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Rebets Y, Tsolis KC, Guðmundsdóttir EE, Koepff J, Wawiernia B, Busche T, Bleidt A, Horbal L, Myronovskyi M, Ahmed Y, Wiechert W, Rückert C, Hamed MB, Bilyk B, Anné J, Friðjónsson Ó, Kalinowski J, Oldiges M, Economou A, Luzhetskyy A. Characterization of Sigma Factor Genes in Streptomyces lividans TK24 Using a Genomic Library-Based Approach for Multiple Gene Deletions. Front Microbiol 2018; 9:3033. [PMID: 30619125 PMCID: PMC6295645 DOI: 10.3389/fmicb.2018.03033] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/23/2018] [Indexed: 12/15/2022] Open
Abstract
Alternative sigma factors control numerous aspects of bacterial life, including adaptation to physiological stresses, morphological development, persistence states and virulence. This is especially true for the physiologically complex actinobacteria. Here we report the development of a robust gene deletions system for Streptomyces lividans TK24 based on a BAC library combined with the λ-Red recombination technique. The developed system was validated by systematically deleting the most highly expressed genes encoding alternative sigma factors and several other regulatory genes within the chromosome of S. lividans TK24. To demonstrate the possibility of large scale genomic manipulations, the major part of the undecylprodigiosin gene cluster was deleted as well. The resulting mutant strains were characterized in terms of morphology, growth parameters, secondary metabolites production and response to thiol-oxidation and cell-wall stresses. Deletion of SLIV_12645 gene encoding S. coelicolor SigR1 ortholog has the most prominent phenotypic effect, resulted in overproduction of actinorhodin and coelichelin P1 and increased sensitivity to diamide. The secreted proteome analysis of SLIV_12645 mutant revealed SigR1 influence on trafficking of proteins involved in cell wall biogenesis and refactoring. The reported here gene deletion system will further facilitate work on S. lividans strain improvement as a host for either secondary metabolites or protein production and will contribute to basic research in streptomycetes physiology, morphological development, secondary metabolism. On the other hand, the systematic deletion of sigma factors encoding genes demonstrates the complexity and conservation of regulatory processes conducted by sigma factors in streptomycetes.
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Affiliation(s)
- Yuriy Rebets
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | | | | | - Joachim Koepff
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | | | - Tobias Busche
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Arne Bleidt
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Liliya Horbal
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Maksym Myronovskyi
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Yousra Ahmed
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Wolfgang Wiechert
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | | | - Mohamed B. Hamed
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Department of Molecular Biology, National Research Centre, Giza, Egypt
| | - Bohdan Bilyk
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Jozef Anné
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | | | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Marco Oldiges
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Anastassios Economou
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Andriy Luzhetskyy
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
- Actinobacteria Metabolic Engineering Group, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany
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Horbal L, Marques F, Nadmid S, Mendes MV, Luzhetskyy A. Secondary metabolites overproduction through transcriptional gene cluster refactoring. Metab Eng 2018; 49:299-315. [DOI: 10.1016/j.ymben.2018.09.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/17/2018] [Accepted: 09/17/2018] [Indexed: 11/26/2022]
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Bilyk B, Horbal L, Luzhetskyy A. Chromosomal position effect influences the heterologous expression of genes and biosynthetic gene clusters in Streptomyces albus J1074. Microb Cell Fact 2017; 16:5. [PMID: 28052753 PMCID: PMC5209838 DOI: 10.1186/s12934-016-0619-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 12/20/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Efforts to construct the Streptomyces host strain with enhanced yields of heterologous product have focussed mostly on engineering of primary metabolism and/or the deletion of endogenous biosynthetic gene clusters. However, other factors, such as chromosome compactization, have been shown to have a significant influence on gene expression levels in bacteria and fungi. The expression of genes and biosynthetic gene clusters may vary significantly depending on their location within the chromosome. Little is known about the position effect in actinomycetes, which are important producers of various industrially relevant bioactive molecules. RESULTS To demonstrate an impact of the chromosomal position effect on the heterologous expression of genes and gene clusters in Streptomyces albus J1074, a transposon mutant library with randomly distributed transposon that includes a β-glucuronidase reporter gene was generated. Reporter gene expression levels have been shown to depend on the position on the chromosome. Using a combination of the transposon system and a φC31-based vector, the aranciamycin biosynthetic cluster was introduced randomly into the S. albus genome. The production levels of aranciamycin varied up to eightfold depending on the location of the gene cluster within the chromosome of S. albus J1074. One of the isolated mutant strains with an artificially introduced attachment site produced approximately 50% more aranciamycin than strains with endogenous attBs. CONCLUSIONS In this study, we demonstrate that expression of the reporter gene and aranciamycin biosynthetic cluster in Streptomyces albus J1074 varies up to eightfold depending on its position on the chromosome. The integration of the heterologous cluster into different locations on the chromosome may significantly influence the titre of the produced substance. This knowledge can be used for the more efficient engineering of Actinobacteria via the relocation of the biosynthetic gene clusters and insertion of additional copies of heterologous constructs in a suitable chromosomal position.
