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Danaeifar M, Mazlomi MA. Combinatorial biosynthesis: playing chess with the metabolism. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2023; 25:171-190. [PMID: 35435779 DOI: 10.1080/10286020.2022.2065265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
Secondary metabolites are a group of natural products that produced by bacteria, fungi and plants. Many applications of these compounds from medicine to industry have been discovered. However, some changes in their structure and biosynthesis mechanism are necessary for their properties to be more suitable and also for their production to be profitable. The main and most useful method to achieve this goal is combinatorial biosynthesis. This technique uses the multi-unit essence of the secondary metabolites biosynthetic enzymes to make changes in their order, structure and also the organism that produces them.
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Affiliation(s)
- Mohsen Danaeifar
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran 1416753955, Iran
| | - Mohammad Ali Mazlomi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran 1416753955, Iran
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Musiol-Kroll EM, Tocchetti A, Sosio M, Stegmann E. Challenges and advances in genetic manipulation of filamentous actinomycetes - the remarkable producers of specialized metabolites. Nat Prod Rep 2019; 36:1351-1369. [PMID: 31517370 DOI: 10.1039/c9np00029a] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: up to February 2019Actinomycetes are Gram positive bacteria of the phylum Actinobacteria. These organisms are one of the most important sources of structurally diverse, clinically used antibiotics and other valuable bioactive products, as well as biotechnologically relevant enzymes. Most strains were discovered by their ability to produce a given molecule and were often poorly characterized, physiologically and genetically. The development of genetic methods for Streptomyces and related filamentous actinomycetes has led to the successful manipulation of antibiotic biosynthesis to attain structural modification of microbial metabolites that would have been inaccessible by chemical means and improved production yields. Moreover, genome mining reveals that actinomycete genomes contain multiple biosynthetic gene clusters (BGCs), however only a few of them are expressed under standard laboratory conditions, leading to the production of the respective compound(s). Thus, to access and activate the so-called "silent" BGCs, to improve their biosynthetic potential and to discover novel natural products methodologies for genetic manipulation are required. Although different methods have been applied for many actinomycete strains, genetic engineering is still remaining very challenging for some "underexplored" and poorly characterized actinomycetes. This review summarizes the strategies developed to overcome the obstacles to genetic manipulation of actinomycetes and allowing thereby rational genetic engineering of this industrially relevant group of microorganisms. At the end of this review we give some tips to researchers with limited or no previous experience in genetic manipulation of actinomycetes. The article covers the most relevant literature published until February 2019.
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Affiliation(s)
- Ewa M Musiol-Kroll
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, Auf der Morgenstelle 28, Tübingen, 72076, Germany.
| | | | | | - Evi Stegmann
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, Auf der Morgenstelle 28, Tübingen, 72076, Germany.
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Baltz RH. Bacteriophage-resistant industrial fermentation strains: from the cradle to CRISPR/Cas9. ACTA ACUST UNITED AC 2018; 45:1003-1006. [DOI: 10.1007/s10295-018-2079-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/30/2018] [Indexed: 01/21/2023]
Abstract
Abstract
Bacteriophage contamination and cell lysis have been recurring issues with some actinomycetes used in the pharmaceutical fermentation industry since the commercialization of streptomycin in the 1940s. In the early years, spontaneous phage-resistant mutants or lysogens were isolated to address the problem. In some cases, multiple phages were isolated from different contaminated fermentors, so strains resistant to multiple phages were isolated to stabilize the fermentation processes. With the advent of recombinant DNA technology, the early scaleup of the Escherichia coli fermentation process for the production of human insulin A and B chains encountered contamination with multiple coliphages. A genetic engineering solution was to clone and express a potent restriction/modification system in the production strains. Very recently, an E. coli fermentation of 1,3-propanediol was contaminated by a coliphage related to T1. CRISPR/Cas9 technology was applied to block future contamination by targeting seven different phage genes for double-strand cleavage. These approaches employing spontaneous mutation, genetic engineering, and synthetic biology can be applied to many current and future microorganisms used in the biotechnology industry.
