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Seibel E, Um S, Dayras M, Bodawatta KH, de Kruijff M, Jønsson KA, Poulsen M, Kim KH, Beemelmanns C. Genome mining for macrolactam-encoding gene clusters allowed for the network-guided isolation of β-amino acid-containing cyclic derivatives and heterologous production of ciromicin A. Commun Chem 2023; 6:257. [PMID: 37985888 PMCID: PMC10662134 DOI: 10.1038/s42004-023-01034-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/19/2023] [Indexed: 11/22/2023] Open
Abstract
β-Amino acid-containing macrolactams represent a structurally diverse group of bioactive natural products derived from polyketides; however we are currently lacking a comprehensive overview about their abundance across bacterial families and the underlying biosynthetic diversity. In this study, we employed a targeted β-amino acid-specific homology-based multi-query search to identify potential bacterial macrolactam producers. Here we demonstrate that approximately 10% of each of the identified actinobacterial genera harbor a biosynthetic gene cluster (BGC) encoding macrolactam production. Based on our comparative study, we propose that mutations occurring in specific regions of polyketide synthases (PKS) are the primary drivers behind the variation in macrolactam ring sizes. We successfully validated two producers of ciromicin A from the genus Amycolatopsis, revised the composition of the biosynthetic gene cluster region mte of macrotermycins, and confirmed the ciromicin biosynthetic pathway through heterologous expression. Additionally, network-based metabolomic analysis uncovered three previously unreported macrotermycin congeners from Amycolatopsis sp. M39. The combination of targeted mining and network-based analysis serves as a powerful tool for identifying macrolactam producers and our studies will catalyze the future discovery of yet unreported macrolactams.
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Affiliation(s)
- Elena Seibel
- Chemical Biology of Microbe-Host Interactions, Leibniz institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
- Anti-Infectives from Microbiota, Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS), Campus E8.1, 66123, Saarbrücken, Germany
| | - Soohyun Um
- Chemical Biology of Microbe-Host Interactions, Leibniz institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Songdogwahak-ro, Incheon, 12983, Republic of Korea
| | - Marie Dayras
- Anti-Infectives from Microbiota, Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS), Campus E8.1, 66123, Saarbrücken, Germany
| | - Kasun H Bodawatta
- Globe Institute, Section for Molecular Ecology and Evolution, University of Copenhagen, 1350, Copenhagen K, Denmark
- Natural History Museum of Denmark - Research and Collections, University of Copenhagen, 2100, Copenhagen East, Denmark
| | - Martinus de Kruijff
- Anti-Infectives from Microbiota, Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS), Campus E8.1, 66123, Saarbrücken, Germany
| | - Knud A Jønsson
- Natural History Museum of Denmark - Research and Collections, University of Copenhagen, 2100, Copenhagen East, Denmark
- Section for Bioinformatics and Genetics, Swedish Museum of Natural History, 114 18, Stockholm, Sweden
| | - Michael Poulsen
- Section for Ecology and Evolution, University of Copenhagen, 2100, Copenhagen East, Denmark
| | - Ki Hyun Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
| | - Christine Beemelmanns
- Chemical Biology of Microbe-Host Interactions, Leibniz institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Beutenbergstraße 11a, 07745, Jena, Germany.
- Anti-Infectives from Microbiota, Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS), Campus E8.1, 66123, Saarbrücken, Germany.
- Saarland University, 66123, Saarbrücken, Germany.
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Schwitalla JW, Le NTH, Um S, Schalk F, Brönstrup M, Baunach M, Beemelmanns C. Heterologous expression of the cryptic mdk gene cluster and structural revision of maduralactomycin A. RSC Adv 2023; 13:34136-34144. [PMID: 38019997 PMCID: PMC10663993 DOI: 10.1039/d3ra05931f] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023] Open
Abstract
After conducting an in silico analysis of the cryptic mdk cluster region and performing transcriptomic studies, an integrative Streptomyces BAC Vector containing the mdk gene sequence was constructed. The heterologous expression of the mdk cluster in Streptomyces albus J1074 resulted in the production of the angucyclic product, seongomycin, which allowed for the assesment of its antibacterial, antiproliferative, and antiviral activities. Heterologous production was further confirmed by targeted knock-out experiments involving key regulators of the biosynthetic pathways. We were further able to revise the core structure of maduralactomycin A, using a computational approach.
