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Hirose J. Diversity and Evolution of Integrative and Conjugative Elements Involved in Bacterial Aromatic Compound Degradation and Their Utility in Environmental Remediation. Microorganisms 2023; 11:microorganisms11020438. [PMID: 36838403 PMCID: PMC9960961 DOI: 10.3390/microorganisms11020438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
Integrative and conjugative elements (ICEs) are mobile DNA molecules that can be transferred through excision, conjugation, and integration into chromosomes. They contribute to the horizontal transfer of genomic islands across bacterial species. ICEs carrying genes encoding aromatic compound degradation pathways are of interest because of their contribution to environmental remediation. Recent advances in DNA sequencing technology have increased the number of newly discovered ICEs in bacterial genomes and have enabled comparative analysis of their evolution. The two different families of ICEs carry various aromatic compound degradation pathway genes. ICEclc and its related ICEs contain a number of members with diverse catabolic capabilities. In addition, the Tn4371 family, which includes ICEs that carry the chlorinated biphenyl catabolic pathway, has been identified. It is apparent that they underwent evolution through the acquisition, deletion, or exchange of modules to adapt to an environmental niche. ICEs have the property of both stability and mobility in the chromosome. Perspectives on the use of ICEs in environmental remediation are also discussed.
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Affiliation(s)
- Jun Hirose
- Department of Applied Chemistry, Faculty of Engineering, University of Miyazaki, Miyazaki 889-2192, Japan
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2
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Cui Z, Luan X, Jiang H, Li Q, Xu G, Sun C, Zheng L, Song Y, Davison PA, Huang WE. Application of a bacterial whole cell biosensor for the rapid detection of cytotoxicity in heavy metal contaminated seawater. CHEMOSPHERE 2018; 200:322-329. [PMID: 29494913 DOI: 10.1016/j.chemosphere.2018.02.097] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 02/13/2018] [Accepted: 02/16/2018] [Indexed: 06/08/2023]
Abstract
A toxicity biosensor Acinetobacter baylyi Tox2 was constructed with the host strain A. baylyi ADP1 harboring a new and medium-copy-number plasmid pWH1274_lux, and was applied to detect the cytotoxicity of heavy metal contaminated seawater. The gene cassette luxCDABE was controlled by constitutively expressed promoter Ptet on pWH1274_lux and the bioluminescence intensity of the biosensor reduces in proportional to the concentrations of toxic compounds. A. baylyi Tox2 exhibits tolerance to salinity, hence it is applicable to seawater samples. A. baylyi Tox2 and Mugilogobius chulae were exposed to different concentrations of heavy metals (Hg2+, Zn2+, Cu2+, and Cd2+) in artificial seawater for performance comparison and Pearson correlation analysis showed a significant correlation (p < 0.01) between A. baylyi Tox2 toxicity detection and the fish (M. chulae) exposure test. This suggests that the performance of A. baylyi Tox2 is comparable to the conventional fish toxicity test in terms of cytotoxicity detection of heavy metal contaminated seawater. Furthermore, A. baylyi Tox2 was used to evaluate cytotoxicity of field-collected seawater samples. The results indicate that there was a significant correlation between the luminescence inhibition ratio (IR) of A. baylyi Tox2 and heavy metal concentrations detected by ICP-MS in the samples. Two seawater samples, which contained a high concentration of total heavy metals, exhibited stronger cytotoxicity than the samples containing low concentrations of heavy metals. In conclusion, A. baylyi Tox2 can be used as an alternative tool to aquatic animals for the evaluation of the cytotoxicity of heavy metal contamination in the marine environment.
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Affiliation(s)
- Zhisong Cui
- Marine Ecology Research Center, First Institute of Oceanography, State Oceanic Administration of China, Qingdao, 266061, China.
| | - Xiao Luan
- Marine Ecology Research Center, First Institute of Oceanography, State Oceanic Administration of China, Qingdao, 266061, China; State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Huichao Jiang
- Shandong Marine Resource and Environment Research Institute, Yantai, 264006, China
| | - Qian Li
- Marine Ecology Research Center, First Institute of Oceanography, State Oceanic Administration of China, Qingdao, 266061, China
| | - Guangfei Xu
- Marine Ecology Research Center, First Institute of Oceanography, State Oceanic Administration of China, Qingdao, 266061, China
| | - Chengjun Sun
- Marine Ecology Research Center, First Institute of Oceanography, State Oceanic Administration of China, Qingdao, 266061, China
| | - Li Zheng
- Marine Ecology Research Center, First Institute of Oceanography, State Oceanic Administration of China, Qingdao, 266061, China
| | - Yizhi Song
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, United Kingdom
| | - Paul A Davison
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, United Kingdom.
