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Stegmüller J, Rodríguez Estévez M, Shu W, Gläser L, Myronovskyi M, Rückert-Reed C, Kalinowski J, Luzhetskyy A, Wittmann C. Systems metabolic engineering of the primary and secondary metabolism of Streptomyces albidoflavus enhances production of the reverse antibiotic nybomycin against multi-resistant Staphylococcus aureus. Metab Eng 2024; 81:123-143. [PMID: 38072358 DOI: 10.1016/j.ymben.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/17/2023] [Accepted: 12/01/2023] [Indexed: 01/23/2024]
Abstract
Nybomycin is an antibiotic compound with proven activity against multi-resistant Staphylococcus aureus, making it an interesting candidate for combating these globally threatening pathogens. For exploring its potential, sufficient amounts of nybomycin and its derivatives must be synthetized to fully study its effectiveness, safety profile, and clinical applications. As native isolates only accumulate low amounts of the compound, superior producers are needed. The heterologous cell factory S. albidoflavus 4N24, previously derived from the cluster-free chassis S. albidoflavus Del14, produced 860 μg L-1 of nybomycin, mainly in the stationary phase. A first round of strain development modulated expression of genes involved in supply of nybomycin precursors under control of the common Perm* promoter in 4N24, but without any effect. Subsequent studies with mCherry reporter strains revealed that Perm* failed to drive expression during the product synthesis phase but that use of two synthetic promoters (PkasOP* and P41) enabled strong constitutive expression during the entire process. Using PkasOP*, several rounds of metabolic engineering successively streamlined expression of genes involved in the pentose phosphate pathway, the shikimic acid pathway, supply of CoA esters, and nybomycin biosynthesis and export, which more than doubled the nybomycin titer to 1.7 mg L-1 in the sixth-generation strain NYB-6B. In addition, we identified the minimal set of nyb genes needed to synthetize the molecule using single-gene-deletion strains. Subsequently, deletion of the regulator nybW enabled nybomycin production to begin during the growth phase, further boosting the titer and productivity. Based on RNA sequencing along the created strain genealogy, we discovered that the nyb gene cluster was unfavorably downregulated in all advanced producers. This inspired removal of a part and the entire set of the four regulatory genes at the 3'-end nyb of the cluster. The corresponding mutants NYB-8 and NYB-9 exhibited marked further improvement in production, and the deregulated cluster was combined with all beneficial targets from primary metabolism. The best strain, S. albidoflavus NYB-11, accumulated up to 12 mg L-1 nybomycin, fifteenfold more than the basic strain. The absence of native gene clusters in the host and use of a lean minimal medium contributed to a selective production process, providing an important next step toward further development of nybomycin.
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Affiliation(s)
- Julian Stegmüller
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Wei Shu
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Maksym Myronovskyi
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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2
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Eckert N, Rebets Y, Horbal L, Zapp J, Herrmann J, Busche T, Müller R, Kalinowski J, Luzhetskyy A. Discovery and overproduction of novel highly bioactive pamamycins through transcriptional engineering of the biosynthetic gene cluster. Microb Cell Fact 2023; 22:233. [PMID: 37964282 PMCID: PMC10644645 DOI: 10.1186/s12934-023-02231-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND Pamamycins are a family of highly bioactive macrodiolide polyketides produced by Streptomyces alboniger as a complex mixture of derivatives with molecular weights ranging from 579 to 705 Daltons. The large derivatives are produced as a minor fraction, which has prevented their isolation and thus studies of chemical and biological properties. RESULTS Herein, we describe the transcriptional engineering of the pamamycin biosynthetic gene cluster (pam BGC), which resulted in the shift in production profile toward high molecular weight derivatives. The pam BGC library was constructed by inserting randomized promoter sequences in front of key biosynthetic operons. The library was expressed in Streptomyces albus strain with improved resistance to pamamycins to overcome sensitivity-related host limitations. Clones with modified pamamycin profiles were selected and the properties of engineered pam BGC were studied in detail. The production level and composition of the mixture of pamamycins was found to depend on balance in expression of the corresponding biosynthetic genes. This approach enabled the isolation of known pamamycins and the discovery of three novel derivatives with molecular weights of 663 Da and higher. One of them, homopamamycin 677A, is the largest described representative of this family of natural products with an elucidated structure. The new pamamycin 663A shows extraordinary activity (IC50 2 nM) against hepatocyte cancer cells as well as strong activity (in the one-digit micromolar range) against a range of Gram-positive pathogenic bacteria. CONCLUSION By employing transcriptional gene cluster refactoring, we not only enhanced the production of known pamamycins but also discovered novel derivatives exhibiting promising biological activities. This approach has the potential for broader application in various biosynthetic gene clusters, creating a sustainable supply and discovery platform for bioactive natural products.
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Affiliation(s)
- Nikolas Eckert
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Yuriy Rebets
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Lilya Horbal
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Josef Zapp
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Jennifer Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany
| | - Tobias Busche
- Center for Biotechnology-CeBiTec, University of Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany
| | - Jörn Kalinowski
- Center for Biotechnology-CeBiTec, University of Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany.
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany.
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Beganovic S, Rückert-Reed C, Sucipto H, Shu W, Gläser L, Patschkowski T, Struck B, Kalinowski J, Luzhetskyy A, Wittmann C. Systems biology of industrial oxytetracycline production in Streptomyces rimosus: the secrets of a mutagenized hyperproducer. Microb Cell Fact 2023; 22:222. [PMID: 37898787 PMCID: PMC10612213 DOI: 10.1186/s12934-023-02215-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 09/26/2023] [Indexed: 10/30/2023] Open
Abstract
BACKGROUND Oxytetracycline which is derived from Streptomyces rimosus, inhibits a wide range of bacteria and is industrially important. The underlying biosynthetic processes are complex and hinder rational engineering, so industrial manufacturing currently relies on classical mutants for production. While the biochemistry underlying oxytetracycline synthesis is known to involve polyketide synthase, hyperproducing strains of S. rimosus have not been extensively studied, limiting our knowledge on fundamental mechanisms that drive production. RESULTS In this study, a multiomics analysis of S. rimosus is performed and wild-type and hyperproducing strains are compared. Insights into the metabolic and regulatory networks driving oxytetracycline formation were obtained. The overproducer exhibited increased acetyl-CoA and malonyl CoA supply, upregulated oxytetracycline biosynthesis, reduced competing byproduct formation, and streamlined morphology. These features were used to synthesize bhimamycin, an antibiotic, and a novel microbial chassis strain was created. A cluster deletion derivative showed enhanced bhimamycin production. CONCLUSIONS This study suggests that the precursor supply should be globally increased to further increase the expression of the oxytetracycline cluster while maintaining the natural cluster sequence. The mutagenized hyperproducer S. rimosus HP126 exhibited numerous mutations, including large genomic rearrangements, due to natural genetic instability, and single nucleotide changes. More complex mutations were found than those typically observed in mutagenized bacteria, impacting gene expression, and complicating rational engineering. Overall, the approach revealed key traits influencing oxytetracycline production in S. rimosus, suggesting that similar studies for other antibiotics could uncover general mechanisms to improve production.
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Affiliation(s)
- Selma Beganovic
- Institute of Systems Biotechnology, Saarland University, Campus A1 5, 66123, Saarbrücken, Germany
| | | | - Hilda Sucipto
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Wei Shu
- Institute of Systems Biotechnology, Saarland University, Campus A1 5, 66123, Saarbrücken, Germany
| | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Campus A1 5, 66123, Saarbrücken, Germany
| | | | - Ben Struck
- Centre for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Centre for Biotechnology, Bielefeld University, Bielefeld, Germany
| | | | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Campus A1 5, 66123, Saarbrücken, Germany. *
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Stierhof M, Myronovskyi M, Zapp J, Luzhetskyy A. Heterologous Production and Biosynthesis of Threonine-16:0dioic acids with a Hydroxamate Moiety. J Nat Prod 2023; 86:2258-2269. [PMID: 37728876 PMCID: PMC10616846 DOI: 10.1021/acs.jnatprod.3c00097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Indexed: 09/21/2023]
Abstract
Dereplication and genome mining in Streptomyces aureus LU18118 combined with heterologous expression of selected biosynthetic gene clusters (BGCs) led to the discovery of various threonine-16:0dioic acids named lipothrenins. Lipothrenins consist of the core elements l-Thr, d-allo-Thr, or Dhb, which are linked to hexadecanedioic acid by an amide bond. The main compound lipothrenin A (1) carries the N-hydroxylated d-allo form of threonine and expresses a siderophore activity. The lipothrenin BGC was analyzed by a series of deletion experiments. As a result, a variety of interesting genes involved in the recruitment and selective activation of linear 16:0dioic acids, amide bond formation, and the epimerization of l-Thr were revealed. Furthermore, a diiron N-oxygenase was identified that may be directly involved in the monooxygenation of the amide bond. This is divergent from the usual hydroxamate formation mechanism in siderophores, which involves hydroxylation of the free amine prior to amide bond formation. Siderophore activity was observed for all N-hydroxylated lipothrenins by application of the CAS assay method.
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Affiliation(s)
- Marc Stierhof
- Department
of Pharmaceutical Biotechnology and Department of Pharmaceutical Biology, Saarland University, 66123 Saarbruecken, Germany
| | - Maksym Myronovskyi
- Department
of Pharmaceutical Biotechnology and Department of Pharmaceutical Biology, Saarland University, 66123 Saarbruecken, Germany
| | - Josef Zapp
- Department
of Pharmaceutical Biotechnology and Department of Pharmaceutical Biology, Saarland University, 66123 Saarbruecken, Germany
| | - Andriy Luzhetskyy
- Department
of Pharmaceutical Biotechnology and Department of Pharmaceutical Biology, Saarland University, 66123 Saarbruecken, Germany
- Helmholtz
Institute for Pharmaceutical Research Saarland, Saarland University, 66123 Saarbruecken, Germany
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Lopatniuk M, Riedel F, Wildfeuer J, Stierhof M, Dahlem C, Kiemer AK, Luzhetskyy A. Development of a Streptomyces-based system for facile thioholgamide library generation and analysis. Metab Eng 2023; 78:48-60. [PMID: 37142115 DOI: 10.1016/j.ymben.2023.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/27/2023] [Accepted: 04/30/2023] [Indexed: 05/06/2023]
Abstract
Derivatizing natural products (NPs) is essential in structure-activity relationship (SAR) studies, compound optimization, and drug development. Ribosomally synthesized and post-translationally modified peptides (RiPPs) represent one of the major classes of natural products. Thioholgamide represents thioamitide - a recently emerged family of RiPPs with unique structures and great potential in anticancer drug development. Although the method for generating the RiPP library by codon substitutions in the precursor peptide gene is straightforward, the techniques to perform RiPP derivatization in Actinobacteria remain limited and time-consuming. Here, we report a facile system for producing a library of randomized thioholgamide derivatives utilizing an optimized Streptomyces host. This technique enabled us to access all possible amino acid substitutions of the thioholgamide molecule, one position at a time. Out of 152 potential derivatives, 85 were successfully detected, revealing the impact of amino acid substitutions on thioholgamide post-translational modifications (PTMs). Moreover, new PTMs were observed among thioholgamide derivatives: thiazoline heterocycles, which have not yet been reported for thioamitides, and S-methylmethionine, which is very rare in nature. The obtained library was subsequently used for thioholgamide SAR studies and stability assays.
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Affiliation(s)
- Maria Lopatniuk
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Florian Riedel
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Julia Wildfeuer
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany; Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Marc Stierhof
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Charlotte Dahlem
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Alexandra K Kiemer
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Andriy Luzhetskyy
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany.
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6
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Dolya B, Hryhorieva O, Sorochynska K, Lopatniuk M, Ostash I, Tseduliak VM, Sterndorff EB, Jørgensen TS, Gren T, Dacyuk Y, Weber T, Luzhetskyy A, Fedorenko V, Ostash B. Properties of Multidrug-Resistant Mutants Derived from Heterologous Expression Chassis Strain Streptomyces albidoflavus J1074. Microorganisms 2023; 11:1176. [PMID: 37317150 DOI: 10.3390/microorganisms11051176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 03/30/2023] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
Streptomyces albidoflavus J1074 is a popular platform to discover novel natural products via the expression of heterologous biosynthetic gene clusters (BGCs). There is keen interest in improving the ability of this platform to overexpress BGCs and, consequently, enable the purification of specialized metabolites. Mutations within gene rpoB for the β-subunit of RNA polymerase are known to increase rifampicin resistance and augment the metabolic capabilities of streptomycetes. Yet, the effects of rpoB mutations on J1074 remained unstudied, and we decided to address this issue. A target collection of strains that we studied carried spontaneous rpoB mutations introduced in the background of the other drug resistance mutations. The antibiotic resistance spectra, growth, and specialized metabolism of the resulting mutants were interrogated using a set of microbiological and analytical approaches. We isolated 14 different rpoB mutants showing various degrees of rifampicin resistance; one of them (S433W) was isolated for the first time in actinomycetes. The rpoB mutations had a major effect on antibiotic production by J1074, as evident from bioassays and LC-MS data. Our data support the idea that rpoB mutations are useful tools to enhance the ability of J1074 to produce specialized metabolites.
