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Beck C, Blin K, Gren T, Jiang X, Mohite OS, Palazzotto E, Tong Y, Charusanti P, Weber T. Metabolic Engineering of Filamentous Actinomycetes. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Genome mining of the Streptomyces avermitilis genome and development of genome-minimized hosts for heterologous expression of biosynthetic gene clusters. ACTA ACUST UNITED AC 2014; 41:233-50. [DOI: 10.1007/s10295-013-1327-x] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 08/04/2013] [Indexed: 12/11/2022]
Abstract
Abstract
To date, several actinomycete genomes have been completed and annotated. Among them, Streptomyces microorganisms are of major pharmaceutical interest because they are a rich source of numerous secondary metabolites. S. avermitilis is an industrial microorganism used for the production of an anthelmintic agent, avermectin, which is a commercially important antiparasitic agent in human and veterinary medicine, and agricultural pesticides. Genome analysis of S. avermitilis provides significant information for not only industrial applications but also understanding the features of this genus. On genome mining of S. avermitilis, the microorganism has been found to harbor at least 38 secondary metabolic gene clusters and 46 insertion sequence (IS)-like sequences on the genome, which have not been searched so far. A significant use of the genome data of Streptomyces microorganisms is the construction of a versatile host for heterologous expression of exogenous biosynthetic gene clusters by genetic engineering. Since S. avermitilis is used as an industrial microorganism, the microorganism is already optimized for the efficient supply of primary metabolic precursors and biochemical energy to support multistep biosynthesis. The feasibility of large-deletion mutants of S. avermitilis has been confirmed by heterologous expression of more than 20 exogenous biosynthetic gene clusters.
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Banh Q, Arenskötter M, Steinbüchel A. Establishment of Tn5096-based transposon mutagenesis in Gordonia polyisoprenivorans. Appl Environ Microbiol 2005; 71:5077-84. [PMID: 16151089 PMCID: PMC1214614 DOI: 10.1128/aem.71.9.5077-5084.2005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The transposons Tn5, Tn10, Tn611, and Tn5096 were characterized regarding transposition in Gordonia polyisoprenivorans strain VH2. No insertional mutants were obtained employing Tn5 or Tn10. The thermosensitive plasmid pCG79 harboring Tn611 integrated into the chromosome of G. polyisoprenivorans; however, the insertional mutants were fairly unstable und reverted frequently to the wild-type phenotype. In contrast, various stable mutants were obtained employing Tn5096-mediated transposon mutagenesis. Auxotrophic mutants, mutants defective or deregulated in carotenoid biosynthesis, and mutants defective in utilization of rubber and/or highly branched isoprenoid hydrocarbons were obtained by integration of plasmid pMA5096 harboring Tn5096 as a whole into the genome. From about 25,000 isolated mutants, the insertion loci of pMA5096 were subsequently mapped in 20 independent mutants in genes which could be related to the above-mentioned metabolic pathways or to putative regulation proteins. Analyses of the genotypes of pMA5096-mediated mutants defective in biodegradation of poly(cis-1,4-isoprene) did not reveal homologues to recently identified genes coding for enzymes catalyzing the initial cleavage of poly(cis-1,4-isoprene). One rubber-negative mutant was disrupted in mcr, encoding an alpha-methylacyl-coenzyme A racemase. This mutant was defective in degradation of poly(cis-1,4-isoprene) and also of highly branched isoprenoid hydrocarbons.