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Furukawa K, Fujihara H. Microbial degradation of polychlorinated biphenyls: Biochemical and molecular features. J Biosci Bioeng 2008; 105:433-49. [PMID: 18558332 DOI: 10.1263/jbb.105.433] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Accepted: 02/04/2008] [Indexed: 11/17/2022]
Affiliation(s)
- Kensuke Furukawa
- Depatment of Food and Bioscience, Faculty of Food and Nutrition, Beppu University, Beppu, Ohita 874-8501, Japan.
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4
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Haines AS, Akhtar P, Stephens ER, Jones K, Thomas CM, Perkins CD, Williams JR, Day MJ, Fry JC. Plasmids from freshwater environments capable of IncQ retrotransfer are diverse and include pQKH54, a new IncP-1 subgroup archetype. MICROBIOLOGY-SGM 2006; 152:2689-2701. [PMID: 16946264 DOI: 10.1099/mic.0.28941-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Nine mercury-resistance plasmids isolated from river epilithon were assessed for their ability to retrotransfer the non-conjugative IncQ plasmid, R300B, derivatives of which have commercial uses that may result in accidental or deliberate release into the environment. Retrotransfer frequencies ranging from 2.1 x 10(-4) to 1.75 x 10(-5) were obtained for five of the nine plasmids--the remaining plasmids showed low or undetectable retrotransfer ability. The majority of the retrotransfer-proficient plasmids could not be classified by the tests used. Classical incompatibility testing with RP4 identified pQKH6, pQKH54 and pQM719 as IncP-1. Hybridization to replicon probes confirmed this for pQKH6 and pQM719 and added pQKH33. PCR with primers designed to amplify trfA and korA regions of IncP-1 plasmids did not identify any other plasmids. Plasmids pQKH6 and pQM719 but not pQKH54 produced similar SphI restriction profiles to the IncP-1beta subgroup. The complete nucleotide sequence of pQKH54 was determined, revealing it to have a complete IncP-1 backbone but belonging to a new distinct subgroup which was designated IncP-1gamma. The results emphasize the ubiquity and diversity of IncP-1 plasmids in the environment but demonstrate that plasmids of as yet unknown groups are also able to retrotransfer IncQ plasmids efficiently.
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Affiliation(s)
- Anthony S Haines
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Parveen Akhtar
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Elton R Stephens
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Karen Jones
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Christopher M Thomas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Caroline D Perkins
- Cardiff School of Biosciences, Cardiff University, PO Box 915, Cardiff CF1 3TL, UK
| | | | - Martin J Day
- Cardiff School of Biosciences, Cardiff University, PO Box 915, Cardiff CF1 3TL, UK
| | - John C Fry
- Cardiff School of Biosciences, Cardiff University, PO Box 915, Cardiff CF1 3TL, UK
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5
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Furukawa K, Suenaga H, Goto M. Biphenyl dioxygenases: functional versatilities and directed evolution. J Bacteriol 2004; 186:5189-96. [PMID: 15292119 PMCID: PMC490896 DOI: 10.1128/jb.186.16.5189-5196.2004] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Kensuke Furukawa
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Hakozaki, Fukuoka 812-8581, Japan.
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6
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Furukawa K. Biochemical and genetic bases of microbial degradation of polychlorinated biphenyls (PCBs). J GEN APPL MICROBIOL 2000; 46:283-296. [PMID: 12483570 DOI: 10.2323/jgam.46.283] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The microbial degradation of polychlorinated biphenyls (PCBs) has been extensively conducted by many workers, and the following general results have been obtained. (1) PCBs are degraded oxidatively by aerobic bacteria and other microorganisms such as white rot fungi. PCBs are also reductively dehalogenated by anaerobic microbial consortia. (2) The biodegradability of PCBs is highly dependent on chlorine substitution, i.e., number and position of chlorine. The degradation and dehalogenation capabilities are also highly strain dependent. (3) Biphenyl-utilizing bacteria can cometabolize many PCB congeners to chlorobenzoates by biphenl-catabolic enzymes. (4) Enzymes involved in the PCB degradation were purified and characterized. Biphenyl dioxygenase, ring-cleavage dioxygenase, and hydrolase are crystallized, and two ring-cleavage dioxygenases are being solved by x-ray crystallography. (5) The bph gene clusters responsible for PCB degradation are cloned from a variety of bacterial strains. The structure and function are analyzed with respect to the evolutionary relationship. (6) The molecular engineering of biphenyl dioxygenases is successfully performed by DNA shuffling, domain exchange, and subunit exchange. The evolved enzymes exhibit wide and enhanced degradation capacities for PCBs and other aromatic compounds.
