1
|
Li Y, Xu Z, Chen P, Zuo C, Chen L, Yan W, Jiao R, Ye Y. Genome Mining and Heterologous Expression Guided the Discovery of Antimicrobial Naphthocyclinones from Streptomyces eurocidicus CGMCC 4.1086. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2914-2923. [PMID: 36731876 DOI: 10.1021/acs.jafc.2c06928] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A type II polyketide synthase biosynthetic gene cluster (nap) was identified in Streptomyces eurocidicus CGMCC 4.1086 via genome mining. The heterologous expression of the cryptic nap gene cluster in Streptomyces albus J1074 generated dimerized aromatic polyketide naphthocyclinones (1-3), whose structures were determined via extensive analysis using nuclear magnetic resonance and high-resolution electrospray ionization mass spectroscopy. The biological pathway of naphthocyclinone synthesis was revealed via in vivo gene deletion, in vitro biochemical reactions, and comparative genomics. Remarkably, 3 played a crucial role in inhibiting Phytophthora capsici and Phytophthora sojae, with EC50 values of 6.1 and 20.2 μg/mL, respectively. Furthermore, 3 exhibited a potent protective effect against P. capsici and P. sojae in greenhouse tests.
Collapse
Affiliation(s)
- Yu Li
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, P. R. China
| | - Zifei Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ping Chen
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, P. R. China
| | - Chen Zuo
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, P. R. China
| | - Liyifan Chen
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, P. R. China
| | - Wei Yan
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, P. R. China
| | - Ruihua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yonghao Ye
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, P. R. China
| |
Collapse
|
2
|
Wu Z, Li Y, Zhang L, Ding Z, Shi G. Microbial production of small peptide: pathway engineering and synthetic biology. Microb Biotechnol 2021; 14:2257-2278. [PMID: 33459516 PMCID: PMC8601181 DOI: 10.1111/1751-7915.13743] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 12/12/2020] [Accepted: 12/13/2020] [Indexed: 01/14/2023] Open
Abstract
Small peptides are a group of natural products with low molecular weights and complex structures. The diverse structures of small peptides endow them with broad bioactivities and suggest their potential therapeutic use in the medical field. The remaining challenge is methods to address the main limitations, namely (i) the low amount of available small peptides from natural sources, and (ii) complex processes required for traditional chemical synthesis. Therefore, harnessing microbial cells as workhorse appears to be a promising approach to synthesize these bioactive peptides. As an emerging engineering technology, synthetic biology aims to create standard, well-characterized and controllable synthetic systems for the biosynthesis of natural products. In this review, we describe the recent developments in the microbial production of small peptides. More importantly, synthetic biology approaches are considered for the production of small peptides, with an emphasis on chassis cells, the evolution of biosynthetic pathways, strain improvements and fermentation.
Collapse
Affiliation(s)
- Zhiyong Wu
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan UniversityWuxiJiangsu Province214122China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
- Jiangsu Provisional Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
| | - Youran Li
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan UniversityWuxiJiangsu Province214122China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
- Jiangsu Provisional Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
| | - Liang Zhang
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan UniversityWuxiJiangsu Province214122China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
- Jiangsu Provisional Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
| | - Zhongyang Ding
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan UniversityWuxiJiangsu Province214122China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
- Jiangsu Provisional Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
| | - Guiyang Shi
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan UniversityWuxiJiangsu Province214122China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
- Jiangsu Provisional Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
| |
Collapse
|
3
|
De BC, Zhang W, Zhang G, Liu Z, Tan B, Zhang Q, Zhang L, Zhang H, Zhu Y, Zhang C. Host-dependent heterologous expression of berninamycin gene cluster leads to linear thiopeptide antibiotics. Org Biomol Chem 2021; 19:8940-8946. [PMID: 34617948 DOI: 10.1039/d1ob01759d] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Berninamycins are a class of thiopeptide antibiotics with potent activity against Gram-positive bacteria. Heterologous expression of the berninamycin (ber) biosynthetic gene cluster from marine-derived Streptomyces sp. SCSIO 11878 in different terrestrial model Streptomyces hosts led to the production of berninamycins A (1) and B (2) in Streptomyces lividans SBT18 and Streptomyces coelicolor M1154, while two new linearized berninamycins J (3) and K (4) were obtained in Streptomyces albus J1074. Their structures were elucidated by detailed interpretation of NMR data and Marfey's method. Bioactivity assays showed that the linear thiopeptides 3 and 4 were less potent than 1 and 2 in antibacterial activity. This work indicates that undefined host-dependent enzymes might be responsible for generating the linear thiopeptides 3 and 4 in S. albus J1074.
Collapse
Affiliation(s)
- Bidhan Chandra De
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Wenjun Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Rd., Nansha District, Guangzhou 511458, China
| | - Guangtao Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Rd., Nansha District, Guangzhou 511458, China
| | - Zhiwen Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.
| | - Bin Tan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Rd., Nansha District, Guangzhou 511458, China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Rd., Nansha District, Guangzhou 511458, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Rd., Nansha District, Guangzhou 511458, China
| | - Haibo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Rd., Nansha District, Guangzhou 511458, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Rd., Nansha District, Guangzhou 511458, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Rd., Nansha District, Guangzhou 511458, China
| |
Collapse
|
4
|
Multi-omics Study of Planobispora rosea, Producer of the Thiopeptide Antibiotic GE2270A. mSystems 2021; 6:e0034121. [PMID: 34156292 PMCID: PMC8269224 DOI: 10.1128/msystems.00341-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Planobispora rosea is the natural producer of the potent thiopeptide antibiotic GE2270A. Here, we present the results of a metabolomics and transcriptomics analysis of P. rosea during production of GE2270A. The data generated provides useful insights into the biology of this genetically intractable bacterium. We characterize the details of the shutdown of protein biosynthesis and the respiratory chain associated with the end of the exponential growth phase. We also provide the first description of the phosphate regulon in P. rosea. Based on the transcriptomics data, we show that both phosphate and iron are limiting P. rosea growth in our experimental conditions. Additionally, we identified and validated a new biosynthetic gene cluster associated with the production of the siderophores benarthin and dibenarthin in P. rosea. Together, the metabolomics and transcriptomics data are used to inform and refine the very first genome-scale metabolic model for P. rosea, which will be a valuable framework for the interpretation of future studies of the biology of this interesting but poorly characterized species. IMPORTANCEPlanobispora rosea is a genetically intractable bacterium used for the production of GE2270A on an industrial scale. GE2270A is a potent thiopeptide antibiotic currently used as a precursor for the synthesis of two compounds under clinical studies for the treatment of Clostridium difficile infection and acne. Here, we present the very first systematic multi-omics investigation of this important bacterium, which provides a much-needed detailed picture of the dynamics of metabolism of P. rosea while producing GE2270A. Author Video: An author video summary of this article is available.
