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Sood U, Müller M, Lan T, Garg G, Singhvi N, Hira P, Singh P, Nigam A, Verma M, Lata P, Kaur H, Kumar A, Rawat CD, Lal S, Aldrich C, Bechthold A, Lal R. Amycolatopsis mediterranei: A Sixty-Year Journey from Strain Isolation to Unlocking Its Potential of Rifamycin Analogue Production by Combinatorial Biosynthesis. JOURNAL OF NATURAL PRODUCTS 2024; 87:424-438. [PMID: 38289177 DOI: 10.1021/acs.jnatprod.3c00686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Ever since the isolation of Amycolatopsis mediterranei in 1957, this strain has been the focus of research worldwide. In the last 60 years or more, our understanding of the taxonomy, development of cloning vectors and conjugation system, physiology, genetics, genomics, and biosynthetic pathway of rifamycin B production in A. mediterranei has substantially increased. In particular, the development of cloning vectors, transformation system, characterization of the rifamycin biosynthetic gene cluster, and the regulation of rifamycin B production by the pioneering work of Heinz Floss have made the rifamycin polyketide biosynthetic gene cluster (PKS) an attractive target for extensive genetic manipulations to produce rifamycin B analogues which could be effective against multi-drug-resistant tuberculosis. Additionally, a better understanding of the regulation of rifamycin B production and the application of newer genomics tools, including CRISPR-assisted genome editing systems, might prove useful to overcome the limitations associated with low production of rifamycin analogues.
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Affiliation(s)
- Utkarsh Sood
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi-110007, India
| | - Moritz Müller
- Institute of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universität, Stefan-Meier-Straße 19, 79104, Freiburg, Germany
| | - Tian Lan
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Gauri Garg
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi-110007, India
| | - Nirjara Singhvi
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, Uttarakhand 248007, India
| | - Princy Hira
- Department of Zoology, Maitreyi College, University of Delhi, Delhi-110003, India
| | - Priya Singh
- Department of Zoology, Maitreyi College, University of Delhi, Delhi-110003, India
| | - Aeshna Nigam
- Department of Zoology, Shivaji College, University of Delhi, Delhi-110027, India
| | - Mansi Verma
- Department of Zoology, Hansraj College, University of Delhi, Delhi-110007, India
| | - Pushp Lata
- Department of Zoology, University of Delhi, Delhi-110007, India
| | - Hardeep Kaur
- Department of Zoology, Ramjas College, University of Delhi, Delhi-110007, India
| | - Abhilash Kumar
- Department of Zoology, Ramjas College, University of Delhi, Delhi-110007, India
| | - Charu Dogra Rawat
- Department of Zoology, Ramjas College, University of Delhi, Delhi-110007, India
| | - Sukanya Lal
- PhiXGen Private Limited, Gurugram, Haryana-122001, India
| | - Courtney Aldrich
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Andreas Bechthold
- Institute of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universität, Stefan-Meier-Straße 19, 79104, Freiburg, Germany
| | - Rup Lal
- PhiXGen Private Limited, Gurugram, Haryana-122001, India
- Acharya Narendra Dev College, University of Delhi, Delhi-110019, India
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Goldfinger V, Spohn M, Rodler JP, Sigle M, Kulik A, Cryle MJ, Rapp J, Link H, Wohlleben W, Stegmann E. Metabolic engineering of the shikimate pathway in Amycolatopsis strains for optimized glycopeptide antibiotic production. Metab Eng 2023; 78:84-92. [PMID: 37244369 DOI: 10.1016/j.ymben.2023.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 05/17/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
Glycopeptide antibiotics (GPA) consist of a glycosylated heptapeptide backbone enriched in aromatic residues originating from the shikimate pathway. Since the enzymatic reactions within the shikimate pathway are highly feedback-regulated, this raises the question as to how GPA producers control the delivery of precursors for GPA assembly. We chose Amycolatopsis balhimycina, the producer of balhimycin, as a model strain for analyzing the key enzymes of the shikimate pathway. A. balhimycina contains two copies each of the key enzymes of the shikimate pathway, deoxy-d-arabino-heptulosonate-7-phosphate synthase (Dahp) and prephenate dehydrogenase (Pdh), with one pair (Dahpsec and Pdhsec) encoded within the balhimycin biosynthetic gene cluster and one pair (Dahpprim and Pdhprim) in the core genome. While overexpression of the dahpsec gene resulted in a significant (>4-fold) increase in balhimycin yield, no positive effects were observed after overexpression of the pdhprim or pdhsec genes. Investigation of allosteric enzyme inhibition revealed that cross-regulation between the tyrosine and phenylalanine pathways plays an important role. Tyrosine, a key precursor of GPAs, was found to be a putative activator of prephenate dehydratase (Pdt), which catalyzes the first step reaction from prephenate to phenylalanine in the shikimate pathway. Surprisingly, overexpression of pdt in A. balhimycina led to an increase in antibiotic production in this modified strain. In order to demonstrate that this metabolic engineering approach is generally applicable to GPA producers, we subsequently applied this strategy to Amycolatopsis japonicum and improved the production of ristomycin A, which is used in diagnosis of genetic disorders. Comparison of "cluster-specific" enzymes with the isoenzymes from the primary metabolism's pathway provided insights into the adaptive mechanisms used by producers to ensure adequate precursor supply and GPA yields. These insights further demonstrate the importance of a holistic approach in bioengineering efforts that takes into account not only peptide assembly but also adequate precursor supply.
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Affiliation(s)
- Valentina Goldfinger
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Marius Spohn
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Jens-Peter Rodler
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbial Bioactive Compounds, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Melanie Sigle
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Andreas Kulik
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbial Bioactive Compounds, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia; EMBL Australia, Monash University, Clayton, VIC, 3800, Australia; ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, VIC, 3800, Australia
| | - Johanna Rapp
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Bacterial Metabolomics, University of Tübingen, Auf der Morgenstelle 25, 72076, Tübingen, Germany
| | - Hannes Link
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Bacterial Metabolomics, University of Tübingen, Auf der Morgenstelle 25, 72076, Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Cluster of Excellence CMFI, Bacterial Metabolomics University of Tübingen, Auf der Morgenstelle 25, 72076, Tübingen, Germany
| | - Wolfgang Wohlleben
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbial Bioactive Compounds, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany.
