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Haber CL, Allen LN, Zhao S, Hanson RS. Methylotrophic bacteria: biochemical diversity and genetics. Science 2010; 221:1147-53. [PMID: 17811506 DOI: 10.1126/science.221.4616.1147] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Bacteria that are able to use methane as a sole carbon and energy source also carry out a broad range of biotransformations, some of which have industrial and environmental significance. Genetic studies on methylotrophs, including the use of recombinant DNA techniques, show promise for the isolation and cloning of genes coding for specific functions.
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Holubová I, Brenner V, Hubácek J. Intergeneric conjugal transfer of Escherichia coli/Methylobacterium sp. shuttle vector. Folia Microbiol (Praha) 1993; 38:277-80. [PMID: 8112692 DOI: 10.1007/bf02898593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
To develop a host-vector system for Methylobacterium sp. using a construct based on a small indigenous methylotrophic plasmid, the E. coli--Methylobacterium sp. shuttle vector pWUBR (12.7 kb, Apr, Tcr) was constructed by joining the E. coli plasmid pBR328 and the cryptic plasmid pWU7 (7.8 kb), isolated from the soil facultative methylotrophic bacterium, Methylobacterium sp. strain M17. Via mobilization by the pDPT51 R plasmid, belonging to the IncP-1 incompatibility group, plasmid pWUBR was transferred into the original host of cryptic plasmid pWU7, strain M17, where a competition between the introduced hybrid plasmid and the indigenous cryptic plasmid took place, and into the plasmidless Methylobacterium sp. strain R2b. The stability of pWUBR in Tcr methylotrophic transconjugants after 25 generations of growth under nonselective conditions was more than 90% in both hosts. The ability to replicate in R2b strain demonstrates that the host spectrum of pWUBR is not restricted to the original host of pWU7 and indicates the possibility to use the present system for other methylotrophs.
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Affiliation(s)
- I Holubová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague
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Brenner V, Holubová I, Benada O, Hubácek J. Characterization of new plasmids from methylotrophic bacteria. Antonie Van Leeuwenhoek 1991; 60:43-8. [PMID: 1796807 DOI: 10.1007/bf00580440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Several tens of methanol-utilizing bacterial strains isolated from soil were screened for the presence of plasmids. From the obligate methylotroph Methylomonas sp. strain R103a plasmid pIH36 (36 kb) was isolated and its restriction map was constructed. In pink-pigmented facultative methylotrophs (PPFM), belonging to the genus Methylobacterium four plasmids were detected: plasmids pIB200 (200 kb) and pIB14 (14 kb) in the strain R15d and plasmids pWU14 (14 kb) and pWU7 (7.8 kb) in the strain M17. Because of the small size and the presence of several unique REN sites (HindIII, EcoRI, NcoI), plasmid pWU7 was chosen for the construction of a vector for cloning in methylotrophs. Cointegrates pKWU7A and pKWU7B were formed between pWU7 and the E. coli plasmid pK19 Kmr, which were checked for conjugative transfer from E. coli into the methylotrophic host.
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Affiliation(s)
- V Brenner
- Institute of Microbiology, Czechoslovak Academy of Sciences, Prague
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Abstract
Methylotrophic bacteria comprise a broad range of obligate aerobic microorganisms, which are able to proliferate on (a number of) compounds lacking carbon-carbon bonds. This contribution will essentially be limited to those organisms that are able to utilize methanol and will cover the physiological, biochemical and genetic aspects of this still diverse group of organisms. In recent years much progress has been made in the biochemical and genetic characterization of pathways and the knowledge of specific reactions involved in methanol catabolism. Only a few of the genetic loci hitherto found have been matched by biochemical experiments through the isolation or demonstration of specific gene products. Conversely, several factors have been identified by biochemical means and were shown to be involved in the methanol dehydrogenase reaction or subsequent electron transfer. For the majority of these components, their genetic loci are unknown. A comprehensive treatise on the regulation and molecular mechanism of methanol oxidation is therefore presented, followed by the data that have become available through the use of genetic analysis. The assemblage of methanol dehydrogenase enzyme, the role of pyrrolo-quinoline quinone, the involvement of accessory factors, the evident translocation of all these components to the periplasm and the dedicated link to the electron transport chain are now accepted and well studied phenomena in a few selected facultative methylotrophs. Metabolic regulation of gene expression, efficiency of energy conservation and the question whether universal rules apply to methylotrophs in general, have so far been given less attention. In order to expand these studies to less well known methylotrophic species initial results concerning such area as genetic mapping, the molecular characterization of specific genes and extrachromosomal genetics will also pass in review.