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Affiliation(s)
- Bohdan Bilyk
- PharmBioTec GmbH, Science Park 1, 66123, Saarbrücken, Germany.,Helmholtz-Institute for Pharmaceutical Research Saarland, Campus, Building C2.3, 66123, Saarbrücken, Germany
| | - Liliya Horbal
- Department of Pharmaceutical Biotechnology, Saarland University, 66123, Saarbrücken, Germany
| | - Andriy Luzhetskyy
- PharmBioTec GmbH, Science Park 1, 66123, Saarbrücken, Germany. .,Helmholtz-Institute for Pharmaceutical Research Saarland, Campus, Building C2.3, 66123, Saarbrücken, Germany. .,Department of Pharmaceutical Biotechnology, Saarland University, 66123, Saarbrücken, Germany.
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Horbal L, Luzhetskyy A. Dual control system - A novel scaffolding architecture of an inducible regulatory device for the precise regulation of gene expression. Metab Eng 2016; 37:11-23. [PMID: 27040671 PMCID: PMC4915818 DOI: 10.1016/j.ymben.2016.03.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/29/2016] [Accepted: 03/30/2016] [Indexed: 12/17/2022]
Abstract
Here, we present a novel scaffolding architecture of an inducible regulatory device. This dual control system is completely silent in the off stage and is coupled to the regulation of gene expression at both the transcriptional and translational levels. This system also functions as an AND gate. We demonstrated the effectiveness of the cumate-riboswitch dual control system for the control of pamamycin production in Streptomyces albus. Placing the cre recombinase gene under the control of this system permitted the construction of synthetic devices with non-volatile memory that sense the signal and respond by altering DNA at the chromosomal level, thereby producing changes that are heritable. In addition, we present a library of synthetic inducible promoters based on the previously described cumate switch. With only one inducer and different promoters, we demonstrate that simultaneous modulation of the expression of several genes to different levels in various operons is possible. Because all modules of the AND gates are functional in bacteria other than Streptomyces, we anticipate that these regulatory devices can be used to control gene expression in other Actinobacteria. The features described in this study make these systems promising tools for metabolic engineering and biotechnology in Actinobacteria.
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Affiliation(s)
- L Horbal
- Helmholtz Institute for Pharmaceutical Research, 66123 Saarbrücken, Germany; University of Saarland, Pharmaceutical Biotechnology, 66123 Saarbrucken, Germany
| | - A Luzhetskyy
- Helmholtz Institute for Pharmaceutical Research, 66123 Saarbrücken, Germany; University of Saarland, Pharmaceutical Biotechnology, 66123 Saarbrucken, Germany.
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Yushchuk O, Ostash B, Pham TH, Luzhetskyy A, Fedorenko V, Truman AW, Horbal L. Characterization of the Post-Assembly Line Tailoring Processes in Teicoplanin Biosynthesis. ACS Chem Biol 2016; 11:2254-64. [PMID: 27285718 DOI: 10.1021/acschembio.6b00018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Actinoplanes teichomyceticus produces teicoplanin (Tcp), a "last resort" lipoglycopeptide antibiotic used to treat severe multidrug resistant infections such as methicillin-resistant Staphylococcus aureus (MRSA). A number of studies have addressed various steps of Tcp biosynthesis using in vitro assays, although the exact sequence of Tcp peptide core tailoring reactions remained speculative. Here, we describe the generation and analysis of a set of A. teichomyceticus mutant strains that have been used to elucidate the sequence of reactions from the Tcp aglycone to mature Tcp. By combining these results with previously published data, we propose an updated order of post-assembly line tailoring processes in Tcp biosynthesis. We also demonstrate that the acyl-CoA-synthetase Tei13* and the type II thioesterase Tei30* are dispensable for Tcp production. Five Tcp derivatives featuring hitherto undescribed combinations of glycosylation and acylation patterns are described. The generation of strains that produce novel Tcp analogues now provides a platform for the production of additional Tcp-like molecules via combinatorial biosynthesis or chemical derivatization.