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Affiliation(s)
- Kensuke Furukawa
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 812-8581, Japan
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7
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Nishi A, Tominaga K, Furukawa K. A 90-kilobase conjugative chromosomal element coding for biphenyl and salicylate catabolism in Pseudomonas putida KF715. J Bacteriol 2000; 182:1949-55. [PMID: 10715002 PMCID: PMC101889 DOI: 10.1128/jb.182.7.1949-1955.2000] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The biphenyl and salicylate metabolic pathways in Pseudomonas putida KF715 are chromosomally encoded. The bph gene cluster coding for the conversion of biphenyl to benzoic acid and the sal gene cluster coding for the salicylate meta-pathway were obtained from the KF715 genomic cosmid libraries. These two gene clusters were separated by 10-kb DNA and were highly prone to deletion when KF715 was grown in nutrient medium. Two types of deletions took place at the region including only the bph genes (ca. 40 kb) or at the region including both the bph and sal genes (ca. 70 kb). A 90-kb DNA region, including both the bph and sal genes (termed the bph-sal element), was transferred by conjugation from KF715 to P. putida AC30. Such transconjugants gained the ability to grow on biphenyl and salicylate as the sole sources of carbon. The bph and sal element was located on the chromosome of the recipient. The bph-sal element in strain AC30 was also highly prone to deletion; however, it could be mobilized to the chromosome of P. putida KT2440 and the two deletion mutants of KF715.
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Affiliation(s)
- A Nishi
- Division of Bioresource and Bioenvironmental Sciences, Graduate School, Kyushu University, Hakozaki, Fukuoka 812-8581, Japan
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8
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Davison AD, Karuso P, Jardine DR, Veal DA. Halopicolinic acids, novel products arising through the degradation of chloro- and bromo-biphenyl by Sphingomonas paucimobilis BPSI-3. Can J Microbiol 1996; 42:66-71. [PMID: 8595598 DOI: 10.1139/m96-009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Sphingomonas paucimobilis BPSI-3 was previously isolated from a mixed microbial consortium growing on biphenyl as the sole source of carbon and energy. Transformation of 4-chlorobiphenyl (4CBP) was demonstrated by this strain, although little or no growth was observed. In minimal salts medium supplemented with 4CBP or bromobiphenyl and dextrose, yellow coloured product(s) were rapidly formed. Gas chromatography-mass spectrometry (GC-MS) revealed single-ring N-heterocyclic compounds that were identified as halopicolinic acids. We believe this to be the first report of such compounds being formed via biological transformation of halobiphenyls. A mechanism is proposed for their formation.
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Affiliation(s)
- A D Davison
- School of Biological Sciences, Macquarie University, Sydney, Australia
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9
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Dunaway-Mariano D, Babbitt PC. On the origins and functions of the enzymes of the 4-chlorobenzoate to 4-hydroxybenzoate converting pathway. Biodegradation 1994; 5:259-76. [PMID: 7765837 DOI: 10.1007/bf00696464] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
This review examines the enzymes of 4-chlorobenzoate to 4-hydroxybenzoate converting pathway found in certain soil bacteria. This pathway consists of three enzymes: 4-chlorobenzoate: Coenzyme A ligase, 4-chlorobenzoyl-Coenzyme A dehalogenase and 4-hydroxybenzoyl-Coenzyme A thioesterase. Recent progress made in the cloning and expression of the pathway genes from assorted bacterial strains is described. Gene order and sequence found among these strains are compared to reveal independent enzyme recruitment strategies. Sequence alignments made between the Pseudomonas sp. strain CBS3 4-chlorobenzoate pathway enzymes and structurally related proteins contained within the protein sequence data banks suggest possible origins in preexisting beta-oxidation pathways. The purification and characterization of the physical and kinetic properties of the pathway enzymes are described. Where possible a comparison of these properties between like enzymes from different bacterial sources are made.
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Affiliation(s)
- D Dunaway-Mariano
- Department of Chemistry and Biochemistry, University of Maryland, College Park 20742
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10
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Lloyd-Jones G, de Jong C, Ogden RC, Duetz WA, Williams PA. Recombination of the
bph
(Biphenyl) Catabolic Genes from Plasmid pWW100 and Their Deletion during Growth on Benzoate. Appl Environ Microbiol 1994; 60:691-6. [PMID: 16349195 PMCID: PMC201367 DOI: 10.1128/aem.60.2.691-696.1994] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas
sp. strain CB406 was isolated from polychlorinated biphenyl-contaminated soil and harbors a nontransmissible plasmid, pWW100, of approximately 200 kb which carries the genes required for biphenyl and 4-chlorobiphenyl catabolism. The catabolic phenotype was mobilized following the construction in vivo of a cointegrate plasmid containing functional upper and lower biphenyl operons inserted into the broad-host-range R plasmid RP4. The Bph
+
phenotype carried by pWW100 was stable in nonselective media but was unstable during growth on benzoate, where the sequential selection of two species of
bph
deletion derivatives occurs at high frequency. This mirrors observations made with TOL plasmids (encoding toluene and xylene catabolism) grown under similar conditions. Subcloning of dioxygenase genes involved in biphenyl catabolism confirmed the localization of the
bph
genes on the wild-type plasmid and the RP4 cointegrate plasmid.