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Affiliation(s)
- Borys Dolya
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Olena Hryhorieva
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Khrystyna Sorochynska
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Maria Lopatniuk
- Department of Pharmacy, Saarland University, 66123 Saarbrucken, Germany
| | - Iryna Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Vasylyna-Marta Tseduliak
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Eva Baggesgaard Sterndorff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Tue Sparholt Jørgensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Tetiana Gren
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Yuriy Dacyuk
- Department of Mineral Geology and Geophysics, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Andriy Luzhetskyy
- Department of Pharmacy, Saarland University, 66123 Saarbrucken, Germany
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Bohdan Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
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Tistechok S, Roman I, Fedorenko V, Luzhetskyy A, Gromyko O. Diversity and bioactive potential of Actinomycetia from the rhizosphere soil of Juniperus excelsa. Folia Microbiol (Praha) 2023:10.1007/s12223-023-01047-x. [PMID: 36947395 PMCID: PMC10031196 DOI: 10.1007/s12223-023-01047-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 11/23/2022] [Accepted: 03/15/2023] [Indexed: 03/23/2023]
Abstract
Microbial natural products are among the main sources of compounds used in the medical biotechnology field for the purpose of drug development. However, as antibiotic resistance in pathogenic microorganisms is known to be increasing dramatically, there exists a need to develop new antibiotics. Actinomycetia have proven to be a good source of biologically active compounds, although the rediscovery of previously known compounds significantly slows down the introduction of new antibiotics. As a consequence, increasing attention is being paid to the isolation of actinomycete strains from previously unexplored sources, which can significantly increase the likelihood of discovering new biologically active compounds. This study investigated the diversity and bioactive potential of 372 actinomycete strains isolated from the rhizosphere soil of Juniperus excelsa M. Bieb. The examined actinomycete strains belonged to 11 genera, namely, Actinoplanes, Actinorectispora, Amycolatopsis, Kribbella, Micrococcus, Micromonospora, Nocardia, Promicromonospora, Rhodococcus, Saccharopolyspora and Streptomyces. The bioactive potential of each isolated actinomycete strain was determined on the basis of its ability to produce antimicrobial metabolites against Gram-positive and Gram-negative bacteria and yeast. Some 159 strains (42.74%) exhibited antimicrobial activity against at least one of the tested microbial strains. The dereplication analysis of the extract of the Streptomyces sp. Je 1-651 strain, which exhibited strong antimicrobial activity, led to the annotation of spiramycins and stambomycins. Moreover, the phylogenetic analysis based on the 16S rRNA gene sequence of the Je 1-651 strain revealed it to be close to the S. ambofaciens.
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Affiliation(s)
- Stepan Tistechok
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine
| | - Ivan Roman
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbruecken, 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbruecken, 66123, Germany
| | - Oleksandr Gromyko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine.
- Microbial Culture Collection of Antibiotic Producers, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine.
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8
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Tseduliak VM, Dolia B, Ostash I, Lopatniuk M, Busche T, Ochi K, Kalinowski J, Luzhetskyy A, Fedorenko V, Ostash B. Mutations within gene XNR_2147 for TetR-like protein enhance lincomycin resistance and endogenous specialized metabolism of Streptomyces albus J1074. J Appl Genet 2023; 64:185-195. [PMID: 36417169 DOI: 10.1007/s13353-022-00738-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022]
Abstract
Streptomyces albus J1074 is one of the most popular heterologous expression platforms among streptomycetes. Identification of new genes and mutations that influence specialized metabolism in this species is therefore of great applied interest. Here, we describe S. albus KO-1304 that was isolated as a spontaneous lincomycin-resistant variant of double rpsLR94G rsmGR15SG40E mutant KO-1295. Besides altered antibiotic resistance profile, KO-1304 exhibited increased antibiotic activity as compared to its parental strains. KO-1304 genome sequencing revealed mutations within gene XNR_2147 encoding putative TetR-like protein. Gene XNR_2146 for efflux protein is the most likely target of repressing action of Xnr_2147. Our data agree with the scenario where lincomycin resistance phenotype of KO-1304 arose from inability of mutated Xnr_2147 protein to repress XNR_2146. Introduction of additional copy of XNR_2146 into wild type strain increased antibiotic activity of the latter, attesting to the practical value of transporter genes for strain improvement.
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Affiliation(s)
- Vasylyna-Marta Tseduliak
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Lviv, 79005, Ukraine
| | - Borys Dolia
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Lviv, 79005, Ukraine
| | - Iryna Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Lviv, 79005, Ukraine
| | - Maria Lopatniuk
- Helmholtz Institute for Pharmaceutical Research, Saarland Campus, Building C2.3, 66123, Saarbrucken, Germany
| | - Tobias Busche
- Technology Platform Genomics, CeBiTec, Bielefeld University, Sequenz 1, 33615, Bielefeld, Germany
| | - Kozo Ochi
- Department of Life Sciences, Hiroshima Institute of Technology, Saeki-Ku, Hiroshima, 731-5193, Japan
| | - Jörn Kalinowski
- Technology Platform Genomics, CeBiTec, Bielefeld University, Sequenz 1, 33615, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Helmholtz Institute for Pharmaceutical Research, Saarland Campus, Building C2.3, 66123, Saarbrucken, Germany
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Lviv, 79005, Ukraine
| | - Bohdan Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Lviv, 79005, Ukraine.
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Tistechok S, Stierhof M, Myronovskyi M, Zapp J, Gromyko O, Luzhetskyy A. Furaquinocins K and L: Novel Naphthoquinone-Based Meroterpenoids from Streptomyces sp. Je 1-369. Antibiotics (Basel) 2022; 11:1587. [PMID: 36358243 PMCID: PMC9686526 DOI: 10.3390/antibiotics11111587] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 10/17/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 10/29/2023] Open
Abstract
Actinomycetes are the most prominent group of microorganisms that produce biologically active compounds. Among them, special attention is focused on bacteria in the genus Streptomyces. Streptomycetes are an important source of biologically active natural compounds that could be considered therapeutic agents. In this study, we described the identification, purification, and structure elucidation of two new naphthoquinone-based meroterpenoids, furaquinocins K and L, from Streptomyces sp. Je 1-369 strain, which was isolated from the rhizosphere soil of Juniperus excelsa (Bieb.). The main difference between furaquinocins K and L and the described furaquinocins was a modification in the polyketide naphthoquinone skeleton. In addition, the structure of furaquinocin L contained an acetylhydrazone fragment, which is quite rare for natural compounds. We also identified a furaquinocin biosynthetic gene cluster in the Je 1-369 strain, which showed similarity (60%) with the furaquinocin B biosynthetic gene cluster from Streptomyces sp. KO-3988. Furaquinocin L showed activity against Gram-positive bacteria without cytotoxic effects.
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Affiliation(s)
- Stepan Tistechok
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Marc Stierhof
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany
| | - Maksym Myronovskyi
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany
| | - Josef Zapp
- Department of Pharmaceutical Biology, Saarland University, 66123 Saarbruecken, Germany
| | - Oleksandr Gromyko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
- Microbial Culture Collection of Antibiotic Producers, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123 Saarbruecken, Germany
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10
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Paulus C, Myronovskyi M, Zapp J, Rodríguez Estévez M, Lopatniuk M, Rosenkränzer B, Palusczak A, Luzhetskyy A. Miramides A–D: Identification of Detoxin-like Depsipeptides after Heterologous Expression of a Hybrid NRPS-PKS Gene Cluster from Streptomyces mirabilis Lu17588. Microorganisms 2022; 10:microorganisms10091752. [PMID: 36144353 PMCID: PMC9503745 DOI: 10.3390/microorganisms10091752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/16/2022] [Accepted: 08/19/2022] [Indexed: 11/30/2022] Open
Abstract
Natural products derived from plants, fungi or bacteria have been used for years in the medicine, agriculture and food industries as they exhibit a variety of beneficial properties, such as antibiotic, antifungal, anticancer, herbicidal and immunosuppressive activities. Compared to synthetic compounds, natural products possess a greater chemical diversity, which is a reason why they are profitable templates for developing pharmaceutical drug candidates and ongoing research on them is inevitable. Performing heterologous expression with unknown gene clusters is the preferred method to activate gene clusters that are not expressed in the wild-type strain under laboratory conditions; thus, this method offers a way to discover new interesting metabolites. Here, we report the gene cluster assembly of a hybrid NRPS-PKS gene cluster from Streptomyces mirabilis Lu17588, which was heterologously expressed in Streptomyces albus Del14. Four new compounds were produced by the obtained strain, which were named miramides A–D. Isolation and structure elucidation revealed similarity of the isolated compounds to the known depsipeptides rimosamides/detoxins.
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Affiliation(s)
- Constanze Paulus
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany
| | - Maksym Myronovskyi
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany
| | - Josef Zapp
- Department of Pharmaceutical Biology, Saarland University, 66123 Saarbruecken, Germany
| | - Marta Rodríguez Estévez
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany
| | - Maria Lopatniuk
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany
| | - Birgit Rosenkränzer
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany
| | - Anja Palusczak
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany
- AMEG Department, Helmholtz Institute for Pharmaceutical Research Saarland, 66123 Saarbruecken, Germany
- Correspondence: ; Tel.: +49-681-302-70200
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11
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Ashraf N, Zafar S, Makitrynskyy R, Bechthold A, Spiteller D, Song L, Anwar MA, Luzhetskyy A, Khan AN, Akhtar K, Khaliq S. Revealing Genome-Based Biosynthetic Potential of Streptomyces sp. BR123 Isolated from Sunflower Rhizosphere with Broad Spectrum Antimicrobial Activity. Antibiotics (Basel) 2022; 11:antibiotics11081057. [PMID: 36009926 PMCID: PMC9405382 DOI: 10.3390/antibiotics11081057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/30/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022] Open
Abstract
Actinomycetes, most notably the genus Streptomyces, have great importance due to their role in the discovery of new natural products, especially for finding antimicrobial secondary metabolites that are useful in the medicinal science and biotechnology industries. In the current study, a genome-based evaluation of Streptomyces sp. isolate BR123 was analyzed to determine its biosynthetic potential, based on its in vitro antimicrobial activity against a broad range of microbial pathogens, including gram-positive and gram-negative bacteria and fungi. A draft genome sequence of 8.15 Mb of Streptomyces sp. isolate BR123 was attained, containing a GC content of 72.63% and 8103 protein coding genes. Many antimicrobial, antiparasitic, and anticancerous compounds were detected by the presence of multiple biosynthetic gene clusters, which was predicted by in silico analysis. A novel metabolite with a molecular mass of 1271.7773 in positive ion mode was detected through a high-performance liquid chromatography linked with mass spectrometry (HPLC-MS) analysis. In addition, another compound, meridamycin, was also identified through a HPLC-MS analysis. The current study reveals the biosynthetic potential of Streptomyces sp. isolate BR123, with respect to the synthesis of bioactive secondary metabolites through genomic and spectrometric analysis. Moreover, the comparative genome study compared the isolate BR123 with other Streptomyces strains, which may expand the knowledge concerning the mechanism involved in novel antimicrobial metabolite synthesis.
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Affiliation(s)
- Neelma Ashraf
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, PO Box 577, Faisalabad 38000, Pakistan
- Department of Chemical Ecology/Biological Chemistry, University of Konstanz, 78457 Konstanz, Germany
- Correspondence: (N.A.); (S.K.); Tel.: +92-41-9201316 (S.K.); Fax: +92-41-92014722 (S.K.)
| | - Sana Zafar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, PO Box 577, Faisalabad 38000, Pakistan
| | - Roman Makitrynskyy
- Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, University of Freiburg, 79104 Freiburg im Breisgau, Germany
| | - Andreas Bechthold
- Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, University of Freiburg, 79104 Freiburg im Breisgau, Germany
| | - Dieter Spiteller
- Department of Chemical Ecology/Biological Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Lijiang Song
- Department of Chemistry, University of Warwick Coventry, Coventry CV4 7AL, UK
| | - Munir Ahmad Anwar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, PO Box 577, Faisalabad 38000, Pakistan
| | - Andriy Luzhetskyy
- Pharmaceutical Biotechnology Campus, Saarland University, Building C2.3, 66123 Saarbrucken, Germany
| | - Ali Nisar Khan
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, PO Box 577, Faisalabad 38000, Pakistan
| | - Kalsoom Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, PO Box 577, Faisalabad 38000, Pakistan
| | - Shazia Khaliq
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, PO Box 577, Faisalabad 38000, Pakistan
- Correspondence: (N.A.); (S.K.); Tel.: +92-41-9201316 (S.K.); Fax: +92-41-92014722 (S.K.)