Collapse
|
5
|
Rational engineering strategies for achieving high-yield, high-quality and high-stability of natural product production in actinomycetes. Metab Eng 2021; 67:198-215. [PMID: 34166765 DOI: 10.1016/j.ymben.2021.06.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/30/2021] [Accepted: 06/19/2021] [Indexed: 12/11/2022]
Abstract
Actinomycetes are recognized as excellent producers of microbial natural products, which have a wide range of applications, especially in medicine, agriculture and stockbreeding. The three main indexes of industrialization (titer, purity and stability) must be taken into overall consideration in the manufacturing process of natural products. Over the past decades, synthetic biology techniques have expedited the development of industrially competitive strains with excellent performances. Here, we summarize various rational engineering strategies for upgrading the performance of industrial actinomycetes, which include enhancing the yield of natural products, eliminating the by-products and improving the genetic stability of engineered strains. Furthermore, the current challenges and future perspectives for optimizing the industrial strains more systematically through combinatorial engineering strategies are also discussed.
Collapse
|
6
|
Recent Advances in the Heterologous Biosynthesis of Natural Products from Streptomyces. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11041851] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Streptomyces is a significant source of natural products that are used as therapeutic antibiotics, anticancer and antitumor agents, pesticides, and dyes. Recently, with the advances in metabolite analysis, many new secondary metabolites have been characterized. Moreover, genome mining approaches demonstrate that many silent and cryptic biosynthetic gene clusters (BGCs) and many secondary metabolites are produced in very low amounts under laboratory conditions. One strain many compounds (OSMAC), overexpression/deletion of regulatory genes, ribosome engineering, and promoter replacement have been utilized to activate or enhance the production titer of target compounds. Hence, the heterologous expression of BGCs by transferring to a suitable production platform has been successfully employed for the detection, characterization, and yield quantity production of many secondary metabolites. In this review, we introduce the systematic approach for the heterologous production of secondary metabolites from Streptomyces in Streptomyces and other hosts, the genome analysis tools, the host selection, and the development of genetic control elements for heterologous expression and the production of secondary metabolites.
Collapse
|
7
|
Nitta K, Breitling R, Takano E, Putri SP, Fukusaki E. Investigation of the effects of actinorhodin biosynthetic gene cluster expression and a rpoB point mutation on the metabolome of Streptomyces coelicolor M1146. J Biosci Bioeng 2021; 131:525-536. [PMID: 33549493 DOI: 10.1016/j.jbiosc.2021.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 02/07/2023]
Abstract
The previously reported Streptomyces coelicolor M1146 is commonly used as a host strain for engineering of secondary metabolite production. In this study, absolute quantification of intracellular and extracellular metabolites of M1146 was performed in mid-log phase and stationary phase to observe major metabolites and the changes that occurred during growth. Decreased levels of central carbon metabolites (glycolysis, TCA cycle, and pentose phosphate pathway) and increased levels of amino acids were observed in stationary phase compared to mid-log phase. Furthermore, comparative metabolome analyses of M1146 upon expression of the actinorhodin biosynthetic gene cluster (M1146+ACT), a point mutation on the rpoB gene encoding RNA polymerase beta-subunit (M1152), and both expression of actinorhodin biosynthetic gene cluster and a rpoB point mutation (M1152+ACT) were performed. M1146+ACT showed higher levels of important cofactors, such as ATP, NADPH, and FMN while M1152 led to higher levels of intracellular S-adenosyl-methionine, acyl-CoAs, and extracellular nucleosides compared to M1146. M1152+ACT exhibited the highest levels of actinorhodin with elevated bases, nucleosides, and nucleotides, such as intracellular PRPP (phosphoribosyl phosphate), ATP, along with extracellular inosine, uridine, and guanine compared to the other three strains, which were considered to be combined effects of actinorhodin gene cluster expression and a rpoB point mutation. Metabolites analysis by means of absolute quantification demonstrated changes in precursors of secondary metabolites before and after phosphate depletion in M1146. Comparative metabolome analysis provided further insights into the effects of actinorhodin gene cluster expression along with a rpoB point mutation on the metabolome of S. coelicolor.
Collapse
Affiliation(s)
- Katsuaki Nitta
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Eriko Takano
- Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Sastia P Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| |
Collapse
|
8
|
Vior NM, Cea-Torrescassana E, Eyles TH, Chandra G, Truman AW. Regulation of Bottromycin Biosynthesis Involves an Internal Transcriptional Start Site and a Cluster-Situated Modulator. Front Microbiol 2020; 11:495. [PMID: 32273872 PMCID: PMC7113386 DOI: 10.3389/fmicb.2020.00495] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 03/06/2020] [Indexed: 01/18/2023] Open
Abstract
Bottromycin is a ribosomally synthesized and post-translationally modified peptide (RiPP) produced by several streptomycetes, including the plant pathogen Streptomyces scabies. There is significant interest in this molecule as it possesses strong antibacterial activity against clinically relevant multidrug resistant pathogens and is structurally distinct from all other antibiotics. However, studies into its efficacy are hampered by poor yields. An understanding of how bottromycin biosynthesis is regulated could aid the development of strategies to increase titres. Here, we use 5′-tag-RNA-seq to identify the transcriptional organization of the gene cluster, which includes an internal transcriptional start site that precedes btmD, the gene that encodes the bottromycin precursor peptide. We show that the gene cluster does not encode a master regulator that controls pathway expression and instead encodes a regulatory gene, btmL, which functions as a modulator that specifically affects the expression of btmD but not genes up- or downstream of btmD. In order to identify non-cluster associated proteins involved in regulation, proteins were identified that bind to the main promoter of the pathway, which precedes btmC. This study provides insights into how this deceptively complex pathway is regulated in the absence of a pathway specific master regulator, and how it might coordinate with the central metabolism of the cell.