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Marker-Free Genome Engineering in Amycolatopsis Using the pSAM2 Site-Specific Recombination System. Microorganisms 2022; 10:microorganisms10040828. [PMID: 35456877 PMCID: PMC9033027 DOI: 10.3390/microorganisms10040828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/07/2022] [Accepted: 04/13/2022] [Indexed: 02/01/2023] Open
Abstract
Actinobacteria of the genus Amycolatopsis are important for antibiotic production and other valuable biotechnological applications such as bioconversion or bioremediation. Despite their importance, tools and methods for their genetic manipulation are less developed than in other actinobacteria such as Streptomyces. We report here the use of the pSAM2 site-specific recombination system to delete antibiotic resistance cassettes used in gene replacement experiments or to create large genomic deletions. For this purpose, we constructed a shuttle vector, replicating in Escherichia coli and Amycolatopsis, expressing the integrase and the excisionase from the Streptomyces integrative and conjugative element pSAM2. These proteins are sufficient for site-specific recombination between the attachment sites attL and attR. We also constructed two plasmids, replicative in E. coli but not in Amycolatopsis, for the integration of the attL and attR sites on each side of a large region targeted for deletion. We exemplified the use of these tools in Amycolatopsis mediterranei by obtaining with high efficiency a marker-free deletion of one single gene in the rifamycin biosynthetic gene cluster or of the entire 90-kb cluster. These robust and simple tools enrich the toolbox for genome engineering in Amycolatopsis.
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Edenhart S, Denneler M, Spohn M, Doskocil E, Kavšček M, Amon T, Kosec G, Smole J, Bardl B, Biermann M, Roth M, Wohlleben W, Stegmann E. Metabolic engineering of Amycolatopsis japonicum for optimized production of [S,S]-EDDS, a biodegradable chelator. Metab Eng 2020; 60:148-156. [PMID: 32302770 DOI: 10.1016/j.ymben.2020.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/23/2020] [Accepted: 04/06/2020] [Indexed: 11/16/2022]
Abstract
The actinomycete Amycolatopsis japonicum is the producer of the chelating compound [S,S]-ethylenediamine-disuccinc acid (EDDS). [S,S]-EDDS is an isomer of ethylenediamine-tetraacetic acid (EDTA), an economically important chelating compound that suffers from an extremely poor degradability. Frequent use of the persistent EDTA in various industrial and domestic applications has caused an accumulation of EDTA in soil as well as in aqueous environments. As a consequence, EDTA is the highest concentrated anthropogenic compound present in water reservoirs. The [S,S]-form of EDDS has chelating properties similar to EDTA, however, in contrast to EDTA it is readily biodegradable. In order to compete with the cost-effective chemical synthesis of EDTA, we aimed to optimize the biotechnological production of [S,S]-EDDS in A. japonicum by using metabolic engineering approaches. Firstly, we integrated several copies of the [S,S]-EDDS biosynthetic genes into the chromosome of A. japonicum and replaced the native zinc responsive promoter with the strong synthetic constitutive promoter SP44*. Secondly, we increased the supply of O-phospho-serine, the direct precursor of [S,S]-EDDS. The combination of these approaches together with the optimized fermentation process led to a significant improvement in [S,S]-EDDS up to 9.8 g/L with a production rate of 4.3 mg/h/g DCW.
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Affiliation(s)
- Simone Edenhart
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen, Microbiology/Biotechnology, University of Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - Marius Denneler
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen, Microbiology/Biotechnology, University of Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - Marius Spohn
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen, Microbiology/Biotechnology, University of Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - Eva Doskocil
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen, Microbiology/Biotechnology, University of Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - Martin Kavšček
- Acies Bio d.o.o., Tehnoloski Park 21, 1000, Ljubljana, Slovenia
| | - Tadeja Amon
- Acies Bio d.o.o., Tehnoloski Park 21, 1000, Ljubljana, Slovenia
| | - Gregor Kosec
- Acies Bio d.o.o., Tehnoloski Park 21, 1000, Ljubljana, Slovenia
| | - Jernej Smole
- Acies Bio d.o.o., Tehnoloski Park 21, 1000, Ljubljana, Slovenia
| | - Bettina Bardl
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Bio Pilot Plant, Beutenbergstr. 11A, 07745, Jena, Germany
| | - Michael Biermann
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Bio Pilot Plant, Beutenbergstr. 11A, 07745, Jena, Germany
| | - Martin Roth
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Bio Pilot Plant, Beutenbergstr. 11A, 07745, Jena, Germany
| | - Wolfgang Wohlleben
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen, Microbiology/Biotechnology, University of Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen, Microbiology/Biotechnology, University of Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Germany.
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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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Gao H, Murugesan B, Hoßbach J, Evans SK, Stark WM, Smith MCM. Integrating vectors for genetic studies in the rare Actinomycete Amycolatopsis marina. BMC Biotechnol 2019; 19:32. [PMID: 31164159 PMCID: PMC6549336 DOI: 10.1186/s12896-019-0521-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 04/30/2019] [Indexed: 11/15/2022] Open
Abstract
Background Few natural product pathways from rare Actinomycetes have been studied due to the difficulty in applying molecular approaches in these genetically intractable organisms. In this study, we sought to identify more integrating vectors, using phage int/attP loci, that would efficiently integrate site-specifically in the rare Actinomycete, Amycolatopsis marina DSM45569. Results Analysis of the genome of A. marina DSM45569 indicated the presence of attB-like sequences for TG1 and R4 integrases. The TG1 and R4 attBs were active in in vitro recombination assays with their cognate purified integrases and attP loci. Integrating vectors containing either the TG1 or R4 int/attP loci yielded exconjugants in conjugation assays from Escherichia coli to A. marina DSM45569. Site-specific recombination of the plasmids into the host TG1 or R4 attB sites was confirmed by sequencing. Conclusions The homologous TG1 and R4 attB sites within the genus Amycolatopsis have been identified. The results indicate that vectors based on TG1 and R4 integrases could be widely applicable in this genus.
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Affiliation(s)
- Hong Gao
- Department of Biology, University of York, York, North Yorkshire, YO10 5DD, UK. .,Present address: School of Science, Engineering & Design, Teesside University, Middlesbrough, TS1 3BX, UK.