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Affiliation(s)
- Quyen Banh
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, D-48149 Münster, Germany
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Blount ZD, Grogan DW. New insertion sequences of Sulfolobus: functional properties and implications for genome evolution in hyperthermophilic archaea. Mol Microbiol 2005; 55:312-25. [PMID: 15612937 DOI: 10.1111/j.1365-2958.2004.04391.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Analyses of complete genomes indicate that insertion sequences (ISs) are abundant and widespread in hyperthermophilic archaea, but few experimental studies have measured their activities in these hosts. As a way to investigate the impact of ISs on Sulfolobus genomes, we identified seven transpositionally active ISs in a widely distributed Sulfolobus species, and measured their functional properties. Six of the seven were found to be distinct from previously described ISs of Sulfolobus, and one of the six could not be assigned to any known IS family. A type II 'Miniature Inverted-repeat Transposable Element' (MITE) related to one of the ISs was also recovered. Rates of transposition of the different ISs into the pyrEF region of their host strains varied over a 250-fold range. The Sulfolobus ISs also differed with respect to target-site selectivity, although several shared an apparent preference for the pyrEF promoter region. Despite the number of distinct ISs assayed and their molecular diversity, only one demonstrated precise excision from the chromosomal target region. The fact that this IS is the only one lacking inverted repeats and target-site duplication suggests that the observed precise excision may be promoted by the IS itself. Sequence searches revealed previously unidentified partial copies of the newly identified ISs in the Sulfolobus tokodaii and Sulfolobus solfataricus genomes. The structures of these fragmentary copies suggest several distinct molecular mechanisms which, in the absence of precise excision, inactivate ISs and gradually eliminate the defective copies from Sulfolobus genomes.
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Affiliation(s)
- Zachary D Blount
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
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Yamasaki M, Miyashita K, Cullum J, Kinashi H. A complex insertion sequence cluster at a point of interaction between the linear plasmid SCP1 and the linear chromosome of Streptomyces coelicolor A3(2). J Bacteriol 2000; 182:3104-10. [PMID: 10809688 PMCID: PMC94495 DOI: 10.1128/jb.182.11.3104-3110.2000] [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: 01/21/2000] [Accepted: 03/13/2000] [Indexed: 11/20/2022] Open
Abstract
The giant linear plasmid SCP1 can integrate into the central region of the linear chromosome of Streptomyces coelicolor A3(2). Nucleotide sequence analysis around the target site for SCP1 integration in strain M145 identified a total of five copies of four insertion sequences (ISs) in a 6.5-kb DNA stretch. Three of the four (IS468, IS469, and IS470) are new IS elements, and the other is IS466. All of these elements contain one open reading frame which encodes a transposase-like protein. Two copies of IS468 (IS468A and -B) are tandemly aligned at the left end of the cluster. Following these, IS469 and IS466 are located in a tail-to-tail orientation with 69.3% identity to each other. IS470 is located at the right end of the cluster. The activities of IS466 and IS468 were demonstrated by transposition experiments and sequence comparison of several copies, respectively.
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Affiliation(s)
- M Yamasaki
- Department of Molecular Biotechnology, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima 739-8527, Japan
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Hopwood DA. Forty years of genetics with Streptomyces: from in vivo through in vitro to in silico. MICROBIOLOGY (READING, ENGLAND) 1999; 145 ( Pt 9):2183-2202. [PMID: 10517572 DOI: 10.1099/00221287-145-9-2183] [Citation(s) in RCA: 205] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- David A Hopwood
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK1
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Gagnat J, Chouayekh H, Gerbaud C, Francou F, Virolle MJ. Disruption of sblA in Streptomyces lividans permits expression of a heterologous alpha-amylase gene in the presence of glucose. MICROBIOLOGY (READING, ENGLAND) 1999; 145 ( Pt 9):2303-2312. [PMID: 10517583 DOI: 10.1099/00221287-145-9-2303] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In a transposition mutant of Streptomyces lividans TK24, the usually glucose-repressible expression of a heterologous alpha-amylase gene (aml) became resistant to glucose repression. The transposon had inserted into an ORF called sblA which encodes a 274 aa product sharing significant sequence similarities with various phosphatases that act on small phosphorylated substrates. sblA was transcribed as a monocistronic mRNA and its transcription was enhanced at the transition phase. Because its transcriptional and putative translational start points coincide, sblA is likely to be translated in the absence of a conventional RBS. The sblA-disrupted mutant is characterized by early growth arrest in glucose-grown cultures and by partial relief of glucose repression of aml expression.