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Affiliation(s)
- Richard H Baltz
- Cognogen Biotechnology Consulting 7636 Andora Drive 34238 Sarasota FL USA
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Streptomyces and Saccharopolyspora hosts for heterologous expression of secondary metabolite gene clusters. J Ind Microbiol Biotechnol 2010; 37:759-72. [DOI: 10.1007/s10295-010-0730-9] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 04/22/2010] [Indexed: 10/19/2022]
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Min Y, Lv H, Zheng Y. Fusion PCR-targeted tylCV gene deletion of Streptomyces fradiae for producing desmycosin, the direct precursor of tilmicosin. Process Biochem 2007. [DOI: 10.1016/j.procbio.2006.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Mo HB, Chen XY, Liu Y, Xia F, Yang KQ. Development of a multifunctional and efficient conjugal plasmid for use in Streptomyces spp. Appl Microbiol Biotechnol 2006; 70:705-10. [PMID: 16532313 DOI: 10.1007/s00253-006-0324-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2005] [Revised: 12/31/2005] [Accepted: 01/03/2006] [Indexed: 11/30/2022]
Abstract
A plasmid, pGB112, has recently been developed to transfer DNA from Escherichia coli to Streptomyces spp via conjugation. This technique made use of (A) E. coli replicon, (B) ampicillin (amp) resistance gene for selection in E. coli and thiostrepton (tsr) resistance gene for selection in Streptomyces, (C) a fragment of SCP2* replicon, (D) a 2.6 kb fragment of tra-cassette which consists of pIJ101 transfer gene (tra) and two ermE promoters, (E) a 0.8 kb fragment of oriT of (IncP) RK2. The results showed that this plasmid was able to transfer plasmid DNA from E. coli to Streptomyces coelicolor via conjugation, and that it could also transfer DNA between Streptomyces strains. Since this plasmid has both pBR322 and SCP2* replicons, it may provide a novel and useful method for genetic operation in E. coli and Streptomyces.
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Affiliation(s)
- H B Mo
- Center of Biochemistry and Molecular Biology [corrected] College of Medical Sciences, Jinan University [corrected] Guangzhou, 510632, People's Republic of China.
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Apichaisataienchote B, Altenbuchner J, Buchenauer H. Isolation and identification of Streptomyces fradiae SU-1 from Thailand and protoplast transformation with the chitinase B Gene from Nocardiopsis prasina OPC-131. Curr Microbiol 2005; 51:116-21. [PMID: 16010517 DOI: 10.1007/s00284-005-4402-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2004] [Accepted: 03/12/2005] [Indexed: 11/26/2022]
Abstract
Thirty-two strains of actinomycetes obtained from soil samples of Thailand were selected. Actinomycete strain SU-1 is the most effective in terms of antagonism of Fusarium moniliforme. It produces antifungal substances on agar medium against F. moniliforme. On the basis of microscopical observations of its morphology and biochemical tests as well as analysis of cell wall and fatty acid pattern, this strain was identified as Streptomyces fradiae. The chitinase gene B (chiB337) from Nocardiopsis prasina OPC-131 was inserted into an integrating plasmid pFIS318, an Escherichia coli-Streptomyces shuttle vector. The new plasmid pFIS319-1 carrying the chitinase gene was used to transform protoplasts of S. fradiae strain SU-1. The obtained recombinant strain SU-1 pFIS319-1 exhibited higher chitinase activity than the wild-type in chitinase induction medium. Chitinase activity after renaturing protein from SDS-PAGE was detected rapidly by using 4-methylumbelliferyl beta-D: -N,N''-diacetylchitobioside as the substrate. S. fradiae SU-1 secreted two chitinases with estimated molecular masses of 26 kDa and 43 kDa whereas the recombinant strain secreted three chitinases of about 26 kDa, 31.5 kDa (ChiB), and 43 kDa. The supernatant of the recombinant strain grown in chitinase induction medium inhibited the hyphal extension of F. moniliforme.
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Affiliation(s)
- Busaya Apichaisataienchote
- Department of Plant Pathology (Tropical Agriculture International Program), Kasetsart University, Khampang Sean, Nakhon Pathom, 73140, Thailand
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Lyutzkanova D, Stoilova-Disheva M, Peltekova V. The restriction-modification system in Streptomyces flavopersicus. Folia Microbiol (Praha) 2001; 46:119-22. [PMID: 11501397 DOI: 10.1007/bf02873588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To clone bifunctional vectors in streptomycetes, it was necessary to define the restriction-modification system of Streptomyces flavopersicus. Plasmid DNA from bifunctional vectors pIJ699 and pXED3-13, isolated from E. coli strains with different methylation systems: E. coli DH5 alpha (dam+ dcm+), E. coli MB5386 (dam dcm), E. coli CB51 (dam dcm+), E. coli NM544 (dam+ dcm), was used for transformation of protoplasts from strain S. flavopersicus. Restriction of dcm-methylated DNA from S. flavopersicus was established. As a host in the intermediate cloning strain E. coli NM544 (dam+ dcm) should be used, as the dcm-transmethylase-dependent strain S. flavopersicus does not process DNA from this strain.