Collapse
Affiliation(s)
- Natalia M Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | | | - Tom H Eyles
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| |
Collapse
|
9
|
DeepRiPP integrates multiomics data to automate discovery of novel ribosomally synthesized natural products. Proc Natl Acad Sci U S A 2019; 117:371-380. [PMID: 31871149 DOI: 10.1073/pnas.1901493116] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Microbial natural products represent a rich resource of evolved chemistry that forms the basis for the majority of pharmacotherapeutics. Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are a particularly interesting class of natural products noted for their unique mode of biosynthesis and biological activities. Analyses of sequenced microbial genomes have revealed an enormous number of biosynthetic loci encoding RiPPs but whose products remain cryptic. In parallel, analyses of bacterial metabolomes typically assign chemical structures to only a minority of detected metabolites. Aligning these 2 disparate sources of data could provide a comprehensive strategy for natural product discovery. Here we present DeepRiPP, an integrated genomic and metabolomic platform that employs machine learning to automate the selective discovery and isolation of novel RiPPs. DeepRiPP includes 3 modules. The first, NLPPrecursor, identifies RiPPs independent of genomic context and neighboring biosynthetic genes. The second module, BARLEY, prioritizes loci that encode novel compounds, while the third, CLAMS, automates the isolation of their corresponding products from complex bacterial extracts. DeepRiPP pinpoints target metabolites using large-scale comparative metabolomics analysis across a database of 10,498 extracts generated from 463 strains. We apply the DeepRiPP platform to expand the landscape of novel RiPPs encoded within sequenced genomes and to discover 3 novel RiPPs, whose structures are exactly as predicted by our platform. By building on advances in machine learning technologies, DeepRiPP integrates genomic and metabolomic data to guide the isolation of novel RiPPs in an automated manner.
Collapse
|
10
|
Sekurova ON, Schneider O, Zotchev SB. Novel bioactive natural products from bacteria via bioprospecting, genome mining and metabolic engineering. Microb Biotechnol 2019; 12:828-844. [PMID: 30834674 PMCID: PMC6680616 DOI: 10.1111/1751-7915.13398] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/15/2019] [Accepted: 02/21/2019] [Indexed: 12/21/2022] Open
Abstract
For over seven decades, bacteria served as a valuable source of bioactive natural products some of which were eventually developed into drugs to treat infections, cancer and immune system-related diseases. Traditionally, novel compounds produced by bacteria were discovered via conventional bioprospecting based on isolation of potential producers and screening their extracts in a variety of bioassays. Over time, most of the natural products identifiable by this approach were discovered, and the pipeline for new drugs based on bacterially produced metabolites started to run dry. This mini-review highlights recent developments in bacterial bioprospecting for novel compounds that are based on several out-of-the-box approaches, including the following: (i) targeting bacterial species previously unknown to produce any bioactive natural products, (ii) exploring non-traditional environmental niches and methods for isolation of bacteria and (iii) various types of 'genome mining' aimed at unravelling genetic potential of bacteria to produce secondary metabolites. All these approaches have already yielded a number of novel bioactive compounds and, if used wisely, will soon revitalize drug discovery pipeline based on bacterial natural products.
Collapse
Affiliation(s)
- Olga N. Sekurova
- Department of PharmacognosyUniversity of ViennaAlthanstraße 141090ViennaAustria
| | - Olha Schneider
- Department of PharmacognosyUniversity of ViennaAlthanstraße 141090ViennaAustria
| | - Sergey B. Zotchev
- Department of PharmacognosyUniversity of ViennaAlthanstraße 141090ViennaAustria
| |
Collapse
|
11
|
Myronovskyi M, Luzhetskyy A. Heterologous production of small molecules in the optimized Streptomyces hosts. Nat Prod Rep 2019; 36:1281-1294. [PMID: 31453623 DOI: 10.1039/c9np00023b] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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.
Collapse
Affiliation(s)
| | - Andriy Luzhetskyy
- Saarland University, Department Pharmacy, Saarbrücken, Germany and Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany.
| |
Collapse
|
12
|
Wang X, Yin S, Bai J, Liu Y, Fan K, Wang H, Yuan F, Zhao B, Li Z, Wang W. Heterologous production of chlortetracycline in an industrial grade Streptomyces rimosus host. Appl Microbiol Biotechnol 2019; 103:6645-6655. [PMID: 31240365 DOI: 10.1007/s00253-019-09970-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/28/2019] [Accepted: 06/05/2019] [Indexed: 01/06/2023]
Abstract
High-yielding industrial Streptomyces producer is usually obtained by multiple rounds of random mutagenesis and screening. These strains have great potential to be developed as the versatile chassis for the discovery and titer improvement of desired heterologous products. Here, the industrial strain Streptomyces rimosus 461, which is a high producer of oxytetracycline, has been engineered as a robust host for heterologous expression of chlortetracycline (CTC) biosynthetic gene cluster. First, the industrial chassis strain SR0 was constructed by deleting the whole oxytetracycline gene cluster of S. rimosus 461. Then, the biosynthetic gene cluster ctc of Streptomyces aureofaciens ATCC 10762 was integrated into the chromosome of SR0. With an additional constitutively expressed cluster-situated activator gene ctcB, the CTC titer of the engineering strain SRC1 immediately reached 1.51 g/L in shaking flask. Then, the CTC titers were upgraded to 2.15 and 3.27 g/L, respectively, in the engineering strains SRC2 and SRC3 with the enhanced ctcB expression. Further, two cluster-situated resistance genes were co-overexpressed with ctcB. The resultant strain produced CTC up to 3.80 g/L in shaking flask fermentation, which represents 38 times increase in comparison with that of the original producer. Overall, SR0 presented in this study have great potential to be used for heterologous production of tetracyclines and other type II polyketides.
Collapse
Affiliation(s)
- Xuefeng Wang
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China.,Hebei Shengxue Dacheng Pharmaceutical Co., Ltd., Shijiazhuang, 051430, Hebei, People's Republic of China
| | - Shouliang Yin
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, People's Republic of China
| | - Jing Bai
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China
| | - Yang Liu
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, People's Republic of China
| | - Keqiang Fan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Huizhuan Wang
- Hebei Shengxue Dacheng Pharmaceutical Co., Ltd., Shijiazhuang, 051430, Hebei, People's Republic of China
| | - Fang Yuan
- Hebei Shengxue Dacheng Pharmaceutical Co., Ltd., Shijiazhuang, 051430, Hebei, People's Republic of China
| | - Baohua Zhao
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China.
| | - Zilong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, People's Republic of China.
