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Ji CH, Je HW, Kim H, Kang HS. Promoter engineering of natural product biosynthetic gene clusters in actinomycetes: concepts and applications. Nat Prod Rep 2024; 41:672-699. [PMID: 38259139 DOI: 10.1039/d3np00049d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Covering 2011 to 2022Low titers of natural products in laboratory culture or fermentation conditions have been one of the challenging issues in natural products research. Many natural product biosynthetic gene clusters (BGCs) are also transcriptionally silent in laboratory culture conditions, making it challenging to characterize the structures and activities of their metabolites. Promoter engineering offers a potential solution to this problem by providing tools for transcriptional activation or optimization of biosynthetic genes. In this review, we summarize the 10 years of progress in promoter engineering approaches in natural products research focusing on the most metabolically talented group of bacteria actinomycetes.
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Affiliation(s)
- Chang-Hun Ji
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea.
| | - Hyun-Woo Je
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea.
| | - Hiyoung Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea.
| | - Hahk-Soo Kang
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea.
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2
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Xia L, Wen J. Available strategies for improving the biosynthesis of surfactin: a review. Crit Rev Biotechnol 2023; 43:1111-1128. [PMID: 36001039 DOI: 10.1080/07388551.2022.2095252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 06/04/2022] [Indexed: 11/03/2022]
Abstract
Surfactin is an excellent biosurfactant with a wide range of application prospects in many industrial fields. However, its low productivity and high cost have largely limited its commercial applications. In this review, the pathways for surfactin synthesis in Bacillus strains are summarized and discussed. Further, the latest strategies for improving surfactin production, including: medium optimization, genome engineering methods (rational genetic engineering, genome reduction, and genome shuffling), heterologous synthesis, and the use of synthetic biology combined with metabolic engineering approaches to construct high-quality artificial cells for surfactin production using xylose, are described. Finally, the prospects for improving surfactin synthesis are discussed in detail.
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Affiliation(s)
- Li Xia
- Key Laboratory of Systems Bioengineering, Ministry of Education, Department of Biological Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
- National Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, People's Republic of China
- Frontier Science Center of the Ministry of Education, Tianjin University, Tianjin, People's Republic of China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering, Ministry of Education, Department of Biological Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
- National Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, People's Republic of China
- Frontier Science Center of the Ministry of Education, Tianjin University, Tianjin, People's Republic of China
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3
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Gu B, Kim DG, Kim DK, Kim M, Kim HU, Oh MK. Heterologous overproduction of oviedomycin by refactoring biosynthetic gene cluster and metabolic engineering of host strain Streptomyces coelicolor. Microb Cell Fact 2023; 22:212. [PMID: 37838667 PMCID: PMC10576301 DOI: 10.1186/s12934-023-02218-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/28/2023] [Indexed: 10/16/2023] Open
Abstract
BACKGROUND Oviedomycin is one among several polyketides known for their potential as anticancer agents. The biosynthetic gene cluster (BGC) for oviedomycin is primarily found in Streptomyces antibioticus. However, because this BGC is usually inactive under normal laboratory conditions, it is necessary to employ systematic metabolic engineering methods, such as heterologous expression, refactoring of BGCs, and optimization of precursor biosynthesis, to allow efficient production of these compounds. RESULTS Oviedomycin BGC was captured from the genome of Streptomyces antibioticus by a newly constructed plasmid, pCBA, and conjugated into the heterologous strain, S. coelicolor M1152. To increase the production of oviedomycin, clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system was utilized in an in vitro setting to refactor the native promoters within the ovm BGC. The target promoters of refactoring were selected based on examination of factors such as transcription levels and metabolite profiling. Furthermore, genome-scale metabolic simulation was applied to find overexpression targets that could enhance the biosynthesis of precursors or cofactors related to oviedomycin production. The combined approach led to a significant increase in oviedomycin production, reaching up to 670 mg/L, which is the highest titer reported to date. This demonstrates the potential of the approach undertaken in this study. CONCLUSIONS The metabolic engineering approach used in this study led to the successful production of a valuable polyketide, oviedomycin, via BGC cloning, promoter refactoring, and gene manipulation of host metabolism aided by genome-scale metabolic simulation. This approach can be also useful for the efficient production of other secondary molecules encoded by 'silent' BGCs.
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Affiliation(s)
- Boncheol Gu
- Department of Chemical & Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Duck Gyun Kim
- Department of Chemical & Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Do-Kyung Kim
- Department of Chemical & Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Minji Kim
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
| | - Min-Kyu Oh
- Department of Chemical & Biological Engineering, Korea University, Seoul, 02841, Republic of Korea.