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Affiliation(s)
- G Lloyd-Jones
- School of Biological Sciences, University of Wales, Bangor, Gwynedd LL57 2UW, United Kingdom
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11
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Springael D, Kreps S, Mergeay M. Identification of a catabolic transposon, Tn4371, carrying biphenyl and 4-chlorobiphenyl degradation genes in Alcaligenes eutrophus A5. J Bacteriol 1993; 175:1674-81. [PMID: 8383664 PMCID: PMC203961 DOI: 10.1128/jb.175.6.1674-1681.1993] [Citation(s) in RCA: 90] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Alcaligenes eutrophus A5 catabolizes biphenyl to CO2 via benzoate and 4-chlorobiphenyl to 4-chlorobenzoate. In curing and conjugation experiments, the A5 endogenous 51-kb IncP1 plasmid pSS50 was found to be dispensable for biphenyl and 4-chlorobiphenyl catabolism. Transfer of the biphenyl- and 4-chlorobiphenyl-degrading phenotype by means of pSS50 was observed at a frequency of 10(-5) per transferred plasmid in matings of A5 with other A. eutrophus strains. Transconjugants harbor enlarged pSS50 derivatives which contain additional genetic information governing the oxidation of biphenyl and 4-chlorobiphenyl to benzoate and 4-chlorobenzoate and originating from the chromosome of strain A5. The following observations indicate that the catabolic genes reside on a 59-kb large transposon (Tn4371) for which a restriction map is presented. (i) Tn4371 transposes between different replicons and at different locations of the same replicon. (ii) Transposition was observed in a Rec- strain of A. eutrophus. (iii) Tn4371 transposes as a single, contiguous piece of DNA. Although an RP4::Tn4371 plasmid was stably maintained in different hosts, the plasmid conferred growth on biphenyl only when present in strains of A. eutrophus and in an Acinetobacter sp. strain.
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Affiliation(s)
- D Springael
- Laboratory of Genetics and Biotechnology, SCK/CEN-VITO, Mol, Belgium
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12
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Layton AC, Sanseverino J, Wallace W, Corcoran C, Sayler GS. Evidence for 4-chlorobenzoic acid dehalogenation mediated by plasmids related to pSS50. Appl Environ Microbiol 1992; 58:399-402. [PMID: 1539985 PMCID: PMC195221 DOI: 10.1128/aem.58.1.399-402.1992] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The biodegradation of 4-chlorobiphenyl usually proceeds through the intermediate 4-chlorobenzoate. Few bacterial strains can degrade 4-chlorobiphenyl to 4-chlorobenzoate and 4-chlorobenzoate to CO2. This study demonstrates that the 4-chlorobiphenyl-degrading Alcaligenes sp. strain ALP83 can degrade 4-chlorobenzoate to 4-hydroxybenzoate. The dehalogenase activity is correlated with a 10-kb fragment carried on plasmid pSS70.
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Affiliation(s)
- A C Layton
- Department of Microbiology, University of Tennessee, Knoxville 37932
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13
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Burlage RS, Bemis LA, Layton AC, Sayler GS, Larimer F. Comparative genetic organization of incompatibility group P degradative plasmids. J Bacteriol 1990; 172:6818-25. [PMID: 2254257 PMCID: PMC210798 DOI: 10.1128/jb.172.12.6818-6825.1990] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Plasmids that encode genes for the degradation of recalcitrant compounds are often examined only for characteristics of the degradative pathways and ignore regions that are necessary for plasmid replication, incompatibility, and conjugation. If these characteristics were known, then the mobility of the catabolic genes between species could be predicted and different catabolic pathways might be combined to alter substrate range. Two catabolic plasmids, pSS50 and pSS60, isolated from chlorobiphenyl-degrading strains and a 3-chlorobenzoate-degrading plasmid, pBR60, were compared with the previously described IncP group (Pseudomonas group P-1) plasmids pJP4 and R751. All three of the former plasmids were also members of the IncP group, although pBR60 is apparently more distantly related. DNA probes specific for known genetic loci were used to determine the order of homologous loci on the plasmids. In all of these plasmids the order is invariant, demonstrating the conservation of this "backbone" region. In addition, all five plasmids display at least some homology with the mercury resistance transposon, Tn501, which has been suggested to be characteristic of the beta subgroup of the IncP plasmids. Plasmids pSS50 and pSS60 have been mapped in detail, and repeat sequences that surround the suspected degradation genes are described.
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Affiliation(s)
- R S Burlage
- Department of Microbiology, University of Tennessee, Knoxville 37932
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