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Affiliation(s)
- Josette Gagnat
- Laboratoire de Biologie et Génétique Moléculaire, Institut de Génétique et Microbiologie, CNRS UMR8621 Bâtiment 400, Université Paris-Sud, F-91405 Orsay Cedex, France1
| | - Hichem Chouayekh
- Laboratoire de Biologie et Génétique Moléculaire, Institut de Génétique et Microbiologie, CNRS UMR8621 Bâtiment 400, Université Paris-Sud, F-91405 Orsay Cedex, France1
| | - Claude Gerbaud
- Laboratoire de Biologie et Génétique Moléculaire, Institut de Génétique et Microbiologie, CNRS UMR8621 Bâtiment 400, Université Paris-Sud, F-91405 Orsay Cedex, France1
| | - François Francou
- Laboratoire de Biologie et Génétique Moléculaire, Institut de Génétique et Microbiologie, CNRS UMR8621 Bâtiment 400, Université Paris-Sud, F-91405 Orsay Cedex, France1
| | - Marie-Joelle Virolle
- Laboratoire de Biologie et Génétique Moléculaire, Institut de Génétique et Microbiologie, CNRS UMR8621 Bâtiment 400, Université Paris-Sud, F-91405 Orsay Cedex, France1
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Healy FG, Bukhalid RA, Loria R. Characterization of an insertion sequence element associated with genetically diverse plant pathogenic Streptomyces spp. J Bacteriol 1999; 181:1562-8. [PMID: 10049389 PMCID: PMC93547 DOI: 10.1128/jb.181.5.1562-1568.1999] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/1998] [Accepted: 12/11/1998] [Indexed: 11/20/2022] Open
Abstract
Streptomycetes are common soil inhabitants, yet few described species are plant pathogens. While the pathogenicity mechanisms remain unclear, previous work identified a gene, nec1, which encodes a putative pathogenicity or virulence factor. nec1 and a neighboring transposase pseudogene, ORFtnp, are conserved among unrelated plant pathogens and absent from nonpathogens. The atypical GC content of nec1 suggests that it was acquired through horizontal transfer events. Our investigation of the genetic organization of regions adjacent to the 3' end of nec1 in Streptomyces scabies 84.34 identified a new insertion sequence (IS) element, IS1629, with homology to other IS elements from prokaryotic animal pathogens. IS1629 is 1,462 bp with 26-bp terminal inverted repeats and encodes a putative 431-amino-acid (aa) transposase. Transposition of IS1629 generates a 10-bp target site duplication. A 77-nucleotide (nt) sequence encompassing the start codon and upstream region of the transposase was identified which could function in the posttranscritpional regulation of transposase synthesis. A functional copy of IS1629 from S. turgidiscabies 94.09 (Hi-C-13) was selected in the transposon trap pCZA126, through its insertion into the lambda cI857 repressor. IS1629 is present in multiple copies in some S. scabies strains and is present in all S. acidiscabies and S. turgidiscabies strains examined. A second copy of IS1629 was identified between ORFtnp and nec1 in S. acidiscabies strains. The diversity of IS1629 hybridization profiles was greatest within S. scabies. IS1629 was absent from the 27 nonpathogenic Streptomyces strains tested. The genetic organization and nucleotide sequence of the nec1-IS1629 region was conserved and identical among representatives of S. acidiscabies and S. turgidiscabies. These findings support our current model for the unidirectional transfer of the ORFtnp-nec1-IS1629 locus from IS1629-containing S. scabies (type II) to S. acidiscabies and S. turgidiscabies.
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Affiliation(s)
- F G Healy
- Department of Plant Pathology, Cornell University, Ithaca, New York 14853, USA
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Volff JN, Altenbuchner J. High-frequency transposition of IS1373, the insertion sequence delimiting the amplifiable element AUD2 of Streptomyces lividans. J Bacteriol 1997; 179:5639-42. [PMID: 9287031 PMCID: PMC179447 DOI: 10.1128/jb.179.17.5639-5642.1997] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
IS1373 is the putative insertion sequence delimiting the amplifiable unit AUD2 of Streptomyces lividans. Two IS1373-derived thiostrepton-resistant transposons, Tn5492 and Tn5494, transposed into multiple sites of the S. lividans chromosome at frequencies as high as 0.4 and 1%, respectively. Hence, IS1373 is a functional insertion sequence and its unique open reading frame, insA, encodes the transposase.
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Affiliation(s)
- J N Volff
- Institut für Industrielle Genetik, Universität Stuttgart, Germany.