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4
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Dietrich D, Jovanovic-Gasovic S, Cao P, Kohlstedt M, Wittmann C. Refactoring the architecture of a polyketide gene cluster enhances docosahexaenoic acid production in Yarrowia lipolytica through improved expression and genetic stability. Microb Cell Fact 2023; 22:199. [PMID: 37773137 PMCID: PMC10540379 DOI: 10.1186/s12934-023-02209-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Long-chain polyunsaturated fatty acids (LC-PUFAs), such as docosahexaenoic acid (DHA), are essential for human health and have been widely used in the food and pharmaceutical industries. However, the limited availability of natural sources, such as oily fish, has led to the pursuit of microbial production as a promising alternative. Yarrowia lipolytica can produce various PUFAs via genetic modification. A recent study upgraded Y. lipolytica for DHA production by expressing a four-gene cluster encoding a myxobacterial PKS-like PUFA synthase, reducing the demand for redox power. However, the genetic architecture of gene expression in Y. lipolytica is complex and involves various control elements, offering space for additional improvement of DHA production. This study was designed to optimize the expression of the PUFA cluster using a modular cloning approach. RESULTS Expression of the monocistronic cluster with each gene under the control of the constitutive TEF promoter led to low-level DHA production. By using the minLEU2 promoter instead and incorporating additional upstream activating UAS1B4 sequences, 5' promoter introns, and intergenic spacers, DHA production was increased by 16-fold. The producers remained stable over 185 h of cultivation. Beneficially, the different genetic control elements acted synergistically: UAS1B elements generally increased expression, while the intron caused gene-specific effects. Mutants with UAS1B16 sequences within 2-8 kb distance, however, were found to be genetically unstable, which limited production performance over time, suggesting the avoidance of long repetitive sequence blocks in synthetic multigene clusters and careful monitoring of genetic stability in producing strains. CONCLUSIONS Overall, the results demonstrate the effectiveness of synthetic heterologous gene clusters to drive DHA production in Y. lipolytica. The combinatorial exploration of different genetic control elements allowed the optimization of DHA production. These findings have important implications for developing Y. lipolytica strains for the industrial-scale production of valuable polyunsaturated fatty acids.
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Affiliation(s)
- Demian Dietrich
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Peng Cao
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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5
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Huang C, Zabala D, de los Santos ELC, Song L, Corre C, Alkhalaf L, Challis G. Parallelized gene cluster editing illuminates mechanisms of epoxyketone proteasome inhibitor biosynthesis. Nucleic Acids Res 2023; 51:1488-1499. [PMID: 36718812 PMCID: PMC9943649 DOI: 10.1093/nar/gkad009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 12/22/2022] [Accepted: 01/06/2023] [Indexed: 02/01/2023] Open
Abstract
Advances in DNA sequencing technology and bioinformatics have revealed the enormous potential of microbes to produce structurally complex specialized metabolites with diverse uses in medicine and agriculture. However, these molecules typically require structural modification to optimize them for application, which can be difficult using synthetic chemistry. Bioengineering offers a complementary approach to structural modification but is often hampered by genetic intractability and requires a thorough understanding of biosynthetic gene function. Expression of specialized metabolite biosynthetic gene clusters (BGCs) in heterologous hosts can surmount these problems. However, current approaches to BGC cloning and manipulation are inefficient, lack fidelity, and can be prohibitively expensive. Here, we report a yeast-based platform that exploits transformation-associated recombination (TAR) for high efficiency capture and parallelized manipulation of BGCs. As a proof of concept, we clone, heterologously express and genetically analyze BGCs for the structurally related nonribosomal peptides eponemycin and TMC-86A, clarifying remaining ambiguities in the biosynthesis of these important proteasome inhibitors. Our results show that the eponemycin BGC also directs the production of TMC-86A and reveal contrasting mechanisms for initiating the assembly of these two metabolites. Moreover, our data shed light on the mechanisms for biosynthesis and incorporation of 4,5-dehydro-l-leucine (dhL), an unusual nonproteinogenic amino acid incorporated into both TMC-86A and eponemycin.
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Affiliation(s)
- Chuan Huang
- Correspondence may also be addressed to Chuan Huang. Tel: +61 03 9905 1750;
| | - Daniel Zabala
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Emmanuel L C de los Santos
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Lijiang Song
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Christophe Corre
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Lona M Alkhalaf
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
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6
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Liu J, Li SM. Genomics-Guided Efficient Identification of 2,5-Diketopiperazine Derivatives from Actinobacteria. Chembiochem 2023; 24:e202200502. [PMID: 36098493 PMCID: PMC10092475 DOI: 10.1002/cbic.202200502] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/12/2022] [Indexed: 02/04/2023]
Abstract
Secondary metabolites derived from microorganism constitute an important part of natural products. Mining of the microbial genomes revealed a large number of uncharacterized biosynthetic gene clusters, indicating their greater potential to synthetize specialized or secondary metabolites (SMs) than identified by classic fermentation and isolation approaches. Various bioinformatics tools have been developed to analyze and identify such gene clusters, thus accelerating significantly the mining process. Heterologous expression of an individual biosynthetic gene cluster has been proven as an efficient way to activate the genes and identify the encoded metabolites that cannot be detected under normal laboratory cultivation conditions. Herein, we describe a concept of genomics-guided approach by performing genome mining and heterologous expression to uncover novel CDPS-derived DKPs and functionally characterize novel tailoring enzymes embedded in the biosynthetic pathways. Recent works focused on the identification of the nucleobase-related and dimeric DKPs are also presented.
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Affiliation(s)
- Jing Liu
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037, Marburg, Germany.,Current address: Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037, Marburg, Germany
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Wu Y, Gong FL, Li S. Leveraging yeast to characterize plant biosynthetic gene clusters. CURRENT OPINION IN PLANT BIOLOGY 2023; 71:102314. [PMID: 36463029 PMCID: PMC10664738 DOI: 10.1016/j.pbi.2022.102314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
Plant biosynthetic gene clusters (BGCs) contain multiple physically clustered non-homologous genes that encode enzymes catalyzing diverse reactions in one plant natural product biosynthetic pathway. A growing number of plant BGCs have emerged as an underlying resource for understanding plant specialized metabolism and evolution, but the characterization remains challenging. Recent studies have demonstrated that baker's yeast can serve as a versatile platform for the characterization of plant BGCs, from single-gene characterization to multiple genes and hitherto unknown putative BGC validation and elucidation. In this review, we will summarize the strategies and examples of the applications of yeast in plant BGC characterization and share our perspective on the development of a systematic pipeline to fully leverage yeast to advance the understanding of plant BGCs and plant natural product biomanufacturing.