| | - Buvani Murugesan
- Department of Biology, University of York, York, North Yorkshire, YO10 5DD, UK
| | - Janina Hoßbach
- Department of Biology, University of York, York, North Yorkshire, YO10 5DD, UK
| | - Stephanie K Evans
- Department of Biology, University of York, York, North Yorkshire, YO10 5DD, UK
| | - W Marshall Stark
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Margaret C M Smith
- Department of Biology, University of York, York, North Yorkshire, YO10 5DD, UK
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Schwarz PN, Roller L, Kulik A, Wohlleben W, Stegmann E. Engineering metabolic pathways in Amycolatopsis japonicum for the optimization of the precursor supply for heterologous brasilicardin congeners production. Synth Syst Biotechnol 2018; 3:56-63. [PMID: 29911199 PMCID: PMC5884276 DOI: 10.1016/j.synbio.2017.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/06/2017] [Accepted: 12/22/2017] [Indexed: 02/08/2023] Open
Abstract
The isoprenoid brasilicardin A is a promising immunosuppressant compound with a unique mode of action, high potency and reduced toxicity compared to today's standard drugs. However, production of brasilicardin has been hampered since the producer strain Nocardia terpenica IFM0406 synthesizes brasilicardin in only low amounts and is a biosafety level 2 organism. Previously, we were able to heterologously express the brasilicardin gene cluster in the nocardioform actinomycete Amycolatopsis japonicum. Four brasilicardin congeners, intermediates of the BraA biosynthesis, were produced. Since chemical synthesis of the brasilicardin core structure has remained elusive we intended to produce high amounts of the brasilicardin backbone for semi synthesis and derivatization. Therefore, we used a metabolic engineering approach to increase heterologous production of brasilicardin in A. japonicum. Simultaneous heterologous expression of genes encoding the MVA pathway and expression of diterpenoid specific prenyltransferases were used to increase the provision of the isoprenoid precursor isopentenyl diphosphate (IPP) and to channel the precursor into the direction of diterpenoid biosynthesis. Both approaches contributed to an elevated heterologous production of the brasilicardin backbone, which can now be used as a starting point for semi synthesis of new brasilicardin congeners with better properties.
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Key Words
- 3HBA, 3-hydroxy-benzoate
- Aact, acetoacetyl CoA thiolase
- BraA, brasilicardin A
- BraB, brasilicardin B
- BraC, brasilicardin C
- BraC-agl, brasilicardin C aglycon
- BraD, brasilicardin D
- BraD-agl, brasilicardin D aglycon
- DMAPP, dimethylallyl diphosphate
- FPP, farnesyl diphosphate
- Fpps, farnesyl diphosphate synthase
- GGPP, geranylgeranyl diphosphate
- GPP, geranyl diphosphate
- Ggpps, geranylgeranyl diphosphate synthase
- GlcNAc, N-acetylglucosamine
- Gpps, geranyl diphosphate synthase
- IPP, isopentenyl diphosphate
- Idi, isopentenyl diphosphate synthase
- Isoprenoids
- MEP, Methylerythritol 4-phosphate
- MVA, mevalonate
- Mevalonate pathway
- Norcardia terpenica IFM0406
- Prenyltransferases
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Affiliation(s)
- Paul N Schwarz
- Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Eberhard Karls University Tübingen, Tübingen, Germany
| | - Luisa Roller
- Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Eberhard Karls University Tübingen, Tübingen, Germany
| | - Andreas Kulik
- Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Eberhard Karls University Tübingen, Tübingen, Germany
| | - Wolfgang Wohlleben
- Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Eberhard Karls University Tübingen, Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Evi Stegmann
- Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Eberhard Karls University Tübingen, Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
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Schwarz PN, Buchmann A, Roller L, Kulik A, Gross H, Wohlleben W, Stegmann E. The Immunosuppressant Brasilicardin: Determination of the Biosynthetic Gene Cluster in the Heterologous HostAmycolatopsis japonicum. Biotechnol J 2017; 13. [DOI: 10.1002/biot.201700527] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/05/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Paul N. Schwarz
- Microbiology/Biotechnology; Interfaculty Institute of Microbiology and Infection Medicine (IMIT); Eberhard Karls University of Tübingen; Tübingen Germany
| | - Anina Buchmann
- Department of Pharmaceutical Biology; Pharmaceutical Institute; Eberhard Karls University of Tübingen; Tübingen Germany
| | - Luisa Roller
- Microbiology/Biotechnology; Interfaculty Institute of Microbiology and Infection Medicine (IMIT); Eberhard Karls University of Tübingen; Tübingen Germany
| | - Andreas Kulik
- Microbiology/Biotechnology; Interfaculty Institute of Microbiology and Infection Medicine (IMIT); Eberhard Karls University of Tübingen; Tübingen Germany
| | - Harald Gross
- Department of Pharmaceutical Biology; Pharmaceutical Institute; Eberhard Karls University of Tübingen; Tübingen Germany
- German Centre for Infection Research (DZIF); Partner Site Tübingen; Tübingen Germany
| | - Wolfgang Wohlleben
- Microbiology/Biotechnology; Interfaculty Institute of Microbiology and Infection Medicine (IMIT); Eberhard Karls University of Tübingen; Tübingen Germany
- German Centre for Infection Research (DZIF); Partner Site Tübingen; Tübingen Germany
| | - Evi Stegmann
- Microbiology/Biotechnology; Interfaculty Institute of Microbiology and Infection Medicine (IMIT); Eberhard Karls University of Tübingen; Tübingen Germany
- German Centre for Infection Research (DZIF); Partner Site Tübingen; Tübingen Germany
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Lei X, Zhang C, Jiang Z, Li X, Shi Y, Liu M, Xie Y, Wang L, Hong B. Complete genome sequence of Amycolatopsis orientalis CPCC200066, the producer of norvancomycin. J Biotechnol 2017; 247:6-10. [PMID: 28216102 DOI: 10.1016/j.jbiotec.2017.02.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 02/13/2017] [Accepted: 02/13/2017] [Indexed: 10/20/2022]
Abstract
Amycolatopsis orientalis CPCC200066 is an actinomycete exploited commercially in China for the production of norvancomycin, an important glycopeptide antibiotic structurally close to the well-known vancomycin. The availability of the complete genome sequence of CPCC200066 would greatly strengthen our understanding of the regulation pattern of norvancomycin biosynthesis and ultimately improve its production, as well as potentiate discoveries of novel bioactive compounds. Here we report the complete genome sequence of A. orientalis CPCC200066, a circular chromosome consisting of 9,490,992bp. Forty putative secondary metabolite biosynthetic gene clusters, including norvancomycin, were predicted, covering 20.3% of the whole genome. To facilitate genetic manipulation of this strain, an efficient transformation system was established by constructing a novel integrative vector pIMBT1, which could be transferred into CPCC200066 by electroporation with high efficiency. ΦBT1 attB sites were also identified in other known Amycolatopsis genomes, indicating pIMBT1's prospect to be a novel vector for genus Amycolatopsis.