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Affiliation(s)
- D Lyutzkanova
- Institute of Microbiology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
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Tuteja D, Dua M, Khanna R, Dhingra N, Khanna M, Kaur H, Saxena DM, Lal R. The importance of homologous recombination in the generation of large deletions in hybrid plasmids in Amycolatopsis mediterranei. Plasmid 2000; 43:1-11. [PMID: 10610815 DOI: 10.1006/plas.1999.1426] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The cloning vector pRL60 was developed previously as a tool for genetic manipulations in Amycolatopsis mediterranei, which produces the commercially and medicinally important antibiotic rifamycin. Here, a method based on intraplasmid recombinations is described for the construction of smaller plasmids in A. mediterranei, which also helped in delimiting the origin of replication (pA-rep) of the parent plasmid. The strategy involved the cloning of a selectable marker, erythromycin resistance gene (ermE), onto plasmids pULAM2 and pULVK2A (derivatives of pRL1), followed by selection of the hybrid or concatemeric plasmids pRL50 and pRL80 (with large homologous repeats) in Escherichia coli GM2163. These hybrid plasmids were then transferred to A. mediterranei DSM 40773 by electroporation, with selection in the presence of different antibiotics. During the process of transformation and selection in A. mediterranei, pRL50 and pRL80 underwent intraplasmid recombinations, yielding derivatives that retained a common region essential for maintenance and replication, as well as the selected resistance genes. This approach produced several smaller plasmids designated pRL51, pRL52, pRL53, pRL60, pRL81, and pRL82. These plasmids, isolated from A. mediterranei DSM 40773, could be transferred to different Amycolatopsis strains at transformation efficiencies ranging from 0.7 x 10(2) to 4 x 10(4) transformants/microg DNA. The electroporation parameters under which maximum transformation efficiencies were obtained varied from strain to strain. Since the isolation of plasmid DNA from Amycolatopsis strains were extremely difficult, a convenient and rapid method of direct transfer of plasmid DNA, i.e., electroduction, was also developed in which the above-described shuttle plasmids were transferred directly from A. mediterranei to E. coli. In addition, the sequence of the minimal (pA-rep, approximately 1.0 kb) of plasmid pRL51 was determined. The nucleotide base sequence of the pA-rep region did not have any clear similarity to the DNA or amino acid sequences in various databases, suggesting that it is unique.
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Affiliation(s)
- D Tuteja
- Department of Zoology, University of Delhi, Delhi-, 110007, India
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Butler AR, Bate N, Cundliffe E. Impact of thioesterase activity on tylosin biosynthesis in Streptomyces fradiae. CHEMISTRY & BIOLOGY 1999; 6:287-92. [PMID: 10322123 DOI: 10.1016/s1074-5521(99)80074-x] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND The polyketide lactone, tylactone, is produced in Streptomyces fradiae by the TylG complex of five multifunctional proteins. As with other type I polyketide synthases, the enzyme catalysing the final elongation step (TylGV) possesses an integral thioesterase domain that is believed to be responsible for chain termination and ring closure to form tylactone, which is then glycosylated to yield tylosin. In common with other macrolide producers, S. fradiae also possesses an additional thioesterase gene (orf5) located within the cluster of antibiotic biosynthetic genes. The function of the Orf5 protein is addressed here. RESULTS Disruption of orf5 reduced antibiotic accumulation in S. fradiae by at least 85%. Under such circumstances, the strain accumulated desmycosin (demycarosyl-tylosin) due to a downstream polar effect on the expression of orf6, which encodes a mycarose biosynthetic enzyme. High levels of desmycosin production were restored in the disrupted strain by complementation with intact orf5, or with the corresponding thioesterase gene, nbmB, from S. narbonensis, but not with DNA encoding the integral thioesterase domain of TylGV. CONCLUSIONS Polyketide metabolism in S. fradiae is strongly dependent on the thioesterase activity encoded by orf5 (tylO). It is proposed that the TylG complex might operate with a significant error frequency and be prone to blockage with aberrant polyketides. A putative editing activity associated with TylO might be essential to unblock the polyketide synthase complex and thereby promote antibiotic accumulation.