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Solenberg PJ, Matsushima P, Stack DR, Wilkie SC, Thompson RC, Baltz RH. Production of hybrid glycopeptide antibiotics in vitro and in Streptomyces toyocaensis. CHEMISTRY & BIOLOGY 1997; 4:195-202. [PMID: 9115410 DOI: 10.1016/s1074-5521(97)90288-x] [Citation(s) in RCA: 132] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND The glycopeptide antibiotics vancomycin and teicoplanin are currently the last line of defence against some microorganisms that are resistant to many drugs. The emergence of vancomycin-resistant and teicoplanin-resistant enterococci underscores the need for more potent antibiotics. The glycosylation patterns of glycopeptides and chemical modifications of the glycosyl moieties have been shown to greatly influence their antibiotic activity, and certain combinations have resulted in highly active new compounds. To explore further the production of more potent glycopeptide antibiotics, we assessed whether glycosyltransferases could be used to produce hybrid compounds that contain various combinations of sugars and peptide cores. RESULTS We cloned five glycosyltransferase genes from Amycolatopsis orientalis strains that produce vancomycin or a related glycopeptide, A82846. The gtfB and gtfE' genes from A. orientalis strains expressed in Escherichia coli produced glucosyltransferase activities that added glucose or xylose to the vancomycin heptapeptide. The GtfE' protein added glucose efficiently to two other heptapeptides related to teicoplanin to produce hybrid glycopeptide antibiotics. The cloned gtfE' gene, driven by the strong constitutive promoter ermEp*, was introduced into Streptomyces toyocaensis, which produces the antibiotic A47934, a heptapeptide related to teicoplanin; recombinant organisms produced glucosyl A47934, a hybrid glycopeptide antibiotic. CONCLUSIONS Cloned glycosyltransferases from glycopeptide antibiotic producers can be used to produce novel hybrid antibiotics, both in vitro and in vivo. Because similar enzymes have differing degrees of substrate specificity, it is advantageous to characterize the substrate specificity with enzymes expressed in E. coli prior to constructing recombinant actinomycetes for production.
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Affiliation(s)
- P J Solenberg
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA.
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Matsushima P, Baltz RH. A gene cloning system for 'Streptomyces toyocaensis'. MICROBIOLOGY (READING, ENGLAND) 1996; 142 ( Pt 2):261-267. [PMID: 8932699 DOI: 10.1099/13500872-142-2-261] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We explored different methods of introducing DNA into 'Streptomyces toyocaensis' and Streptomyces virginiae to construct stable recombinant strains. Plasmid pIJ702 isolated from Streptomyces lividans transformed protoplasts of 'S. toyocaensis' at a frequency of 7 x 10(3) transformants (mu g DNA)-1. pIJ702 prepared from 'S. toyocaensis' transformed 'S. toyocaensis' protoplasts at a frequency of 1 center dot 5 x 10(5) (mu g DNA)-1, suggesting that 'S. toyocaensis' expresses restriction and modification. Plasmid pRHB126 was transduced by bacteriophage FP43 into 'S. toyocaensis' at a frequency of 1.2 x 10(-6) (p.f.u)-1. Plasmids pOJ436 and pRHB304 were introduced into 'S. toyocaensis' by conjugation from Escherichia coli S17-1 at frequencies of about 2 x 10(-4) and 1 x 10(-4) per recipient, respectively. Analysis of several exconjugants indicated that pOJ436 and pRHB304 inserted into a unique phiC31 attB site and that some of the insertions had minimal deleterious effects on glycopeptide A47934 production. The results indicate that 'S. toyocaensis' is a suitable host for gene cloning, whereas S. virginiae does not appear to be.