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, People's Republic of China.
| |
Collapse
|
13
|
van der Heul HU, Bilyk BL, McDowall KJ, Seipke RF, van Wezel GP. Regulation of antibiotic production in Actinobacteria: new perspectives from the post-genomic era. Nat Prod Rep 2019; 35:575-604. [PMID: 29721572 DOI: 10.1039/c8np00012c] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: 2000 to 2018 The antimicrobial activity of many of their natural products has brought prominence to the Streptomycetaceae, a family of Gram-positive bacteria that inhabit both soil and aquatic sediments. In the natural environment, antimicrobial compounds are likely to limit the growth of competitors, thereby offering a selective advantage to the producer, in particular when nutrients become limited and the developmental programme leading to spores commences. The study of the control of this secondary metabolism continues to offer insights into its integration with a complex lifecycle that takes multiple cues from the environment and primary metabolism. Such information can then be harnessed to devise laboratory screening conditions to discover compounds with new or improved clinical value. Here we provide an update of the review we published in NPR in 2011. Besides providing the essential background, we focus on recent developments in our understanding of the underlying regulatory networks, ecological triggers of natural product biosynthesis, contributions from comparative genomics and approaches to awaken the biosynthesis of otherwise silent or cryptic natural products. In addition, we highlight recent discoveries on the control of antibiotic production in other Actinobacteria, which have gained considerable attention since the start of the genomics revolution. New technologies that have the potential to produce a step change in our understanding of the regulation of secondary metabolism are also described.
Collapse
|
14
|
O'Neill EC, Schorn M, Larson CB, Millán-Aguiñaga N. Targeted antibiotic discovery through biosynthesis-associated resistance determinants: target directed genome mining. Crit Rev Microbiol 2019; 45:255-277. [PMID: 30985219 DOI: 10.1080/1040841x.2019.1590307] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Intense competition between microbes in the environment has directed the evolution of antibiotic production in bacteria. Humans have harnessed these natural molecules for medicinal purposes, magnifying them from environmental concentrations to industrial scale. This increased exposure to antibiotics has amplified antibiotic resistance across bacteria, spurring a global antimicrobial crisis and a search for antibiotics with new modes of action. Genetic insights into these antibiotic-producing microbes reveal that they have evolved several resistance strategies to avoid self-toxicity, including product modification, substrate transport and binding, and target duplication or modification. Of these mechanisms, target duplication or modification will be highlighted in this review, as it uniquely links an antibiotic to its mode of action. We will further discuss and propose a strategy to mine microbial genomes for these genes and their associated biosynthetic gene clusters to discover novel antibiotics using target directed genome mining.
Collapse
Affiliation(s)
- Ellis C O'Neill
- a Department of Plant Sciences, University of Oxford , Oxford , Oxfordshire , UK
| | - Michelle Schorn
- b Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California , San Diego , CA , USA
| | - Charles B Larson
- b Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California , San Diego , CA , USA
| | - Natalie Millán-Aguiñaga
- c Universidad Autónoma de Baja California, Facultad de Ciencias Marinas , Ensenada , Baja California , México
| |
Collapse
|
15
|
Nepal KK, Wang G. Streptomycetes: Surrogate hosts for the genetic manipulation of biosynthetic gene clusters and production of natural products. Biotechnol Adv 2019; 37:1-20. [PMID: 30312648 PMCID: PMC6343487 DOI: 10.1016/j.biotechadv.2018.10.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/04/2018] [Accepted: 10/05/2018] [Indexed: 12/23/2022]
Abstract
Due to the worldwide prevalence of multidrug-resistant pathogens and high incidence of diseases such as cancer, there is an urgent need for the discovery and development of new drugs. Nearly half of the FDA-approved drugs are derived from natural products that are produced by living organisms, mainly bacteria, fungi, and plants. Commercial development is often limited by the low yield of the desired compounds expressed by the native producers. In addition, recent advances in whole genome sequencing and bioinformatics have revealed an abundance of cryptic biosynthetic gene clusters within microbial genomes. Genetic manipulation of clusters in the native host is commonly used to awaken poorly expressed or silent gene clusters, however, the lack of feasible genetic manipulation systems in many strains often hinders our ability to engineer the native producers. The transfer of gene clusters into heterologous hosts for expression of partial or entire biosynthetic pathways is an approach that can be used to overcome this limitation. Heterologous expression also facilitates the chimeric fusion of different biosynthetic pathways, leading to the generation of "unnatural" natural products. The genus Streptomyces is especially known to be a prolific source of drugs/antibiotics, its members are often used as heterologous expression hosts. In this review, we summarize recent applications of Streptomyces species, S. coelicolor, S. lividans, S. albus, S. venezuelae and S. avermitilis, as heterologous expression systems.
Collapse
Affiliation(s)
- Keshav K Nepal
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 U.S. 1 North, Fort Pierce, FL 34946, USA
| | - Guojun Wang
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 U.S. 1 North, Fort Pierce, FL 34946, USA.
| |
Collapse
|
16
|
Abstract
Although considerable knowledge of the biosynthetic machinery of thiopeptide antibiotics has been accumulated, the regulation of their production remains unclear. In this issue of Cell Chemical Biology, Li et al. (2018) have now characterized a key transcription factor and suggest its feedback regulation by biosynthesis intermediates and the final product.
Collapse
Affiliation(s)
- Claudia Roessler
- Friedrich Schiller University, Institute of Organic and Macromolecular Chemistry, Humboldtstr. 10, D-07743 Jena, Germany
| | - Hans-Dieter Arndt
- Friedrich Schiller University, Institute of Organic and Macromolecular Chemistry, Humboldtstr. 10, D-07743 Jena, Germany.
| |
Collapse
|
17
|
Ichikawa H, Bashiri G, Kelly WL. Biosynthesis of the Thiopeptins and Identification of an F 420H 2-Dependent Dehydropiperidine Reductase. J Am Chem Soc 2018; 140:10749-10756. [PMID: 30118217 PMCID: PMC6193465 DOI: 10.1021/jacs.8b04238] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Thiopeptins are highly decorated thiopeptide antibiotics similar in structure to thiostrepton A and harbor two unusual features. All thiopeptins contain a thioamide, a rare moiety among natural products, and a subset of thiopeptins present with a piperidine in the core macrocycle rather than the more oxidated dehydropiperidine or pyridine rings typically observed in the thiopeptides. Here, we report the identification of the thiopeptin biosynthetic gene ( tpn) cluster in Streptomyces tateyamensis and the gene product, TpnL, which shows sequence similarity to (deaza)flavin-dependent oxidoreductases. Heterologous expression of TpnL in the thiostrepton A producer Streptomyces laurentii led to the production of a piperidine-containing analogue. Binding studies revealed that TpnL preferentially binds the deazaflavin cofactor coenzyme F420, and in vitro reconstitution of TpnL activity confirmed that this enzyme is an F420H2-dependent dehydropiperidine reductase. The identification of TpnL and its activity establishes the basis for the piperidine-containing series a thiopeptides, one of the five main structural groups of this diverse family of antibiotics.
