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Khomenkov VG, Shevelev AB, Zhukov VG, Zagustina NA, Bezborodov AM, Popov VO. Organization of metabolic pathways and molecular-genetic mechanisms of xenobiotic degradation in microorganisms: A review. APPL BIOCHEM MICRO+ 2011. [DOI: 10.1134/s0003683808020014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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2
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Ohtsubo Y, Genka H, Komatsu H, Nagata Y, Tsuda M. High-temperature-induced transposition of insertion elements in burkholderia multivorans ATCC 17616. Appl Environ Microbiol 2005; 71:1822-8. [PMID: 15812007 PMCID: PMC1082539 DOI: 10.1128/aem.71.4.1822-1828.2005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An efficient and quantitative method to analyze the transposition of various insertion sequence (IS) elements in Burkholderia multivorans ATCC 17616 was devised. pGEN500, a plasmid carrying a Bacillus subtilis-derived sacB gene, was introduced into ATCC 17616 cells, and 25% of their sucrose-resistant derivatives were found to carry various IS elements on pGEN500. A PCR-based experimental protocol, in which a mixture of several specific primer pairs was used, revealed that pGEN500 captured, in addition to five previously reported IS elements (IS401, IS402, IS406, IS407, and IS408), three novel IS elements, ISBmu1, ISBmu2, and ISBmu3. The global transposition frequency of these IS elements was enhanced more than sevenfold under a high-temperature condition (42 degrees C) but not under oxidative stress or starvation conditions. To our knowledge, this is the first report demonstrating the elevated transposition activities of several IS elements at a high temperature. The efficient experimental protocol developed in this study will be useful in quantitatively and simultaneously investigating various IS elements, as well as in capturing novel functional mobile elements from a wide variety of bacteria.
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Affiliation(s)
- Yoshiyuki Ohtsubo
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan.
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3
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Nagata Y, Matsuda M, Komatsu H, Imura Y, Sawada H, Ohtsubo Y, Tsuda M. Organization and localization of the dnaA and dnaK gene regions on the multichromosomal genome of Burkholderia multivorans ATCC 17616. J Biosci Bioeng 2005; 99:603-10. [PMID: 16233838 DOI: 10.1263/jbb.99.603] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2005] [Accepted: 03/24/2005] [Indexed: 01/22/2023]
Abstract
The Burkholderia multivorans strain ATCC 17616 carries three circular chromosomes with sizes of 3.4, 2.5, and 0.9 Mb. To reveal the distribution and organization of the genes for fundamental cell functions on the genome of this bacterium, the dnaA and dnaK gene regions of ATCC 17616 were cloned and characterized. The gene organization of the dnaA region was rnpA-rmpH-dnaA-dnaN-gyrB with a single consensus DnaA-binding box (TTATCCACA) between the rmpH and dnaA genes. This intergenic region, however, did not work as an autonomously replicating sequence in ATCC 17616. On the other hand, the gene organization of the dnaK region was grpE-orf1 (gene for thioredoxin homologue)-dnaK-dnaJ-pabB (gene for p-aminobenzoate synthetase component homologue). A putative heat-shock promoter that showed good homology to the sigma32-dependent promoter consensus sequence in Escherichia coli was found upstream of the grpE gene, suggesting that these five genes constitute an operon. In M9 succinate minimal medium the dnaJ mutant grew more slowly than the wild-type strain, indicating that this operon is functional. Pulsed-field gel electrophoresis and Southern blot analyses indicated that both the dnaA and dnaK gene regions exist as single copies on the 3.4 Mb chromosome.
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Affiliation(s)
- Yuji Nagata
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan.