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Affiliation(s)
- Yinan Wu
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Franklin L Gong
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Sijin Li
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA.
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8
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Xu Z, Park TJ, Cao H. Advances in mining and expressing microbial biosynthetic gene clusters. Crit Rev Microbiol 2023; 49:18-37. [PMID: 35166616 DOI: 10.1080/1040841x.2022.2036099] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Natural products (NPs) especially the secondary metabolites originated from microbes exhibit great importance in biomedical, industrial and agricultural applications. However, mining biosynthetic gene clusters (BGCs) to produce novel NPs has been hindered owing that a large population of environmental microbes are unculturable. In the past decade, strategies to explore BGCs directly from (meta)genomes have been established along with the fast development of high-throughput sequencing technologies and the powerful bioinformatics data-processing tools, which greatly expedited the exploitations of novel BGCs from unculturable microbes including the extremophilic microbes. In this review, we firstly summarized the popular bioinformatics tools and databases available to mine novel BGCs from (meta)genomes based on either pure cultures or pristine environmental samples. Noticeably, approaches rooted from machine learning and deep learning with focuses on the prediction of ribosomally synthesized and post-translationally modified peptides (RiPPs) were dramatically increased in recent years. Moreover, synthetic biology techniques to express the novel BGCs in culturable native microbes or heterologous hosts were introduced. This working pipeline including the discovery and biosynthesis of novel NPs will greatly advance the exploitations of the abundant but unexplored microbial BGCs.
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Affiliation(s)
- Zeling Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China
| | - Tae-Jin Park
- HME Healthcare Co., Ltd, Suwon-si, Republic of Korea
| | - Huiluo Cao
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
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9
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Zabed HM, Akter S, Rupani PF, Akor J, Zhang Y, Zhao M, Zhang C, Ragauskas AJ, Qi X. Biocatalytic gateway to convert glycerol into 3-hydroxypropionic acid in waste-based biorefineries: Fundamentals, limitations, and potential research strategies. Biotechnol Adv 2023; 62:108075. [PMID: 36502965 DOI: 10.1016/j.biotechadv.2022.108075] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 12/14/2022]
Abstract
Microbial conversion of bioenergy-derived waste glycerol into value-added chemicals has emerged as an important bioprocessing technology due to its eco-friendliness, feasible technoeconomics, and potential to provide sustainability in biodiesel and bioethanol production. Glycerol is an abundant liquid waste from bioenergy plants with a projected volume of 6 million tons by 2025, accounting for about 10% of biodiesel and 2.5% of bioethanol yields. 3-Hydroxypropionic acid (3-HP) is a major product of glycerol bioconversion, which is the third largest biobased platform compound with expected market size and value of 3.6 million tons/year and USD 10 billion/year, respectively. Despite these biorefinery values, 3-HP biosynthesis from glycerol is still at an immature stage of commercial exploitation. The main challenges behind this immaturity are the toxic effects of 3-HPA on cells, the distribution of carbon flux to undesirable pathways, low tolerance of cells to glycerol and 3-HP, co-factor dependence of enzymes, low enzyme activity and stability, and the problems of substrate inhibition and specificity of enzymes. To address these challenges, it is necessary to understand the fundamentals of glycerol bioconversion and 3-HP production in terms of metabolic pathways, related enzymes, cell factories, midstream process configurations, and downstream 3-HP recovery, as discussed in this review critically and comprehensively. It is equally important to know the current challenges and limitations in 3-HP production, which are discussed in detail along with recent research efforts and remaining gaps. Finally, possible research strategies are outlined considering the recent technological advances in microbial biosynthesis, aiming to attract further research efforts to achieve a sustainable and industrially exploitable 3-HP production technology. By discussing the use of advanced tools and strategies to overcome the existing challenges in 3-HP biosynthesis, this review will attract researchers from many other similar biosynthesis technologies and provide a common gateway for their further development.
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Affiliation(s)
- Hossain M Zabed
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Suely Akter
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Parveen Fatemah Rupani
- Department of Chemical Engineering, Ku Luven, Jan De Nayerlaan 5, 2860 Sint-Katelijne-Waver, Belgium
| | - Joseph Akor
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Yufei Zhang
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Mei Zhao
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Cunsheng Zhang
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Arthur J Ragauskas
- Department of Chemical and Biomolecular Engineering, University of Tennessee Knoxville, Knoxville, TN 37996, USA; Department of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon, The University of Tennessee Institute of Agriculture, Knoxville, TN 37996, USA; UTK-ORNL Joint Institute for Biological Science, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
| | - Xianghui Qi
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China; School of Life Sciences, Guangzhou University, Guangzhou 510,006, Guangdong Province, China.