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Affiliation(s)
- Oleksandr Yushchuk
- Department
of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Bohdan Ostash
- Department
of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Thu H. Pham
- Department
of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Andriy Luzhetskyy
- Department
of Pharmaceutical Biotechnology, Saarland University, Campus, Saarbrucken, Germany
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Center for Infectious Research (HZI), Saarbrucken, Germany
| | - Victor Fedorenko
- Department
of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Andrew W. Truman
- Department
of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Liliya Horbal
- Department
of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
- Department
of Pharmaceutical Biotechnology, Saarland University, Campus, Saarbrucken, Germany
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Fedorenko V, Genilloud O, Horbal L, Marcone GL, Marinelli F, Paitan Y, Ron EZ. Antibacterial Discovery and Development: From Gene to Product and Back. Biomed Res Int 2015; 2015:591349. [PMID: 26339625 PMCID: PMC4538407 DOI: 10.1155/2015/591349] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/30/2014] [Accepted: 01/13/2015] [Indexed: 12/23/2022]
Abstract
Concern over the reports of antibiotic-resistant bacterial infections in hospitals and in the community has been publicized in the media, accompanied by comments on the risk that we may soon run out of antibiotics as a way to control infectious disease. Infections caused by Enterococcus faecium, Staphylococcus aureus, Klebsiella species, Clostridium difficile, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, and other Enterobacteriaceae species represent a major public health burden. Despite the pharmaceutical sector's lack of interest in the topic in the last decade, microbial natural products continue to represent one of the most interesting sources for discovering and developing novel antibacterials. Research in microbial natural product screening and development is currently benefiting from progress that has been made in other related fields (microbial ecology, analytical chemistry, genomics, molecular biology, and synthetic biology). In this paper, we review how novel and classical approaches can be integrated in the current processes for microbial product screening, fermentation, and strain improvement.
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Affiliation(s)
- Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv 79005, Ukraine
| | - Olga Genilloud
- Fundación MEDINA, Health Sciences Technology Park, 18016 Granada, Spain
| | - Liliya Horbal
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv 79005, Ukraine
| | - Giorgia Letizia Marcone
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
- The Protein Factory, Interuniversity Centre Politecnico di Milano, ICRM CNR Milano, and University of Insubria, 21100 Varese, Italy
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
- The Protein Factory, Interuniversity Centre Politecnico di Milano, ICRM CNR Milano, and University of Insubria, 21100 Varese, Italy
| | - Yossi Paitan
- Clinical Microbiology Laboratory, Meir Medical Center, 44281 Kfar Saba, Israel
| | - Eliora Z. Ron
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 6997801 Tel Aviv, Israel
- Galilee Research Institute (MIGAL), 11016 Kiryat Shmona, Israel
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Horbal L, Kobylyanskyy A, Truman AW, Zaburranyi N, Ostash B, Luzhetskyy A, Marinelli F, Fedorenko V. The pathway-specific regulatory genes, tei15* and tei16*, are the master switches of teicoplanin production in Actinoplanes teichomyceticus. Appl Microbiol Biotechnol 2014; 98:9295-309. [PMID: 25104028 DOI: 10.1007/s00253-014-5969-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/16/2014] [Accepted: 07/18/2014] [Indexed: 12/01/2022]
Abstract
Pathogenic antibiotic-resistant bacteria are an unprecedented threat to health care worldwide. The range of antibiotics active against these bacteria is narrow; it includes teicoplanin, a "last resort" drug, which is produced by the filamentous actinomycete Actinoplanes teichomyceticus. In this report, we determine the functions of tei15* and tei16*, pathway-specific regulatory genes that code for StrR- and LuxR-type transcriptional factors, respectively. The products of these genes are master switches of teicoplanin biosynthesis, since their inactivation completely abolished antibiotic production. We show that Tei15* positively regulates the transcription of at least 17 genes in the cluster, whereas the targets of Tei16* still remain unknown. Integration of tei15* or tei16* under the control of the aminoglycoside resistance gene aac(3)IV promoter into attBϕC31 site of the A. teichomyceticus chromosome increased teicoplanin productivity to nearly 1 g/L in TM1 industrial medium. The expression of these genes from the moderate copy number episomal vector pKC1139 led to 3-4 g/L teicoplanin, while under the same conditions, wild type produced approximately 100 mg/L. This shows that a significant increase in teicoplanin production can be achieved by a single step of genetic manipulation of the wild-type strain by increasing the expression of the tei regulatory genes. This confirms that natural product yields can be increased using rational engineering once suitable genetic tools have been developed. We propose that this new technology for teicoplanin overproduction might now be transferred to industrial mutants of A. teichomyceticus.