Collapse
Affiliation(s)
- Hiro Ichikawa
- School of Chemistry and Biochemistry and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ghader Bashiri
- Laboratory of Structural Biology and Maurice Wilkins Center for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Wendy L. Kelly
- School of Chemistry and Biochemistry and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| |
Collapse
|
18
|
Zhang Y, Chen M, Bruner SD, Ding Y. Heterologous Production of Microbial Ribosomally Synthesized and Post-translationally Modified Peptides. Front Microbiol 2018; 9:1801. [PMID: 30135682 PMCID: PMC6092494 DOI: 10.3389/fmicb.2018.01801] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/17/2018] [Indexed: 12/30/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides, or RiPPs, which have mainly isolated from microbes as well as plants and animals, are an ever-expanding group of peptidic natural products with diverse chemical structures and biological activities. They have emerged as a major category of secondary metabolites partly due to a myriad of microbial genome sequencing endeavors and the availability of genome mining software in the past two decades. Heterologous expression of RiPP gene clusters mined from microbial genomes, which are often silent in native producers, in surrogate hosts such as Escherichia coli and Streptomyces strains can be an effective way to elucidate encoded peptides and produce novel derivatives. Emerging strategies have been developed to facilitate the success of the heterologous expression by targeting multiple synthetic biology levels, including individual proteins, pathways, metabolic flux and hosts. This review describes recent advances in heterologous production of RiPPs, mainly from microbes, with a focus on E. coli and Streptomyces strains as the surrogate hosts.
Collapse
Affiliation(s)
- Yi Zhang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Manyun Chen
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Steven D Bruner
- Department of Chemistry, University of Florida, Gainesville, FL, United States
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
| |
Collapse
|
19
|
Mevaere J, Goulard C, Schneider O, Sekurova ON, Ma H, Zirah S, Afonso C, Rebuffat S, Zotchev SB, Li Y. An orthogonal system for heterologous expression of actinobacterial lasso peptides in Streptomyces hosts. Sci Rep 2018; 8:8232. [PMID: 29844351 PMCID: PMC5974421 DOI: 10.1038/s41598-018-26620-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 05/15/2018] [Indexed: 12/05/2022] Open
Abstract
Lasso peptides are ribosomally synthesized and post-translationally modified peptides produced by bacteria. They are characterized by an unusual lariat-knot structure. Targeted genome scanning revealed a wide diversity of lasso peptides encoded in actinobacterial genomes, but cloning and heterologous expression of these clusters turned out to be problematic. To circumvent this, we developed an orthogonal expression system for heterologous production of actinobacterial lasso peptides in Streptomyces hosts based on a newly-identified regulatory circuit from Actinoalloteichus fjordicus. Six lasso peptide gene clusters, mainly originating from marine Actinobacteria, were chosen for proof-of-concept studies. By varying the Streptomyces expression hosts and a small set of culture conditions, three new lasso peptides were successfully produced and characterized by tandem MS. The newly developed expression system thus sets the stage to uncover and bioengineer the chemo-diversity of actinobacterial lasso peptides. Moreover, our data provide some considerations for future bioprospecting efforts for such peptides.
Collapse
Affiliation(s)
- Jimmy Mevaere
- Laboratory « Molecules of Communication and Adaptation of Microorganisms » (MCAM, UMR 7245 CNRS-MNHN), Sorbonne Universités, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, 75005, Paris, France
| | - Christophe Goulard
- Laboratory « Molecules of Communication and Adaptation of Microorganisms » (MCAM, UMR 7245 CNRS-MNHN), Sorbonne Universités, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, 75005, Paris, France
| | - Olha Schneider
- Department of Biotechnology, Norwegian University of Science and Technology NTNU, N-7491, Trondheim, Norway
| | - Olga N Sekurova
- Department of Pharmacognosy, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
| | - Haiyan Ma
- Laboratory « Molecules of Communication and Adaptation of Microorganisms » (MCAM, UMR 7245 CNRS-MNHN), Sorbonne Universités, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, 75005, Paris, France.,Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Séverine Zirah
- Laboratory « Molecules of Communication and Adaptation of Microorganisms » (MCAM, UMR 7245 CNRS-MNHN), Sorbonne Universités, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, 75005, Paris, France
| | - Carlos Afonso
- Normandie Université, INSA Rouen, UNIROUEN, CNRS, COBRA, Rouen, France
| | - Sylvie Rebuffat
- Laboratory « Molecules of Communication and Adaptation of Microorganisms » (MCAM, UMR 7245 CNRS-MNHN), Sorbonne Universités, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, 75005, Paris, France
| | - Sergey B Zotchev
- Department of Pharmacognosy, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria.
| | - Yanyan Li
- Laboratory « Molecules of Communication and Adaptation of Microorganisms » (MCAM, UMR 7245 CNRS-MNHN), Sorbonne Universités, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, 75005, Paris, France.
| |
Collapse
|
20
|
Schwarz PN, Buchmann A, Roller L, Kulik A, Gross H, Wohlleben W, Stegmann E. The Immunosuppressant Brasilicardin: Determination of the Biosynthetic Gene Cluster in the Heterologous HostAmycolatopsis japonicum. Biotechnol J 2017; 13. [DOI: 10.1002/biot.201700527] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/05/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Paul N. Schwarz
- Microbiology/Biotechnology; Interfaculty Institute of Microbiology and Infection Medicine (IMIT); Eberhard Karls University of Tübingen; Tübingen Germany
| | - Anina Buchmann
- Department of Pharmaceutical Biology; Pharmaceutical Institute; Eberhard Karls University of Tübingen; Tübingen Germany
| | - Luisa Roller
- Microbiology/Biotechnology; Interfaculty Institute of Microbiology and Infection Medicine (IMIT); Eberhard Karls University of Tübingen; Tübingen Germany
| | - Andreas Kulik
- Microbiology/Biotechnology; Interfaculty Institute of Microbiology and Infection Medicine (IMIT); Eberhard Karls University of Tübingen; Tübingen Germany
| | - Harald Gross
- Department of Pharmaceutical Biology; Pharmaceutical Institute; Eberhard Karls University of Tübingen; Tübingen Germany
- German Centre for Infection Research (DZIF); Partner Site Tübingen; Tübingen Germany
| | - Wolfgang Wohlleben
- Microbiology/Biotechnology; Interfaculty Institute of Microbiology and Infection Medicine (IMIT); Eberhard Karls University of Tübingen; Tübingen Germany
- German Centre for Infection Research (DZIF); Partner Site Tübingen; Tübingen Germany
| | - Evi Stegmann
- Microbiology/Biotechnology; Interfaculty Institute of Microbiology and Infection Medicine (IMIT); Eberhard Karls University of Tübingen; Tübingen Germany
- German Centre for Infection Research (DZIF); Partner Site Tübingen; Tübingen Germany
| |
Collapse
|
21
|
Linares-Otoya L, Linares-Otoya V, Armas-Mantilla L, Blanco-Olano C, Crüsemann M, Ganoza-Yupanqui ML, Campos-Florian J, König GM, Schäberle TF. Identification and heterologous expression of the kocurin biosynthetic gene cluster. MICROBIOLOGY-SGM 2017; 163:1409-1414. [PMID: 28942758 DOI: 10.1099/mic.0.000538] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The antibiotically bioactive thiopeptide compound kocurin was identified in extracts from a newly isolated Kocuria rosea strain. The axenic strain was retrieved from a soil sample of the intertidal area at the Paracas National Park, Peru. The genetic basis of this promising natural product with activity against methicillin-resistant Staphylococcus aureus (MRSA) strains was revealed by comparative genome analysis of this new isolate and other reported thiopeptide producer strains. The functionality of the predicted gene locus was experimentally proven by heterologous expression in Streptomyces coelicolor M1146. Expression of the gene cluster under the control of a constitutive promoter enabled the transgenic strain to produce kocurin in selected media. The kocurin biosynthetic gene cluster comprises nine open reading frames and spans around 12 kbp of the genome.