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Affiliation(s)
- Xuan Lei
- Key Laboratory of Biotechnology of Antibiotics, The National Health and Family Planning Commission (NHFPC), Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Cong Zhang
- Key Laboratory of Biotechnology of Antibiotics, The National Health and Family Planning Commission (NHFPC), Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Zhibo Jiang
- Key Laboratory of Biotechnology of Antibiotics, The National Health and Family Planning Commission (NHFPC), Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xingxing Li
- Key Laboratory of Biotechnology of Antibiotics, The National Health and Family Planning Commission (NHFPC), Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yuanyuan Shi
- Key Laboratory of Biotechnology of Antibiotics, The National Health and Family Planning Commission (NHFPC), Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ming Liu
- Immunology Program Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yunying Xie
- Key Laboratory of Biotechnology of Antibiotics, The National Health and Family Planning Commission (NHFPC), Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Lifei Wang
- Key Laboratory of Biotechnology of Antibiotics, The National Health and Family Planning Commission (NHFPC), Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Bin Hong
- Key Laboratory of Biotechnology of Antibiotics, The National Health and Family Planning Commission (NHFPC), Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
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An Efficient Method To Generate Gene Deletion Mutants of the Rapamycin-Producing Bacterium Streptomyces iranensis HM 35. Appl Environ Microbiol 2016; 82:3481-3492. [PMID: 27037115 DOI: 10.1128/aem.00371-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 03/28/2016] [Indexed: 01/22/2023] Open
Abstract
UNLABELLED Streptomyces iranensis HM 35 is an alternative rapamycin producer to Streptomyces rapamycinicus Targeted genetic modification of rapamycin-producing actinomycetes is a powerful tool for the directed production of rapamycin derivatives, and it has also revealed some key features of the molecular biology of rapamycin formation in S. rapamycinicus. The approach depends upon efficient conjugational plasmid transfer from Escherichia coli to Streptomyces, and the failure of this step has frustrated its application to Streptomyces iranensis HM 35. Here, by systematically optimizing the process of conjugational plasmid transfer, including screening of various media, and by defining optimal temperatures and concentrations of antibiotics and Ca(2+) ions in the conjugation media, we have achieved exconjugant formation for each of a series of gene deletions in S. iranensis HM 35. Among them were rapK, which generates the starter unit for rapamycin biosynthesis, and hutF, encoding a histidine catabolizing enzyme. The protocol that we have developed may allow efficient generation of targeted gene knockout mutants of Streptomyces species that are genetically difficult to manipulate. IMPORTANCE The developed protocol of conjugational plasmid transfer from Escherichia coli to Streptomyces iranensis may allow efficient generation of targeted gene knockout mutants of other genetically difficult to manipulate, but valuable, Streptomyces species.
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11
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Spohn M, Wohlleben W, Stegmann E. Elucidation of the zinc-dependent regulation inAmycolatopsis japonicumenabled the identification of the ethylenediamine-disuccinate ([S,S]-EDDS) genes. Environ Microbiol 2016; 18:1249-63. [DOI: 10.1111/1462-2920.13159] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/13/2015] [Accepted: 11/27/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Marius Spohn
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen, Microbiology/Biotechnology; University of Tuebingen; 72076 Tuebingen Germany
| | - Wolfgang Wohlleben
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen, Microbiology/Biotechnology; University of Tuebingen; 72076 Tuebingen Germany
- Partner Site Tuebingen; German Centre for Infection Research (DZIF); Tuebingen Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen, Microbiology/Biotechnology; University of Tuebingen; 72076 Tuebingen Germany
- Partner Site Tuebingen; German Centre for Infection Research (DZIF); Tuebingen Germany
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12
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Allard N, Garneau D, Poulin-Laprade D, Burrus V, Brzezinski R, Roy S. A diaminopimelic acid auxotrophic Escherichia coli donor provides improved counterselection following intergeneric conjugation with actinomycetes. Can J Microbiol 2015; 61:565-74. [PMID: 26166710 DOI: 10.1139/cjm-2015-0041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Considering the medical, biotechnological, and economical importance of actinobacteria, there is a continuous need to improve the tools for genetic engineering of a broad range of these microorganisms. Intergeneric conjugation has proven to be a valuable yet imperfect tool for this purpose. The natural resistance of many actinomycetes to nalidixic acid (Nal) is generally exploited to eliminate the sensitive Escherichia coli donor strain following conjugation. Nevertheless, Nal can delay growth and have other unexpected effects on the recipient strain. To provide an improved alternative to antibiotics, we propose a postconjugational counterselection using a diaminopimelic acid (DAP) auxotrophic donor strain. The DAP-negative phenotype was obtained by introducing a dapA deletion into the popular methylase-negative donor strain E. coli ET12567/pUZ8002. The viability of ET12567 and its ΔdapA mutant exposed to DAP deprivation or Nal selection were compared in liquid pure culture and after mating with Streptomyces coelicolor. Results showed that death of the E. coli ΔdapA Nal-sensitive donor strain occurred more efficiently when subjected to DAP deprivation than when exposed to Nal. Our study shows that postconjugational counterselection based on DAP deprivation circumvents the use of antibiotics and will facilitate the transfer of plasmids into actinomycetes with high biotechnological potential, yet currently not accessible to conjugative techniques.
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Affiliation(s)
- Nancy Allard
- Centre d'étude et de valorisation de la diversité microbienne (CEVDM), Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500, boulevard de l'Université, Sherbrooke, QC J1K 2R1, Canada.,Centre d'étude et de valorisation de la diversité microbienne (CEVDM), Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500, boulevard de l'Université, Sherbrooke, QC J1K 2R1, Canada
| | - Daniel Garneau
- Centre d'étude et de valorisation de la diversité microbienne (CEVDM), Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500, boulevard de l'Université, Sherbrooke, QC J1K 2R1, Canada.,Centre d'étude et de valorisation de la diversité microbienne (CEVDM), Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500, boulevard de l'Université, Sherbrooke, QC J1K 2R1, Canada
| | - Dominic Poulin-Laprade
- Centre d'étude et de valorisation de la diversité microbienne (CEVDM), Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500, boulevard de l'Université, Sherbrooke, QC J1K 2R1, Canada.,Centre d'étude et de valorisation de la diversité microbienne (CEVDM), Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500, boulevard de l'Université, Sherbrooke, QC J1K 2R1, Canada
| | - Vincent Burrus
- Centre d'étude et de valorisation de la diversité microbienne (CEVDM), Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500, boulevard de l'Université, Sherbrooke, QC J1K 2R1, Canada.,Centre d'étude et de valorisation de la diversité microbienne (CEVDM), Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500, boulevard de l'Université, Sherbrooke, QC J1K 2R1, Canada
| | - Ryszard Brzezinski
- Centre d'étude et de valorisation de la diversité microbienne (CEVDM), Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500, boulevard de l'Université, Sherbrooke, QC J1K 2R1, Canada.,Centre d'étude et de valorisation de la diversité microbienne (CEVDM), Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500, boulevard de l'Université, Sherbrooke, QC J1K 2R1, Canada