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12
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Syrvatka V, Rabets A, Gromyko O, Luzhetskyy A, Fedorenko V. Scandium-microorganism interactions in new biotechnologies. Trends Biotechnol 2022; 40:1088-1101. [PMID: 35346528 DOI: 10.1016/j.tibtech.2022.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/17/2022] [Accepted: 02/23/2022] [Indexed: 12/19/2022]
Abstract
Scandium (Sc) plays a special role in high-tech industries because of its wide application in green, space, and defense technologies. However, Sc mining and purification are problematic due to political, technological, and environmental difficulties. The deficit of this element limits global technological development. One sustainable solution to this problem is to use microorganisms to extract Sc from ore and waste, as well as to concentrate and separate it from other elements. Sc also demonstrates attractive metabolic effects on microbes that is of great interest in white biotechnology. Sc increases the production of proteins and secondary metabolites and activates poorly expressed genes. This review offers a comprehensive analysis of current knowledge on the application of Sc-microorganism interactions in promising biotechnologies, its perspectives, and future challenges.
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Affiliation(s)
- Vasyl Syrvatka
- Genetics and Biotechnology Department, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Andrii Rabets
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Oleksandr Gromyko
- Genetics and Biotechnology Department, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Andriy Luzhetskyy
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Victor Fedorenko
- Genetics and Biotechnology Department, Ivan Franko National University of Lviv, Lviv, Ukraine.
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13
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Shuai H, Myronovskyi M, Rosenkränzer B, Paulus C, Nadmid S, Stierhof M, Kolling D, Luzhetskyy A. Novel Biosynthetic Route to the Isoquinoline Scaffold. ACS Chem Biol 2022; 17:598-608. [PMID: 35253423 DOI: 10.1021/acschembio.1c00869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Isoquinoline alkaloids are a large class of natural products with a broad range of biological activities, including antimicrobial, antitumor, antileukemic and anti-inflammatory properties. Although mostly found in plants, isoquinolines can also be found in the extracts of bacterial and fungal cultures. Regardless of the origin, most of the reported biosynthetic routes for isoquinolines use tyrosine as a main biosynthetic precursor. Here, we report the identification of a new biosynthetic pathway for production of isoquinolinequinone alkaloid mansouramycin D in Streptomyces albus Del14. Using feeding, mass spectrometry, and nuclear magnetic resonance spectroscopy, we demonstrate that tryptophan serves instead of tyrosine as a main mansouramycin biosynthetic precursor. The biosynthetic genes were identified in the chromosome of the strain by using gene inactivation and heterologous expression. Insights into the biosynthesis of mansouramycins are also presented.
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Affiliation(s)
- Hui Shuai
- Department of Pharmaceutical Biotechnology, University of Saarland, Campus Building C2 3, 66123 Saarbruecken, Germany
| | - Maksym Myronovskyi
- Department of Pharmaceutical Biotechnology, University of Saarland, Campus Building C2 3, 66123 Saarbruecken, Germany
| | - Birgit Rosenkränzer
- Department of Pharmaceutical Biotechnology, University of Saarland, Campus Building C2 3, 66123 Saarbruecken, Germany
| | - Constanze Paulus
- Department of Pharmaceutical Biotechnology, University of Saarland, Campus Building C2 3, 66123 Saarbruecken, Germany
| | - Suvd Nadmid
- Department of Pharmaceutical Biotechnology, University of Saarland, Campus Building C2 3, 66123 Saarbruecken, Germany
| | - Marc Stierhof
- Department of Pharmaceutical Biotechnology, University of Saarland, Campus Building C2 3, 66123 Saarbruecken, Germany
| | - Dominik Kolling
- Department of Pharmaceutical Biotechnology, University of Saarland, Campus Building C2 3, 66123 Saarbruecken, Germany
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, University of Saarland, Campus Building C2 3, 66123 Saarbruecken, Germany
- Department of Metabolic Engineering of Actinomycetes, Helmholtz-Institute for Pharmaceutical Research Saarland, Campus Building E8 1, 66123 Saarbruecken, Germany
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14
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Sikandar A, Lopatniuk M, Luzhetskyy A, Müller R, Koehnke J. Total In Vitro Biosynthesis of the Thioamitide Thioholgamide and Investigation of the Pathway. J Am Chem Soc 2022; 144:5136-5144. [PMID: 35263083 DOI: 10.1021/jacs.2c00402] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Thioholgamides are ribosomally synthesized and posttranslationally modified peptides (RiPPs), with potent activity against cancerous cell lines and an unprecedented structure. Despite being one of the most structurally and chemically complex RiPPs, very few biosynthetic steps have been elucidated. Here, we report the complete in vitro reconstitution of the biosynthetic pathway. We demonstrate that thioamidation is the first step and acts as a gatekeeper for downstream processing. Thr dehydration follows thioamidation, and our studies reveal that both these modifications require the formation of protein complexes─ThoH/I and ThoC/D. Harnessing the power of AlphaFold, we deduce that ThoD acts as a lyase and also proposes putative catalytic residues. ThoF catalyzes the oxidative decarboxylation of the terminal Cys, and the subsequent macrocyclization is facilitated by ThoE. This is followed by Ser dehydration, which is also carried out by ThoC/D. ThoG is responsible for histidine bis-N-methylation, which is a prerequisite for His β-hydroxylation─a modification carried out by ThoJ. The last step of the pathway is the removal of the leader peptide by ThoK to afford mature thioholgamide.
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Affiliation(s)
- Asfandyar Sikandar
- Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI) and Department of Pharmacy at Saarland University (UdS), Campus E8.1, 66123 Saarbrücken, Germany
| | - Maria Lopatniuk
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Andriy Luzhetskyy
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI) and Department of Pharmacy at Saarland University (UdS), Campus E8.1, 66123 Saarbrücken, Germany.,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Jesko Koehnke
- Workgroup Structural Biology of Biosynthetic Enzymes, HIPS, HZI, UdS, 66123 Saarbrücken, Germany.,School of Chemistry, University of Glasgow, Glasgow G12 8QQ, United Kingdom
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15
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Kolling D, Stierhof M, Lasch C, Myronovskyi M, Luzhetskyy A. A Promiscuous Halogenase for the Derivatization of Flavonoids. Molecules 2021; 26:molecules26206220. [PMID: 34684801 PMCID: PMC8539768 DOI: 10.3390/molecules26206220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 11/17/2022] Open
Abstract
Halogenation often improves the bioactive properties of natural products and is used in pharmaceutical research for the generation of new potential drug leads. High regio- and stereospecificity, simple reaction conditions and straightforward downstream processing are the main advantages of halogenation using enzymatic biocatalysts compared to chemical synthetic approaches. The identification of new promiscuous halogenases for the modification of various natural products is of great interest in modern drug discovery. In this paper, we report the identification of a new promiscuous FAD-dependent halogenase, DklH, from Frankia alni ACN14a. The identified halogenase readily modifies various flavonoid compounds, including those with well-studied biological activities. This halogenase has been demonstrated to modify not only flavones and isoflavones, but also flavonols, flavanones and flavanonols. The structural requirements for DklH substrate recognition were determined using a feeding approach. The homology model of DklH and the mechanism of substrate recognition are also proposed in this paper.
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Affiliation(s)
- Dominik Kolling
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (D.K.); (M.S.); (C.L.); (M.M.)
| | - Marc Stierhof
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (D.K.); (M.S.); (C.L.); (M.M.)
| | - Constanze Lasch
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (D.K.); (M.S.); (C.L.); (M.M.)
| | - Maksym Myronovskyi
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (D.K.); (M.S.); (C.L.); (M.M.)
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (D.K.); (M.S.); (C.L.); (M.M.)
- AMEG Department, Helmholtz Institute for Pharmaceutical Research Saarland, 66123 Saarbruecken, Germany
- Correspondence: ; Tel.: +49-681-302-70200
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16
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Paulus C, Zapp J, Luzhetskyy A. New Scabimycins A-C Isolated from Streptomyces acidiscabies (Lu19992). Molecules 2021; 26:5922. [PMID: 34641466 PMCID: PMC8513078 DOI: 10.3390/molecules26195922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/24/2021] [Accepted: 09/26/2021] [Indexed: 11/16/2022] Open
Abstract
Peptide natural products displaying a wide range of biological activities have become important drug candidates over the years. Microorganisms have been a powerful source of such bioactive peptides, and Streptomyces have yielded many novel natural products thus far. In an effort to uncover such new, meaningful compounds, the metabolome of Streptomyces acidiscabies was analyzed thoroughly. Three new compounds, scabimycins A-C (1-3), were discovered, and their chemical structures were elucidated by NMR spectroscopy. The relative and absolute configurations were determined using ROESY NMR experiments and advanced Marfey's method.
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Affiliation(s)
- Constanze Paulus
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany;
| | - Josef Zapp
- Department of Pharmaceutical Biology, Saarland University, 66123 Saarbrücken, Germany;
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany;
- AMEG Department, Helmholtz Institute for Pharmaceutical Research Saarland, 66123 Saarbrücken, Germany
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17
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Miethke M, Pieroni M, Weber T, Brönstrup M, Hammann P, Halby L, Arimondo PB, Glaser P, Aigle B, Bode HB, Moreira R, Li Y, Luzhetskyy A, Medema MH, Pernodet JL, Stadler M, Tormo JR, Genilloud O, Truman AW, Weissman KJ, Takano E, Sabatini S, Stegmann E, Brötz-Oesterhelt H, Wohlleben W, Seemann M, Empting M, Hirsch AKH, Loretz B, Lehr CM, Titz A, Herrmann J, Jaeger T, Alt S, Hesterkamp T, Winterhalter M, Schiefer A, Pfarr K, Hoerauf A, Graz H, Graz M, Lindvall M, Ramurthy S, Karlén A, van Dongen M, Petkovic H, Keller A, Peyrane F, Donadio S, Fraisse L, Piddock LJV, Gilbert IH, Moser HE, Müller R. Towards the sustainable discovery and development of new antibiotics. Nat Rev Chem 2021; 5:726-749. [PMID: 37118182 PMCID: PMC8374425 DOI: 10.1038/s41570-021-00313-1] [Citation(s) in RCA: 350] [Impact Index Per Article: 116.7] [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] [Accepted: 07/01/2021] [Indexed: 02/08/2023]
Abstract
An ever-increasing demand for novel antimicrobials to treat life-threatening infections caused by the global spread of multidrug-resistant bacterial pathogens stands in stark contrast to the current level of investment in their development, particularly in the fields of natural-product-derived and synthetic small molecules. New agents displaying innovative chemistry and modes of action are desperately needed worldwide to tackle the public health menace posed by antimicrobial resistance. Here, our consortium presents a strategic blueprint to substantially improve our ability to discover and develop new antibiotics. We propose both short-term and long-term solutions to overcome the most urgent limitations in the various sectors of research and funding, aiming to bridge the gap between academic, industrial and political stakeholders, and to unite interdisciplinary expertise in order to efficiently fuel the translational pipeline for the benefit of future generations. ![]()
Antimicrobial resistance is an increasing threat to public health and encouraging the development of new antimicrobials is one of the most important ways to address the problem. This Roadmap article aims to bring together industrial, academic and political partners, and proposes both short-term and long-term solutions to this challenge.
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Affiliation(s)
- Marcus Miethke
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Marco Pieroni
- Food and Drug Department, University of Parma, Parma, Italy
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Mark Brönstrup
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Chemical Biology (CBIO), Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Peter Hammann
- Infectious Diseases & Natural Product Research at EVOTEC, and Justus Liebig University Giessen, Giessen, Germany
| | - Ludovic Halby
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, Paris, France
| | - Paola B Arimondo
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, Paris, France
| | - Philippe Glaser
- Ecology and Evolution of Antibiotic Resistance Unit, Microbiology Department, Institut Pasteur, CNRS UMR3525, Paris, France
| | | | - Helge B Bode
- Department of Biosciences, Goethe University Frankfurt, Frankfurt, Germany.,Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, Marburg, Germany
| | - Rui Moreira
- Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Yanyan Li
- Unit MCAM, CNRS, National Museum of Natural History (MNHN), Paris, France
| | - Andriy Luzhetskyy
- Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Jean-Luc Pernodet
- Institute for Integrative Biology of the Cell (I2BC) & Microbiology Department, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Marc Stadler
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Microbial Drugs (MWIS), Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | | | | | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Kira J Weissman
- Molecular and Structural Enzymology Group, Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Eriko Takano
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, United Kingdom
| | - Stefano Sabatini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Evi Stegmann
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Wolfgang Wohlleben
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Myriam Seemann
- Institute for Chemistry UMR 7177, University of Strasbourg/CNRS, ITI InnoVec, Strasbourg, France
| | - Martin Empting
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Brigitta Loretz
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
| | - Claus-Michael Lehr
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
| | - Alexander Titz
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Jennifer Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Timo Jaeger
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Silke Alt
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | | | | | - Andrea Schiefer
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Kenneth Pfarr
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Achim Hoerauf
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Heather Graz
- Biophys Ltd., Usk, Monmouthshire, United Kingdom
| | - Michael Graz
- School of Law, University of Bristol, Bristol, United Kingdom
| | | | | | - Anders Karlén
- Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | | | - Hrvoje Petkovic
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, University Hospital, Saarbrücken, Germany
| | | | | | - Laurent Fraisse
- Drugs for Neglected Diseases initiative (DNDi), Geneva, Switzerland
| | - Laura J V Piddock
- The Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Ian H Gilbert
- Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Heinz E Moser
- Novartis Institutes for BioMedical Research (NIBR), Emeryville, CA USA
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
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18
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Lasch C, Stierhof M, Estévez MR, Myronovskyi M, Zapp J, Luzhetskyy A. Bonsecamin: A New Cyclic Pentapeptide Discovered through Heterologous Expression of a Cryptic Gene Cluster. Microorganisms 2021; 9:microorganisms9081640. [PMID: 34442719 PMCID: PMC8400726 DOI: 10.3390/microorganisms9081640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/01/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 11/16/2022] Open
Abstract
The intriguing structural complexity of molecules produced by natural organisms is uncontested. Natural scaffolds serve as an important basis for the development of molecules with broad applications, e.g., therapeutics or agrochemicals. Research in recent decades has demonstrated that by means of classic metabolite extraction from microbes only a small portion of natural products can be accessed. The use of genome mining and heterologous expression approaches represents a promising way to discover new natural compounds. In this paper we report the discovery of a novel cyclic pentapeptide called bonsecamin through the heterologous expression of a cryptic NRPS gene cluster from Streptomyces albus ssp. chlorinus NRRL B-24108 in Streptomyces albus Del14. The new compound was successfully isolated and structurally characterized using NMR. The minimal set of genes required for bonsecamin production was determined through bioinformatic analysis and gene deletion experiments. A biosynthetic route leading to the production of bonsecamin is proposed in this paper.