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Affiliation(s)
- A R Butler
- Department of Biochemistry University of Leicester Leicester, LE1 7RH, UK
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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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Vrijbloed JW, van Hylckama Vlieg J, van der Put NM, Hessels GI, Dijkhuizen L. Molecular cloning with a pMEA300-derived shuttle vector and characterization of the Amycolatopsis methanolica prephenate dehydratase gene. J Bacteriol 1995; 177:6666-9. [PMID: 7592448 PMCID: PMC177523 DOI: 10.1128/jb.177.22.6666-6669.1995] [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: 01/26/2023] Open
Abstract
An efficient restriction barrier for methylated DNA in the actinomycete Amycolatopsis methanolica could be avoided by using a nonmethylating Escherichia coli strain for DNA isolations. The A. methanolica prephenate dehydratase gene was cloned from a gene bank in a pMEA300-derived shuttle vector in E. coli and characterized.
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Affiliation(s)
- J W Vrijbloed
- Department of Microbiology, University of Groningen, Haren, The Netherlands
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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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Holmalahti J, Raatikainen O, Wright A. Transformable mutants of a biopesticide strainStreptomyces griseoviridis K61. J Ind Microbiol Biotechnol 1993. [DOI: 10.1007/bf01583722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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MacNeil T, Gewain KM, MacNeil DJ. Deletion analysis of the avermectin biosynthetic genes of Streptomyces avermitilis by gene cluster displacement. J Bacteriol 1993; 175:2552-63. [PMID: 8478321 PMCID: PMC204556 DOI: 10.1128/jb.175.9.2552-2563.1993] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Streptomyces avermitilis produces a group of glycosylated, methylated macrocyclic lactones, the avermectins, which have potent anthelmintic activity. A homologous recombination strategy termed gene cluster displacement was used to construct Neor deletion strains with defined endpoints and to clone the corresponding complementary DNA encoding functions for avermectin biosynthesis (avr). Thirty-five unique deletions of 0.5 to > 100 kb over a continuous 150-kb region were introduced into S. avermitilis. Analysis of the avermectin phenotypes of the deletion-containing strains defined the extent and ends of the 95-kb avr gene cluster, identified a regulatory region, and mapped several avr functions. A 60-kb region in the central portion determines the synthesis of the macrolide ring. A 13-kb region at one end of the cluster is responsible for synthesis and attachment of oleandrose disaccharide. A 10-kb region at the other end has functions for positive regulation and C-5 O methylation. Physical analysis of the deletions and of in vivo-cloned fragments refined a 130-kb physical map of the avr gene cluster region.
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Affiliation(s)
- T MacNeil
- Department of Microbial Chemotherapeutics and Molecular Genetics, Merck Research Laboratories, Rahway, New Jersey 07065
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Palomeque-Messia P, Quittre V, Leyh-Bouille M, Nguyen-Distèche M, Gershater CJ, Dacey IK, Dusart J, Van Beeumen J, Ghuysen JM. Secretion by overexpression and purification of the water-soluble Streptomyces K15 DD-transpeptidase/penicillin-binding protein. Biochem J 1992; 288 ( Pt 1):87-91. [PMID: 1445284 PMCID: PMC1132083 DOI: 10.1042/bj2880087] [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: 12/27/2022]
Abstract
Though synthesized with a cleavable signal peptide and devoid of membrane anchors, the 262-amino-acid-residue Streptomyces K15 DD-transpeptidase/penicillin-binding protein is membrane-bound. Overexpression in Streptomyces lividans resulted in the export of an appreciable amount of the synthesized protein (4 mg/litre of culture supernatant). The water-soluble enzyme was purified close to protein homogeneity with a yield of 75%. It requires the presence of 0.5 M-NaCl to remain soluble. It is indistinguishable from the detergent-extract wild-type enzyme with respect to molecular mass, thermostability, transpeptidase activity and penicillin-binding capacity.