| | - Sébastien Roy
- Centre d'étude et de valorisation de la diversité microbienne (CEVDM), Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500, boulevard de l'Université, Sherbrooke, QC J1K 2R1, Canada.,Centre d'étude et de valorisation de la diversité microbienne (CEVDM), Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500, boulevard de l'Université, Sherbrooke, QC J1K 2R1, Canada
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13
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Stegmann E, Albersmeier A, Spohn M, Gert H, Weber T, Wohlleben W, Kalinowski J, Rückert C. Complete genome sequence of the actinobacterium Amycolatopsis japonica MG417-CF17T (=DSM 44213T) producing (S,S)-N,N′-ethylenediaminedisuccinic acid. J Biotechnol 2014; 189:46-7. [DOI: 10.1016/j.jbiotec.2014.08.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 08/25/2014] [Indexed: 10/24/2022]
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14
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Overproduction of Ristomycin A by activation of a silent gene cluster in Amycolatopsis japonicum MG417-CF17. Antimicrob Agents Chemother 2014; 58:6185-96. [PMID: 25114137 DOI: 10.1128/aac.03512-14] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The emergence of antibiotic-resistant pathogenic bacteria within the last decades is one reason for the urgent need for new antibacterial agents. A strategy to discover new anti-infective compounds is the evaluation of the genetic capacity of secondary metabolite producers and the activation of cryptic gene clusters (genome mining). One genus known for its potential to synthesize medically important products is Amycolatopsis. However, Amycolatopsis japonicum does not produce an antibiotic under standard laboratory conditions. In contrast to most Amycolatopsis strains, A. japonicum is genetically tractable with different methods. In order to activate a possible silent glycopeptide cluster, we introduced a gene encoding the transcriptional activator of balhimycin biosynthesis, the bbr gene from Amycolatopsis balhimycina (bbrAba), into A. japonicum. This resulted in the production of an antibiotically active compound. Following whole-genome sequencing of A. japonicum, 29 cryptic gene clusters were identified by genome mining. One of these gene clusters is a putative glycopeptide biosynthesis gene cluster. Using bioinformatic tools, ristomycin (syn. ristocetin), a type III glycopeptide, which has antibacterial activity and which is used for the diagnosis of von Willebrand disease and Bernard-Soulier syndrome, was deduced as a possible product of the gene cluster. Chemical analyses by high-performance liquid chromatography and mass spectrometry (HPLC-MS), tandem mass spectrometry (MS/MS), and nuclear magnetic resonance (NMR) spectroscopy confirmed the in silico prediction that the recombinant A. japonicum/pRM4-bbrAba synthesizes ristomycin A.
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15
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Optimization of transconjugation and characterization of attB integration site for Streptomyces cinnamoneus producing transglutaminase. Biologia (Bratisl) 2014. [DOI: 10.2478/s11756-014-0408-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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16
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Sioud S, Karray-Rebai I, Aouissaoui H, Aigle B, Bejar S, Mellouli L. Targeted Gene Disruption of the Cyclo (L-Phe, L-Pro) Biosynthetic Pathway in Streptomyces sp. US24 Strain. J Biomed Biotechnol 2012; 2007:91409. [PMID: 17710112 PMCID: PMC1940057 DOI: 10.1155/2007/91409] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Accepted: 03/30/2007] [Indexed: 12/05/2022] Open
Abstract
We have previously isolated a new actinomycete strain from Tunisian soil called Streptomyces sp. US24, and have shown that it produces two bioactive molecules including a Cyclo (L-Phe, L-Pro) diketopiperazine (DKP). To identify the structural genes responsible for the synthesis of this DKP derivative, a PCR amplification (696 bp) was carried out using the Streptomyces sp. US24 genomic DNA as template and two degenerate oligonucleotides designed by analogy with genes encoding peptide synthetases (NRPS). The detection of DKP derivative biosynthetic pathway of the Streptomyces sp. US24 strain was then achieved by gene disruption via homologous recombination using a suicide vector derived from the conjugative plasmid pSET152 and containing the PCR product. Chromatography analysis, biological tests and spectroscopic studies of supernatant cultures of the wild-type Streptomyces sp. US24 strain and three mutants obtained by this gene targeting disruption approach showed that the amplified DNA fragment is required for Cyclo (L-Phe, L-Pro) biosynthesis in Streptomyces sp. US24 strain. This DKP derivative seems to be produced either directly via a nonribosomal pathway or as a side product in the course of nonribosomal synthesis of a longer peptide.
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Affiliation(s)
- Samiha Sioud
- Laboratory of Prokaryotic Enzymes and Metabolites, Centre of Biotechnology of Sfax, Road of Sidi Mansour Km 6, P.O. Box K, 3038 Sfax, Tunisia
| | - Ines Karray-Rebai
- Laboratory of Prokaryotic Enzymes and Metabolites, Centre of Biotechnology of Sfax, Road of Sidi Mansour Km 6, P.O. Box K, 3038 Sfax, Tunisia
| | - Hedi Aouissaoui
- Laboratory of Prokaryotic Enzymes and Metabolites, Centre of Biotechnology of Sfax, Road of Sidi Mansour Km 6, P.O. Box K, 3038 Sfax, Tunisia
| | - Bertrand Aigle
- Laboratory of Genetics and Microbiology, UMR/INRA 1128, IFR 110, Faculty of Sciences and Techniques, University Henri Poincaré, 54506 Vandoeuvre-lès-Nancy, France
| | - Samir Bejar
- Laboratory of Prokaryotic Enzymes and Metabolites, Centre of Biotechnology of Sfax, Road of Sidi Mansour Km 6, P.O. Box K, 3038 Sfax, Tunisia
| | - Lotfi Mellouli
- Laboratory of Prokaryotic Enzymes and Metabolites, Centre of Biotechnology of Sfax, Road of Sidi Mansour Km 6, P.O. Box K, 3038 Sfax, Tunisia
- *Lotfi Mellouli:
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17
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Chauhan G, Pant KK, Nigam KDP. Extraction of Nickel from Spent Catalyst Using Biodegradable Chelating Agent EDDS. Ind Eng Chem Res 2012. [DOI: 10.1021/ie300580v] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Garima Chauhan
- Department of Chemical Engineering, Indian Institute of Technology, Delhi −110016, India
| | - Kamal K. Pant
- Department of Chemical Engineering, Indian Institute of Technology, Delhi −110016, India
| | - Krishna D. P. Nigam
- Department of Chemical Engineering, Indian Institute of Technology, Delhi −110016, India
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18
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Baltz RH. Streptomyces temperate bacteriophage integration systems for stable genetic engineering of actinomycetes (and other organisms). ACTA ACUST UNITED AC 2012; 39:661-72. [DOI: 10.1007/s10295-011-1069-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 11/23/2011] [Indexed: 12/21/2022]
Abstract
Abstract
ϕC31, ϕBT1, R4, and TG1 are temperate bacteriophages with broad host specificity for species of the genus Streptomyces. They form lysogens by integrating site-specifically into diverse attB sites located within individual structural genes that map to the conserved core region of streptomycete linear chromosomes. The target genes containing the ϕC31, ϕBT1, R4, and TG1 attB sites encode a pirin-like protein, an integral membrane protein, an acyl-CoA synthetase, and an aminotransferase, respectively. These genes are highly conserved within the genus Streptomyces, and somewhat conserved within other actinomycetes. In each case, integration is mediated by a large serine recombinase that catalyzes unidirectional recombination between the bacteriophage attP and chromosomal attB sites. The unidirectional nature of the integration mechanism has been exploited in genetic engineering to produce stable recombinants of streptomycetes, other actinomycetes, eucaryotes, and archaea. The ϕC31 attachment/integration (Att/Int) system has been the most widely used, and it has been coupled with the ϕBT1 Att/Int system to facilitate combinatorial biosynthesis of novel lipopeptide antibiotics in Streptomyces fradiae.