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Affiliation(s)
- Constanze Lasch
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (C.L.); (M.S.); (M.R.E.); (M.M.)
| | - Marc Stierhof
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (C.L.); (M.S.); (M.R.E.); (M.M.)
| | - Marta Rodríguez Estévez
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (C.L.); (M.S.); (M.R.E.); (M.M.)
| | - Maksym Myronovskyi
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (C.L.); (M.S.); (M.R.E.); (M.M.)
| | - Josef Zapp
- Department of Pharmaceutical Biology, Saarland University, 66123 Saarbruecken, Germany;
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (C.L.); (M.S.); (M.R.E.); (M.M.)
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123 Saarbruecken, Germany
- Correspondence: ; Tel.: +49-681-302-70200
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19
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Stierhof M, Myronovskyi M, Zapp J, Luzhetskyy A. Discovery and Heterologous Production of New Cyclic Depsibosamycins. Microorganisms 2021; 9:microorganisms9071396. [PMID: 34203385 PMCID: PMC8303602 DOI: 10.3390/microorganisms9071396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 06/03/2021] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 11/16/2022] Open
Abstract
Streptomyces are producers of valuable secondary metabolites with unique scaffolds that perform a plethora of biological functions. Nonribosomal peptides are of special interest due to their variety and complexity. They are synthesized by nonribosomal peptide synthetases, large biosynthetic machineries that are encoded in the genome of many Streptomyces species. The identification of new peptides and the corresponding biosynthetic gene clusters is of major interest since knowledge can be used to facilitate combinatorial biosynthesis and chemical semisynthesis of natural products. The recently discovered bosamycins are linear octapeptides with an interesting 5-OMe tyrosine moiety and various modifications at the N-terminus. In this study, the new cyclic depsibosamycins B, C, and D from Streptomyces aurantiacus LU19075 were discovered. In comparison to the linear bosamycins B, C, and D, which were also produced by the strain, the cyclic depsibosamycins showed a side-chain-to-tail lactonization of serine and glycine, leading to a ring of four amino acids. In silico identification and heterologous expression of the depsibosamycin (dbm) gene cluster indicated that the cyclic peptides, rather than the linear derivatives, are the main products of the cluster.
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Affiliation(s)
- Marc Stierhof
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (M.S.); (M.M.)
| | - Maksym Myronovskyi
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (M.S.); (M.M.)
| | - Josef Zapp
- Department of Pharmaceutical Biology, Saarland University, 66123 Saarbruecken, Germany;
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (M.S.); (M.M.)
- AMEG Department, Helmholtz Institute for Pharmaceutical Research Saarland, 66123 Saarbrücken, Germany
- Correspondence: ; Tel.: +49-681-3027-0200
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20
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Gläser L, Kuhl M, Stegmüller J, Rückert C, Myronovskyi M, Kalinowski J, Luzhetskyy A, Wittmann C. Superior production of heavy pamamycin derivatives using a bkdR deletion mutant of Streptomyces albus J1074/R2. Microb Cell Fact 2021; 20:111. [PMID: 34082758 PMCID: PMC8176718 DOI: 10.1186/s12934-021-01602-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 03/16/2021] [Accepted: 05/27/2021] [Indexed: 11/17/2022] Open
Abstract
Background Pamamycins are macrodiolides of polyketide origin which form a family of differently large homologues with molecular weights between 579 and 663. They offer promising biological activity against pathogenic fungi and gram-positive bacteria. Admittedly, production titers are very low, and pamamycins are typically formed as crude mixture of mainly smaller derivatives, leaving larger derivatives rather unexplored so far. Therefore, strategies that enable a more efficient production of pamamycins and provide increased fractions of the rare large derivatives are highly desired. Here we took a systems biology approach, integrating transcription profiling by RNA sequencing and intracellular metabolite analysis, to enhance pamamycin production in the heterologous host S. albus J1074/R2. Results Supplemented with l-valine, the recombinant producer S. albus J1074/R2 achieved a threefold increased pamamycin titer of 3.5 mg L−1 and elevated fractions of larger derivatives: Pam 649 was strongly increased, and Pam 663 was newly formed. These beneficial effects were driven by increased availability of intracellular CoA thioesters, the building blocks for the polyketide, resulting from l-valine catabolism. Unfavorably, l-valine impaired growth of the strain, repressed genes of mannitol uptake and glycolysis, and suppressed pamamycin formation, despite the biosynthetic gene cluster was transcriptionally activated, restricting production to the post l-valine phase. A deletion mutant of the transcriptional regulator bkdR, controlling a branched-chain amino acid dehydrogenase complex, revealed decoupled pamamycin biosynthesis. The regulator mutant accumulated the polyketide independent of the nutrient status. Supplemented with l-valine, the novel strain enabled the biosynthesis of pamamycin mixtures with up to 55% of the heavy derivatives Pam 635, Pam 649, and Pam 663: almost 20-fold more than the wild type. Conclusions Our findings open the door to provide rare heavy pamamycins at markedly increased efficiency and facilitate studies to assess their specific biological activities and explore this important polyketide further. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01602-6.
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Affiliation(s)
- Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Martin Kuhl
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Julian Stegmüller
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Maksym Myronovskyi
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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21
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Kuhl M, Rückert C, Gläser L, Beganovic S, Luzhetskyy A, Kalinowski J, Wittmann C. Microparticles enhance the formation of seven major classes of natural products in native and metabolically engineered actinobacteria through accelerated morphological development. Biotechnol Bioeng 2021; 118:3076-3093. [PMID: 33974270 DOI: 10.1002/bit.27818] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 03/04/2021] [Revised: 04/17/2021] [Accepted: 04/30/2021] [Indexed: 11/09/2022]
Abstract
Actinobacteria provide a rich spectrum of bioactive natural products and therefore display an invaluable source towards commercially valuable pharmaceuticals and agrochemicals. Here, we studied the use of inorganic talc microparticles (hydrous magnesium silicate, 3MgO·4SiO2 ·H2 O, 10 µm) as a general supplement to enhance natural product formation in this important class of bacteria. Added to cultures of recombinant Streptomyces lividans, talc enhanced production of the macrocyclic peptide antibiotic bottromycin A2 and its methylated derivative Met-bottromycin A2 up to 109 mg L-1 , the highest titer reported so far. Hereby, the microparticles fundamentally affected metabolism. With 10 g L-1 talc, S. lividans grew to 40% smaller pellets and, using RNA sequencing, revealed accelerated morphogenesis and aging, indicated by early upregulation of developmental regulator genes such as ssgA, ssgB, wblA, sigN, and bldN. Furthermore, the microparticles re-balanced the expression of individual bottromycin cluster genes, resulting in a higher macrocyclization efficiency at the level of BotAH and correspondingly lower levels of non-cyclized shunt by-products, driving the production of mature bottromycin. Testing a variety of Streptomyces species, talc addition resulted in up to 13-fold higher titers for the RiPPs bottromycin and cinnamycin, the alkaloid undecylprodigiosin, the polyketide pamamycin, the tetracycline-type oxytetracycline, and the anthramycin-analogs usabamycins. Moreover, talc addition boosted production in other actinobacteria, outside of the genus of Streptomyces: vancomycin (Amycolatopsis japonicum DSM 44213), teicoplanin (Actinoplanes teichomyceticus ATCC 31121), and the angucyclinone-type antibiotic simocyclinone (Kitasatospora sp.). For teicoplanin, the microparticles were even crucial to activate production. Taken together, the use of talc was beneficial in 75% of all tested cases and optimized natural and heterologous hosts forming the substance of interest with clusters under native and synthetic control. Given its simplicity and broad benefits, microparticle-supplementation appears as an enabling technology in natural product research of these most important microbes.
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Affiliation(s)
- Martin Kuhl
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Selma Beganovic
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
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22
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Koshla O, Lopatniuk M, Borys O, Misaki Y, Kravets V, Ostash I, Shemediuk A, Ochi K, Luzhetskyy A, Fedorenko V, Ostash B. Genetically engineered rpsL merodiploidy impacts secondary metabolism and antibiotic resistance in Streptomyces. World J Microbiol Biotechnol 2021; 37:62. [PMID: 33730177 DOI: 10.1007/s11274-021-03030-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 10/08/2020] [Accepted: 03/08/2021] [Indexed: 11/28/2022]
Abstract
Certain point mutations within gene for ribosomal protein S12, rpsL, are known to dramatically change physiological traits of bacteria, most prominently antibiotic resistance and production of various metabolites. The rpsL mutants are usually searched among spontaneous mutants resistant to aminoglycoside antibiotics, such as streptomycin or paromomycin. The shortcomings of traditional selection are as follows: random rpsL mutants may carry undesired genome alterations; many rpsL mutations cannot be isolated because they are either not associated with increased antibiotic resistance or non-viable in the absence of intact rpsLWT gene. Introduction of mutant rpsL alleles in the rpsLWT background can be used to circumvent these obstacles. Here we take the latter approach and report the generation and properties of a set of stable rpsL merodiploids for Streptomyces albus J1074. We identified several rpsL alleles that enhance endogenous and heterologous antibiotic production by this strain and show that rpsLWTrpsLK88E merodiploid displays increased streptomycin resistance. We further tested several promising rpsL alleles in two more strains, Streptomyces cyanogenus S136 and Streptomyces ghanaensis ATCC14672. In S136, plasmid-borne rpsLK88E+P91S and rpsLK88R led to elevated landomycin production; no changes were detected for ATCC14672 merodiploids. Our data outline the prospects for and limitations to rpsL merodiploids as a tool for rapid enhancement of secondary metabolism in Streptomyces.
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Affiliation(s)
- Oksana Koshla
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv, 79005, Ukraine
| | - Maria Lopatniuk
- Helmholtz Institute for Pharmaceutical Research, Saarland Campus, Building C2.3, 66123, Saarbrucken, Germany
| | - Oksana Borys
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv, 79005, Ukraine
| | - Yuya Misaki
- Department of Life Sciences, Hiroshima Institute of Technology, Saeki-ku, Hiroshima, 731-5193, Japan
| | - Volodymyr Kravets
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv, 79005, Ukraine
| | - Iryna Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv, 79005, Ukraine
| | - Anastasiia Shemediuk
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv, 79005, Ukraine
| | - Kozo Ochi
- Department of Life Sciences, Hiroshima Institute of Technology, Saeki-ku, Hiroshima, 731-5193, Japan
| | - Andriy Luzhetskyy
- Helmholtz Institute for Pharmaceutical Research, Saarland Campus, Building C2.3, 66123, Saarbrucken, Germany
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv, 79005, Ukraine
| | - Bohdan Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv, 79005, Ukraine.