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Affiliation(s)
- Patti Matsushima
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Richard H Baltz
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
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Vertès AA, Asai Y, Inui M, Kobayashi M, Kurusu Y, Yukawa H. Transposon mutagenesis of coryneform bacteria. MOLECULAR & GENERAL GENETICS : MGG 1994; 245:397-405. [PMID: 7808388 DOI: 10.1007/bf00302251] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The Corynebacterium glutamicum insertion sequence IS31831 was used to construct two artificial transposons: Tn31831 and miniTn31831. The transposition vectors were based on a gram-negative replication origin and do not replicate in coryneform bacteria. Strain Brevibacterium flavum MJ233C was mutagenized by miniTn31831 at an efficiency of 4.3 x 10(4) mutants per microgram DNA. Transposon insertions occurred at different locations on the chromosome and produced a variety of mutants. Auxotrophs could be recovered at a frequency of approximately 0.2%. Transposition of IS31831 derivatives led not only to simple insertion, but also to cointegrate formation (5%). No multiple insertions were observed. Chromosomal loci of B. flavum corresponding to auxotrophic and pigmentation mutants could be rescued in Escherichia coli, demonstrating that these transposable elements are useful genetic tools for studying the biology of coryneform bacteria.
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Affiliation(s)
- A A Vertès
- Mitsubishi Petrochemical Co., Ltd., Tsukuba Research Center, Ibaraki, Japan
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Abstract
Transposons derived from the Streptomyces lividans insertion sequence IS493 are useful for the genetic analysis and manipulation of a number of Streptomyces spp. Tn5099-10, an IS493 derivative that contains a spontaneous deletion terminating in the left inverted repeat (IR-L), transposed at a 1000-fold higher frequency in Streptomyces griseofuscus, and at a tenfold higher frequency in Streptomyces fradiae, than the IS493 derivatives, Tn5096 and Tn5099. The IR-L from Tn5099-10 was used to construct a cassette which hypertransposes from plasmids containing the transposon genes, ORFA and ORFB, outside of the inverted repeats. The target sequences of two Tn5099-10 insertions conformed to the consensus target sequence of the other IS493 derivatives, gNCaNTgNNy (where lower-case letters indicate that other nt have been observed at this position and N is any nt). Transposition mutant libraries of S. griseofuscus and S. fradiae can be easily prepared in broth culture by using the hypertransposing elements and a temperature-sensitive delivery plasmid.
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Affiliation(s)
- P J Solenberg
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285
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Matsushima P, Broughton MC, Turner JR, Baltz RH. Conjugal transfer of cosmid DNA from Escherichia coli to Saccharopolyspora spinosa: effects of chromosomal insertions on macrolide A83543 production. Gene 1994; 146:39-45. [PMID: 8063103 DOI: 10.1016/0378-1119(94)90831-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Cosmid pOJ436, containing large inserts of Saccharopolyspora spinosa (Ss) DNA, was transferred by conjugation from Escherichia coli to Ss an integrated into the chromosome, apparently by homologous recombination, at high frequencies (10(-5) to 10(-4) per recipient). Transfer was mediated by the plasmid RP4 (RK2) transfer functions in E. coli, and the RK2 oriT function located on pOJ436 [Bierman et al., Gene 116 (1992) 43-49]. pOJ436 lacking Ss DNA, or containing a small insert (approx. 2 kb) of Ss DNA, conjugated from E. coli and integrated at either of two bacteriophage phi C31 attB sites at low frequency (approx. 10(-7) per recipient). Exconjugants containing homologous inserts or inserts at the phi C31 attB sites were stable in the absence of antibiotic selection, and most produced control levels of tetracyclic macrolide A83543 factors. Some exconjugants contained similar kinds of large deletions and were defective in macrolide production.
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Affiliation(s)
- P Matsushima
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285
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Brolle DF, Pape H, Hopwood DA, Kieser T. Analysis of the transfer region of the Streptomyces plasmid SCP2. Mol Microbiol 1993; 10:157-70. [PMID: 7968512 DOI: 10.1111/j.1365-2958.1993.tb00912.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
pIJ903, a bifunctional derivative of the 31.4 kb low-copy-number, conjugative Streptomyces plasmid SCP2*, was mutagenized in Streptomyces lividans using Tn4560. Mutant plasmids differing in their transfer frequencies, chromosome mobilization abilities, pock formation, and complementation properties were isolated. The mutations defined five transfer-related genes, traA, traB, traC, traD and spd, clustered in a region of 9 kb. The deduced sequences of the putative TraA and TraB proteins showed no overall similarity to known protein sequences, but the phenotype of traA mutant plasmids and sequence motifs in the putative TraA protein suggested that it might be a DNA helicase.