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4
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Tsang JSH. Molecular biology of the Burkholderia cepacia complex. ADVANCES IN APPLIED MICROBIOLOGY 2004; 54:71-91. [PMID: 15251276 DOI: 10.1016/s0065-2164(04)54002-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Jimmy S H Tsang
- Molecular Microbiology Laboratory, Department of Botany, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
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5
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Liu L, Spilker T, Coenye T, LiPuma JJ. Identification by subtractive hybridization of a novel insertion element specific for two widespread Burkholderia cepacia genomovar III strains. J Clin Microbiol 2003; 41:2471-6. [PMID: 12791867 PMCID: PMC156561 DOI: 10.1128/jcm.41.6.2471-2476.2003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Species of the Burkholderia cepacia complex cause chronic and life-threatening infections in persons with cystic fibrosis. Epidemic strains infect multiple patients, reside primarily in genomovar III, and have an apparent enhanced capacity for human infection and/or interpatient transmission. By using subtractive hybridization, a novel insertion element, designated IS1363, was identified in epidemic strain PHDC, known to infect many cystic fibrosis patients in the mid-Atlantic region of the United States. IS1363 was also found in most isolates of the ET12 lineage, responsible for infecting large numbers of patients in Ontario, Canada, and the United Kingdom. Southern blot analysis demonstrated that whereas multiple copies of IS1363 were present in strain PHDC, only one copy was present in ET12 isolates. IS1363 was used to probe a collection of 943 B. cepacia complex isolates, representing all nine genomovars, recovered from 761 cystic fibrosis patients or the natural environment. IS1363 was not found in other genomovar III strains and, with the exception of B. ambifaria, was absent from other B. cepacia complex species. Genotyping analyses of all IS1363-positive isolates demonstrated that strain PHDC was more widely distributed in the United States than previously appreciated; 212 cystic fibrosis patients in 24 states were identified as being infected with PHDC.
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Affiliation(s)
- Lixia Liu
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan 48109-0646, USA
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6
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Miché L, Faure D, Blot M, Cabanne-Giuli E, Balandreau J. Detection and activity of insertion sequences in environmental strains of Burkholderia. Environ Microbiol 2001; 3:766-73. [PMID: 11846770 DOI: 10.1046/j.1462-2920.2001.00251.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The presence of two insertion sequences, IS406 and IS407, was tested by polymerase chain reaction (PCR) amplification in 25 strains representing 15 Burkholderia species and the close relative Ralstonia pickettii. A total of 50% of the 25 strains contained at least one of the two insertion sequences (ISs) and a statistically significant correlation was found between the occurrences of IS406 and IS407. Moreover, PCR-RFLP studies of the amplified fragments showed that IS406 is largely conserved among all the strains tested, whereas IS407 is rather polymorphic. Transposition activity was studied in Burkholderia vietnamiensis TVV75, using the pGBG1 target plasmid. This entrapping plasmid permitted the isolation and characterization of three active IS, able to activate the plasmid-borne tetA gene after transposition. Sequencing permitted the identification of these mobile genetic elements as isoforms of IS402, IS407 and IS1416. PCR amplification products provided IS probes, which were used to determine the copy-numbers of IS402, IS407 and IS1416 in the genome of B. vietnamiensis TVV75, by Southern blotting. Copy numbers are 12, 3 and 11 respectively. To our knowledge, this is the first description of active insertion sequences in B. vietnamiensis.
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Affiliation(s)
- L Miché
- Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, Université Claude Bernard Lyon 1, 69622 Villeurbanne cedex, France
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7
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Schneider D, Faure D, Noirclerc-Savoye M, Barrière AC, Coursange E, Blot M. A broad-host-range plasmid for isolating mobile genetic elements in gram-negative bacteria. Plasmid 2000; 44:201-7. [PMID: 10964631 DOI: 10.1006/plas.2000.1483] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Plasmid pGBG1 was constructed to isolate mobile genetic elements in a wide variety of gram-negative bacteria. The mutation target, carried on a broad-host-range vector, allows positive selection for tetracycline resistance. In tests using several gram-negative bacteria we could detect transposition events of either insertion sequences or transposons. A new insertion sequence (IS) element was identified in Ralstonia eutropha.
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Affiliation(s)
- D Schneider
- Plasticité et Expression des Génomes Microbiens, CNRS EP2029, CEA LRC N degrees 12, Université Joseph Fourier, 460 rue de la Piscine, Grenoble Cedex 9, F-38041, France
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8
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Chang HK, Zylstra GJ. Role of quinolinate phosphoribosyl transferase in degradation of phthalate by Burkholderia cepacia DBO1. J Bacteriol 1999; 181:3069-75. [PMID: 10322007 PMCID: PMC93761 DOI: 10.1128/jb.181.10.3069-3075.1999] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two distinct regions of DNA encode the enzymes needed for phthalate degradation by Burkholderia cepacia DBO1. A gene coding for an enzyme (quinolinate phosphoribosyl transferase) involved in the biosynthesis of NAD+ was identified between these two regions by sequence analysis and functional assays. Southern hybridization experiments indicate that DBO1 and other phthalate-degrading B. cepacia strains have two dissimilar genes for this enzyme, while non-phthalate-degrading B. cepacia strains have only a single gene. The sequenced gene was labeled ophE, due to the fact that it is specifically induced by phthalate as shown by lacZ gene fusions. Insertional knockout mutants lacking ophE grow noticeably slower on phthalate while exhibiting normal rates of growth on other substrates. The fact that elevated levels of quinolinate phosphoribosyl transferase enhance growth on phthalate stems from the structural similarities between phthalate and quinolinate: phthalate is a competitive inhibitor of this enzyme and the phthalate catabolic pathway cometabolizes quinolinate. The recruitment of this gene for growth on phthalate thus gives B. cepacia an advantage over other phthalate-degrading bacteria in the environment.