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Affiliation(s)
- G E de Vries
- Department of Microbiology, University of Groningen, Haren, The Netherlands
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Isolation and characterization of Paracoccus denitrificans mutants with increased conjugation frequencies and pleiotropic loss of a (nGATCn) DNA-modifying property. Arch Microbiol 1989. [DOI: 10.1007/bf00447011] [Citation(s) in RCA: 103] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Schmidhauser TJ, Ditta G, Helinski DR. Broad-host-range plasmid cloning vectors for gram-negative bacteria. BIOTECHNOLOGY (READING, MASS.) 1988; 10:287-332. [PMID: 2850044 DOI: 10.1016/b978-0-409-90042-2.50021-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Araki Y, Inoue M, Hashimoto H. Characterization and mobilization of nonconjugative plasmids encoding resistance to streptomycin and sulfanilamide. Microbiol Immunol 1987; 31:1107-11. [PMID: 3444425 DOI: 10.1111/j.1348-0421.1987.tb01342.x] [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: 01/05/2023]
Abstract
Most of nonconjugative streptomycin (Sm)- and sulfanilamide (Su)- resistance of clinical isolates belonging to various species of Enterobacteriaceae and Pseudomonas were encoded by an Inc Q plasmid, molecular size of which was 5.5 Md. The SmSu plasmids were efficiently mobilized by Inc P plasmids between E. coli strains. Inc I group and Inc F group plasmids could mobilize the Inc Q plasmids at lower efficiencies. The Inc Q plasmid was also mobilized to various species of Enterobacteriaceae at high frequencies without accompanying the conjugative Inc P plasmid; as a result, most of the SmSu-resistant transconjugants were nontransferable. The above results may explain the wide distribution of nonconjugative SmSu strains among clinical isolates.
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Affiliation(s)
- Y Araki
- Laboratory of Drug Resistance in Bacteria, Gunma University School of Medicine
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Al-Taho N, Warner P. Restoration of phenotype inEscherichia coliauxotrophs by pULB113-mediated mobilisation from methylotrophic bacteria. FEMS Microbiol Lett 1987. [DOI: 10.1111/j.1574-6968.1987.tb02129.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Nešvera J, Hochmannová J, Holubová I, Čejka K. Transfer of IncW plasmids into methylotrophic bacteria by conjugation and mobilization. Appl Microbiol Biotechnol 1987. [DOI: 10.1007/bf00253899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Nunn DN, Lidstrom ME. Isolation and complementation analysis of 10 methanol oxidation mutant classes and identification of the methanol dehydrogenase structural gene of Methylobacterium sp. strain AM1. J Bacteriol 1986; 166:581-90. [PMID: 3009411 PMCID: PMC214644 DOI: 10.1128/jb.166.2.581-590.1986] [Citation(s) in RCA: 120] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
A method has been developed for the direct selection of methanol oxidation mutants of the facultative methylotroph Methylobacterium sp. strain AM1 (formerly Pseudomonas sp. strain AM1). Using this direct selection technique, we have isolated mutants of Methylobacterium sp. strain AM1 that are no longer capable of growth on methanol but retain the ability to grow on methylamine. These methanol oxidation (Mox) mutants were complemented with a genomic clone bank of this organism constructed in the broad-host-range cosmid pVK100, and subcloning and Tn5 mutagenesis experiments have assigned the Mox mutants to 10 distinct complementation groups. Using an open reading frame beta-galactosidase fusion vector and antibodies specific for Methylobacterium sp. strain AM1 methanol dehydrogenase, we have identified the methanol dehydrogenase structural gene and determined the direction of transcription. The results suggest that the synthesis and utilization of an active methanol dehydrogenase in this organism requires at least 10 different gene functions.