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Affiliation(s)
- Richard H Baltz
- CognoGen Biotechnology Consulting 6438 North Olney Street 46220 Indianapolis IN USA
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19
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Cai Z, Chen Q, Wang H, He Y, Wang W, Zhao X, Ye Q. Degradation of the novel herbicide ZJ0273 by Amycolatopsis sp. M3-1 isolated from soil. Appl Microbiol Biotechnol 2012; 96:1371-9. [PMID: 22249724 DOI: 10.1007/s00253-011-3867-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Revised: 12/19/2011] [Accepted: 12/22/2011] [Indexed: 11/30/2022]
Abstract
ZJ0273, propyl 4-(2-(4,6-dimethoxypyrimidin-2-yloxy) benzylamino) benzoate, is a novel and broad-spectrum herbicide. In this study, 15 bacteria capable of utilizing ZJ0273 as the sole carbon source were isolated from soil. One of the isolates belonged to the family Amycolatopsis and was designated to Amycolatopsis sp. M3-1; at 30°C and pH 7.0, degradation rate of ZJ0273 could reach at 59.3% and 68.5% in 25 days and 60 days, respectively. Furthermore, six metabolites (M1-M6) during the degradation of ZJ0273 by Amycolatopsis sp. M3-1 were identified by a combination with multi-position (14)C-labeled compounds (B-ZJ0273 and C-ZJ0273), chromatography, liquid scintillation spectrometer, and LC-MS, a novel pathway of ZJ0273 degradation by Amycolatopsis sp. M3-1 was proposed based on the identified metabolites and their biodegradation courses. ZJ0273 was initially hydrolyzed into M1 (4-(2-(4,6-dimethoxypyrimidin-2-yloxy) benzylamino) benzoic acid), then further oxidized into M3 (2-(4,6-dimethoxypyrimidin-2-yloxy) benzoic acid). M1 also could undergo a carbonylation into M2 (4-(2-(4,6-dimethoxypyrimidin-2-yloxy) benzamido) benzoic acid), and then its C-N and C-O bonds were cleaved to yield M3 (2-(4,6-dimethoxypyrimidin-2-yloxy) benzoic acid) and M4 (4,6-dimethoxypyrimidin-2-ol), respectively. Moreover, another two new metabolites, M5 (2-(4-hydroxy, 6-methoxypyrimidin-2-yloxy) benzoic acid) and M6 (2, 4-dihydroxy-pyrimidine) were found. M5 was formed through de-methyl of M3 and then hydrolyzed into M6.
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Affiliation(s)
- Zhiqiang Cai
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of the Ministry of Agriculture, Zhejiang University, Hangzhou, 310029, China.
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Marcone GL, Foulston L, Binda E, Marinelli F, Bibb M, Beltrametti F. Methods for the genetic manipulation of Nonomuraea sp. ATCC 39727. J Ind Microbiol Biotechnol 2010; 37:1097-103. [DOI: 10.1007/s10295-010-0807-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 08/04/2010] [Indexed: 10/19/2022]
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21
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Marcone GL, Carrano L, Marinelli F, Beltrametti F. Protoplast preparation and reversion to the normal filamentous growth in antibiotic-producing uncommon actinomycetes. J Antibiot (Tokyo) 2010; 63:83-8. [PMID: 20057514 DOI: 10.1038/ja.2009.127] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protoplast preparation, regeneration and fusion represent essential tools for those poorly studied biotechnologically valuable microorganisms inapplicable with the current molecular biology protocols. The protoplast production and regeneration method developed for Planobispora rosea and using the combination of hen egg-white lysozyme (HEWL) and Streptomyces globisporus mutanolysin was applied to a set of antibiotic-producing filamentous actinomycetes belonging to the Streptosporangiaceae, Micromonosporaceae and Streptomycetaceae. 10(7)-10(9) protoplasts were obtained from 100 ml of culture, after incubation times in the digestion solution ranging from a few hours to 1 or 2 days depending on the strain. The efficiency of protoplast reversion to the normal filamentous growth varied from 0.1 to nearly 50%. Analysis of cell wall peptidoglycan in three representative strains (Nonomuraea sp. ATCC 39727, Actinoplanes teichomyceticus ATCC 31121 and Streptomyces coelicolor A3(2)) has evidenced structural variations in the glycan strand and in the peptide chain, which may account for the different response to cell digestion and protoplast regeneration treatments.
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Integrative gene cloning and expression system for Streptomyces sp. US 24 and Streptomyces sp. TN 58 bioactive molecule producing strains. J Biomed Biotechnol 2009; 2009:464986. [PMID: 19547659 PMCID: PMC2699437 DOI: 10.1155/2009/464986] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 03/26/2009] [Indexed: 11/17/2022] Open
Abstract
Streptomyces sp. US 24 and Streptomyces sp. TN 58, two strains producing interesting bioactive molecules, were successfully transformed using E. coli ET12567 (pUZ8002), as a conjugal donor, carrying the integrative plasmid pSET152. For the Streptomyces sp. US 24 strain, two copies of this plasmid were tandemly integrated in the chromosome, whereas for Streptomyces sp. TN 58, the integration was in single copy at the attB site. Plasmid pSET152 was inherited every time for all analysed Streptomyces sp. US 24 and Streptomyces sp. TN 58 exconjugants under nonselective conditions. The growth, morphological differentiation, and active molecules production of all studied pSET152 integrated exconjugants were identical to those of wild type strains. Consequently, conjugal transfer using pSET152 integration system is a suitable means of genes transfer and expression for both studied strains. To validate the above gene transfer system, the glucose isomerase gene (xylA) from Streptomyces sp. SK was expressed in strain Streptomyces sp. TN 58. Obtained results indicated that heterologous glucose isomerase could be expressed and folded effectively. Glucose isomerase activity of the constructed TN 58 recombinant strain is of about eighteenfold higher than that of the Streptomyces sp. SK strain. Such results are certainly of importance due to the potential use of improved strains in biotechnological process for the production of high-fructose syrup from starch.