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10
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Weihmann R, Kubicki S, Bitzenhofer NL, Domröse A, Bator I, Kirschen LM, Kofler F, Funk A, Tiso T, Blank LM, Jaeger KE, Drepper T, Thies S, Loeschcke A. The modular pYT vector series employed for chromosomal gene integration and expression to produce carbazoles and glycolipids in P. putida. FEMS MICROBES 2022; 4:xtac030. [PMID: 37333445 PMCID: PMC10117823 DOI: 10.1093/femsmc/xtac030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/03/2022] [Accepted: 12/16/2022] [Indexed: 10/22/2023] Open
Abstract
The expression of biosynthetic genes in bacterial hosts can enable access to high-value compounds, for which appropriate molecular genetic tools are essential. Therefore, we developed a toolbox of modular vectors, which facilitate chromosomal gene integration and expression in Pseudomonas putida KT2440. To this end, we designed an integrative sequence, allowing customisation regarding the modes of integration (random, at attTn7, or into the 16S rRNA gene), promoters, antibiotic resistance markers as well as fluorescent proteins and enzymes as transcription reporters. We thus established a toolbox of vectors carrying integrative sequences, designated as pYT series, of which we present 27 ready-to-use variants along with a set of strains equipped with unique 'landing pads' for directing a pYT interposon into one specific copy of the 16S rRNA gene. We used genes of the well-described violacein biosynthesis as reporter to showcase random Tn5-based chromosomal integration leading to constitutive expression and production of violacein and deoxyviolacein. Deoxyviolacein was likewise produced after gene integration into the 16S rRNA gene of rrn operons. Integration in the attTn7 site was used to characterise the suitability of different inducible promoters and successive strain development for the metabolically challenging production of mono-rhamnolipids. Finally, to establish arcyriaflavin A production in P. putida for the first time, we compared different integration and expression modes, revealing integration at attTn7 and expression with NagR/PnagAa to be most suitable. In summary, the new toolbox can be utilised for the rapid generation of various types of P. putida expression and production strains.
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Affiliation(s)
- Robin Weihmann
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Sonja Kubicki
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Nora Lisa Bitzenhofer
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Andreas Domröse
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Isabel Bator
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Lisa-Marie Kirschen
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Franziska Kofler
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Aileen Funk
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Till Tiso
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Lars M Blank
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Bio-and Geosciences IBG 1: Biotechnology, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Stephan Thies
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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11
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Zheng X, Li Y, Guan M, Wang L, Wei S, Li YC, Chang CY, Xu Z. Biomimetic Total Synthesis of the Spiroindimicin Family of Natural Products. Angew Chem Int Ed Engl 2022; 61:e202208802. [PMID: 35904849 DOI: 10.1002/anie.202208802] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Indexed: 12/24/2022]
Abstract
A unified strategy for the biomimetic total synthesis of the spiroindimicin family of natural products was reported. Key transformations include a one-pot two-enzyme-catalyzed oxidative dimerization of L-tryptophan/5-chloro-L-tryptophan to afford the bis-indole precursors chromopyrrolic acid/5',5''-dichloro-chromopyrrolic acid, and regioselective C3'-C2'' and C3'-C4'' bond formation converting a common bis-indole skeleton to two skeletally different natural products, including (±)-spiroindimicins D and G with a [5,5] spiro-ring skeleton, and (±)-spiroindimicins A and H with a [5,6] spiro-ring skeleton, respectively.
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Affiliation(s)
- Xikang Zheng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Yan Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Mengtie Guan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Lingyue Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Shilong Wei
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Yi-Cheng Li
- Department of Biological Sciences and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, P. R. China
| | - Chin-Yuan Chang
- Department of Biological Sciences and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, P. R. China
| | - Zhengren Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
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12
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Zheng X, Li Y, Guan M, Wang L, Wei S, Li YC, Chang CY, Xu Z. Biomimetic Total Synthesis of the Spiroindimicin Family of Natural Products. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xikang Zheng
- Peking University State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences CHINA
| | - Yan Li
- Peking University State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences CHINA
| | - Mengtie Guan
- Peking University State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences CHINA
| | - Lingyue Wang
- Peking University State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences CHINA
| | - Shilong Wei
- Peking University State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences CHINA
| | - Yi-Cheng Li
- National Yang Ming Chiao Tung University Department of Biological Sciences and Technology TAIWAN
| | - Chin-Yuan Chang
- National Yang Ming Chiao Tung University Department of Biological Sciences and Technology TAIWAN
| | - Zhengren Xu
- Peking University State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences 38 Xueyuan Road, Haidian District 100191 Beijing CHINA
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13
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Almeida H, Tsang A, Diallo AB. Improving candidate Biosynthetic Gene Clusters in fungi through reinforcement learning. Bioinformatics 2022; 38:3984-3991. [PMID: 35762945 PMCID: PMC9364373 DOI: 10.1093/bioinformatics/btac420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 05/17/2022] [Accepted: 06/23/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Precise identification of Biosynthetic Gene Clusters (BGCs) is a challenging task. Performance of BGC discovery tools is limited by their capacity to accurately predict components belonging to candidate BGCs, often overestimating cluster boundaries. To support optimizing the composition and boundaries of candidate BGCs, we propose reinforcement learning approach relying on protein domains and functional annotations from expert curated BGCs. RESULTS The proposed reinforcement learning method aims to improve candidate BGCs obtained with state-of-the-art tools. It was evaluated on candidate BGCs obtained for two fungal genomes, Aspergillus niger and Aspergillus nidulans. The results highlight an improvement of the gene precision by above 15% for TOUCAN, fungiSMASH and DeepBGC; and cluster precision by above 25% for fungiSMASH and DeepBCG, allowing these tools to obtain almost perfect precision in cluster prediction. This can pave the way of optimizing current prediction of candidate BGCs in fungi, while minimizing the curation effort required by domain experts. AVAILABILITY AND IMPLEMENTATION https://github.com/bioinfoUQAM/RL-bgc-components. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hayda Almeida
- Departement d’Informatique, UQAM, Montréal, QC H2X 3Y7, Canada,Centre for Structural and Functional Genomics, Concordia University, Montréal, QC H4B 1R6, Canada,Laboratoire d’Algèbre, de Combinatoire, et d’Informatique Mathématique (LACIM), UQAM, Montréal, QC H2X 3Y, Canada
| | - Adrian Tsang
- Departement d’Informatique, UQAM, Montréal, QC H2X 3Y7, Canada,Centre for Structural and Functional Genomics, Concordia University, Montréal, QC H4B 1R6, Canada
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14
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Recent Advances in the Heterologous Expression of Biosynthetic Gene Clusters for Marine Natural Products. Mar Drugs 2022; 20:md20060341. [PMID: 35736144 PMCID: PMC9225448 DOI: 10.3390/md20060341] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/11/2022] [Accepted: 05/20/2022] [Indexed: 12/29/2022] Open
Abstract
Marine natural products (MNPs) are an important source of biologically active metabolites, particularly for therapeutic agent development after terrestrial plants and nonmarine microorganisms. Sequencing technologies have revealed that the number of biosynthetic gene clusters (BGCs) in marine microorganisms and the marine environment is much higher than expected. Unfortunately, the majority of them are silent or only weakly expressed under traditional laboratory culture conditions. Furthermore, the large proportion of marine microorganisms are either uncultivable or cannot be genetically manipulated. Efficient heterologous expression systems can activate cryptic BGCs and increase target compound yield, allowing researchers to explore more unknown MNPs. When developing heterologous expression of MNPs, it is critical to consider heterologous host selection as well as genetic manipulations for BGCs. In this review, we summarize current progress on the heterologous expression of MNPs as a reference for future research.