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Affiliation(s)
- D F Brolle
- John Innes Institute, John Innes Centre, Norwich, UK
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Abstract
Over the past year, dramatic developments in the technology for isolating and manipulating genes for polyketide synthases have been reported. Significant progress has been made in understanding the mechanisms by which these complex enzymes generate the carbon chains of the polyketides, a highly versatile class of natural products. With the demonstration of the production of novel metabolites by synthase engineering, the stage is excitingly set for rationally manipulating synthase 'programming' to generate tailor-made carbon chains.
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Affiliation(s)
- D A Hopwood
- Genetics Department, John Innes Institute, John Innes Centre, Norwich, UK
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Rezsöhazy R, Hallet B, Delcour J, Mahillon J. The IS4 family of insertion sequences: evidence for a conserved transposase motif. Mol Microbiol 1993; 9:1283-95. [PMID: 7934941 DOI: 10.1111/j.1365-2958.1993.tb01258.x] [Citation(s) in RCA: 127] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The eight IS231 variants characterized so far (IS231 A-F, V and W) display similar transposases with an overall 40% identity. Comparison with all the prokaryotic transposable elements sequenced so far revealed that the IS231 transposases share two conserved regions with those of 35 other insertion sequences of wide origins. These insertion sequences, defining the IS4 family, have a common bipartite organization of their ends and are divided into two similarity groups. Interestingly, the transposase domains conserved within this family display similarities with the well known integrase domain shared by transposases of the IS3 and IS15 families, and integrases of retroelements. This domain is also found in IS30-related elements and Tn7 TnsB protein. Amino acid residues conserved throughout all these prokaryotic and eukaryotic mobile genetic elements define a major transposase/integrase motif, likely to play an important role in the transposition process.
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Affiliation(s)
- R Rezsöhazy
- Unité de Génétique, Université Catholique de Louvain, Louvain-La-Neuve, Belgium
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Ikeda H, Takada Y, Pang CH, Tanaka H, Omura S. Transposon mutagenesis by Tn4560 and applications with avermectin-producing Streptomyces avermitilis. J Bacteriol 1993; 175:2077-82. [PMID: 8384619 PMCID: PMC204307 DOI: 10.1128/jb.175.7.2077-2082.1993] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The Tn3-like Streptomyces transposon Tn4560 was used to mutagenize Streptomyces avermitilis, the producer of anthelmintic avermectins and the cell growth inhibitor oligomycin. Tn4560 transposed in this strain from a temperature-sensitive plasmid to the chromosome and from the chromosome to a plasmid with an apparent frequency of about 10(-4) to 10(-3) at both 30 and 39 degrees C. Auxotrophic and antibiotic nonproducing mutations were, however, obtained only with cultures that were kept at 37 or 39 degrees C. About 0.1% of the transposon inserts obtained at 39 degrees C caused auxotrophy or abolished antibiotic production. The sites of insertion into the S. avermitilis chromosome were mapped. Chromosomal DNA fragments containing Tn4560 insertions in antibiotic production genes were cloned onto a Streptomyces plasmid with temperature-sensitive replication and used to transport transposon mutations to other strains, using homologous recombination. This technique was used to construct an avermectin production strain that no longer makes the toxic oligomycin.
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Affiliation(s)
- H Ikeda
- School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
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Chen CW, Yu TW, Chung HM, Chou CF. Discovery and characterization of a new transposable element, Tn4811, in Streptomyces lividans 66. J Bacteriol 1992; 174:7762-9. [PMID: 1332944 PMCID: PMC207491 DOI: 10.1128/jb.174.23.7762-7769.1992] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Transposition of a new 5.4-kb transposon, Tn4811, of Streptomyces lividans to the melC operon of Streptomyces antibioticus on plasmid pIJ702 was discovered. The nucleotide sequence of this copy of Tn4811, which contained an imperfect (9 of 11 bp) terminal inverted repeat, five putative Streptomyces coding sequences for an oxidoreductase and its transcription regulator, and three transposition-related proteins, was determined. SLP- strains of S. lividans contained one copy (A) of Tn4811, while SLP2+ strains contained an additional copy (B) on the SLP2 plasmid. The nucleotide sequences at three insertion junctions of Tn4811 were determined. Copy B lacked 41 bp from the left end. At the other five junctions the duplication of a putative 3-bp target sequence (TGA) was observed. A sequence of less than 3 kb homologous to Tn4811 was present in S. antibioticus. DNA homologous to Tn4811 was not detected in 14 other Streptomyces species.