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Malhotra S, Majumdar S, Kumar M, Bhasin VK, Gartemann KH, Lal R. Nucleotide sequence of plasmid pA387 ofAmycolatopsis benzoatilytica and construction of a conjugative shuttle vector. J Basic Microbiol 2008; 48:177-85. [DOI: 10.1002/jobm.200700326] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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24
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Application of conjugation using ϕC31 att/int system for Actinoplanes teichomyceticus, a producer of teicoplanin. Biotechnol Lett 2008; 30:1233-8. [DOI: 10.1007/s10529-008-9671-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Revised: 02/09/2008] [Accepted: 02/12/2008] [Indexed: 11/25/2022]
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Functional analysis of a BarX homologue (SngA) as a pleiotropic regulator in Streptomyces natalensis. Arch Microbiol 2008; 189:569-77. [DOI: 10.1007/s00203-008-0349-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2007] [Revised: 12/22/2007] [Accepted: 01/04/2008] [Indexed: 11/29/2022]
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Identification by gene deletion analysis of barS2, a gene involved in the biosynthesis of gamma-butyrolactone autoregulator in Streptomyces virginiae. Arch Microbiol 2007; 189:367-74. [PMID: 18034227 DOI: 10.1007/s00203-007-0327-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2007] [Revised: 07/26/2007] [Accepted: 11/06/2007] [Indexed: 10/22/2022]
Abstract
Virginiae butanolide (VB) is a member of the gamma-butyrolactone autoregulators and triggers the production of streptogramin antibiotics virginiamycin M1 and S in Streptomyces virginiae. A VB biosynthetic gene (barS2) was localized in a 10-kb regulatory island which controls the virginiamycin biosynthesis/resistance of S. virginiae, and analyzed by gene disruption/complementation. The barS2 gene is flanked by barS1, another VB biosynthetic gene catalyzing stereospecific reduction of an A-factor-type precursor into a VB-type compound, and barX encoding a pleiotropic regulator for virginiamycin biosynthesis. The deduced product of barS2 possessed moderate similarity to a putative dehydrogenase of Streptomyces venezuelae, encoded by jadW2 located in similar gene arrangement to that in the regulatory island of S. virginiae. A barS2-disruptant (strain IC152), created by means of homologous recombination, showed no differences in growth in liquid medium or morphology on solid medium compared to a wild-type strain, suggesting that BarS2 does not play any role in primary metabolism or morphological differentiation of S. virginiae. In contrast, no initiation of virginiamycin production or VB production was detected with the strain IC152 until 18 h of cultivation, at which time full production of virginiamycin occurs in the wild-type strain. The delayed virginiamycin production of the strain IC152 was fully restored to the level of the wild-type strain either by the exogenous addition of VB or by complementation of the intact barS2 gene, indicating that the lack of VB production at the initiation phase of virginiamycin production is the sole reason for the defect of virginiamycin production, and the barS2 gene is of primary importance for VB biosynthesis in S. virginiae.
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Kim MK, Ha HS, Choi SU. Conjugal transfer using the bacteriophage ϕC31 att/int system and properties of the attB site in Streptomyces ambofaciens. Biotechnol Lett 2007; 30:695-9. [DOI: 10.1007/s10529-007-9586-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2007] [Revised: 10/22/2007] [Accepted: 10/24/2007] [Indexed: 11/29/2022]
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Beltrametti F, Barucco D, Rossi R, Selva E, Marinelli F. Protoplast Fusion and Gene Recombination in the Uncommon Actinomycete Planobispora rosea Producing GE2270. J Antibiot (Tokyo) 2007; 60:447-54. [PMID: 17721003 DOI: 10.1038/ja.2007.57] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An efficient method for protoplast generation for the uncommon actinomycete Planobispora rosea, the producer of the thiazolylpeptide antibiotic GE2270, was developed using a combination of hen egg white lysozyme and Streptomyces globisporus mutanolysin. This method converted more than 70% of vegetative mycelium to protoplasts, which were then regenerated with 50% efficiency in an optimized medium. When P. rosea protoplasts were efficiently fused, recombination between different antibiotic (streptomycin and gentamicin) resistance markers originated sensitive strains (str(s)gen(s)) at frequencies as high as 18% and double resistant fusants (str(r)gen(r)) at frequencies as high as 29%. Double resistant fusants showed GE2270 productivity intermediate between the productivity of the parental strains. Protoplast generation and fusion in P. rosea makes whole genome shuffling feasible as an approach to be used alternately with classical random mutagenesis in industrial strain improvement programs.
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Malhotra S, Lal R. The genus Amycolatopsis: Indigenous plasmids, cloning vectors and gene transfer systems. Indian J Microbiol 2007; 47:3-14. [PMID: 23100633 DOI: 10.1007/s12088-007-0003-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Revised: 01/27/2007] [Accepted: 01/31/2007] [Indexed: 11/30/2022] Open
Abstract
The genus Amycolatopsis is a member of the phylogenetic group nocardioform actinomycetes. Most of the members of the genus Amycolatopsis are known to produce antibiotics. Additionally, members of this genus have been reported to metabolize aromatic compounds as the sole sources of carbon and energy. Development of genetic manipulation in Amycolatopsis has progressed slowly due to paucity of genetic tools and methods. The occurrence of indigenous plasmids in different species of Amycolatopsis is not very common. Till date, only three indigenous plasmids viz., pMEA100, pMEA300 and pA387 have been reported in Amycolatopsis species. Various vectors based on the indigenous plasmids, pMEA100, pMEA300 and pA387, have been constructed. These vectors have proved useful for molecular genetics studies of actinomycetes. Molecular genetic work with Amycolatopsis strains is not easy, since transformation methods have to be developed, or at least optimized, for each particular strain. Nonetheless, methods for efficient transformation (polyethyleneglycol (PEG) induced protoplast transformation, transformation by electroporation and direct transformation) have been developed and used successfully for the introduction of DNA into several Amycolatopsis species. The construction of plasmid cloning vectors and the development of gene transfer systems has opened up possibilities for studying the molecular genetics of these bacteria.