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15
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Advances in Biosynthesis of Natural Products from Marine Microorganisms. Microorganisms 2021; 9:microorganisms9122551. [PMID: 34946152 PMCID: PMC8706298 DOI: 10.3390/microorganisms9122551] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/27/2021] [Accepted: 12/07/2021] [Indexed: 01/01/2023] Open
Abstract
Natural products play an important role in drug development, among which marine natural products are an underexplored resource. This review summarizes recent developments in marine natural product research, with an emphasis on compound discovery and production methods. Traditionally, novel compounds with useful biological activities have been identified through the chromatographic separation of crude extracts. New genome sequencing and bioinformatics technologies have enabled the identification of natural product biosynthetic gene clusters in marine microbes that are difficult to culture. Subsequently, heterologous expression and combinatorial biosynthesis have been used to produce natural products and their analogs. This review examines recent examples of such new strategies and technologies for the development of marine natural products.
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16
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Li H, Pan Y, Liu G. Multiplying the heterologous production of spinosad through tandem amplification of its biosynthetic gene cluster in Streptomyces coelicolor. Microb Biotechnol 2021; 15:1550-1560. [PMID: 34796664 PMCID: PMC9049625 DOI: 10.1111/1751-7915.13965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 10/21/2021] [Indexed: 12/14/2022] Open
Abstract
Heterologous expression of the biosynthetic gene cluster (BGC) is important for studying the microbial natural products (NPs), especially for those kept in silent or poorly expressed in their original strains. Here, we cloned the spinosad BGC through the Cas9-Assisted Targeting of Chromosome segments and amplified it to five copies through a ZouA-dependent DNA amplification system in Streptomyces coelicolor M1146. The resulting strain produced 1253.9 ± 78.2 μg l-1 of spinosad, which was about 224-fold compared with that of the parent strain carrying only one copy of the spinosad BGC. Moreover, we further increased spinosad to 1958.9 ± 73.5 μg l-1 by the dynamic regulation of intracellular triacylglycerol degradation. Our study indicates that tandem amplification of the targeted gene cluster is particularly suitable to enhance the heterologous production of valuable NPs with efficiency and simplicity.
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Affiliation(s)
- Hong Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuanyuan Pan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Gang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100864, China
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17
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Ji CH, Kim H, Je HW, Kwon H, Lee D, Kang HS. Top-down synthetic biology approach for titer improvement of clinically important antibiotic daptomycin in Streptomyces roseosporus. Metab Eng 2021; 69:40-49. [PMID: 34737068 DOI: 10.1016/j.ymben.2021.10.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/09/2021] [Accepted: 10/29/2021] [Indexed: 12/21/2022]
Abstract
Secondary metabolites are produced at low titers by native producers due to tight regulations of their productions in response to environmental conditions. Synthetic biology provides a rational engineering principle for transcriptional optimization of secondary metabolite BGCs (biosynthetic gene clusters). Here, we demonstrate the use of synthetic biology principles for the development of a high-titer strain of the clinically important antibiotic daptomycin. Due to the presence of large NRPS (non-ribosomal peptide synthetase) genes with multiple direct repeats, we employed a top-down approach that allows transcriptional optimization of genes in daptomycin BGC with the minimum inputs of synthetic DNAs. The repeat-free daptomycin BGC was created through partial codon-reprogramming of a NRPS gene and cloned into a shuttle BAC vector, allowing BGC refactoring in a host with a powerful recombination system. Then, transcriptions of functionally divided operons were sequentially optimized through three rounds of DBTL (design-build-test-learn) cycles that resulted in up to ~2300% improvement in total lipopeptide titers compared to the wild-type strain. Upon decanoic acid feeding, daptomycin accounted for ∼ 40% of total lipopeptide production. To the best of our knowledge, this is the highest improvement of daptomycin titer ever achieved through genetic engineering of S. roseosporus. The top-down engineering approach we describe here could be used as a general strategy for the development of high-titer industrial strains of secondary metabolites produced by BGCs containing genes of large multi-modular NRPS and PKS enzymes.
