: 10.1111/j.1365-2958.1994.tb00999.x. [DOI] [PubMed] [Google Scholar]
- Prentki P., Teter B., Chandler M., Galas D. J. Functional promoters created by the insertion of transposable element IS1. J Mol Biol. 1986 Oct 5;191(3):383–393. doi: 10.1016/0022-2836(86)90134-8. [DOI] [PubMed] [Google Scholar]
- Rodley P. D., Römling U., Tümmler B. A physical genome map of the Burkholderia cepacia type strain. Mol Microbiol. 1995 Jul;17(1):57–67. doi: 10.1111/j.1365-2958.1995.mmi_17010057.x. [DOI] [PubMed] [Google Scholar]
- Scordilis G. E., Ree H., Lessie T. G. Identification of transposable elements which activate gene expression in Pseudomonas cepacia. J Bacteriol. 1987 Jan;169(1):8–13. doi: 10.1128/jb.169.1.8-13.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Shields M. S., Reagin M. J., Gerger R. R., Campbell R., Somerville C. TOM, a new aromatic degradative plasmid from Burkholderia (Pseudomonas) cepacia G4. Appl Environ Microbiol. 1995 Apr;61(4):1352–1356. doi: 10.1128/aem.61.4.1352-1356.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Shields M. S., Reagin M. J. Selection of a Pseudomonas cepacia strain constitutive for the degradation of trichloroethylene. Appl Environ Microbiol. 1992 Dec;58(12):3977–3983. doi: 10.1128/aem.58.12.3977-3983.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Thompson J. D., Higgins D. G., Gibson T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994 Nov 11;22(22):4673–4680. doi: 10.1093/nar/22.22.4673. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tomasek P. H., Frantz B., Sangodkar U. M., Haugland R. A., Chakrabarty A. M. Characterization and nucleotide sequence determination of a repeat element isolated from a 2,4,5-T degrading strain of Pseudomonas cepacia. Gene. 1989;76(2):227–238. doi: 10.1016/0378-1119(89)90163-7. [DOI] [PubMed] [Google Scholar]
- Vieira J., Messing J. New pUC-derived cloning vectors with different selectable markers and DNA replication origins. Gene. 1991 Apr;100:189–194. doi: 10.1016/0378-1119(91)90365-i. [DOI] [PubMed] [Google Scholar]
- Wheatcroft R., Laberge S. Identification and nucleotide sequence of Rhizobium meliloti insertion sequence ISRm3: similarity between the putative transposase encoded by ISRm3 and those encoded by Staphylococcus aureus IS256 and Thiobacillus ferrooxidans IST2. J Bacteriol. 1991 Apr;173(8):2530–2538. doi: 10.1128/jb.173.8.2530-2538.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wood M. S., Byrne A., Lessie T. G. IS406 and IS407, two gene-activating insertion sequences for Pseudomonas cepacia. Gene. 1991 Aug 30;105(1):101–105. doi: 10.1016/0378-1119(91)90519-h. [DOI] [PubMed] [Google Scholar]
- Wood M. S., Lory C., Lessie T. G. Activation of the lac genes of Tn951 by insertion sequences from Pseudomonas cepacia. J Bacteriol. 1990 Apr;172(4):1719–1724. doi: 10.1128/jb.172.4.1719-1724.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Yates J. R., Cunningham R. P., Holmes D. S. IST2: an insertion sequence from Thiobacillus ferrooxidans. Proc Natl Acad Sci U S A. 1988 Oct;85(19):7284–7287. doi: 10.1073/pnas.85.19.7284. [DOI] [PMC free article] [PubMed] [Google Scholar]