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Harms N, de Vries GE, Maurer K, Veltkamp E, Stouthamer AH. Isolation and characterization of Paracoccus denitrificans mutants with defects in the metabolism of one-carbon compounds. J Bacteriol 1985; 164:1064-70. [PMID: 3905763 PMCID: PMC219298 DOI: 10.1128/jb.164.3.1064-1070.1985] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Mutants deficient in the metabolism of one-carbon compounds have been obtained by treating Paracoccus denitrificans with the mutagen N-methyl-N'-nitro-N-nitrosoguanidine. Mutants were selected without enrichment procedures by newly developed plate screening tests. The obtained mutants were characterized by their growth responses, cytochrome composition, enzyme activities, and immunogenic reaction with antisera against methanol dehydrogenase. By these criteria five mutant classes could be distinguished. Class I mutants are involved in the expression of methanol dehydrogenase. Three mutants of this class have a defect in the structural gene. A double mutant was found with defects in the expression of both methanol dehydrogenase and hydrogenase. Class II mutants have a defect in a regulatory gene involved in the regulation of both methanol dehydrogenase and methylamine dehydrogenase. Class III mutants are deficient in formaldehyde metabolism. A defect may exist in the expression of a second non-NAD-linked formaldehyde dehydrogenase which was postulated to be involved in C1 metabolism. Class IV mutants are deficient in cytochrome c. Mutants of class V have a defect in synthesis of the molybdenum cofactor essential for the function of formate dehydrogenase.
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Mapping of some genes involved in C-1 metabolism in the facultative methylotroph Methylobacterium sp strain AM1 (Pseudomonas AM1). Arch Microbiol 1985. [DOI: 10.1007/bf00411043] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Priefer UB, Simon R, Pühler A. Extension of the host range of Escherichia coli vectors by incorporation of RSF1010 replication and mobilization functions. J Bacteriol 1985; 163:324-30. [PMID: 3891734 PMCID: PMC219116 DOI: 10.1128/jb.163.1.324-330.1985] [Citation(s) in RCA: 120] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The broad-host-range vectors pSUP104, pSUP106, pSUP204, pSUP304, and pSUP404 are based on conventional Escherichia coli vectors (such as pBR325 and pACYC184) which have been modified to include the mobilization and broad-host-range replication functions of the IncQ plasmid RSF1010. These vector plasmids now can be maintained in a wide range of bacterial genera including Rhizobium, Agrobacterium, and Pseudomonas. They are efficiently mobilized by RP4 and thus are of particular interest for bacteria refractory to transformation. They offer the selection markers and cloning sites characteristic of the basic E. coli vectors. Therefore, they can be applied and adapted to a variety of cloning strategies. However, the cloning of very large fragments (e.g., in cosmid hybrids of pSUP106) was found to affect the stability of the recombinant molecules in a Rec+ background. This instability was not observed with smaller inserts of about 5 kilobases.