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Affiliation(s)
- C W Chen
- Institute of Genetics, National Yang-Ming Medical College, Taipei, Taiwan, Republic of China
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Baltz RH, Hahn DR, McHenney MA, Solenberg PJ. Transposition of Tn5096 and related transposons in Streptomyces species. Gene X 1992; 115:61-5. [PMID: 1319378 DOI: 10.1016/0378-1119(92)90541-v] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
IS493 is an insertion sequence isolated from Streptomyces lividans by a method designed to 'trap' transposable elements. IS493 was converted to functional transposons by cloning antibiotic-resistance-encoding genes between ORF-A and ORF-B of IS493 or near the left-end inverted repeat of the element. Tn5096 transposed relatively randomly in several Streptomyces species. Tn5096 can be introduced into streptomycetes on temperature-sensitive vectors by protoplast transformation, FP43-mediated transduction, or by conjugation from Escherichia coli. We have shown that additional genes can be inserted in Tn5096 without disrupting transposition, and that Tn5096 insertions in a tylosin (Ty)-producing strain of Streptomyces fradiae frequently cause no deleterious effects on Ty production. A promoter probe transposon, Tn5099, containing a promoterless xylE gene, transposed in Streptomyces griseofuscus and S. fradiae, and transcriptional fusions were readily identified.
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Affiliation(s)
- R H Baltz
- Lilly Research Laboratories, Indianapolis, IN 46285
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Guilhot C, Gicquel B, Davies J, Martín C. Isolation and analysis of IS6120, a new insertion sequence from Mycobacterium smegmatis. Mol Microbiol 1992; 6:107-13. [PMID: 1310791 DOI: 10.1111/j.1365-2958.1992.tb00842.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Insertion sequence IS6120 from Mycobacterium smegmatis was identified by its ability to transpose into different sites in the lambda repressor gene, cl857, carried on an Escherichia coli/mycobacteria shuttle plasmid. IS6120 is a novel 1.5 kb insertion sequence, which has 24-bp imperfect terminal inverted repeats and generates 9-bp duplications of the target DNA following insertion. IS6120 is present in at least three copies in M. smegmatis but was not found in other species, including Mycobacterium tuberculosis. Nucleotide sequence analysis revealed that IS6120 contains two open reading frames, one of which encodes a putative transposase with similarities to those found in IS256 from Staphylococcus aureus, IST2 from Thiobacillus ferrooxidans, and ISRm3 from Rhizobium meliloti. The fact that IS6120 does not recognize a consensus target sequence for insertion and has no homologous sequences in the other strains studied makes IS6120 useful for transposon mutagenesis in mycobacteria.
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Affiliation(s)
- C Guilhot
- Unité de Génie Microbiologique (URA1300 du CNRS), Institut Pasteur, Paris, France
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24
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Abstract
Tn5099, a promoter probe transposon for Streptomyces spp., was constructed by inserting a promoterless xylE gene and a hygromycin resistance gene into IS493. Tn5099 transposed into different sites in the Streptomyces griseofuscus genome, and the xylE reporter gene was expressed in some of the transposition mutants. Strains containing Tn5099 insertions that gave regulated expression of the xylE gene were identified.
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Affiliation(s)
- D R Hahn
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285
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McHenney MA, Baltz RH. Transposition of Tn5096 from a temperature-sensitive transducible plasmid in Streptomyces spp. J Bacteriol 1991; 173:5578-81. [PMID: 1653214 PMCID: PMC208276 DOI: 10.1128/jb.173.17.5578-5581.1991] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Transposon Tn5096 was inserted into a derivative of the temperature-sensitive plasmid pMT660 containing the bacteriophage FP43 pac site. The resulting plasmid, pRHB126, was transduced by FP43 into several Streptomyces species. Tn5096 transposed from pRHB126 into different sites in the genomes of Streptomyces ambofaciens, Streptomyces cinnamonensis, Streptomyces coelicolor A3(2), Streptomyces fradiae, Streptomyces griseofuscus, and Streptomyces thermotolerans.