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23
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Pikl Š, Carrillo Rincón AF, Slemc L, Goranovič D, Avbelj M, Gjuračić K, Sucipto H, Stare K, Baebler Š, Šala M, Guo M, Luzhetskyy A, Petković H, Magdevska V. Multiple copies of the oxytetracycline gene cluster in selected Streptomyces rimosus strains can provide significantly increased titers. Microb Cell Fact 2021; 20:47. [PMID: 33596911 PMCID: PMC7890619 DOI: 10.1186/s12934-021-01522-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 10/08/2020] [Accepted: 01/19/2021] [Indexed: 11/23/2022] Open
Abstract
Background Natural products are a valuable source of biologically active compounds that have applications in medicine and agriculture. One disadvantage with natural products is the slow, time-consuming strain improvement regimes that are necessary to ensure sufficient quantities of target compounds for commercial production. Although great efforts have been invested in strain selection methods, many of these technologies have not been improved in decades, which might pose a serious threat to the economic and industrial viability of such important bioprocesses. Results In recent years, introduction of extra copies of an entire biosynthetic pathway that encodes a target product in a single microbial host has become a technically feasible approach. However, this often results in minor to moderate increases in target titers. Strain stability and process reproducibility are the other critical factors in the industrial setting. Industrial Streptomyces rimosus strains for production of oxytetracycline are one of the most economically efficient strains ever developed, and thus these represent a very good industrial case. To evaluate the applicability of amplification of an entire gene cluster in a single host strain, we developed and evaluated various gene tools to introduce multiple copies of the entire oxytetracycline gene cluster into three different Streptomyces rimosus strains: wild-type, and medium and high oxytetracycline-producing strains. We evaluated the production levels of these engineered S. rimosus strains with extra copies of the oxytetracycline gene cluster and their stability, and the oxytetracycline gene cluster expression profiles; we also identified the chromosomal integration sites. Conclusions This study shows that stable and reproducible increases in target secondary metabolite titers can be achieved in wild-type and in high oxytetracycline-producing strains, which always reflects the metabolic background of each independent S. rimosus strain. Although this approach is technically very demanding and requires systematic effort, when combined with modern strain selection methods, it might constitute a very valuable approach in industrial process development.
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Affiliation(s)
- Špela Pikl
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | | | - Lucija Slemc
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | | | - Martina Avbelj
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | | | - Hilda Sucipto
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany.,Helmholtz-Institut für Pharmazeutische Forschung Saarland, Saarbrücken, Germany
| | - Katja Stare
- National Institute of Biology, Večna pot 111, Ljubljana, Slovenia
| | - Špela Baebler
- National Institute of Biology, Večna pot 111, Ljubljana, Slovenia
| | - Martin Šala
- National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Meijin Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Andriy Luzhetskyy
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany.,Helmholtz-Institut für Pharmazeutische Forschung Saarland, Saarbrücken, Germany
| | - Hrvoje Petković
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
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Kuhl M, Gläser L, Rebets Y, Rückert C, Sarkar N, Hartsch T, Kalinowski J, Luzhetskyy A, Wittmann C. Back Cover Image, Volume 117, Number 12, December 2020. Biotechnol Bioeng 2020. [DOI: 10.1002/bit.27066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Martin Kuhl
- Institute of Systems Biotechnology Saarland University Saarbrücken Germany
| | - Lars Gläser
- Institute of Systems Biotechnology Saarland University Saarbrücken Germany
| | - Yuriy Rebets
- Department of Pharmacy, Pharmaceutical Biotechnology Saarland University Saarbrücken Germany
| | | | | | | | - Jörn Kalinowski
- Center for Biotechnology Bielefeld University Bielefeld Germany
| | - Andriy Luzhetskyy
- Department of Pharmacy, Pharmaceutical Biotechnology Saarland University Saarbrücken Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology Saarland University Saarbrücken Germany
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25
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Gummerlich N, Rebets Y, Paulus C, Zapp J, Luzhetskyy A. Targeted Genome Mining-From Compound Discovery to Biosynthetic Pathway Elucidation. Microorganisms 2020; 8:microorganisms8122034. [PMID: 33352664 PMCID: PMC7765855 DOI: 10.3390/microorganisms8122034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 11/29/2020] [Revised: 12/13/2020] [Accepted: 12/15/2020] [Indexed: 11/16/2022] Open
Abstract
Natural products are an important source of novel investigational compounds in drug discovery. Especially in the field of antibiotics, Actinobacteria have been proven to be a reliable source for lead structures. The discovery of these natural products with activity- and structure-guided screenings has been impeded by the constant rediscovery of previously identified compounds. Additionally, a large discrepancy between produced natural products and biosynthetic potential in Actinobacteria, including representatives of the order Pseudonocardiales, has been revealed using genome sequencing. To turn this genomic potential into novel natural products, we used an approach including the in-silico pre-selection of unique biosynthetic gene clusters followed by their systematic heterologous expression. As a proof of concept, fifteen Saccharothrixespanaensis genomic library clones covering predicted biosynthetic gene clusters were chosen for expression in two heterologous hosts, Streptomyceslividans and Streptomycesalbus. As a result, two novel natural products, an unusual angucyclinone pentangumycin and a new type II polyketide synthase shunt product SEK90, were identified. After purification and structure elucidation, the biosynthetic pathways leading to the formation of pentangumycin and SEK90 were deduced using mutational analysis of the biosynthetic gene cluster and feeding experiments with 13C-labelled precursors.
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Affiliation(s)
- Nils Gummerlich
- Department of Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123 Saarbrücken, Germany; (N.G.); (Y.R.); (C.P.)
| | - Yuriy Rebets
- Department of Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123 Saarbrücken, Germany; (N.G.); (Y.R.); (C.P.)
| | - Constanze Paulus
- Department of Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123 Saarbrücken, Germany; (N.G.); (Y.R.); (C.P.)
| | - Josef Zapp
- Department of Pharmaceutical Biology, Saarland University, Campus C2.3, 66123 Saarbrücken, Germany;
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123 Saarbrücken, Germany; (N.G.); (Y.R.); (C.P.)
- Actinobacteria Metabolic Engineering Group, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Campus E8.1, 66123 Saarbrücken, Germany
- Correspondence: ; Tel.: +49-681-302-70200
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26
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Marques F, Luzhetskyy A, Mendes MV. Engineering Corynebacterium glutamicum with a comprehensive genomic library and phage-based vectors. Metab Eng 2020; 62:221-234. [DOI: 10.1016/j.ymben.2020.08.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/17/2020] [Accepted: 08/10/2020] [Indexed: 12/18/2022]
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Abstract
Thioviridamide-like compounds, including thioholgamides, are ribosomally synthesized and post-translationally modified peptide natural products with potent anticancer cell activity and an unprecedented structure. Very little is known about their biosynthesis, and we were intrigued by the β-hydroxy-N1, N3-dimethylhistidinium moiety found in these compounds. Here we report the construction of a heterologous host capable of producing thioholgamide with a 15-fold increased yield compared to the wild-type strain. A knockout of thoJ, encoding a predicted nonheme monooxygenase, shows that ThoJ is essential for thioholgamide β-hydroxylation. The crystal structure of ThoJ exhibits a typical mono/dioxygenase fold with conserved key active-site residues. Yet, ThoJ possesses a very large substrate binding pocket that appears suitable to receive a cyclic thioholgamide intermediate for hydroxylation. The improved production of the heterologous host will enable the dissection of the individual biosynthetic steps involved in biosynthesis of this exciting RiPP family.
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Affiliation(s)
- Asfandyar Sikandar
- Workgroup Structural Biology of Biosynthetic Enzymes, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus Geb. E8.1, 66123 Saarbrücken, Germany
| | - Maria Lopatniuk
- Department Microbial Natural Products, Actinobacteria Metabolic Engineering Group, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, CampusC2.3, 66123 Saarbrücken, Germany
| | - Andriy Luzhetskyy
- Department Microbial Natural Products, Actinobacteria Metabolic Engineering Group, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, CampusC2.3, 66123 Saarbrücken, Germany
| | - Jesko Koehnke
- Workgroup Structural Biology of Biosynthetic Enzymes, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus Geb. E8.1, 66123 Saarbrücken, Germany
- School of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K
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28
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Lasch C, Gummerlich N, Myronovskyi M, Palusczak A, Zapp J, Luzhetskyy A. Loseolamycins: A Group of New Bioactive Alkylresorcinols Produced after Heterologous Expression of a Type III PKS from Micromonospora endolithica. Molecules 2020; 25:molecules25204594. [PMID: 33050154 PMCID: PMC7587189 DOI: 10.3390/molecules25204594] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 11/22/2022] Open
Abstract
Natural products are a valuable source of biologically active compounds with potential applications in medicine and agriculture. Unprecedented scaffold diversity of natural products and biocatalysts from their biosynthetic pathways are of fundamental importance. Heterologous expression and refactoring of natural product biosynthetic pathways are generally regarded as a promising approach to discover new secondary metabolites of microbial origin. Here, we present the identification of a new group of alkylresorcinols after transcriptional activation and heterologous expression of the type III polyketide synthase of Micromonospora endolithica. The most abundant compounds loseolamycins A1 and A2 have been purified and their structures were elucidated by NMR. Loseolamycins contain an unusual branched hydroxylated aliphatic chain which is provided by the host metabolism and is incorporated as a starter fatty acid unit. The isolated loseolamycins show activity against gram-positive bacteria and inhibit the growth of the monocot weed Agrostis stolonifera in a germination assay. The biosynthetic pathway leading to the production of loseolamycins is proposed in this paper.
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Affiliation(s)
- Constanze Lasch
- Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (C.L.); (N.G.); (M.M.); (A.P.)
| | - Nils Gummerlich
- Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (C.L.); (N.G.); (M.M.); (A.P.)
| | - Maksym Myronovskyi
- Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (C.L.); (N.G.); (M.M.); (A.P.)
| | - Anja Palusczak
- Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (C.L.); (N.G.); (M.M.); (A.P.)
| | - Josef Zapp
- Pharmaceutical Biology, Saarland University, 66123 Saarbruecken, Germany;
| | - Andriy Luzhetskyy
- Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (C.L.); (N.G.); (M.M.); (A.P.)
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123 Saarbruecken, Germany
- Correspondence: ; Tel.: +49-681-302-70200
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Kuhl M, Gläser L, Rebets Y, Rückert C, Sarkar N, Hartsch T, Kalinowski J, Luzhetskyy A, Wittmann C. Microparticles globally reprogram Streptomyces albus toward accelerated morphogenesis, streamlined carbon core metabolism, and enhanced production of the antituberculosis polyketide pamamycin. Biotechnol Bioeng 2020; 117:3858-3875. [PMID: 32808679 DOI: 10.1002/bit.27537] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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: 05/19/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 12/18/2022]
Abstract
Streptomyces spp. are a rich source for natural products with recognized industrial value, explaining the high interest to improve and streamline the performance of in these microbes. Here, we studied the production of pamamycins, macrodiolide homologs with a high activity against multiresistant pathogenic microbes, using recombinant Streptomyces albus J1074/R2. Talc particles (hydrous magnesium silicate, 3MgO·4SiO2 ·H2 O) of micrometer size, added to submerged cultures of the recombinant strain, tripled pamamycin production up to 50 mg/L. Furthermore, they strongly affected morphology, reduced the size of cell pellets formed by the filamentous microbe during the process up to sixfold, and shifted the pamamycin spectrum to larger derivatives. Integrated analysis of transcriptome and precursor (CoA thioester) supply of particle-enhanced and control cultures provided detailed insights into the underlying molecular changes. The microparticles affected the expression of 3,341 genes (56% of all genes), revealing a global and fundamental impact on metabolism. Morphology-associated genes, encoding major regulators such as SsgA, RelA, EshA, Factor C, as well as chaplins and rodlins, were found massively upregulated, indicating that the particles caused a substantially accelerated morphogenesis. In line, the pamamycin cluster was strongly upregulated (up to 1,024-fold). Furthermore, the microparticles perturbed genes encoding for CoA-ester metabolism, which were mainly activated. The altered expression resulted in changes in the availability of intracellular CoA-esters, the building blocks of pamamycin. Notably, the ratio between methylmalonyl CoA and malonyl-CoA was increased fourfold. Both metabolites compete for incorporation into pamamycin so that the altered availability explained the pronounced preference for larger derivatives in the microparticle-enhanced process. The novel insights into the behavior of S. albus in response to talc appears of general relevance to further explore and upgrade the concept of microparticle enhanced cultivation, widely used for filamentous microbes.