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Affiliation(s)
- Jan W Schwitalla
- Chemical Biology of Microbe-Host Interactions, Hans-Knöll Institute (HKI) Beutenbergstraße 11a 07745 Jena Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) Campus E8 66123 Saarbrücken Germany
| | - Ngoc-Thao-Hien Le
- Department of Pharmaceutical Sciences, Natural Products and Food Research and Analysis (NatuRA), University of Antwerp Universiteitsplein 1 B-2610 Antwerp Belgium
| | - Soohyun Um
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University Incheon 21983 South Korea
| | - Felix Schalk
- Chemical Biology of Microbe-Host Interactions, Hans-Knöll Institute (HKI) Beutenbergstraße 11a 07745 Jena Germany
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research Inhoffenstrasse 7 D-38124 Braunschweig Germany
| | - Martin Baunach
- Institute of Pharmaceutical Biology, University of Bonn Nussallee 6 53115 Bonn Germany
| | - Christine Beemelmanns
- Chemical Biology of Microbe-Host Interactions, Hans-Knöll Institute (HKI) Beutenbergstraße 11a 07745 Jena Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) Campus E8 66123 Saarbrücken Germany
- Saarland University 66123 Saarbrücken Germany
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Mitousis L, Thoma Y, Musiol-Kroll EM. An Update on Molecular Tools for Genetic Engineering of Actinomycetes-The Source of Important Antibiotics and Other Valuable Compounds. Antibiotics (Basel) 2020; 9:E494. [PMID: 32784409 PMCID: PMC7460540 DOI: 10.3390/antibiotics9080494] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 02/06/2023] Open
Abstract
The first antibiotic-producing actinomycete (Streptomyces antibioticus) was described by Waksman and Woodruff in 1940. This discovery initiated the "actinomycetes era", in which several species were identified and demonstrated to be a great source of bioactive compounds. However, the remarkable group of microorganisms and their potential for the production of bioactive agents were only partially exploited. This is caused by the fact that the growth of many actinomycetes cannot be reproduced on artificial media at laboratory conditions. In addition, sequencing, genome mining and bioactivity screening disclosed that numerous biosynthetic gene clusters (BGCs), encoded in actinomycetes genomes are not expressed and thus, the respective potential products remain uncharacterized. Therefore, a lot of effort was put into the development of technologies that facilitate the access to actinomycetes genomes and activation of their biosynthetic pathways. In this review, we mainly focus on molecular tools and methods for genetic engineering of actinomycetes that have emerged in the field in the past five years (2015-2020). In addition, we highlight examples of successful application of the recently developed technologies in genetic engineering of actinomycetes for activation and/or improvement of the biosynthesis of secondary metabolites.
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Affiliation(s)
| | | | - Ewa M. Musiol-Kroll
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (L.M.); (Y.T.)
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Chhiba-Govindjee VP, van der Westhuyzen CW, Bode ML, Brady D. Bacterial nitrilases and their regulation. Appl Microbiol Biotechnol 2019; 103:4679-4692. [DOI: 10.1007/s00253-019-09776-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 12/25/2022]
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Noguchi Y, Kashiwagi N, Uzura A, Ogino C, Kondo A, Ikeda H, Sota M. Development of a strictly regulated xylose-induced expression system in Streptomyces. Microb Cell Fact 2018; 17:151. [PMID: 30241528 PMCID: PMC6149001 DOI: 10.1186/s12934-018-0991-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 09/05/2018] [Indexed: 12/12/2022] Open
Abstract
Background Genetic tools including constitutive and inducible promoters have been developed over the last few decades for strain engineering in Streptomyces. Inducible promoters are useful for controlling gene expression, however only a limited number are applicable to Streptomyces. The aim of this study is to develop a controllable protein expression system based on an inducible promoter using sugar inducer, which has not yet been widely applied in Streptomyces. Results To determine a candidate promoter, inducible protein expression was first examined in Streptomyces avermitilis MA-4680 using various carbon sources. Xylose isomerase (xylA) promoter derived from xylose (xyl) operon was selected due to strong expression of xylose isomerase (XylA) in the presence of d-xylose. Next, a xylose-inducible protein expression system was constructed by investigating heterologous protein expression (chitobiase as a model protein) driven by the xylA promoter in Streptomyces lividans. Chitobiase activity was detected at high levels in S. lividans strain harboring an expression vector with xylA promoter (pXC), under both xylose-induced and non-induced conditions. Thus, S. avermitilis xylR gene, which encodes a putative repressor of xyl operon, was introduced into constructed vectors in order to control protein expression by d-xylose. Among strains constructed in the study, XCPR strain harboring pXCPR vector exhibited strict regulation of protein expression. Chitobiase activity in the XCPR strain was observed to be 24 times higher under xylose-induced conditions than that under non-induced conditions. Conclusion In this study, a strictly regulated protein expression system was developed based on a xylose-induced system. As far as we could ascertain, this is the first report of engineered inducible protein expression in Streptomyces by means of a xylose-induced system. This system might be applicable for controllable expression of toxic products or in the field of synthetic biology using Streptomyces strains. Electronic supplementary material The online version of this article (10.1186/s12934-018-0991-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuji Noguchi
- Nagase R&D Center, Nagase & Co., Ltd., 2-2-3 Murotani, Nishi-ku, Kobe, Hyogo, 651-2241, Japan
| | - Norimasa Kashiwagi
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Atsuko Uzura
- Nagase R&D Center, Nagase & Co., Ltd., 2-2-3 Murotani, Nishi-ku, Kobe, Hyogo, 651-2241, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.,RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Haruo Ikeda
- Laboratory of Microbial Engineering, Kitasato Institute for Life Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Masahiro Sota
- Nagase R&D Center, Nagase & Co., Ltd., 2-2-3 Murotani, Nishi-ku, Kobe, Hyogo, 651-2241, Japan
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