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Bierman M, Logan R, O'Brien K, Seno ET, Rao RN, Schoner BE. Plasmid cloning vectors for the conjugal transfer of DNA from Escherichia coli to Streptomyces spp. Gene 1992; 116:43-9. [PMID: 1628843 DOI: 10.1016/0378-1119(92)90627-2] [Citation(s) in RCA: 1146] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have constructed cloning vectors for the conjugal transfer of DNA from Escherichia coli to Streptomyces spp. All vectors contain the 760-bp oriT fragment from the IncP plasmid, RK2. Transfer functions need to be supplied in trans by the E. coli donor strain. We have incorporated into these vectors selectable antibiotic-resistance markers (AmR, ThR, SpR) that function in Streptomyces spp. and other features that should allow for: (i) integration via homologous recombination between cloned DNA and the Streptomyces spp. chromosome, (ii) autonomous replication, or (iii) site-specific integration at the bacteriophage phi C31 attachment site. Shuttle cosmids for constructing genomic libraries and bacteriophage P1 cloning vector capable of accepting approx. 100-kb fragments are also described. A simple mating procedure has been developed for the conjugal transfer of these vectors from E. coli to Streptomyces spp. that involves plating of the donor strain and either germinated spores or mycelial fragments of the recipient strain. We have shown that several of these vectors can be introduced into Streptomyces fradiae, a strain that is notoriously difficult to transform by PEG-mediated protoplast transformation.
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Affiliation(s)
- M Bierman
- Lilly Research Laboratories, A Division of Eli Lilly and Company, Indianapolis, IN 46285-0424
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18
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Efficient transformation ofMicromonospora melanosporea protoplasts byStreptomyces plasmid. Curr Microbiol 1991. [DOI: 10.1007/bf02104137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Hussain HA, Ritchie DA. High frequency transformation of Streptomyces niveus protoplasts by plasmid DNA. THE JOURNAL OF APPLIED BACTERIOLOGY 1991; 71:422-7. [PMID: 1761435 DOI: 10.1111/j.1365-2672.1991.tb03811.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A procedure has been developed for transforming protoplasts of the novobiocin producing strain Streptomyces niveus at high frequency. This required the isolation of strains LH13 and LH20 defective in DNA restriction from the wild type (ATCC 19793) which is transformed at very low frequencies. The LH13 and LH20 derivatives were obtained by curing pIJ702 DNA from the few S. niveus transformed protoplasts obtained by transformation of the wild type with high concentrations of pIJ702 DNA. Protoplasts of S. niveus strains LH13 and LH20 produced about 10(6) transformants/micrograms DNA with modified pIJ702 DNA derived by replication in S. niveus. Unmodified DNA (derived from replication in S: lividans) from a series of pIJ101, SCP2 and pSN2-based derivatives, gave transformation frequencies in the range of 10(2)-10(3) transformants/micrograms DNA. Optimal conditions for the formation and transformation of S. niveus protoplasts are described.
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Affiliation(s)
- H A Hussain
- Department of Genetics and Microbiology, University of Liverpool, UK
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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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Posno M, Leer RJ, van Luijk N, van Giezen MJF, Heuvelmans PTHM, Lokman BC, Pouwels PH. Incompatibility of
Lactobacillus
Vectors with Replicons Derived from Small Cryptic
Lactobacillus
Plasmids and Segregational Instability of the Introduced Vectors. Appl Environ Microbiol 1991; 57:1822-1828. [PMID: 16348515 PMCID: PMC183475 DOI: 10.1128/aem.57.6.1822-1828.1991] [Citation(s) in RCA: 146] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Three new
Lactobacillus
vectors based on cryptic
Lactobacillus
plasmids were constructed. The shuttle vector pLP3537 consists of a 2.3-kb plasmid from
Lactobacillus pentosus
MD353, an erythromycin resistance gene from
Staphylococcus aureus
plasmid pE194, and pUC19 as a replicon for
Escherichia coli
. The vectors pLPE317 and pLPE323, which do not contain
E. coli
sequences, were generated by introducing the erythromycin resistance gene of pE194 into a 1.7- and a 2.3-kb plasmid from
L. pentosus
MD353, respectively. These vectors and the shuttle vector pLP825 (M. Posno, R. J. Leer, J. M. M. van Rijn, B. C. Lokman, and P. H. Pouwels, p. 397-401,
in
A. T. Ganesan and J. A. Hoch, ed., Genetics and biotechnology of bacilli, vol. 2, 1988) could be introduced by electroporation into
Lactobacillus casei, L. pentosus, L. plantarum, L. acidophilus, L. fermentum
, and
L. brevis
strains with similar efficiencies. Transformation efficiencies were strain dependent and varied from 10
2
to 10
7
transformants per μg of DNA. Plasmid DNA analysis of
L. pentosus
MD353 transformants revealed that the introduction of pLP3537 or pLPE323 was invariably accompanied by loss of the endogenous 2.3-kb plasmid. Remarkably, pLPE317 could only be introduced into an
L. pentosus
MD353 strain that had been previously cured of its endogenous 1.7-kb plasmid. The curing phenomena are most likely to be explained by the incompatibility of the vectors and resident plasmids.