Collapse
Affiliation(s)
- Luis Linares-Otoya
- Institute for Insect Biotechnology, Justus Liebig University of Giessen, Giessen, Germany.,Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany.,Research Centre for Sustainable Development Uku Pacha, Peru
| | - Virginia Linares-Otoya
- Research Centre for Sustainable Development Uku Pacha, Peru.,Department of Pharmacology, Faculty of Pharmacy and Biochemistry, National University of Trujillo, Trujillo, Peru
| | - Lizbeth Armas-Mantilla
- Department of Pharmacology, Faculty of Pharmacy and Biochemistry, National University of Trujillo, Trujillo, Peru
| | - Cyntia Blanco-Olano
- Department of Pharmacology, Faculty of Pharmacy and Biochemistry, National University of Trujillo, Trujillo, Peru
| | - Max Crüsemann
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Mayar L Ganoza-Yupanqui
- Department of Pharmacology, Faculty of Pharmacy and Biochemistry, National University of Trujillo, Trujillo, Peru
| | - Julio Campos-Florian
- Department of Pharmacology, Faculty of Pharmacy and Biochemistry, National University of Trujillo, Trujillo, Peru
| | - Gabriele M König
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany.,German Centre for Infection Research (DZIF) Partner Site Bonn, Cologne, Germany
| | - Till F Schäberle
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany.,Institute for Insect Biotechnology, Justus Liebig University of Giessen, Giessen, Germany.,German Centre for Infection Research (DZIF) Partner Site Bonn, Cologne, Germany
| |
Collapse
|
22
|
Prezioso SM, Brown NE, Goldberg JB. Elfamycins: inhibitors of elongation factor-Tu. Mol Microbiol 2017; 106:22-34. [PMID: 28710887 DOI: 10.1111/mmi.13750] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2017] [Indexed: 01/26/2023]
Abstract
Elfamycins are a relatively understudied group of antibiotics that target the essential process of translation through impairment of EF-Tu function. For the most part, the utility of these compounds has been as laboratory tools for the study of EF-Tu and the ribosome, as their poor pharmacokinetic profile and solubility has prevented implementation as therapeutic agents. However, due to the slowing of the antibiotic pipeline and the rapid emergence of resistance to approved antibiotics, this group is being reconsidered. Some researchers are using screens for novel naturally produced variants, while others are making directed, systematic chemical improvements on publically disclosed compounds. As an example of the latter approach, a GE2270 A derivative, LFF571, has completed phase 2 clinical trials, thus demonstrating the potential for elfamycins to become more prominent antibiotics in the future.
Collapse
Affiliation(s)
- Samantha M Prezioso
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Emory University School of Medicine, Atlanta, GA 30322, USA.,Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nicole E Brown
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Joanna B Goldberg
- Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.,Emory+Children's Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, GA 30322, USA
| |
Collapse
|
23
|
Basitta P, Westrich L, Rösch M, Kulik A, Gust B, Apel AK. AGOS: A Plug-and-Play Method for the Assembly of Artificial Gene Operons into Functional Biosynthetic Gene Clusters. ACS Synth Biol 2017; 6:817-825. [PMID: 28182401 DOI: 10.1021/acssynbio.6b00319] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The generation of novel secondary metabolites by reengineering or refactoring biochemical pathways is a rewarding but also challenging goal of synthetic biology. For this, the development of tools for the reconstruction of secondary metabolite gene clusters as well as the challenge of understanding the obstacles in this process is of great interest. The artificial gene operon assembly system (AGOS) is a plug-and-play method developed as a tool to consecutively assemble artificial gene operons into a destination vector and subsequently express them under the control of a de-repressed promoter in a Streptomyces host strain. AGOS was designed as a set of entry plasmids for the construction of artificial gene operons and a SuperCos1 based destination vector, into which the constructed operons can be assembled by Red/ET-mediated recombination. To provide a proof-of-concept of this method, we disassembled the well-known novobiocin biosynthetic gene cluster into four gene operons, encoding for the different moieties of novobiocin. We then genetically reorganized these gene operons with the help of AGOS to finally obtain the complete novobiocin gene cluster again. The production of novobiocin precursors and of novobiocin could successfully be detected by LC-MS and LC-MS/MS. Furthermore, we demonstrated that the omission of terminator sequences only had a minor impact on product formation in our system.