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Affiliation(s)
- Liliya Horbal
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
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Horbal L, Kobylyanskyy A, Yushchuk O, Zaburannyi N, Luzhetskyy A, Ostash B, Marinelli F, Fedorenko V. Evaluation of heterologous promoters for genetic analysis of Actinoplanes teichomyceticus--Producer of teicoplanin, drug of last defense. J Biotechnol 2013; 168:367-72. [PMID: 24161919 DOI: 10.1016/j.jbiotec.2013.10.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 10/09/2013] [Accepted: 10/15/2013] [Indexed: 10/26/2022]
Abstract
Actinoplanes teichomyceticus is the only known producer of the valuable glycopeptide antibiotic teicoplanin. Random mutagenesis and selection were extensively applied to teicoplanin producers, while the gene engineering methods were not used, because of the paucity of genetic tools for A. teichomyceticus. Particularly, availability of promoters of different strength that are functional in Actinoplanes would be very useful for overexpression of beneficial genes. Here we report the use of a glucuronidase reporter system (gusA) for studying transcriptional activity in A. teichomyceticus and describe the behavior of a set of heterologous promoters in this strain. We reveal several elements that exceed in their strength the well-established Streptomyces promoter ermEp, underscoring the utility of the gusA reporter for Actinoplanes sp. Remarkable overproduction of teicoplanin was achieved by constructing strains carrying additional copies of the regulatory gene tcp28 under the control of one of the two most active promoters, moeE5p and actp, discovered in this study.
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Affiliation(s)
- Liliya Horbal
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st, Lviv 79005, Ukraine
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Horbal L, Rebets Y, Rabyk M, Makitrynskyy R, Luzhetskyy A, Fedorenko V, Bechthold A. SimReg1 is a master switch for biosynthesis and export of simocyclinone D8 and its precursors. AMB Express 2012; 2:1. [PMID: 22214346 PMCID: PMC3261101 DOI: 10.1186/2191-0855-2-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 01/03/2012] [Indexed: 11/10/2022] Open
Abstract
Analysis of the simocyclinone biosynthesis (sim) gene cluster of Streptomyces antibioticus Tü6040 led to the identification of a putative pathway specific regulatory gene simReg1. In silico analysis places the SimReg1 protein in the OmpR-PhoB subfamily of response regulators. Gene replacement of simReg1 from the S. antibioticus chromosome completely abolishes simocyclinone production indicating that SimReg1 is a key regulator of simocyclinone biosynthesis. Results of the DNA-shift assays and reporter gene expression analysis are consistent with the idea that SimReg1 activates transcription of simocyclinone biosynthesis, transporter genes, regulatory gene simReg3 and his own transcription. The presence of extracts (simocyclinone) from S. antibioticus Tü6040 × pSSimR1-1 could dissociate SimReg1 from promoter regions. A preliminary model for regulation of simocyclinone biosynthesis and export is discussed.
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Rebets Y, Boll R, Horbal L, Fedorenko V, Bechthold A. Production of avilamycin A is regulated by AviC1 and AviC2, two transcriptional activators. J Antibiot (Tokyo) 2009; 62:461-4. [PMID: 19609289 DOI: 10.1038/ja.2009.63] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yuriy Rebets
- Institut für Pharmazeutische Wissenschaften, Pharmazeutische Biologie und Biotechnologie, Universität Freiburg, Freiburg im Breisgau, Germany
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