Lactobacillus
vectors are generally rapidly lost when cells are cultivated in the absence of selective pressure. However, pLPE323 is stable in three of four
Lactobacillus
strains tested so far.
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Affiliation(s)
- M Posno
- TNO Medical Biological Laboratory, P.O. Box 45, 2280 AA Rijswijk, The Netherlands
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22
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Abstract
FP43 is a temperate bacteriophage for Streptomyces griseofuscus that forms plaques on many Streptomyces species. FP43 virions contain 56 kb of double-strand DNA that is circularly permuted and terminally redundant, and contains 65% G + C. A physical map of the FP43 genome was constructed, and the origin for headful packaging (pac) was localized to an 8.8-kb region of the genome (hft) that mediates high-frequency transduction by FP43 of plasmid pRHB101. The phage attachment site (attP), a replication origin (rep), a region that inhibits plaque formation (pin), and a 3-kb deletion (rpt) that caused a 100-fold reduction in plasmid transduction were mapped.
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Affiliation(s)
- D R Hahn
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285
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23
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Hillemann D, Pühler A, Wohlleben W. Gene disruption and gene replacement in Streptomyces via single stranded DNA transformation of integration vectors. Nucleic Acids Res 1991; 19:727-31. [PMID: 2017360 PMCID: PMC333703 DOI: 10.1093/nar/19.4.727] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
For the isolation of single stranded plasmid DNA, various E. coli and E. coli-Streptomyces shuttle plasmids were equipped with the phage f1 replication origin. The transformation of some representative Streptomyces species with plasmid vectors occurred irrespective of whether single or double stranded DNA was used. In contrast, the transformation of Streptomyces was 10 to 100 times more efficient when an integration vector was in the single stranded form as opposed to the double stranded form. Streptomyces viridochromogenes was transformed by single stranded DNA integration vectors in order to replace the pat by the tsr gene and generate mutants unable to synthesize phosphinothricin-tripeptide (PTT).
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Affiliation(s)
- D Hillemann
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, FRG
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24
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Kuhstoss S, Richardson MA, Rao RN. Plasmid cloning vectors that integrate site-specifically in Streptomyces spp. Gene 1991; 97:143-6. [PMID: 1995427 DOI: 10.1016/0378-1119(91)90022-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cloning vectors based on the Streptomyces ambofaciens plasmid pSAM2 and the streptomycete phage phi C31 were developed for use in Streptomyces spp. These vectors replicate in Escherichia coli but integrate by site-specific recombination in Streptomyces spp. Both pSAM2-based and phi C31-based vectors transformed a number of different Streptomyces spp; however, the phi C31-based vectors consistently transformed at higher frequencies than pSAM2-based vectors. Southern analysis indicated that the phi C31-based vectors integrated at a unique site in the S. ambofaciens chromosome, while the pSAM2-based vectors gave complex patterns which could indicate structural instability or use of multiple loci. Both types of vectors utilize the apramycin (Am)-resistance gene which can be selected in E. coli and Streptomyces spp. with either Am or the commercially available antibiotic Geneticin (G418).
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Affiliation(s)
- S Kuhstoss
- Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, IN 46285
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25
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Muchová J, Lacová B, Godány A, Sevcíková B. Highly transformable mutants of Streptomyces aureofaciens containing restriction-modification systems. J Basic Microbiol 1991; 31:141-7. [PMID: 1652638 DOI: 10.1002/jobm.3620310213] [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: 12/28/2022]
Abstract
Streptomyces aureofaciens 13 is a mutant defective in chlortetracycline production. It was chosen as a potentially useful host for gene cloning in investigations of the organization of the biosynthetic genes for the tetracycline antibiotic pathway. From the Streptomyces aureofaciens 13 strain, three suitable clones were used for our work. The conditions for optimal formation and efficient transformation of protoplasts with plasmid DNAs have been determined. Transformation frequencies of about 10(4) to 10(5) per microgram of plasmid DNA were obtained when plasmids were isolated from Streptomyces strains. From the patterns of restriction enzyme digestion of plasmid DNA isolated from Streptomyces aureofaciens transformants, it was observed that the clones express modification systems which render plasmid DNAs resistant to cleavage by HindIII and EcoRI. Additionally, one of the clones produces the restriction endonuclease Sau13I (isoschizomer of SauI). The presence of the restriction-modification system of Sau13I does not reduce the efficiency of plasmid transformation.