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Affiliation(s)
- Chang-Hun Ji
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Hiyoung Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Hyun-Woo Je
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Haeun Kwon
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Dongho Lee
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Hahk-Soo Kang
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
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Park J, Yim SS, Wang HH. High-Throughput Transcriptional Characterization of Regulatory Sequences from Bacterial Biosynthetic Gene Clusters. ACS Synth Biol 2021; 10:1859-1873. [PMID: 34288650 DOI: 10.1021/acssynbio.0c00639] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Recent efforts to sequence, survey, and functionally characterize the diverse biosynthetic capabilities of bacteria have identified numerous Biosynthetic Gene Clusters (BGCs). Genes found within BGCs are typically transcriptionally silent, suggesting their expression is tightly regulated. To better elucidate the underlying mechanisms and principles that govern BGC regulation on a DNA sequence level, we employed high-throughput DNA synthesis and multiplexed reporter assays to build and to characterize a library of BGC-derived regulatory sequences. Regulatory sequence transcription levels were measured in the Actinobacteria Streptomyces albidoflavus J1074, a popular model strain from a genus rich in BGC diversity. Transcriptional activities varied over 1000-fold in range and were used to identify key features associated with expression, including GC content, transcription start sites, and sequence motifs. Furthermore, we demonstrated that transcription levels could be modulated through coexpression of global regulatory proteins. Lastly, we developed and optimized a S. albidoflavus cell-free expression system for rapid characterization of regulatory sequences. This work helps to elucidate the regulatory landscape of BGCs and provides a diverse library of characterized regulatory sequences for rational engineering and activation of cryptic BGCs.
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Affiliation(s)
- Jimin Park
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York 10032, United States
- Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Sung Sun Yim
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York 10032, United States
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Harris H. Wang
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York 10032, United States
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032, United States
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19
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Li R, Shi H, Zhao X, Liu X, Duan Q, Song C, Chen H, Zheng W, Shen Q, Wang M, Wang X, Gong K, Yin J, Zhang Y, Li A, Fu J. Development and application of an efficient recombineering system for Burkholderia glumae and Burkholderia plantarii. Microb Biotechnol 2021; 14:1809-1826. [PMID: 34191386 PMCID: PMC8313284 DOI: 10.1111/1751-7915.13840] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 05/13/2021] [Accepted: 05/13/2021] [Indexed: 02/07/2023] Open
Abstract
The lambda phage Red proteins Redα/Redβ/Redγ and Rac prophage RecE/RecT proteins are powerful tools for precise and efficient genetic manipulation but have been limited to only a few prokaryotes. Here, we report the development and application of a new recombineering system for Burkholderia glumae and Burkholderia plantarii based on three Rac bacteriophage RecET-like operons, RecETheBDU8 , RecEThTJI49 and RecETh1h2eYI23 , which were obtained from three different Burkholderia species. Recombineering experiments indicated that RecEThTJI49 and RecETh1h2eYI23 showed higher recombination efficiency compared to RecETheBDU8 in Burkholderia glumae PG1. Furthermore, all of the proteins currently categorized as hypothetical proteins in RecETh1h2eYI23, RecEThTJI49 and RecETheBDU8 may have a positive effect on recombination in B. glumae PG1 except for the h2 protein in RecETh1h2eYI23 . Additionally, RecETYI23 combined with exonuclease inhibitors Pluγ or Redγ exhibited equivalent recombination efficiency compared to Redγβα in Escherichia coli, providing potential opportunity of recombineering in other Gram-negative bacteria for its loose host specificity. Using recombinase-assisted in situ insertion of promoters, we successfully activated three cryptic non-ribosomal peptide synthetase biosynthetic gene clusters in Burkholderia strains, resulting in the generation of a series of lipopeptides that were further purified and characterized. Compound 7 exhibited significant potential anti-inflammatory activity by inhibiting lipopolysaccharide-stimulated nitric oxide production in RAW 264.7 macrophages. This recombineering system may greatly enhance functional genome research and the mining of novel natural products in the other species of the genus Burkholderia after optimization of a protocol.
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Affiliation(s)
- Ruijuan Li
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Hongbo Shi
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Xiaoyu Zhao
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Xianqi Liu
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Qiong Duan
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Chaoyi Song
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Hanna Chen
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Wentao Zheng
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Qiyao Shen
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Maoqin Wang
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Xue Wang
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Kai Gong
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Jia Yin
- Hunan Provincial Key Laboratory of Animal Intestinal Function and RegulationCollege of Life SciencesHunan Normal UniversityChangshaHunan410081China
| | - Youming Zhang
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Aiying Li
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Jun Fu
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
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20
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Sharma V, Kaur R, Salwan R. Streptomyces: host for refactoring of diverse bioactive secondary metabolites. 3 Biotech 2021; 11:340. [PMID: 34221811 DOI: 10.1007/s13205-021-02872-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/31/2021] [Indexed: 12/22/2022] Open
Abstract
Microbial secondary metabolites are intensively explored due to their demands in pharmaceutical, agricultural and food industries. Streptomyces are one of the largest sources of secondary metabolites having diverse applications. In particular, the abundance of secondary metabolites encoding biosynthetic gene clusters and presence of wobble position in Streptomyces strains make it potential candidate as a native or heterologous host for secondary metabolite production including several cryptic gene clusters expression. Here, we have discussed the developments in Streptomyces strains genome mining, its exploration as a suitable host and application of synthetic biology for refactoring genetic systems for developing chassis for enhanced as well as novel secondary metabolites with reduced genome and cleaned background.