Collapse
Affiliation(s)
- Patrick Basitta
- Pharmaceutical
Biology, Pharmaceutical Institute, University of Tübingen, Auf
der Morgenstelle 8, Tübingen, 72076, Germany
| | - Lucia Westrich
- Pharmaceutical
Biology, Pharmaceutical Institute, University of Tübingen, Auf
der Morgenstelle 8, Tübingen, 72076, Germany
| | - Manuela Rösch
- Pharmaceutical
Biology, Pharmaceutical Institute, University of Tübingen, Auf
der Morgenstelle 8, Tübingen, 72076, Germany
| | | | - Bertolt Gust
- Pharmaceutical
Biology, Pharmaceutical Institute, University of Tübingen, Auf
der Morgenstelle 8, Tübingen, 72076, Germany
| | - Alexander Kristian Apel
- Pharmaceutical
Biology, Pharmaceutical Institute, University of Tübingen, Auf
der Morgenstelle 8, Tübingen, 72076, Germany
| |
Collapse
|
24
|
Elucidating and engineering thiopeptide biosynthesis. World J Microbiol Biotechnol 2017; 33:119. [DOI: 10.1007/s11274-017-2283-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 05/03/2017] [Indexed: 01/15/2023]
|
25
|
Nah HJ, Pyeon HR, Kang SH, Choi SS, Kim ES. Cloning and Heterologous Expression of a Large-sized Natural Product Biosynthetic Gene Cluster in Streptomyces Species. Front Microbiol 2017; 8:394. [PMID: 28360891 PMCID: PMC5350119 DOI: 10.3389/fmicb.2017.00394] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 02/24/2017] [Indexed: 12/14/2022] Open
Abstract
Actinomycetes family including Streptomyces species have been a major source for the discovery of novel natural products (NPs) in the last several decades thanks to their structural novelty, diversity and complexity. Moreover, recent genome mining approach has provided an attractive tool to screen potentially valuable NP biosynthetic gene clusters (BGCs) present in the actinomycetes genomes. Since many of these NP BGCs are silent or cryptic in the original actinomycetes, various techniques have been employed to activate these NP BGCs. Heterologous expression of BGCs has become a useful strategy to produce, reactivate, improve, and modify the pathways of NPs present at minute quantities in the original actinomycetes isolates. However, cloning and efficient overexpression of an entire NP BGC, often as large as over 100 kb, remain challenging due to the ineffectiveness of current genetic systems in manipulating large NP BGCs. This mini review describes examples of actinomycetes NP production through BGC heterologous expression systems as well as recent strategies specialized for the large-sized NP BGCs in Streptomyces heterologous hosts.
Collapse
Affiliation(s)
- Hee-Ju Nah
- Department of Biological Engineering, Inha University Incheon, South Korea
| | - Hye-Rim Pyeon
- Department of Biological Engineering, Inha University Incheon, South Korea
| | - Seung-Hoon Kang
- Department of Biological Engineering, Inha University Incheon, South Korea
| | - Si-Sun Choi
- Department of Biological Engineering, Inha University Incheon, South Korea
| | - Eung-Soo Kim
- Department of Biological Engineering, Inha University Incheon, South Korea
| |
Collapse
|
26
|
Burkhart BJ, Schwalen CJ, Mann G, Naismith JH, Mitchell DA. YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function. Chem Rev 2017; 117:5389-5456. [PMID: 28256131 DOI: 10.1021/acs.chemrev.6b00623] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
With advances in sequencing technology, uncharacterized proteins and domains of unknown function (DUFs) are rapidly accumulating in sequence databases and offer an opportunity to discover new protein chemistry and reaction mechanisms. The focus of this review, the formerly enigmatic YcaO superfamily (DUF181), has been found to catalyze a unique phosphorylation of a ribosomal peptide backbone amide upon attack by different nucleophiles. Established nucleophiles are the side chains of Cys, Ser, and Thr which gives rise to azoline/azole biosynthesis in ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products. However, much remains unknown about the potential for YcaO proteins to collaborate with other nucleophiles. Recent work suggests potential in forming thioamides, macroamidines, and possibly additional post-translational modifications. This review covers all knowledge through mid-2016 regarding the biosynthetic gene clusters (BGCs), natural products, functions, mechanisms, and applications of YcaO proteins and outlines likely future research directions for this protein superfamily.
Collapse
Affiliation(s)
| | | | - Greg Mann
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom
| | - James H Naismith
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom.,State Key Laboratory of Biotherapy, Sichuan University , Sichuan, China
| | | |
Collapse
|
27
|
Reconstitution and Minimization of a Micrococcin Biosynthetic Pathway in Bacillus subtilis. J Bacteriol 2016; 198:2431-8. [PMID: 27381911 DOI: 10.1128/jb.00396-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 06/24/2016] [Indexed: 12/23/2022] Open
Abstract
UNLABELLED Thiopeptides represent one of several families of highly modified peptide antibiotics that hold great promise for natural product engineering. These macrocyclic peptides are produced by a combination of ribosomal synthesis and extensive posttranslational modification by dedicated processing enzymes. We previously identified a compact, plasmid-borne gene cluster for the biosynthesis of micrococcin P1 (MP1), an archetypal thiopeptide antibiotic. In an effort to genetically dissect this pathway, we have reconstituted it in Bacillus subtilis Successful MP1 production required promoter engineering and the reassembly of essential biosynthetic genes in a modular plasmid. The resulting system allows for rapid pathway manipulation, including protein tagging and gene deletion. We find that 8 processing proteins are sufficient for the production of MP1 and that the tailoring enzyme TclS catalyzes a C-terminal reduction step that distinguishes MP1 from its sister compound micrococcin P2. IMPORTANCE The emergence of antibiotic resistance is one of the most urgent human health concerns of our day. A crucial component in an integrated strategy for countering antibiotic resistance is the ability to engineer pathways for the biosynthesis of natural and derivatized antimicrobial compounds. In this study, the model organism B. subtilis was employed to reconstitute and genetically modularize a 9-gene system for the biosynthesis of micrococcin, the founding member of a growing family of thiopeptide antibiotics.