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Meyer RJ, Lin LS, Kim K, Brasch MA. Broad host-range plasmid R1162: replication, incompatibility, and copy-number control. BASIC LIFE SCIENCES 1985; 30:173-88. [PMID: 2990408 DOI: 10.1007/978-1-4613-2447-8_16] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Dijkhuizen L, Harder W, de Boer L, van Boven A, Clement W, Bron S, Venema G. Genetic manipulation of the restricted facultative methylotroph Hyphomicrobium X by the R-plasmid-mediated introduction of the Escherichia coli pdh genes. Arch Microbiol 1984; 139:311-8. [PMID: 6393893 DOI: 10.1007/bf00408372] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The inability of Hyphomicrobium X to grow on compounds such as pyruvate and succinate is most likely due to the absence of a functional pyruvate dehydrogenase (PDH) complex. Further support for this was sought by studying the effect of the introduction of the Escherichia coli pdh genes in Hyphomicrobium X on the pattern of substrate utilization by the latter organism. These genes were cloned by in vivo techniques using the broad-host range conjugative plasmid RP4::Mucts. Plasmid RP4 derivatives containing pdh genes were selected by their ability to complement a pyruvate dehydrogenase deletion mutant of E. coli, strain JRG746 recA (ace-1pd) delta 18. The plasmids thus obtained could be transferred through an intermediary host (C600 recA), selecting only for an antibiotic resistance coded for by RP4 and back into JRG746 or other E. coli pdh mutants, upon which they still conferred the wild type phenotype. Enzyme assays showed that the latter strains, when carrying plasmid RP4'pdh1 also possessed PDH complex activity. Conjugation between the auxotrophic E. coli JRG746 (RP4'pdh1) strain and Hyphomicrobium X on pyruvate minimal agar gave rise to progeny which, on the basis of its morphology (stalked bacteria), their ability to grow on C1-compounds and to denitrify (now also with pyruvate) were identified as hyphomicrobia. This Hyphomicrobium X transconjugant was also able to grow in minimal medium with succinate, but no other novel growth substrates have been identified so far.(ABSTRACT TRUNCATED AT 250 WORDS)
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Abstract
A series of cloning vectors has been constructed based on the broad-host-range plasmid R300B. One of these vectors, pGSS33, has a size of 13.4 kb and carries four antibiotic resistance genes [ampicillin (Apr), chloramphenicol (Cmr), streptomycin (Smr) and tetracycline (Tcr)], all of which have restriction sites for insertional inactivation. The derivation, structure and uses of the plasmids are described.
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Frey J, Bagdasarian M, Feiss D, Franklin FC, Deshusses J. Stable cosmid vectors that enable the introduction of cloned fragments into a wide range of gram-negative bacteria. Gene 1983; 24:299-308. [PMID: 6315541 DOI: 10.1016/0378-1119(83)90090-2] [Citation(s) in RCA: 100] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A cosmid cloning system has been developed which is useful for the construction of genomic libraries and the introduction of clones into a broad range of bacterial species. The cosmids pMMB33 and pMMB34 allow selective cloning into their unique BamHI site of 36-kb DNA fragments generated by BamHI, Sau3A and MboI partial digestion. This selective cloning is achieved by a strategy that avoids formation of polycosmids without a dephosphorylation step. It uses two unique recognition sites within the vectors for endoncleases that generate blunt-ended DNA fragments for the preparation of left and right cosmid "arms". An alternative method that uses the unique EcoRI and SstI sites and dephosphorylation of the cosmid arms prior to BamHI digestion is also outlined and discussed. The DNA is first cloned with either vector into a rec- E. coli strain, where clones can be maintained stably, and can then be introduced by mobilization into a wide range of Gram-negative species to permit the study of gene expression and complementation. Because mobilization is much more efficient than transformation, the vector has the advantage that it can be transferred between bacterial species that specify different restriction systems, where transformation appears to be inefficient. The vectors have been used to generate gene libraries from the chromosomal DNA of several Pseudomonas and a Thiobacillus species. The genes specifying myo-inositol transport from Pseudomonas strain JD34 have been cloned with this system.
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Monteiro M, Typas M, Moffett B, Bainbridge B. Isolation and characterization of a high molecular weight plasmid from the obligate methanol-utilising bacteriumMethylomonas (Methanomonas) methylovora. FEMS Microbiol Lett 1982. [DOI: 10.1111/j.1574-6968.1982.tb00074.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Meyer R, Laux R, Boch G, Hinds M, Bayly R, Shapiro JA. Broad-host-range IncP-4 plasmid R1162: effects of deletions and insertions on plasmid maintenance and host range. J Bacteriol 1982; 152:140-50. [PMID: 6288654 PMCID: PMC221385 DOI: 10.1128/jb.152.1.140-150.1982] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
R1162 is an 8.7-kilobase (kb) broad-host-range replicon encoding resistance to streptomycin and sulfa drugs. In vitro deletion of 1.8-kb DNA between coordinates 3.0 and 5.3 kb did not affect plasmid maintenance, but a Tn1 insertion at coordinate 6.3 kb led to a recessive defect in plasmid maintenance. The only cis-acting region necessary for plasmid replication appears to lie between the Tn1 insertion at coordinate 6.3 kb and a second Tn1 insertion at coordinate 6.5 kb. All R1162 sequences between position 6.5 kb and the EcoRI site at coordinate 8.7/0 kb were dispensible for replication in Escherichia coli and Pseudomonas putida. Plasmids carrying insertions in a variety of restriction sites in an R1162::Tn1 derivative were unstable in P. putida but stable in E. coli. Tn5 insertions in R1162 showed a hot spot at coordinate 7.5 kb. A Tn5 insertion at coordinate 8.2 kb appeared to mark the 3' end of the streptomycin phosphotransferase coding sequence. All R1162::Tn5 derivatives showed specific instability in Pseudomonas strains but not in E. coli. The instability could be relieved by internal deletions of Tn5 sequences. In the haloaromatic-degrading Pseudomonas sp. strain B13, introduction of an unstable R1162::Tn5 plasmid led to loss of ability to utilize m-chlorobenzoate as a growth substrate. Our results showed that alteration of plasmid sequence organization in nonessential regions can result in restriction of plasmid host range.