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Affiliation(s)
- Vivek Sharma
- University Centre for Research and Development, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Randhir Kaur
- University Centre for Research and Development, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Richa Salwan
- College of Horticulture and Forestry, Dr YS Parmar University of Horticulture and Forestry, Neri, Hamirpur, Himachal Pradesh 177001 India
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21
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Wu J, Xin Y, Kong J, Guo T. Genetic tools for the development of recombinant lactic acid bacteria. Microb Cell Fact 2021; 20:118. [PMID: 34147119 PMCID: PMC8214781 DOI: 10.1186/s12934-021-01607-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/07/2021] [Indexed: 12/11/2022] Open
Abstract
Lactic acid bacteria (LAB) are a phylogenetically diverse group with the ability to convert soluble carbohydrates into lactic acid. Many LAB have a long history of safe use in fermented foods and are recognized as food-grade microorganisms. LAB are also natural inhabitants of the human intestinal tract and have beneficial effects on health. Considering these properties, LAB have potential applications as biotherapeutic vehicles to delivery cytokines, antigens and other medicinal molecules. In this review, we summarize the development of, and advances in, genome manipulation techniques for engineering LAB and the expected future development of such genetic tools. These methods are crucial for us to maximize the value of LAB. We also discuss applications of the genome-editing tools in enhancing probiotic characteristics and therapeutic functionalities of LAB.
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Affiliation(s)
- Jiapeng Wu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Yongping Xin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Jian Kong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China.
| | - Tingting Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China.
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22
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Li L, Maclntyre LW, Brady SF. Refactoring biosynthetic gene clusters for heterologous production of microbial natural products. Curr Opin Biotechnol 2021; 69:145-152. [PMID: 33476936 PMCID: PMC8238852 DOI: 10.1016/j.copbio.2020.12.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 12/03/2020] [Accepted: 12/15/2020] [Indexed: 02/08/2023]
Abstract
Microbial natural products (NPs) are of paramount importance in human medicine, animal health and plant crop protection. Large-scale microbial genome and metagenomic mining has revealed tremendous biosynthetic potential to produce new NPs. However a majority of NP biosynthetic gene clusters (BGCs) are functionally inaccessible under standard laboratory conditions. BGC refactoring and heterologous expression provide a promising synthetic biology approach to NP discovery, yield optimization and combinatorial biosynthesis studies. In this review, we summarize the recent advances pertaining to the heterologous production of bacterial and fungal NPs, with an emphasis on next-generation transcriptional regulatory modules, novel BGC refactoring techniques and optimized heterologous hosts.
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Affiliation(s)
- Lei Li
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States
| | - Logan W Maclntyre
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States.
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23
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Alam K, Hao J, Zhang Y, Li A. Synthetic biology-inspired strategies and tools for engineering of microbial natural product biosynthetic pathways. Biotechnol Adv 2021; 49:107759. [PMID: 33930523 DOI: 10.1016/j.biotechadv.2021.107759] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/28/2021] [Accepted: 04/23/2021] [Indexed: 02/08/2023]
Abstract
Microbial-derived natural products (NPs) and their derivative products are of great importance and used widely in many fields, especially in pharmaceutical industries. However, there is an immediate need to establish innovative approaches, strategies, and techniques to discover new NPs with novel or enhanced biological properties, due to the less productivity and higher cost on traditional drug discovery pipelines from natural bioresources. Revealing of untapped microbial cryptic biosynthetic gene clusters (BGCs) using DNA sequencing technology and bioinformatics tools makes genome mining possible for NP discovery from microorganisms. Meanwhile, new approaches and strategies in the area of synthetic biology offer great potentials for generation of new NPs by engineering or creating synthetic systems with improved and desired functions. Development of approaches, strategies and tools in synthetic biology can facilitate not only exploration and enhancement in supply, and also in the structural diversification of NPs. Here, we discussed recent advances in synthetic biology-inspired strategies, including bioinformatics and genetic engineering tools and approaches for identification, cloning, editing/refactoring of candidate biosynthetic pathways, construction of heterologous expression hosts, fitness optimization between target pathways and hosts and detection of NP production.
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Affiliation(s)
- Khorshed Alam
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
| | - Jinfang Hao
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
| | - Aiying Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
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24
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Gao S, Xu X, Zeng W, Xu S, Lyv Y, Feng Y, Kai G, Zhou J, Chen J. Efficient Biosynthesis of (2 S)-Eriodictyol from (2 S)-Naringenin in Saccharomyces cerevisiae through a Combination of Promoter Adjustment and Directed Evolution. ACS Synth Biol 2020; 9:3288-3297. [PMID: 33226782 DOI: 10.1021/acssynbio.0c00346] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The compound (2S)-eriodictyol is an important flavonoid that can be derived from (2S)-naringenin through flavonoid 3'-hydroxylase (F3'H) catalyzation. F3'H is a cytochrome P450 enzyme that requires a cytochrome P450 reductase (CPR) to function. However, P450s have limited applications in industrial scale biosynthesis, owing to their low activity. Here, an efficient SmF3'H and a matched SmCPR were identified from Silybum marianum. To improve the efficiency of SmF3'H, we established a high-throughput detection method for (2S)-eriodictyol, in which the promoter combination of SmF3'H and SmCPR were optimized in Saccharomyces cerevisiae. The results revealed that SmF3'H/SmCPR should be expressed by using promoters with similar and strong expression levels. Furthermore, directed evolution was applied to further improve the efficiency of SmF3'H/SmCPR. With the optimized promoter and mutated combinations SmF3'HD285N/SmCPRI453V, the (2S)-eriodictyol titer was improved to 3.3 g/L, the highest titer in currently available reports. These results indicated that S. cerevisiae is an ideal platform for functional expression of flavonoid related P450 enzymes.