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Affiliation(s)
- Martin Kuhl
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Yuriy Rebets
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | | | | | | | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
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Erdenetsogt U, Nadmid S, Paulus C, Chanagsuren G, Dolgor E, Gotov C, Dahse HM, Luzhetskyy A, Dagvadorj E. Bioactive flavonoids from plant extract of Pyrethrum pulchrum and its acute toxicity. Nat Prod Res 2020; 35:5960-5963. [DOI: 10.1080/14786419.2020.1806271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Uugangerel Erdenetsogt
- Department of Chemistry, School of Biomedicine, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | - Suvd Nadmid
- School of Pharmacy, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | - Constanze Paulus
- Department of Chemistry, University of Zürich, Zürich, Switzerland
| | - Ganchimeg Chanagsuren
- School of Medicine, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | - Erdenechimeg Dolgor
- School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Choijamts Gotov
- Department of Pharmacology, Otoch Manramba University of Mongolia, Ulaanbaatar, Mongolia
| | - Hans-Martin Dahse
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany
| | - Andriy Luzhetskyy
- Actinomycet Metabolic Engineering, Helmholtz-Institute for Pharmaceutical Research Saarland, Saarbrucken, Germany
| | - Enkhmaa Dagvadorj
- Department of Chemistry, School of Biomedicine, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
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Shuai H, Myronovskyi M, Nadmid S, Luzhetskyy A. Identification of a Biosynthetic Gene Cluster Responsible for the Production of a New Pyrrolopyrimidine Natural Product-Huimycin. Biomolecules 2020; 10:biom10071074. [PMID: 32708402 PMCID: PMC7439116 DOI: 10.3390/biom10071074] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/14/2020] [Accepted: 07/16/2020] [Indexed: 12/27/2022] Open
Abstract
Pyrrolopyrimidines are an important class of natural products with a broad spectrum of biological activities, including antibacterial, antifungal, antiviral, anticancer or anti-inflammatory. Here, we present the identification of a biosynthetic gene cluster from the rare actinomycete strain Kutzneria albida DSM 43870, which leads to the production of huimycin, a new member of the pyrrolopyrimidine family of compounds. The huimycin gene cluster was successfully expressed in the heterologous host strain Streptomyces albus Del14. The compound was purified, and its structure was elucidated by means of nuclear magnetic resonance spectroscopy. The minimal huimycin gene cluster was identified through sequence analysis and a series of gene deletion experiments. A model for huimycin biosynthesis is also proposed in this paper.
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Affiliation(s)
- Hui Shuai
- Pharmazeutische Biotechnologie, Universität des Saarlandes, 66123 Saarbrücken, Germany; (H.S.); (M.M.); (S.N.)
| | - Maksym Myronovskyi
- Pharmazeutische Biotechnologie, Universität des Saarlandes, 66123 Saarbrücken, Germany; (H.S.); (M.M.); (S.N.)
| | - Suvd Nadmid
- Pharmazeutische Biotechnologie, Universität des Saarlandes, 66123 Saarbrücken, Germany; (H.S.); (M.M.); (S.N.)
- School of Pharmacy, Mongolian National University of Medical Sciences, S. Zorig Street, 14210 Ulaanbaatar, Mongolia
| | - Andriy Luzhetskyy
- Pharmazeutische Biotechnologie, Universität des Saarlandes, 66123 Saarbrücken, Germany; (H.S.); (M.M.); (S.N.)
- Helmholtz-Institut für Pharmazeutische Forschung Saarland, 66123 Saarbrücken, Germany
- Correspondence: ; Tel.: +49-0681-70223
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Dahlem C, Siow WX, Lopatniuk M, Tse WKF, Kessler SM, Kirsch SH, Hoppstädter J, Vollmar AM, Müller R, Luzhetskyy A, Bartel K, Kiemer AK. Thioholgamide A, a New Anti-Proliferative Anti-Tumor Agent, Modulates Macrophage Polarization and Metabolism. Cancers (Basel) 2020; 12:cancers12051288. [PMID: 32438733 PMCID: PMC7281193 DOI: 10.3390/cancers12051288] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 04/09/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 12/24/2022] Open
Abstract
Natural products represent powerful tools searching for novel anticancer drugs. Thioholgamide A (thioA) is a ribosomally synthesized and post-translationally modified peptide, which has been identified as a product of Streptomyces sp. MUSC 136T. In this study, we provide a comprehensive biological profile of thioA, elucidating its effects on different hallmarks of cancer in tumor cells as well as in macrophages as crucial players of the tumor microenvironment. In 2D and 3D in vitro cell culture models thioA showed potent anti-proliferative activities in cancer cells at nanomolar concentrations. Anti-proliferative actions were confirmed in vivo in zebrafish embryos. Cytotoxicity was only induced at several-fold higher concentrations, as assessed by live-cell microscopy and biochemical analyses. ThioA exhibited a potent modulation of cell metabolism by inhibiting oxidative phosphorylation, as determined in a live-cell metabolic assay platform. The metabolic modulation caused a repolarization of in vitro differentiated and polarized tumor-promoting human monocyte-derived macrophages: ThioA-treated macrophages showed an altered morphology and a modulated expression of genes and surface markers. Taken together, the metabolic regulator thioA revealed low activities in non-tumorigenic cells and an interesting anti-cancer profile by orchestrating different hallmarks of cancer, both in tumor cells as well as in macrophages as part of the tumor microenvironment.
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Affiliation(s)
- Charlotte Dahlem
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany; (C.D.); (S.M.K.); (J.H.)
| | - Wei Xiong Siow
- Department of Pharmacy, Pharmaceutical Biology, Ludwig-Maximilians-University of Munich, Butenandtstrasse 5-13, 81377 Munich, Germany; (W.X.S.); (A.M.V.); (K.B.)
| | - Maria Lopatniuk
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany; (M.L.); (A.L.)
| | - William K. F. Tse
- Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan;
| | - Sonja M. Kessler
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany; (C.D.); (S.M.K.); (J.H.)
- Department of Pharmacology for Natural Sciences, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Susanne H. Kirsch
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Campus E8 1, 66123 Saarbrücken, Germany; (S.H.K.); (R.M.)
| | - Jessica Hoppstädter
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany; (C.D.); (S.M.K.); (J.H.)
| | - Angelika M. Vollmar
- Department of Pharmacy, Pharmaceutical Biology, Ludwig-Maximilians-University of Munich, Butenandtstrasse 5-13, 81377 Munich, Germany; (W.X.S.); (A.M.V.); (K.B.)
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Campus E8 1, 66123 Saarbrücken, Germany; (S.H.K.); (R.M.)
- Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
| | - Andriy Luzhetskyy
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany; (M.L.); (A.L.)
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Campus E8 1, 66123 Saarbrücken, Germany; (S.H.K.); (R.M.)
| | - Karin Bartel
- Department of Pharmacy, Pharmaceutical Biology, Ludwig-Maximilians-University of Munich, Butenandtstrasse 5-13, 81377 Munich, Germany; (W.X.S.); (A.M.V.); (K.B.)
| | - Alexandra K. Kiemer
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany; (C.D.); (S.M.K.); (J.H.)
- Correspondence: ; Tel.: +49-681-302-57301
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Myronovskyi M, Rosenkränzer B, Stierhof M, Petzke L, Seiser T, Luzhetskyy A. Identification and Heterologous Expression of the Albucidin Gene Cluster from the Marine Strain Streptomyces Albus Subsp. Chlorinus NRRL B-24108. Microorganisms 2020; 8:microorganisms8020237. [PMID: 32050690 PMCID: PMC7074753 DOI: 10.3390/microorganisms8020237] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 01/14/2020] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 12/05/2022] Open
Abstract
Herbicides with new modes of action and safer toxicological and environmental profiles are needed to manage the evolution of weeds that are resistant to commercial herbicides. The unparalleled structural diversity of natural products makes these compounds a promising source for new herbicides. In 2009, a novel nucleoside phytotoxin, albucidin, with broad activity against grass and broadleaf weeds was isolated from a strain of Streptomyces albus subsp. chlorinus NRRL B-24108. Here, we report the identification and heterologous expression of the previously uncharacterized albucidin gene cluster. Through a series of gene inactivation experiments, a minimal set of albucidin biosynthetic genes was determined. Based on gene annotation and sequence homology, a model for albucidin biosynthesis was suggested. The presented results enable the construction of producer strains for a sustainable supply of albucidin for biological activity studies.
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Affiliation(s)
- Maksym Myronovskyi
- Pharmazeutische Biotechnologie, Universität des Saarlandes, 66123 Saarbrücken, Germany; (M.M.); (B.R.); (M.S.)
| | - Birgit Rosenkränzer
- Pharmazeutische Biotechnologie, Universität des Saarlandes, 66123 Saarbrücken, Germany; (M.M.); (B.R.); (M.S.)
| | - Marc Stierhof
- Pharmazeutische Biotechnologie, Universität des Saarlandes, 66123 Saarbrücken, Germany; (M.M.); (B.R.); (M.S.)
| | - Lutz Petzke
- BASF SE, 67056 Ludwigshafen, Germany; (L.P.); (T.S.)
| | - Tobias Seiser
- BASF SE, 67056 Ludwigshafen, Germany; (L.P.); (T.S.)
| | - Andriy Luzhetskyy
- Pharmazeutische Biotechnologie, Universität des Saarlandes, 66123 Saarbrücken, Germany; (M.M.); (B.R.); (M.S.)
- Helmholtz-Institut für Pharmazeutische Forschung Saarland, 66123 Saarbrücken, Germany
- Correspondence: ; Tel.: +49-681-302-70200
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Rodríguez Estévez M, Gummerlich N, Myronovskyi M, Zapp J, Luzhetskyy A. Benzanthric Acid, a Novel Metabolite From Streptomyces albus Del14 Expressing the Nybomycin Gene Cluster. Front Chem 2020; 7:896. [PMID: 31998688 PMCID: PMC6965495 DOI: 10.3389/fchem.2019.00896] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 09/04/2019] [Accepted: 12/12/2019] [Indexed: 11/17/2022] Open
Abstract
Streptomycetes constitute a diverse bacterial group able to produce a wide variety of secondary metabolites with potential applications in the pharmacy industry. However, the genes responsible for the biosynthesis of these compounds are very frequently inactive or expressed at very low levels under standard laboratory cultivation conditions. Therefore, the activation or upregulation of secondary metabolite biosynthesis genes is a crucial step for the discovery of new bioactive natural products. We have recently reported the discovery of the biosynthetic genes for the antibiotic nybomycin (nyb genes) in Streptomyces albus subsp. chlorinus. The nyb genes were expressed in the heterologous host Streptomyces albus Del14, which produces not only nybomycin, but also a novel compound. In this study, we describe the isolation, purification, and structure elucidation of the new substance named benzanthric acid.
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Affiliation(s)
| | - Nils Gummerlich
- Pharmaceutical Biotechnology, University of Saarland, Saarbrücken, Germany
| | - Maksym Myronovskyi
- Pharmaceutical Biotechnology, University of Saarland, Saarbrücken, Germany
| | - Josef Zapp
- Department of Pharmacy, Institute of Pharmaceutical Biology, University of Saarland, Saarbrücken, Germany
| | - Andriy Luzhetskyy
- Pharmaceutical Biotechnology, University of Saarland, Saarbrücken, Germany.,Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
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Ahmed Y, Rebets Y, Estévez MR, Zapp J, Myronovskyi M, Luzhetskyy A. Engineering of Streptomyces lividans for heterologous expression of secondary metabolite gene clusters. Microb Cell Fact 2020; 19:5. [PMID: 31918711 PMCID: PMC6950998 DOI: 10.1186/s12934-020-1277-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [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: 05/20/2019] [Accepted: 01/02/2020] [Indexed: 12/04/2022] Open
Abstract
Background Heterologous expression of secondary metabolite gene clusters is used to achieve increased production of desired compounds, activate cryptic gene clusters, manipulate clusters from genetically unamenable strains, obtain natural products from uncultivable species, create new unnatural pathways, etc. Several Streptomyces species are genetically engineered for use as hosts for heterologous expression of gene clusters. S. lividans TK24 is one of the most studied and genetically tractable actinobacteria, which remain untapped. It was therefore important to generate S. lividans chassis strains with clean metabolic backgrounds. Results In this study, we generated a set of S. lividans chassis strains by deleting endogenous gene clusters and introducing additional φC31 attB loci for site-specific integration of foreign DNA. In addition to the simplified metabolic background, the engineered S. lividans strains had better growth characteristics than the parental strain in liquid production medium. The utility of the developed strains was validated by expressing four secondary metabolite gene clusters responsible for the production of different classes of natural products. Engineered strains were found to be superior to the parental strain in production of heterologous natural products. Furthermore, S. lividans-based strains were better producers of amino acid-based natural products than other tested common hosts. Expression of a Streptomyces albus subsp. chlorinus NRRL B-24108 genomic library in the modified S. lividans ΔYA9 and S. albus Del14 strains resulted in the production of 7 potentially new compounds, only one of which was produced in both strains. Conclusion The constructed S. lividans-based strains are a great complement to the panel of heterologous hosts for actinobacterial secondary metabolite gene expression. The expansion of the number of such engineered strains will contribute to an increased success rate in isolation of new natural products originating from the expression of genomic and metagenomic libraries, thus raising the chance to obtain novel biologically active compounds.
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Affiliation(s)
- Yousra Ahmed
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Yuriy Rebets
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | | | - Josef Zapp
- Pharmazeutische Biologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Maksym Myronovskyi
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Andriy Luzhetskyy
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany. .,Helmholtz-Institut für Pharmazeutische Forschung Saarland, Saarbrücken, Germany.