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Affiliation(s)
- H K Chang
- Biotechnology Center for Agriculture and the Environment, Cook College, Rutgers University, New Brunswick, New Jersey 08901-8520, USA
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9
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Romine MF, Stillwell LC, Wong KK, Thurston SJ, Sisk EC, Sensen C, Gaasterland T, Fredrickson JK, Saffer JD. Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199. J Bacteriol 1999; 181:1585-602. [PMID: 10049392 PMCID: PMC93550 DOI: 10.1128/jb.181.5.1585-1602.1999] [Citation(s) in RCA: 238] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The complete 184,457-bp sequence of the aromatic catabolic plasmid, pNL1, from Sphingomonas aromaticivorans F199 has been determined. A total of 186 open reading frames (ORFs) are predicted to encode proteins, of which 79 are likely directly associated with catabolism or transport of aromatic compounds. Genes that encode enzymes associated with the degradation of biphenyl, naphthalene, m-xylene, and p-cresol are predicted to be distributed among 15 gene clusters. The unusual coclustering of genes associated with different pathways appears to have evolved in response to similarities in biochemical mechanisms required for the degradation of intermediates in different pathways. A putative efflux pump and several hypothetical membrane-associated proteins were identified and predicted to be involved in the transport of aromatic compounds and/or intermediates in catabolism across the cell wall. Several genes associated with integration and recombination, including two group II intron-associated maturases, were identified in the replication region, suggesting that pNL1 is able to undergo integration and excision events with the chromosome and/or other portions of the plasmid. Conjugative transfer of pNL1 to another Sphingomonas sp. was demonstrated, and genes associated with this function were found in two large clusters. Approximately one-third of the ORFs (59 of them) have no obvious homology to known genes.
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Affiliation(s)
- M F Romine
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
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Kallastu A, Hõrak R, Kivisaar M. Identification and characterization of IS1411, a new insertion sequence which causes transcriptional activation of the phenol degradation genes in Pseudomonas putida. J Bacteriol 1998; 180:5306-12. [PMID: 9765560 PMCID: PMC107577 DOI: 10.1128/jb.180.20.5306-5312.1998] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/1998] [Accepted: 08/09/1998] [Indexed: 11/20/2022] Open
Abstract
A new insertion sequence (IS element), IS1411, was identified downstream of the phenol degradation genes pheBA that originated from plasmid DNA of Pseudomonas sp. strain EST1001. According to sequence analysis, IS1411 belongs to a new family of IS elements that has recently been named the ISL3 family (J. Mahillon and M. Chandler, Microbiol. Mol. Biol. Rev. 62:725-774, 1998). IS1411 generates 8-bp duplication of the target DNA and carries 24-bp inverted repeats (IRs), highly homologous to the IRs of other IS elements belonging to this family. IS1411 was discovered as a result of insertional activation of promoterless pheBA genes in Pseudomonas putida due to the presence of outward-directed promoters at the left end of IS1411. Both promoters located on the IS element have sequences that are similar to the consensus sequence of Escherichia coli sigma70. IS1411 can produce IS circles, and the circle formation is enhanced when two copies of the element are present in the same plasmid.