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Abstract
Regions of plasmid DNA encoding characteristic properties of the IncQ (P-4) group plasmid R1162 were identified by mutagenesis and in vitro cloning. Coding sequences sufficient for expression of incompatibility and efficient conjugal mobilization by plasmid R751 were found to be linked to the origin of DNA replication. In contrast, there was a region remote from the origin, and active in trans, that was required for plasmid maintenance. A derivative that was temperature sensitive for stability was isolated. The defect mapped at or near the region required for plasmid maintenance and resulted in far fewer copies of supercoiled plasmid DNA per cell under permissive conditions. A second region required for stability was also identified from the behavior of a deletion derivative of R1162, which did not, however, show an altered number of supercoiled plasmid DNA copies. Finally, a plasmid DNA mutation resulting in a substantially higher copy number was isolated. Plasmid reconstruction experiments suggested that the mutation was linked to the replicative origin.
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Abstract
SUMMARYThe broad host-range non-conjugative IncQ plasmid RSF1010 was mobilised with 100% efficiency in membrane filter matings, both inE. coliK12 andP. aeruginosaPAO, by broad host-range conjugative IncP plasmids. No homology between RSF1010 and an IncP plasmid could be detected. InE. coli, IncIα and IncX plasmids, but not IncF, IncN or IncW plasmids, were also relatively efficient at mobilising RSF1010, while inP. aeruginosa, R91–5 (IncP-10) was highly efficient, but pMG5 (IncP-2) and FP2 (IncP-8) were very inefficient. IncP plasmids also mobilised several plasmids derived from RSF1010 for use as in vectors inin vitrorecombination experiments very efficiently, and pSC101 quite efficiently: this reduces the level of biological containment possible with these plasmids.
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Abstract
A pBR322:RSF1010 composite plasmid, constructed in vitro, was used as a cloning vector in Pseudomonas aeruginosa. This nonamplifiable plasmid, pMW79, has a molecular weight of 8.4 X 10(6) and exists as a multicopy plasmid in both P. aeruginosa and Escherichia coli. In P. aeruginosa strain PAO2003, pMW79 conferred resistance to carbenicillin and tetracycline. Characterization of pMW79 with restriction enzymes revealed that four enzymes (BamHI, SalI, HindIII, and HpaI) cleaved the plasmid at unique restriction sites. Cloning P. aeruginosa chromosomal deoxyribonucleic acid fragments into the BamHI or SalI site of pMW79 inactivated the tetracycline resistance gene. Thus, cells carrying recombinant plasmids could be identified by their carbenicillin resistance, tetracycline sensitivity phenotype. Deoxyribonucleic acid fragments of approximately 0.5 to 7.0 megadaltons were inserted into pMW79, and the recombinant plasmids were stably maintained in a recombination-deficient (recA) P. aeruginosa host.
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Shapiro JA, Charbit A, Benson S, Caruso M, Laux R, Meyer R, Banuett F. Perspectives for genetic engineering of hydrocarbon oxidizing bacteria. BASIC LIFE SCIENCES 1981; 18:243-72. [PMID: 6944066 DOI: 10.1007/978-1-4684-3980-9_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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