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Rebets Y, Nadmid S, Paulus C, Dahlem C, Herrmann J, Hübner H, Rückert C, Kiemer AK, Gmeiner P, Kalinowski J, Müller R, Luzhetskyy A. Perquinoline A–C: neuartige bakterielle Tetrahydroisochinoline mit einer bemerkenswerten Biosynthese. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
- Department of Pharmacy Pharmaceutical Biotechnology University of Saarland Campus, Bld. C2 3 Saarbrucken 66123 Deutschland
| | - Suvd Nadmid
- Department of Pharmacy Pharmaceutical Biotechnology University of Saarland Campus, Bld. C2 3 Saarbrucken 66123 Deutschland
| | - Constanze Paulus
- Department of Pharmacy Pharmaceutical Biotechnology University of Saarland Campus, Bld. C2 3 Saarbrucken 66123 Deutschland
| | - Charlotte Dahlem
- Department of Pharmacy Pharmaceutical Biology University of Saarland Campus, Bld. C2 3 Saarbrucken 66123 Deutschland
| | - Jennifer Herrmann
- Department Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Campus, Bld. 8 1 Saarbrucken 66123 Deutschland
| | - Harald Hübner
- Department of Chemistry and Pharmacy Friedrich-Alexander-Universität Erlangen-Nürnberg Nikolaus-Fiebiger-Straße 10 91058 Erlangen Deutschland
| | - Christian Rückert
- Center for Biotechnology – CeBiTec University of Bielefeld Universitätsstraße 25 33615 Bielefeld Deutschland
| | - Alexandra K. Kiemer
- Department of Pharmacy Pharmaceutical Biology University of Saarland Campus, Bld. C2 3 Saarbrucken 66123 Deutschland
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy Friedrich-Alexander-Universität Erlangen-Nürnberg Nikolaus-Fiebiger-Straße 10 91058 Erlangen Deutschland
| | - Jörn Kalinowski
- Center for Biotechnology – CeBiTec University of Bielefeld Universitätsstraße 25 33615 Bielefeld Deutschland
| | - Rolf Müller
- Department Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Campus, Bld. 8 1 Saarbrucken 66123 Deutschland
| | - Andriy Luzhetskyy
- Department of Pharmacy Pharmaceutical Biotechnology University of Saarland Campus, Bld. C2 3 Saarbrucken 66123 Deutschland
- Department Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Campus, Bld. 8 1 Saarbrucken 66123 Deutschland
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Abstract
Time span of literature covered: 2010-2018The genome mining of streptomycetes has revealed their great biosynthetic potential to produce novel natural products. One of the most promising exploitation routes of this biosynthetic potential is the refactoring and heterologous expression of corresponding biosynthetic gene clusters in a panel of specifically selected and optimized chassis strains. This article will review selected recent reports on heterologous production of natural products in streptomycetes. In the first part, the importance of heterologous production for drug discovery will be discussed. In the second part, the review will discuss recently developed genetic control elements (such as promoters, ribosome binding sites, terminators) and their application to achieve successful heterologous expression of biosynthetic gene clusters. Finally, the most widely used Streptomyces hosts for heterologous expression of biosynthetic gene clusters will be compared in detail. The article will be of interest to natural product chemists, molecular biologists, pharmacists and all individuals working in the natural products drug discovery field.
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Affiliation(s)
| | - Andriy Luzhetskyy
- Saarland University, Department Pharmacy, Saarbrücken, Germany and Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany.
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Rebets Y, Nadmid S, Paulus C, Dahlem C, Herrmann J, Hübner H, Rückert C, Kiemer AK, Gmeiner P, Kalinowski J, Müller R, Luzhetskyy A. Perquinolines A-C: Unprecedented Bacterial Tetrahydroisoquinolines Involving an Intriguing Biosynthesis. Angew Chem Int Ed Engl 2019; 58:12930-12934. [PMID: 31310031 DOI: 10.1002/anie.201905538] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Indexed: 01/15/2023]
Abstract
Metabolic profiling of Streptomyces sp. IB2014/016-6 led to the identification of three new tetrahydroisoquinoline natural products, perquinolines A-C (1-3). Labelled precursor feeding studies and the cloning of the pqr biosynthetic gene cluster revealed that 1-3 are assembled by the action of several unusual enzymes. The biosynthesis starts with the condensation of succinyl-CoA and l-phenylalanine catalyzed by the amino-7-oxononanoate synthase-like enzyme PqrA, representing rare chemistry in natural product assembly. The second condensation and cyclization events are conducted by PqrG, an enzyme resembling an acyl-CoA ligase. Last, ATP-grasp RimK-type ligase PqrI completes the biosynthesis by transferring a γ-aminobutyric acid or β-alanine moiety. The discovered pathway represents a new route for assembling the tetrahydroisoquinoline cores of natural products.
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Affiliation(s)
- Yuriy Rebets
- Department of Pharmacy, Pharmaceutical Biotechnology, University of Saarland, Campus, Bld. C2 3, Saarbrucken, 66123, Germany
| | - Suvd Nadmid
- Department of Pharmacy, Pharmaceutical Biotechnology, University of Saarland, Campus, Bld. C2 3, Saarbrucken, 66123, Germany
| | - Constanze Paulus
- Department of Pharmacy, Pharmaceutical Biotechnology, University of Saarland, Campus, Bld. C2 3, Saarbrucken, 66123, Germany
| | - Charlotte Dahlem
- Department of Pharmacy, Pharmaceutical Biology, University of Saarland, Campus, Bld. C2 3, Saarbrucken, 66123, Germany
| | - Jennifer Herrmann
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Campus, Bld. 8 1, Saarbrucken, 66123, Germany
| | - Harald Hübner
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Strasse 10, 91058, Erlangen, Germany
| | - Christian Rückert
- Center for Biotechnology-CeBiTec, University of Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Alexandra K Kiemer
- Department of Pharmacy, Pharmaceutical Biology, University of Saarland, Campus, Bld. C2 3, Saarbrucken, 66123, Germany
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Strasse 10, 91058, Erlangen, Germany
| | - Jörn Kalinowski
- Center for Biotechnology-CeBiTec, University of Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Campus, Bld. 8 1, Saarbrucken, 66123, Germany
| | - Andriy Luzhetskyy
- Department of Pharmacy, Pharmaceutical Biotechnology, University of Saarland, Campus, Bld. C2 3, Saarbrucken, 66123, Germany.,Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Campus, Bld. 8 1, Saarbrucken, 66123, Germany
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Lopatniuk M, Myronovskyi M, Nottebrock A, Busche T, Kalinowski J, Ostash B, Fedorenko V, Luzhetskyy A. Effect of “ribosome engineering” on the transcription level and production of S. albus indigenous secondary metabolites. Appl Microbiol Biotechnol 2019; 103:7097-7110. [DOI: 10.1007/s00253-019-10005-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 06/11/2019] [Accepted: 06/30/2019] [Indexed: 01/31/2023]
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40
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Koshla O, Yushchuk O, Ostash I, Dacyuk Y, Myronovskyi M, Jäger G, Süssmuth RD, Luzhetskyy A, Byström A, Kirsebom LA, Ostash B. Gene miaA for post-transcriptional modification of tRNA XXA is important for morphological and metabolic differentiation in Streptomyces. Mol Microbiol 2019; 112:249-265. [PMID: 31017319 DOI: 10.1111/mmi.14266] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2019] [Indexed: 12/14/2022]
Abstract
Members of actinobacterial genus Streptomyces possess a sophisticated life cycle and are the deepest source of bioactive secondary metabolites. Although morphogenesis and secondary metabolism are subject to transcriptional co-regulation, streptomycetes employ an additional mechanism to initiate the aforementioned processes. This mechanism is based on delayed translation of rare leucyl codon UUA by the only cognate tRNALeu UAA (encoded by bldA). The bldA-based genetic switch is an extensively documented example of translational regulation in Streptomyces. Yet, after five decades since the discovery of bldA, factors that shape its function and peculiar conditionality remained elusive. Here we address the hypothesis that post-transcriptional tRNA modifications play a role in tRNA-based mechanisms of translational control in Streptomyces. Particularly, we studied two Streptomyces albus J1074 genes, XNR_1074 (miaA) and XNR_1078 (miaB), encoding tRNA (adenosine(37)-N6)-dimethylallyltransferase and tRNA (N6-isopentenyl adenosine(37)-C2)-methylthiotransferase respectively. These enzymes produce, in a sequential manner, a hypermodified ms2 i6 A37 residue in most of the A36-A37-containing tRNAs. We show that miaB and especially miaA null mutant of S. albus possess altered morphogenesis and secondary metabolism. We provide genetic evidence that miaA deficiency impacts translational level of gene expression, most likely through impaired decoding of codons UXX and UUA in particular.
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Affiliation(s)
- Oksana Koshla
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Lviv, 79005, Ukraine
| | - Oleksandr Yushchuk
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Lviv, 79005, Ukraine
| | - Iryna Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Lviv, 79005, Ukraine
| | - Yuriy Dacyuk
- Department of Physics of Earth, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Lviv, 79005, Ukraine
| | - Maksym Myronovskyi
- Helmholtz Institute for Pharmaceutical Research, Saarland Campus, Building C2.3, Saarbrucken, 66123, Germany
| | - Gunilla Jäger
- Department of Molecular Biology, Umeå University, 6K och 6L, Sjukhusområdet, Umeå, 90197, Sweden
| | - Roderich D Süssmuth
- Institut für Chemie, Technische Universität Berlin, Straβe des 17 Juni 124/TC2, Berlin, 10623, Germany
| | - Andriy Luzhetskyy
- Helmholtz Institute for Pharmaceutical Research, Saarland Campus, Building C2.3, Saarbrucken, 66123, Germany
| | - Anders Byström
- Department of Molecular Biology, Umeå University, 6K och 6L, Sjukhusområdet, Umeå, 90197, Sweden
| | - Leif A Kirsebom
- Uppsala Biomedicinska Centrum BMC, Uppsala University, Husargatan 3, Box 596, Uppsala, 75124, Sweden
| | - Bohdan Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Lviv, 79005, Ukraine
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41
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Kuzhyk Y, Lopatniuk M, Luzhetskyy A, Fedorenko V, Ostash B. Genome Engineering Approaches to Improve Nosokomycin A Production by Streptomyces ghanaensis B38.3. Indian J Microbiol 2019; 59:109-111. [PMID: 30728639 DOI: 10.1007/s12088-018-0761-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 05/02/2018] [Accepted: 09/21/2018] [Indexed: 10/28/2022] Open
Abstract
Here we describe our efforts to improve the levels of phosphoglycolipid antibiotic nosokomycin A production by Streptomyces ghanaensis ATCC14672 via genome engineering approaches. Introduction of two extra copies of leucyl tRNA (UUA) gene bldA and one copy of moenomycin biosynthesis gene cluster led, on average, to threefold increase in nosokomycin A titers (up to 1.5 mg/L). Our results validate genome engineering approach as a viable strategy to improve moenomycin production.
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Affiliation(s)
- Yuriy Kuzhyk
- 1Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Rm. 102, Lviv, 79005 Ukraine
| | - Maria Lopatniuk
- 2Actinobacteria Metabolic Engineering Group, Helmholtz-Institute for Pharmaceutical Research Saarland, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Andriy Luzhetskyy
- 2Actinobacteria Metabolic Engineering Group, Helmholtz-Institute for Pharmaceutical Research Saarland, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Victor Fedorenko
- 1Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Rm. 102, Lviv, 79005 Ukraine
| | - Bohdan Ostash
- 1Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Rm. 102, Lviv, 79005 Ukraine
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42
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Sehin Y, Koshla O, Dacyuk Y, Zhao R, Ross R, Myronovskyi M, Limbach PA, Luzhetskyy A, Walker S, Fedorenko V, Ostash B. Gene ssfg_01967 (miaB) for tRNA modification influences morphogenesis and moenomycin biosynthesis in Streptomyces ghanaensis ATCC14672. Microbiology (Reading) 2019; 165:233-245. [PMID: 30543507 PMCID: PMC7003650 DOI: 10.1099/mic.0.000747] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 10/31/2018] [Indexed: 12/26/2022]
Abstract
Streptomyces ghanaensis ATCC14672 is remarkable for its production of phosphoglycolipid compounds, moenomycins, which serve as a blueprint for the development of a novel class of antibiotics based on inhibition of peptidoglycan glycosyltransferases. Here we employed mariner transposon (Tn) mutagenesis to find new regulatory genes essential for moenomycin production. We generated a library of 3000 mutants which were screened for altered antibiotic activity. Our focus centred on a single mutant, HIM5, which accumulated lower amounts of moenomycin and was impaired in morphogenesis as compared to the parental strain. HIM5 carried the Tn insertion within gene ssfg_01967 for putative tRNA (N6-isopentenyl adenosine(37)-C2)-methylthiotransferase, or MiaB, and led to a reduced level of thiomethylation at position 37 in the anticodon of S. ghanaensis transfer ribonucleic acid (tRNA). It is likely that the mutant phenotype of HIM5 stems from the way in which ssfg_01967::Tn influences translation of the rare leucine codon UUA in several genes for moenomycin production and life cycle progression in S. ghanaensis. This is the first report showing that quantitative changes in tRNA modification status in Streptomyces have physiological consequences.