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Affiliation(s)
- A Kallastu
- Estonian Biocentre and Institute of Molecular and Cell Biology, Tartu University, EE2400 Tartu, Estonia
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11
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Gonzalez CF, Pettit EA, Valadez VA, Provin EM. Mobilization, cloning, and sequence determination of a plasmid-encoded polygalacturonase from a phytopathogenic Burkholderia (Pseudomonas) cepacia. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 1997; 10:840-851. [PMID: 9304858 DOI: 10.1094/mpmi.1997.10.7.840] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Phytopathogenic strains of Burkholderia cepacia (synonym Pseudomonas cepacia) produce endopolygalacturonase, whereas strains of clinical and soil origin do not. Growth of a phytopathogenic strain (ATCC25416) at elevated temperatures resulted in nonpectolytic derivatives that were either cured of a resident plasmid or contained a plasmid of reduced mass. The resident 200-kb plasmid (pPEC320) in strain ATCC25416 was tagged with Tn5-Mob. The pPEC320::Tn5-Mob (pPEC321) plasmid was mobilized in B. cepacia strains of soil and clinical origin. Transconjugants containing pPEC321 expressed the endopolygalacturonase and showed differential activity on plant tissue. No evidence for self-transfer of pPEC320 or the tagged derivative was observed. A 285-kb cloned fragment from pPEC320 containing the plasmid-borne pehA gene was sequenced and compared to the pehA gene from Erwinia carotovora subsp. carotovora and Ralstonia solanacearum and the polygalacturonase sequence from Lycopersicon esculentum.
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Affiliation(s)
- C F Gonzalez
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station 77843-2132, USA.
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12
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Segonds C, Bingen E, Couetdic G, Mathy S, Brahimi N, Marty N, Plesiat P, Michel-Briand Y, Chabanon G. Genotypic analysis of Burkholderia cepacia isolates from 13 French cystic fibrosis centers. J Clin Microbiol 1997; 35:2055-60. [PMID: 9230381 PMCID: PMC229902 DOI: 10.1128/jcm.35.8.2055-2060.1997] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Burkholderia cepacia has been involved in outbreaks of pulmonary infection among patients with cystic fibrosis (CF), and the spread of a highly transmissible clone has been reported throughout the United Kingdom and Canada. These data prompted a DNA-based typing study of the strains recovered in French CF centers. Ninety-five isolates recovered from 71 patients attending 13 CF centers in 9 regions of France were characterized by randomly amplified polymorphic DNA (RAPD) analysis and pulsed-field gel electrophoresis (PFGE). Twenty-one genotypes were identified among the 95 isolates, and the results of RAPD and PFGE were concordant for 89 isolates (94%). Cross-colonization was demonstrated in 7 of the 13 CF centers. The investigation of serial isolates showed that most chronically colonized patients harbored a single B. cepacia strain. A geographically clustered distribution of B. cepacia genotypes was observed, except for one genotype, which was detected in four regions but was proven to be different from the genotype of the British-Canadian highly transmissible strain. The present study confirms the ability of B. cepacia to spread among CF communities in France and the importance of epidemiological surveys in the institution of prevention policies.
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Affiliation(s)
- C Segonds
- Laboratoire de Bactériologie-Virologie-Hygiène, CHU Rangueil, Toulouse, France
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13
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Hübner A, Hendrickson W. A fusion promoter created by a new insertion sequence, IS1490, activates transcription of 2,4,5-trichlorophenoxyacetic acid catabolic genes in Burkholderia cepacia AC1100. J Bacteriol 1997; 179:2717-23. [PMID: 9098071 PMCID: PMC179022 DOI: 10.1128/jb.179.8.2717-2723.1997] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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.
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Affiliation(s)
- A Hübner
- Department of Microbiology and Immunology, University of Illinois, Chicago 60612, USA
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14
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Lessie TG, Hendrickson W, Manning BD, Devereux R. Genomic complexity and plasticity of Burkholderia cepacia. FEMS Microbiol Lett 1996; 144:117-28. [PMID: 8900054 DOI: 10.1111/j.1574-6968.1996.tb08517.x] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Burkholderia cepacia has attracted attention because of its extraordinary degradative abilities and its potential as a pathogen for plants and for humans. This bacterium was formerly considered to belong to the genus Pseudomonas in the gamma-subclass of the Proteobacteria, but recently has been assigned to the beta-subclass is based on rrn gene sequence analyses and other key phenotypic characteristics. The B. cepacia genome is comprised of multiple chromosomes and is rich in insertion sequences. These two features may have played a key role in the evolution of novel degradative functions and the unusual adaptability of this bacterium.
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Affiliation(s)
- T G Lessie
- Department of Microbiology, University of Massachusetts, Amherst 01003, USA.