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Affiliation(s)
- J Muchová
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Czechoslovakia
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26
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Richardson MA, Kuhstoss S, Huber ML, Ford L, Godfrey O, Turner JR, Rao RN. Cloning of spiramycin biosynthetic genes and their use in constructing Streptomyces ambofaciens mutants defective in spiramycin biosynthesis. J Bacteriol 1990; 172:3790-8. [PMID: 2193916 PMCID: PMC213357 DOI: 10.1128/jb.172.7.3790-3798.1990] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Several cosmid clones from Streptomyces ambofaciens containing the spiramycin resistance gene srmB were introduced into S. fradiae PM73, a mutant defective in tylosin synthesis, resulting in tylosin synthesis. The DNA responsible for this complementation was localized to a 10.5-kilobase EcoRI fragment. A 32-kilobase DNA segment which included the srmB spiramycin resistance gene and DNA which complemented the defect in strain PM73 were mutagenized in vivo with Tn10 carrying the gene for Nmr (which is expressed in Streptomyces spp.) or in vitro by insertional mutagenesis with a drug resistance gene (Nmr) cassette. When these mutagenized DNA segments were crossed into the S. ambofaciens chromosome, three mutant classes blocked in spiramycin synthesis were obtained. One mutant accumulated two precursors of spiramycin, platenolide I and platenolide II. Two mutants, when cofermented with the platenolide-accumulating mutant, produced spiramycin. Tylactone supplementation of these two mutants resulted in the synthesis of a group of compounds exhibiting antibiotic activity. Two other mutants failed to coferment with any of the other mutants or to respond to tylactone supplementation.
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Affiliation(s)
- M A Richardson
- Lilly Research Laboratories, Division of Eli Lilly and Company, Indianapolis, Indiana 46285
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27
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Matsushima P, McHenney MA, Baltz RH. Transduction and transformation of plasmid DNA in Streptomyces fradiae strains that express different levels of restriction. J Bacteriol 1989; 171:3080-4. [PMID: 2542216 PMCID: PMC210018 DOI: 10.1128/jb.171.6.3080-3084.1989] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We constructed nonrestricting strains of Streptomyces fradiae blocked in different steps in tylosin biosynthesis. Plasmid transformation frequencies were 10(3)- to 10(4)-fold higher and bacteriophage plating efficiencies were 10(4)- to 10(8)-fold higher in the nonrestricting strains than in the restricting strains. The efficiencies of transduction of plasmid pRHB101 in S. fradiae strains varied by over 1,000-fold, depending on growth conditions, and optimum transduction frequencies were obtained when cells were grown to mid-exponential phase at 39 degrees C. Under these conditions, restricting and nonrestricting strains were transduced at frequencies that differed by only two- to fivefold.
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Affiliation(s)
- P Matsushima
- Department of Molecular Genetics, Lilly Research Laboratories, Indianapolis, Indiana 46285
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28
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Matsushima P, Baltz RH. Streptomyces lipmanii expresses two restriction systems that inhibit plasmid transformation and bacteriophage plaque formation. J Bacteriol 1989; 171:3128-32. [PMID: 2722743 PMCID: PMC210025 DOI: 10.1128/jb.171.6.3128-3132.1989] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Bacteriophage host range studies suggested that several beta-lactam-producing streptomycetes express similar restriction-modification systems. Streptomyces lipmanii LE32 expressed two restriction-modification systems, designated SliI and SliII. A mutant strain, PM87, was defective only in SliI restriction but expressed both SliI and SliII modification. Streptomyces sp. strain A57986, a natural isolate partially deficient in the expression of SliI and SliII restriction, nevertheless modified bacteriophage DNA for both SliI and SliII specificities. Protoplasts of PM87 and A57986 were transformed by several plasmids, and the modified plasmids isolated from these strains transformed wild-type S. lipmanii efficiently.