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Affiliation(s)
- S Malhotra
- Department of Zoology, University of Delhi, Delhi, 110 007 India
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Lee KM, Lee CK, Choi SU, Park HR, Kitani S, Nihira T, Hwang YI. Cloning and in vivo functional analysis by disruption of a gene encoding the gamma-butyrolactone autoregulator receptor from Streptomyces natalensis. Arch Microbiol 2005; 184:249-57. [PMID: 16228193 DOI: 10.1007/s00203-005-0047-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Revised: 09/15/2005] [Accepted: 09/19/2005] [Indexed: 11/24/2022]
Abstract
A gene encoding a gamma-butyrolactone autoregulator receptor, which has a common activity as DNA-binding transcriptional repressors controlling secondary metabolism and/or morphological differentiation in Streptomyces, was cloned from a natamycin producer, Streptomyces natalensis. PCR using the primers designed for the two highly conserved regions of Streptomyces autoregulator receptors (BarA, FarA, ScbR, and ArpA) gave a 102-bp band. The sequence of this band had a high similarity to the expected region of a receptor gene. By genomic Southern hybridization with the 102-bp insert as a probe, a 687-bp intact receptor gene (sngR) was obtained from S. natalensis. To clarify the in vivo function of sngR, a sngR-disrupted strain was constructed, and the phenotypes were compared with those of the wild-type strain. The sngR-disruptants started natamycin production 6 h earlier and showed a 4.6-fold higher production of natamycin than the wild-type strain. In addition, the sporulation began earlier and the number of spores was tenfold more abundant than that of the wild-type strain. All the phenotypes were restored back to the original phenotypes of the wild-type strain by complementation with the intact sngR, indicating that the autoregulator receptor protein of S. natalensis acts as a primary negative regulator both on the biosynthesis of natamycin and sporulation.
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Affiliation(s)
- Kang-Mu Lee
- Department of Food Science and Biotechnology, Division of Life Science, Kyungnam University, 449 Wolyong-Dong, Masan 631-701, Republic of Korea
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Blaesing F, Mühlenweg A, Vierling S, Ziegelin G, Pelzer S, Lanka E. Introduction of DNA into Actinomycetes by bacterial conjugation from E. coli—An evaluation of various transfer systems. J Biotechnol 2005; 120:146-61. [PMID: 16095742 DOI: 10.1016/j.jbiotec.2005.06.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2005] [Revised: 05/19/2005] [Accepted: 06/10/2005] [Indexed: 11/17/2022]
Abstract
Gene transfer is a basic requirement for optimizing bioactive natural substances produced by an increasing number of industrially used microorganisms. We have analyzed quantitatively horizontal gene transfer from Escherichia coli to Actinomycetes. The efficiencies of DNA transfer of four different systems were compared that consist of conjugative and mobilizable plasmids with a broad-host range. Three novel binary vector set-ups were constructed based on: (i) the IncQ group of mobilizable plasmids (RSF1010), (ii) IncQ-like pTF-FC2 and (iii) pSB102 that belongs to a new class of broad-host-range plasmids. The established system based on the IncPalpha group of conjugative plasmids served as the reference. For all plasmids constructed, we confirmed the functional integrity of the selected transfer machineries by intrageneric matings between E. coli strains. We demonstrate that the transfer systems introduced in this study are efficient in mediating gene transfer from E. coli to Actinomycetes and are possible alternatives for gene transfer into Actinomycetes for which the IncPalpha-based transfer system is not applicable. The use of plasmids that integrate into the recipients' chromosomes compared to that of plasmids replicating autonomously is shown to allow the access to a wider range of hosts.
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Affiliation(s)
- Franca Blaesing
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 63-73, D-14195 Berlin, Germany
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Choi SU, Lee CK, Hwang YI, Kinoshita H, Nihira T. Cloning and functional analysis by gene disruption of a gene encoding a gamma-butyrolactone autoregulator receptor from Kitasatospora setae. J Bacteriol 2004; 186:3423-30. [PMID: 15150228 PMCID: PMC415744 DOI: 10.1128/jb.186.11.3423-3430.2004] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gamma-butyrolactone autoregulator receptors of the genus Streptomyces have a common activity as DNA-binding transcriptional repressors, controlling secondary metabolism and/or morphological differentiation. A gene encoding a gamma-butyrolactone autoregulator receptor was cloned from a bafilomycin B1 producer, Kitasatospora setae, for the first time from a non-Streptomyces genus of actinomycetes, and its function was evaluated by in vitro and in vivo analyses. The gene fragment was initially cloned by PCR with primers designed from two highly conserved regions of Streptomyces autoregulator receptors (BarA, FarA, ScbR, and ArpA), followed by genomic Southern hybridization yielding a 7-kb BamHI fragment on which a 654-bp receptor gene (ksbA) was identified. The recombinant KsbA protein demonstrated clear binding activity toward 3H-labeled autoregulators, especially toward [3H]SCB1, confirming that ksbA encodes a real autoregulator receptor of K. setae. To clarify the in vivo function of ksbA, a ksbA-disrupted strain was constructed by means of homologous recombination after introducing a ksbA disruption construct via transconjugation from Escherichia coli. No difference in morphology was found between the wild-type strain and the ksbA disruptants. However, the ksbA disruptants started producing bafilomycin 18 h earlier than the wild-type strain and showed a 2.4-fold-higher accumulation of bafilomycin. The phenotype was restored to the original wild-type phenotype by complementation with intact ksbA, indicating that the autoregulator receptor protein of K. setae acts as a primary negative regulator of the biosynthesis of bafilomycin but plays no role in cytodifferentiation of K. setae. This indicates that, unlike the A-factor receptor of Streptomyces griseus, the autoregulator receptor (ksbA) of K. setae belongs to a family of autoregulator receptors which control secondary metabolism but play no role in morphological differentiation.
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Affiliation(s)
- Sun-Uk Choi
- International Center for Biotechnology, Osaka University, Suita, Osaka 565-0871, Japan
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Dhingra G, Kumari R, Bala S, Majumdar S, Malhotra S, Sharma P, Lal S, Cullum J, Lal R. Development of cloning vectors and transformation methods for Amycolatopsis. J Ind Microbiol Biotechnol 2003; 30:195-204. [PMID: 12687493 DOI: 10.1007/s10295-003-0040-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2002] [Accepted: 01/08/2003] [Indexed: 10/23/2022]
Abstract
The genus Amycolatopsis is of industrial importance, as its species are known to produce commercial antibiotics. It belongs to the family Pseudonocardiaceae and has an eventful taxonomic history. Initially strains were identified as Streptomyces, then later as Nocardia. However, based on biochemical, morphological and molecular features, the genus Amycolatopsis, containing seventeen species, was created. The development of molecular genetic techniques for this group has been slow. The scarcity of molecular genetic tools including stable plasmids, antibiotic resistance markers, transposons, reporter genes, cloning vectors, and high efficiency transformation protocols has made progress slow, but efforts in the past decade have led to the development of cloning vectors and transformation methods for these organisms. Some of the cloning vectors have broad host range (pRL series) whereas others have limited host range (pMEA300 and pMEA100). The cloning vector pMEA300 has been completely sequenced, while only the minimal replicon (pA- rep) has been sequenced from pRL plasmids. Direct transformation of mycelia and electroporation are the most widely applicable methods for transforming species of Amycolatopsis. Conjugational transfer from Escherichia coli has been reported only in the species A. japonicum, and gene disruption and replacements using homologous recombination are now possible in some strains.
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Affiliation(s)
- Gauri Dhingra
- Molecular Biology Laboratory, University of Delhi, Department of Zoology, Delhi 110007, India
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