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15
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Eisen JA, Benito MI, Walbot V. Sequence similarity of putative transposases links the maize Mutator autonomous element and a group of bacterial insertion sequences. Nucleic Acids Res 1994; 22:2634-6. [PMID: 8041625 PMCID: PMC308220 DOI: 10.1093/nar/22.13.2634] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The Mutator transposable element system of maize is the most active transposable element system characterized in higher plants. While Mutator has been used to generate and tag thousands of new maize mutants, the mechanism and regulation of its transposition are poorly understood. The Mutator autonomous element, MuDR, encodes two proteins: MURA and MURB. We have detected an amino acid sequence motif shared by MURA and the putative transposases of a group of bacterial insertion sequences. Based on this similarity we believe that MURA is the transposase of the Mutator system. In addition we have detected two rice cDNAs in genbank with extensive similarity to MURA. This sequence similarity suggests that a Mutator-like element is present in rice. We believe that Mutator, a group of bacterial insertion sequences, and an uncharacterized rice transposon represent members of a family of transposable elements.
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Affiliation(s)
- J A Eisen
- Department of Biological Sciences, Stanford University, CA 94305-5020
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Abstract
Macrorestriction fragment analysis of DNA from Pseudomonas cepacia 17616, in conjunction with Southern hybridization experiments using junction fragments containing rare restriction enzyme sites as probes, indicated that this bacterium contains three large circular replicons of 3.4, 2.5, and 0.9 megabases (Mb). Inclusion of the 170-kb cryptic plasmid present in this strain gave an overall estimate of genome size of 7 Mb. Other Southern hybridization experiments indicated that the three large replicons contained rRNA genes as well as insertion sequence elements identified previously in this strain. The distribution of SwaI, PacI, and PmeI sites on the three replicons was determined. A derivative of Tn5-751 carrying a SwaI site was used to inactivate and map genes on the 2.5- and 3.4-Mb replicons. Mutants were isolated in which the 2.5- and 0.9-Mb replicons had been reduced in size to 1.8 and 0.65 Mb, respectively. The loss of DNA from the 2.5-Mb replicon was associated with lysine auxotrophy, beta-lactamase deficiency, and failure to utilize ribitol and trehalose as carbon and energy sources. DNA fragments corresponding in size to randomly linearized forms of the different replicons were detected in unrestricted DNA by pulsed-field gel electrophoresis. The results provide a framework for further genetic analysis of strain 17616 and for evaluation of the genomic complexities of other P. cepacia isolates.
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Affiliation(s)
- H P Cheng
- Department of Microbiology, University of Massachusetts, Amherst 01002
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17
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Larsen GY, Stull TL, Burns JL. Marked phenotypic variability in Pseudomonas cepacia isolated from a patient with cystic fibrosis. J Clin Microbiol 1993; 31:788-92. [PMID: 7681845 PMCID: PMC263564 DOI: 10.1128/jcm.31.4.788-792.1993] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Characterization of the epidemiology of Pseudomonas cepacia colonization in cystic fibrosis is difficult because of the phenotypic variability of isolates. A single sputum culture may yield colonies which differ in morphology, antibiotic susceptibility, and pigment production. We examined serial P. cepacia isolates from a cystic fibrosis patient which the clinical laboratory identified as separate strains; these were selected on the basis of isolation date and culture site. An attempt was made to sample at multiple time points and, at a single time point, from three different culture sites. Ribotype analysis, using both the standard Southern blot technique and a recently reported method which uses the polymerase chain reaction, was used to distinguish unique P. cepacia strains. Characterization included comparison of antibiotic susceptibility, plasmid content, and outer membrane protein (OMP) patterns. rRNA analysis demonstrated that all isolates had the same ribotype, consistent with their being derivatives of the same strain. Antibiotic susceptibility testing revealed variability among both same-date and same-site isolates. Screening for plasmid DNA identified three groups of isolates; both same-date and same-site isolates demonstrated variability. OMP profiles were similar, but at least six distinct patterns were identified. For the six same-date isolates, five different OMP patterns were identified. For the 10 same-site isolates from different dates, five of the six OMP patterns were represented. We have demonstrated marked phenotypic variability in 14 strains of P. cepacia isolated from different sites and at different times from a single colonized patient. Ribotyping identified all the isolates as derivatives of a single strain; thus, the diversity of phenotypes appears to be the result of differential gene expression.