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Affiliation(s)
- P Matsushima
- Department of Molecular Genetics, Lilly Research Laboratories, Indianapolis, Indiana 46285
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29
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MacNeil DJ. Characterization of a unique methyl-specific restriction system in Streptomyces avermitilis. J Bacteriol 1988; 170:5607-12. [PMID: 3056907 PMCID: PMC211658 DOI: 10.1128/jb.170.12.5607-5612.1988] [Citation(s) in RCA: 128] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Streptomyces avermitilis contains a unique restriction system that restricts plasmid DNA containing N6-methyladenine or 5-methylcytosine. Shuttle vectors isolated from Escherichia coli RR1 or plasmids isolated from modification-proficient Streptomyces spp. cannot be directly introduced into S. avermitilis. This restriction barrier can be overcome by first transferring plasmids into Streptomyces lividans or a modification-deficient E. coli strain and then into S. avermitilis. The transformation frequency was reduced greater than 1,000-fold when plasmid DNA was modified by dam or TaqI methylases to contain N6-methyladenine or by AluI, HhaI, HphI methylases to contain 5-methylcytosine. Methyl-specific restriction appears to be common in Streptomyces spp., since either N6-methyladenine-specific or 5-methylcytosine-specific restriction was observed in seven of nine strains tested.
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Affiliation(s)
- D J MacNeil
- Exploratory Microbiology and Genetics, Merck Sharp & Dohme Research Laboratories, Rahway, New Jersey 07065
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30
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Hutchinson CR. Prospects for the discovery of new (hybrid) antibiotics by genetic engineering of antibiotic-producing bacteria. Med Res Rev 1988; 8:557-67. [PMID: 3057300 DOI: 10.1002/med.2610080406] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- C R Hutchinson
- School of Pharmacy, Department of Bacteriology, University of Wisconsin, Madison 53706
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31
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McHenney MA, Baltz RH. Transduction of plasmid DNA in Streptomyces spp. and related genera by bacteriophage FP43. J Bacteriol 1988; 170:2276-82. [PMID: 3360743 PMCID: PMC211118 DOI: 10.1128/jb.170.5.2276-2282.1988] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A segment (hft) of bacteriophage FP43 DNA cloned into plasmid pIJ702 mediated high-frequency transduction of the resulting plasmid (pRHB101) by FP43 in Streptomyces griseofuscus. The transducing particles contained linear concatemers of plasmid DNA. Lysates of FP43 prepared on S. griseofuscus containing pRHB101 also transduced many other Streptomyces species, including several that restrict plaque formation by FP43 and at least two that produce restriction endonucleases that cut pRHB101 DNA. Transduction efficiencies in different species were influenced by the addition of anti-FP43 antiserum to the transduction plates, the temperature for cell growth before transduction, the multiplicity of infection, and the host on which the transducing lysate was prepared. FP43 lysates prepared on S. griseofuscus(pRHB101) also transduced species of Streptoverticillium, Chainia, and Saccharopolyspora.
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Affiliation(s)
- M A McHenney
- Department of Molecular Genetics, Lilly Research Laboratories, Indianapolis, Indiana 46285
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32
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Matsushima P, Baltz RH. recA gene of Escherichia coli complements defects in DNA repair and mutagenesis in Streptomyces fradiae JS6 (mcr-6). J Bacteriol 1987; 169:4834-6. [PMID: 3308856 PMCID: PMC213863 DOI: 10.1128/jb.169.10.4834-4836.1987] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Streptomyces fradiae JS6 (mcr-6) is a mutant which is defective in repair of DNA damage induced by a variety of chemical mutagens and UV light. JS6 is also defective in error-prone (mutagenic) DNA repair (J. Stonesifer and R. H. Baltz, Proc. Natl. Acad. Sci. USA 82:1180-1183, 1985). The recA gene of Escherichia coli, cloned in a bifunctional vector that replicates in E. coli and Streptomyces spp., complemented the mutation in S. fradiae JS6, indicating that E. coli and S. fradiae express similar SOS responses and that the mcr+ gene product of S. fradiae is functionally analogous to the protein encoded by the recA gene of E. coli.
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Affiliation(s)
- P Matsushima
- Department of Molecular Genetics, Eli Lilly and Company, Indianapolis, Indiana 46285
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33
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Hutchinson CR. The impact of genetic engineering on the commercial production of antibiotics by Streptomyces and related bacteria. Appl Biochem Biotechnol 1987; 16:169-90. [PMID: 3332755 DOI: 10.1007/bf02798365] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Developments in Streptomyces genetics that have laid a foundation for this field over the past ten years are reviewed and discussed to suggest how this knowledge might useful for improving the commercial production of antibiotics. This brief analysis predicts a bright future for the application of Streptomyces genetics in antibiotic production.
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Affiliation(s)
- C R Hutchinson
- School of Pharmacy, University of Wisconsin, Madison 53706
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