Collapse
|
28
|
Bekiesch P, Basitta P, Apel AK. Challenges in the Heterologous Production of Antibiotics inStreptomyces. Arch Pharm (Weinheim) 2016; 349:594-601. [DOI: 10.1002/ardp.201600058] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/27/2016] [Accepted: 05/06/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Paulina Bekiesch
- Pharmaceutical Biology; Pharmaceutical Institute; Eberhard-Karls-Universität Tübingen; Tübingen Germany
- German Centre for Infection Research (DZIF); Partner Site Tübingen; Tübingen Germany
| | - Patrick Basitta
- Pharmaceutical Biology; Pharmaceutical Institute; Eberhard-Karls-Universität Tübingen; Tübingen Germany
- German Centre for Infection Research (DZIF); Partner Site Tübingen; Tübingen Germany
| | - Alexander K. Apel
- Pharmaceutical Biology; Pharmaceutical Institute; Eberhard-Karls-Universität Tübingen; Tübingen Germany
- German Centre for Infection Research (DZIF); Partner Site Tübingen; Tübingen Germany
| |
Collapse
|
29
|
A Streptomyces coelicolor host for the heterologous expression of Type III polyketide synthase genes. Microb Cell Fact 2015; 14:145. [PMID: 26376792 PMCID: PMC4573997 DOI: 10.1186/s12934-015-0335-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 09/03/2015] [Indexed: 11/30/2022] Open
Abstract
Background Recent advances in genome sequencing, combined with bioinformatic analysis, has led to the identification of numerous novel natural product gene clusters, particularly in actinomycetes of terrestrial and marine origin. Many of these gene clusters encode uncharacterised Type III polyketide synthases. To facilitate the study of these genes and their potentially novel products, we set out to construct an actinomycete expression host specifically designed for the heterologous expression of Type III PKS genes and their gene clusters. Results A derivative of Streptomyces coelicolor A3(2) designed for the expression of Type III polyketide synthase (PKS) genes was constructed from the previously engineered expression strain S. coelicolor M1152 [Δact Δred Δcpk Δcda rpoB(C1298T)] by removal of all three of the endogenous Type III PKS genes (gcs,srsA,rppA) by PCR targeting. The resulting septuple deletion mutant, M1317, proved to be an effective surrogate host for the expression of actinobacterial Type III PKS genes: expression of the reintroduced gcs gene from S. coelicolor and of the heterologous rppA gene from Streptomyces venezuelae under the control of the constitutive ermE* promoter resulted in copious production of germicidin and flaviolin, respectively. Conclusions The newly constructed expression host S. coelicolor M1317 should be particularly useful for the discovery and analysis of new Type III polyketide metabolites.
Collapse
|
30
|
Beites T, Mendes MV. Chassis optimization as a cornerstone for the application of synthetic biology based strategies in microbial secondary metabolism. Front Microbiol 2015; 6:906. [PMID: 26441855 PMCID: PMC4563238 DOI: 10.3389/fmicb.2015.00906] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 08/19/2015] [Indexed: 02/06/2023] Open
Abstract
The increased number of bacterial genome sequencing projects has generated over the last years a large reservoir of genomic information. In silico analysis of this genomic data has renewed the interest in bacterial bioprospecting for bioactive compounds by unveiling novel biosynthetic gene clusters of unknown or uncharacterized metabolites. However, only a small fraction of those metabolites is produced under laboratory-controlled conditions; the remaining clusters represent a pool of novel metabolites that are waiting to be “awaken”. Activation of the biosynthetic gene clusters that present reduced or no expression (known as cryptic or silent clusters) by heterologous expression has emerged as a strategy for the identification and production of novel bioactive molecules. Synthetic biology, with engineering principles at its core, provides an excellent framework for the development of efficient heterologous systems for the expression of biosynthetic gene clusters. However, a common problem in its application is the host-interference problem, i.e., the unpredictable interactions between the device and the host that can hamper the desired output. Although an effort has been made to develop orthogonal devices, the most proficient way to overcome the host-interference problem is through genome simplification. In this review we present an overview on the strategies and tools used in the development of hosts/chassis for the heterologous expression of specialized metabolites biosynthetic gene clusters. Finally, we introduce the concept of specialized host as the next step of development of expression hosts.
Collapse
Affiliation(s)
- Tiago Beites
- I3S Instituto de Investigação e Inovação em Saúde, Universidade do Porto Porto, Portugal ; Instituto de Biologia Molecular e Celular, Universidade do Porto Porto, Portugal
| | - Marta V Mendes
- I3S Instituto de Investigação e Inovação em Saúde, Universidade do Porto Porto, Portugal ; Instituto de Biologia Molecular e Celular, Universidade do Porto Porto, Portugal
| |
Collapse
|
31
|
Tocchetti A, Bordoni R, Gallo G, Petiti L, Corti G, Alt S, Cruz JCS, Salzano AM, Scaloni A, Puglia AM, De Bellis G, Peano C, Donadio S, Sosio M. A Genomic, Transcriptomic and Proteomic Look at the GE2270 Producer Planobispora rosea, an Uncommon Actinomycete. PLoS One 2015. [PMID: 26207753 PMCID: PMC4514598 DOI: 10.1371/journal.pone.0133705] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We report the genome sequence of Planobispora rosea ATCC 53733, a mycelium-forming soil-dweller belonging to one of the lesser studied genera of Actinobacteria and producing the thiopeptide GE2270. The P. rosea genome presents considerable convergence in gene organization and function with other members in the family Streptosporangiaceae, with a significant number (44%) of shared orthologs. Patterns of gene expression in P. rosea cultures during exponential and stationary phase have been analyzed using whole transcriptome shotgun sequencing and by proteome analysis. Among the differentially abundant proteins, those involved in protein metabolism are particularly represented, including the GE2270-insensitive EF-Tu. Two proteins from the pbt cluster, directing GE2270 biosynthesis, slightly increase their abundance values over time. While GE2270 production starts during the exponential phase, most pbt genes, as analyzed by qRT-PCR, are down-regulated. The exception is represented by pbtA, encoding the precursor peptide of the ribosomally synthesized GE2270, whose expression reached the highest level at the entry into stationary phase.
Collapse
Affiliation(s)
| | - Roberta Bordoni
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | | | - Luca Petiti
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | - Giorgio Corti
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | | | | | | | | | | | - Gianluca De Bellis
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | - Clelia Peano
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
- * E-mail: (CP); (MS)
| | | | - Margherita Sosio
- NAICONS Srl, Milano, Italy
- KtedoGen Srl, Milano, Italy
- * E-mail: (CP); (MS)
| |
Collapse
|
32
|
Production of specialized metabolites by Streptomyces coelicolor A3(2). ADVANCES IN APPLIED MICROBIOLOGY 2014; 89:217-66. [PMID: 25131404 DOI: 10.1016/b978-0-12-800259-9.00006-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The actinomycetes are well-known bioactive natural product producers, comprising the Streptomycetes, the richest drug-prolific family in all kingdoms, producing therapeutic compounds for the areas of infection, cancer, circulation, and immunity. Completion and annotation of many actinomycete genomes has highlighted further how proficient these bacteria are in specialized metabolism, which have been largely underexploited in traditional screening programs. The genome sequence of the model strain Streptomyces coelicolor A3(2), and subsequent development of genomics-driven approaches to understand its large specialized metabolome, has been key in unlocking the high potential of specialized metabolites for natural product genomics-based drug discovery. This review discusses systematically the biochemistry and genetics of each of the specialized metabolites of S. coelicolor and describes metabolite transport processes for excretion and complex regulatory patterns controlling biosynthesis.
Collapse
|