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Affiliation(s)
- G Y Larsen
- Division of Infectious Disease, Children's Hospital and Medical Center, Seattle, Washington 98105
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18
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van der Meer JR, de Vos WM, Harayama S, Zehnder AJ. Molecular mechanisms of genetic adaptation to xenobiotic compounds. Microbiol Rev 1992; 56:677-94. [PMID: 1480115 PMCID: PMC372894 DOI: 10.1128/mr.56.4.677-694.1992] [Citation(s) in RCA: 226] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Microorganisms in the environment can often adapt to use xenobiotic chemicals as novel growth and energy substrates. Specialized enzyme systems and metabolic pathways for the degradation of man-made compounds such as chlorobiphenyls and chlorobenzenes have been found in microorganisms isolated from geographically separated areas of the world. The genetic characterization of an increasing number of aerobic pathways for degradation of (substituted) aromatic compounds in different bacteria has made it possible to compare the similarities in genetic organization and in sequence which exist between genes and proteins of these specialized catabolic routes and more common pathways. These data suggest that discrete modules containing clusters of genes have been combined in different ways in the various catabolic pathways. Sequence information further suggests divergence of catabolic genes coding for specialized enzymes in the degradation of xenobiotic chemicals. An important question will be to find whether these specialized enzymes evolved from more common isozymes only after the introduction of xenobiotic chemicals into the environment. Evidence is presented that a range of genetic mechanisms, such as gene transfer, mutational drift, and genetic recombination and transposition, can accelerate the evolution of catabolic pathways in bacteria. However, there is virtually no information concerning the rates at which these mechanisms are operating in bacteria living in nature and the response of such rates to the presence of potential (xenobiotic) substrates. Quantitative data on the genetic processes in the natural environment and on the effect of environmental parameters on the rate of evolution are needed.
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Affiliation(s)
- J R van der Meer
- Department of Microbiology, Wageningen Agricultural University, The Netherlands
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19
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Sayre P, Miller RV. Bacterial mobile genetic elements: importance in assessing the environmental fate of genetically engineered sequences. Plasmid 1991; 26:151-71. [PMID: 1661425 DOI: 10.1016/0147-619x(91)90040-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- P Sayre
- Office of Toxic Substances, U.S. Environmental Protection Agency, Washington, D.C. 20460
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Wood MS, Byrne A, Lessie TG. IS406 and IS407, two gene-activating insertion sequences for Pseudomonas cepacia. Gene X 1991; 105:101-5. [PMID: 1718819 DOI: 10.1016/0378-1119(91)90519-h] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We have determined the nucleotide sequences of IS406 (1368 bp) and IS407 (1236 bp), two insertion sequence (IS) elements isolated from Pseudomonas cepacia 249 on the basis of their abilities to activate the expression of the lac genes of Tn951. IS406 and IS407 when inserted into the lac promoter/operator region of Tn951 generated, respectively, duplications of 8 and 4 bp of target DNA. IS406 had 41-bp terminal inverted repeat (IR) sequences with eleven mismatches. IR-L (left) contained a 12-bp motif present at the ends of Tn2501. In other respects, IS406 was distinct from previously described bacterial IS elements listed in the GenBank and EMBL databases. IS407 had 49-bp terminal IRs with 18 mismatches. IR-R (right) contained an outwardly directed sigma 70-like promoter. IS407 was closely related to IS476 and ISR1 from Xanthomonas and Rhizobium sp., respectively.
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Affiliation(s)
- M S Wood
- Department of Microbiology, University of Massachusetts, Amherst 01003
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Abstract
IS402, a transposable gene-activating element isolated on the basis of its ability to increase expression of the Tn1 bla gene in Pseudomonas cepacia, was cloned from pTGL52 into the vector, pBluescript KS+, and its nucleotide (nt) sequence was determined. This 914-bp element had terminal inverted repeats of 17 bp with a single mismatch, and upon insertion into Tn1 generated a direct target duplication of 3 bp. Comparison of its nt sequence with the GenBank and EMBL databases indicated that IS402 is unrelated to previously described bacterial IS elements.
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Affiliation(s)
- A A Ferrante
- Department of Microbiology, University of Massachusetts, Amherst 01003
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Labes G, Simon R. Isolation of DNA insertion elements from Rhizobium meliloti which are able to promote transcription of adjacent genes. Plasmid 1990; 24:235-9. [PMID: 1963950 DOI: 10.1016/0147-619x(90)90007-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In order to select insertion sequences able to promote transcription of flanking genes (ISp elements), three mobilizable RSF1010 derived vectors were constructed. Using promoterless antibiotic resistance genes, ISp elements ranging from 0.75 to 2.9 kb were isolated from Escherichia coli and Rhizobium meliloti. Restriction and hybridization experiments revealed that identical ISp elements could be isolated from different R. meliloti strains and that one of these is similar to an insertion sequence found previously in R. meliloti 2011.
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Affiliation(s)
- G Labes
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Germany
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