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Affiliation(s)
- M A McHenney
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285
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Hahn DR, Solenberg PJ, McHenney MA, Baltz RH. Transposition and transduction of plasmid DNA inStreptomyces spp. ACTA ACUST UNITED AC 1991; 7:229-34. [PMID: 1369329 DOI: 10.1007/bf01577649] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
To expand the application of molecular genetics to many different streptomycete species, we have been developing two potentially widely applicable methodologies: transposon mutagenesis and plasmid transduction. We constructed three transposons from the Streptomyces lividans insertion sequence IS493. Tn5096 and Tn5097 contain an apramycin resistance gene inserted in different orientations between the two open reading frames of IS493. These transposons transpose from different plasmids into many different sites in the Streptomyces griseofuscus chromosome and into its resident linear plasmids. Tn5099 contains a promoterless xylE gene and a hygromycin-resistance gene inserted in IS493 close to one end. Tn5099 transposes in S. griseofuscus giving operon fusions in some cases that drive expression of the xylE gene product, catechol deoxygenase, giving yellow colonies in the presence of catechol. We have also developed plasmid vectors that can be transduced into many streptomycete species by bacteriophage FP43. We describe the characterization of FP43 and mapping of several bacteriophage functions. The region of cloned FP43 DNA essential for plasmid transduction includes the origin for headful packaging.
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Affiliation(s)
- D R Hahn
- Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, IN 46285
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Solenberg PJ, Baltz RH. Transposition of Tn5096 and other IS493 derivatives in Streptomyces griseofuscus. J Bacteriol 1991; 173:1096-104. [PMID: 1846854 PMCID: PMC207229 DOI: 10.1128/jb.173.3.1096-1104.1991] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Tn5096 was constructed by inserting an apramycin resistance gene, aac(3)IV, into IS493 from Streptomyces lividans. By using conventional and pulsed-field gel electrophoresis, Tn5096 and related transposons were shown to insert into many different locations in the Streptomyces griseofuscus chromosome and in two linear plasmids. On insertion into the target site CANTg, 3 bp appeared to be duplicated. Independent transpositions were obtained by delivery of the transposon from a temperature-sensitive plasmid. The frequency of auxotrophy among cultures containing transpositions was about 0.2%.
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Affiliation(s)
- P J Solenberg
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285
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Rodicio MR, Alvarez MA, Chater KF. Isolation and genetic structure of IS112, an insertion sequence responsible for the inactivation of the SalI restriction-modification system of Streptomyces albus G. MOLECULAR & GENERAL GENETICS : MGG 1991; 225:142-7. [PMID: 1847988 DOI: 10.1007/bf00282652] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
IS112 is a transposable element identified in Streptomyces albus G by its frequent mutagenic insertion into the genes for the SalI restriction-modification system. IS112 is present in several copies in the genome of S. albus G. Homologous sequences were detected in other Streptomyces strains. Sequence analysis revealed that IS112 has a length of 883 bp with a GC content of 67.4%. The copy that was isolated contained imperfect inverted repeats (16/20 match) at its ends and was flanked by a 2 bp duplication at the target site, which was located within the gene (salIR) for the SalI endonuclease. A long open reading frame (ORF) encoding a putative polypeptide of 256-253 amino acids spans almost the entire sequence. Significant homology was detected between this polypeptide and that corresponding to ORFB of IS493, an insertion sequence recently isolated from Streptomyces lividans 66.
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Kieser T, Hopwood DA. Genetic manipulation of Streptomyces: integrating vectors and gene replacement. Methods Enzymol 1991; 204:430-58. [PMID: 1943784 DOI: 10.1016/0076-6879(91)04023-h] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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New nucleotide sequence data on the EMBL File Server. Nucleic Acids Res 1989; 17:9511-24. [PMID: 2587282 PMCID: PMC335188 DOI: 10.1093/nar/17.22.9511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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