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Affiliation(s)
- Yuliia Sehin
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv 79005, Ukraine
| | - Oksana Koshla
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv 79005, Ukraine
| | - Yuriy Dacyuk
- Department of Physics of the Earth, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv 79005, Ukraine
| | - Ruoxia Zhao
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, 318 College Dr, 404 Crosley Tower, Cincinnati OH 45221-0172, USA
| | - Robert Ross
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, 318 College Dr, 404 Crosley Tower, Cincinnati OH 45221-0172, USA
| | - Maksym Myronovskyi
- Helmholtz Institute for Pharmaceutical Research Saarland Campus, Building C2.3, 66123 Saarbrucken, Germany
| | - Patrick A. Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, 318 College Dr, 404 Crosley Tower, Cincinnati OH 45221-0172, USA
| | - Andriy Luzhetskyy
- Helmholtz Institute for Pharmaceutical Research Saarland Campus, Building C2.3, 66123 Saarbrucken, Germany
| | - Suzanne Walker
- Department of Microbiology and Immunobiology, Harvard Medical School, 4 Blackfan Circle, Boston, MA 02115, USA
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv 79005, Ukraine
| | - Bohdan Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv 79005, Ukraine
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43
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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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44
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Hamed MB, Vrancken K, Bilyk B, Koepff J, Novakova R, van Mellaert L, Oldiges M, Luzhetskyy A, Kormanec J, Anné J, Karamanou S, Economou A. Monitoring Protein Secretion in Streptomyces Using Fluorescent Proteins. Front Microbiol 2018; 9:3019. [PMID: 30581427 PMCID: PMC6292873 DOI: 10.3389/fmicb.2018.03019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 09/27/2018] [Accepted: 11/22/2018] [Indexed: 01/25/2023] Open
Abstract
Fluorescent proteins are a major cell biology tool to analyze protein sub-cellular topology. Here we have applied this technology to study protein secretion in the Gram-positive bacterium Streptomyces lividans TK24, a widely used host for heterologous protein secretion biotechnology. Green and monomeric red fluorescent proteins were fused behind Sec (SPSec) or Tat (SPTat) signal peptides to direct them through the respective export pathway. Significant secretion of fluorescent eGFP and mRFP was observed exclusively through the Tat and Sec pathways, respectively. Plasmid over-expression was compared to a chromosomally integrated spSec-mRFP gene to allow monitoring secretion under high and low level synthesis in various media. Fluorimetric detection of SPSec-mRFP recorded folded states, while immuno-staining detected even non-folded topological intermediates. Secretion of SPSec-mRFP is unexpectedly complex, is regulated independently of cell growth phase and is influenced by the growth regime. At low level synthesis, highly efficient secretion occurs until it is turned off and secretory preforms accumulate. At high level synthesis, the secretory pathway overflows and proteins are driven to folding and subsequent degradation. High-level synthesis of heterologous secretory proteins, whether secretion competent or not, has a drastic effect on the endogenous secretome, depending on their secretion efficiency. These findings lay the foundations of dissecting how protein targeting and secretion are regulated by the interplay between the metabolome, secretion factors and stress responses in the S. lividans model.
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Affiliation(s)
- Mohamed Belal Hamed
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Molecular Biology Department, National Research Centre, Dokki, Egypt
| | - Kristof Vrancken
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | | | - Joachim Koepff
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Renata Novakova
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lieve van Mellaert
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Marco Oldiges
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Andriy Luzhetskyy
- Helmholtz-Zentrum für Infektionsforschung GmbH, Braunschweig, Germany
| | - Jan Kormanec
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jozef Anné
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Spyridoula Karamanou
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Anastassios Economou
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
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45
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Rodríguez Estévez M, Myronovskyi M, Gummerlich N, Nadmid S, Luzhetskyy A. Heterologous Expression of the Nybomycin Gene Cluster from the Marine Strain Streptomyces albus subsp. chlorinus NRRL B-24108. Mar Drugs 2018; 16:md16110435. [PMID: 30400361 PMCID: PMC6265801 DOI: 10.3390/md16110435] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 10/26/2018] [Accepted: 10/31/2018] [Indexed: 11/16/2022] Open
Abstract
Streptomycetes represent an important reservoir of active secondary metabolites with potential applications in the pharmaceutical industry. The gene clusters responsible for their production are often cryptic under laboratory growth conditions. Characterization of these clusters is therefore essential for the discovery of new microbial pharmaceutical drugs. Here, we report the identification of the previously uncharacterized nybomycin gene cluster from the marine actinomycete Streptomyces albus subsp. chlorinus through its heterologous expression. Nybomycin has previously been reported to act against quinolone-resistant Staphylococcus aureus strains harboring a mutated gyrA gene but not against those with intact gyrA. The nybomycin-resistant mutants generated from quinolone-resistant mutants have been reported to be caused by a back-mutation in the gyrA gene that restores susceptibility to quinolones. On the basis of gene function assignment from bioinformatics analysis, we suggest a model for nybomycin biosynthesis.
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Affiliation(s)
| | - Maksym Myronovskyi
- Pharmazeutische Biotechnologie, Universität des Saarlandes, 66123 Saarbrücken, Germany.
| | - Nils Gummerlich
- Pharmazeutische Biotechnologie, Universität des Saarlandes, 66123 Saarbrücken, Germany.
| | - Suvd Nadmid
- Pharmazeutische Biotechnologie, Universität des Saarlandes, 66123 Saarbrücken, Germany.
| | - Andriy Luzhetskyy
- Pharmazeutische Biotechnologie, Universität des Saarlandes, 66123 Saarbrücken, Germany.
- Helmholtz-Institut für Pharmazeutische Forschung Saarland, 66123 Saarbrücken, Germany.
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46
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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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Paulus C, Rebets Y, Zapp J, Rückert C, Kalinowski J, Luzhetskyy A. New Alpiniamides From Streptomyces sp. IB2014/011-12 Assembled by an Unusual Hybrid Non-ribosomal Peptide Synthetase Trans-AT Polyketide Synthase Enzyme. Front Microbiol 2018; 9:1959. [PMID: 30186270 PMCID: PMC6113372 DOI: 10.3389/fmicb.2018.01959] [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: 05/04/2018] [Accepted: 08/02/2018] [Indexed: 11/13/2022] Open
Abstract
The environment of Lake Baikal is a well-known source of microbial diversity. The strain Streptomyces sp. IB2014/011-12, isolated from samples collected at Lake Baikal, was found to exhibit potent activity against Gram-positive bacteria. Here, we report isolation and characterization of linear polyketide alpiniamide A (1) and its new derivatives B-D (2-5). The structures of alpiniamides A-D were established and their relative configuration was determined by combination of partial Murata's method and ROESY experiment. The absolute configuration of alpiniamide A was established through Mosher's method. The gene cluster, responsible for the biosynthesis of alpiniamides (alp) has been identified by genome mining and gene deletion experiments. The successful expression of the cloned alp gene cluster in a heterologous host supports these findings. Analysis of the architecture of the alp gene cluster and the feeding of labeled precursors elucidated the alpiniamide biosynthetic pathway. The biosynthesis of alpiniamides is an example of a rather simple polyketide assembly line generating unusual chemical diversity through the combination of domain/module skipping and double bond migration events.
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Affiliation(s)
- Constanze Paulus
- Helmholtz-Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
- Department for Pharmaceutical Biotechnology, University of Saarland, Saarbrücken, Germany
| | - Yuriy Rebets
- Department for Pharmaceutical Biotechnology, University of Saarland, Saarbrücken, Germany
| | - Josef Zapp
- Department for Pharmaceutical Biotechnology, University of Saarland, Saarbrücken, Germany
| | - Christian Rückert
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Helmholtz-Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
- Department for Pharmaceutical Biotechnology, University of Saarland, Saarbrücken, Germany
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48
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Yushchuk O, Ostash I, Vlasiuk I, Gren T, Luzhetskyy A, Kalinowski J, Fedorenko V, Ostash B. Heterologous AdpA transcription factors enhance landomycin production in Streptomyces cyanogenus S136 under a broad range of growth conditions. Appl Microbiol Biotechnol 2018; 102:8419-8428. [PMID: 30056513 DOI: 10.1007/s00253-018-9249-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 05/16/2018] [Revised: 07/09/2018] [Accepted: 07/14/2018] [Indexed: 01/14/2023]
Abstract
Streptomyces cyanogenus S136 is the only known producer of landomycin A (LaA), one of the largest glycosylated angucycline antibiotics possessing strong antiproliferative properties. There is rising interest in elucidation of mechanisms of action of landomycins, which, in turn, requires access to large quantities of the pure compounds. Overproduction of LaA has been achieved in the past through manipulation of cluster-situated regulatory genes. However, other components of the LaA biosynthetic regulatory network remain unknown. To fill this gap, we elucidated the contribution of AdpA family pleiotropic regulators in landomycin production via expression of adpA genes of different origins in S. cyanogenus S136. Overexpression of the native S. cyanogenus S136 adpA ortholog had no effect on landomycin titers. In the same time, expression of several heterologous adpA genes led to significantly increased landomycin production under different cultivation conditions. Hence, heterologous adpA genes are a useful tool to enhance or activate landomycin production by S. cyanogenus. Our ongoing research effort is focused on identification of mutations that render S. cyanogenus AdpA nonfunctional.
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Affiliation(s)
- Oleksandr Yushchuk
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Rm. 102, Lviv, 79005, Ukraine
| | - Iryna Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Rm. 102, Lviv, 79005, Ukraine
| | - Iryna Vlasiuk
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Rm. 102, Lviv, 79005, Ukraine
| | - Tetiana Gren
- Technology Platform Genomics, CeBiTec, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Actinobacteria Metabolic Engineering Group, Saarland University, UdS Campus C2 3, 66123, Saarbrucken, Germany
| | - Joern Kalinowski
- Technology Platform Genomics, CeBiTec, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Rm. 102, Lviv, 79005, Ukraine
| | - Bohdan Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Rm. 102, Lviv, 79005, Ukraine.
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49
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Busche T, Tsolis KC, Koepff J, Rebets Y, Rückert C, Hamed MB, Bleidt A, Wiechert W, Lopatniuk M, Yousra A, Anné J, Karamanou S, Oldiges M, Kalinowski J, Luzhetskyy A, Economou A. Multi-Omics and Targeted Approaches to Determine the Role of Cellular Proteases in Streptomyces Protein Secretion. Front Microbiol 2018; 9:1174. [PMID: 29915569 PMCID: PMC5994538 DOI: 10.3389/fmicb.2018.01174] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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: 03/22/2018] [Accepted: 05/15/2018] [Indexed: 01/29/2023] Open
Abstract
Gram-positive Streptomyces bacteria are profuse secretors of polypeptides using complex, yet unknown mechanisms. Many of their secretory proteins are proteases that play important roles in the acquisition of amino acids from the environment. Other proteases regulate cellular proteostasis. To begin dissecting the possible role of proteases in Streptomyces secretion, we applied a multi-omics approach. We probed the role of the 190 proteases of Streptomyces lividans strain TK24 in protein secretion in defined media at different stages of growth. Transcriptomics analysis revealed transcripts for 93% of these proteases and identified that 41 of them showed high abundance. Proteomics analysis identified 57 membrane-embedded or secreted proteases with variations in their abundance. We focused on 17 of these proteases and putative inhibitors and generated strains deleted of their genes. These were characterized in terms of their fitness, transcriptome and secretome changes. In addition, we performed a targeted analysis in deletion strains that also carried a secretion competent mRFP. One strain, carrying a deletion of the gene for the regulatory protease FtsH, showed significant global changes in overall transcription and enhanced secretome and secreted mRFP levels. These data provide a first multi-omics effort to characterize the complex regulatory mechanisms of protein secretion in Streptomyces lividans and lay the foundations for future rational manipulation of this process.
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Affiliation(s)
- Tobias Busche
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany.,Institute for Biology-Microbiology, Freie Universität Berlin, Berlin, Germany
| | - Konstantinos C Tsolis
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Joachim Koepff
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Jülich, Germany
| | - Yuriy Rebets
- Helmholtz-Zentrum für Infektionsforschung GmbH, Braunschweig, Germany.,Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | | | - Mohamed B Hamed
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Department of Molecular Biology, National Research Centre, Giza, Egypt
| | - Arne Bleidt
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Jülich, Germany
| | - Wolfgang Wiechert
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Jülich, Germany
| | - Mariia Lopatniuk
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Ahmed Yousra
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Jozef Anné
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Spyridoula Karamanou
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Marco Oldiges
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Jülich, Germany.,Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Helmholtz-Zentrum für Infektionsforschung GmbH, Braunschweig, Germany
| | - Anastassios Economou
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
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Rebets Y, Schmelz S, Gromyko O, Tistechok S, Petzke L, Scrima A, Luzhetskyy A. Design, development and application of whole-cell based antibiotic-specific biosensor. Metab Eng 2018; 47:263-270. [DOI: 10.1016/j.ymben.2018.03.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/16/2018] [Accepted: 03/29/2018] [Indexed: 01/25/2023]
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