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Affiliation(s)
- Song Gao
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Xiaoyu Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Weizhu Zeng
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Sha Xu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yunbin Lyv
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yue Feng
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Guoyin Kai
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Jian Chen
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
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25
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Wei X, Chen L, Tang JW, Matsuda Y. Discovery of Pyranoviolin A and Its Biosynthetic Gene Cluster in Aspergillus violaceofuscus. Front Microbiol 2020; 11:562063. [PMID: 33117309 PMCID: PMC7575713 DOI: 10.3389/fmicb.2020.562063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/16/2020] [Indexed: 12/02/2022] Open
Abstract
A new polyketide-non-ribosomal peptide hybrid molecule, pyranoviolin A (1), was discovered from the genome-sequenced fungus Aspergillus violaceofuscus CBS 115571 and was characterized to be the first pyranonigrin analog harboring the C-3 methoxy group. Examination of the genome sequence of the fungus identified a putative biosynthetic gene cluster of 1, which was designated as the pyv cluster. The gene deletion experiment of the polyketide synthase (PKS)-non-ribosomal peptide synthetase (NRPS) hybrid gene in the cluster confirmed the involvement of the pyv cluster in the pyranoviolin A biosynthesis. Finally, a plausible biosynthetic route leading to 1 has been proposed based on the bioinformatic analysis. Our study indicates that metabolite analysis of genome-sequenced microorganisms whose metabolites have been largely unexplored facilitates the discovery of new secondary metabolites along with their biosynthetic gene clusters.
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Affiliation(s)
- Xingxing Wei
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Lin Chen
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Jian-Wei Tang
- Department of Ocean Science and Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong, China.,City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
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26
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Zhou Q, Ning S, Luo Y. Coordinated regulation for nature products discovery and overproduction in Streptomyces. Synth Syst Biotechnol 2020; 5:49-58. [PMID: 32346621 PMCID: PMC7176746 DOI: 10.1016/j.synbio.2020.04.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/04/2020] [Accepted: 04/08/2020] [Indexed: 12/19/2022] Open
Abstract
Streptomyces is an important treasure trove for natural products discovery. In recent years, many scientists focused on the genetic modification and metabolic regulation of Streptomyces to obtain diverse bioactive compounds with high yields. This review summarized the commonly used regulatory strategies for natural products discovery and overproduction in Streptomyces from three main aspects, including regulator-related strategies, promoter engineering, as well as other strategies employing transposons, signal factors, or feedback regulations. It is expected that the metabolic regulation network of Streptomyces will be elucidated more comprehensively to shed light on natural products research in the future.
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Affiliation(s)
- Qun Zhou
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Shuqing Ning
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Yunzi Luo
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China
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27
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Markina NM, Kotlobay AA, Tsarkova AS. Heterologous Metabolic Pathways: Strategies for Optimal Expression in Eukaryotic Hosts. Acta Naturae 2020; 12:28-39. [PMID: 32742725 PMCID: PMC7385092 DOI: 10.32607/actanaturae.10966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 04/29/2020] [Indexed: 11/20/2022] Open
Abstract
Heterologous pathways are linked series of biochemical reactions occurring in a host organism after the introduction of foreign genes. Incorporation of metabolic pathways into host organisms is a major strategy used to increase the production of valuable secondary metabolites. Unfortunately, simple introduction of the pathway genes into the heterologous host in most cases does not result in successful heterologous expression. Extensive modification of heterologous genes and the corresponding enzymes on many different levels is required to achieve high target metabolite production rates. This review summarizes the essential techniques used to create heterologous biochemical pathways, with a focus on the key challenges arising in the process and the major strategies for overcoming them.
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Affiliation(s)
- N. M. Markina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
- Planta LLC, Moscow, 121205 Russia
| | - A. A. Kotlobay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - A. S. Tsarkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
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28
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Kim H, Ji CH, Je HW, Kim JP, Kang HS. mpCRISTAR: Multiple Plasmid Approach for CRISPR/Cas9 and TAR-Mediated Multiplexed Refactoring of Natural Product Biosynthetic Gene Clusters. ACS Synth Biol 2020; 9:175-180. [PMID: 31800222 DOI: 10.1021/acssynbio.9b00382] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Multiplexed refactoring provides a tool for rapid transcriptional optimization of biosynthetic gene clusters (BGCs) through simultaneous replacement of multiple native promoters with synthetic counterparts. Here, we present the mpCRISTAR, a multiple plasmid-based CRISPR/Cas9 and TAR (transformation-associated recombination), that enables a rapid and highly efficient, multiplexed refactoring of natural product BGCs in yeast. A series of CRISPR plasmids with different auxotrophic markers that could be stably maintained in yeast cells were constructed to express multiple gRNAs simultaneously. We demonstrated the multiplexing capacity of mpCRISTAR using the actinorhodin biosynthetic gene cluster as a model cluster. mpCRISTAR1, in which each CRISPR plasmid expresses one gRNA, allows for simultaneous replacement of up to four promoter sites with nearly 100% efficiency. By expressing two gRNAs from one CRISPR plasmid, termed mpCRISTAR2, we simultaneously replaced a total of six and eight promoter sites with 68% and 32% efficiency, respectively. The mpCRISTAR could be performed iteratively using two different auxotrophic markers, allowing for refactoring of any type of BGC regardless of their operon complexities. The mpCRISTAR platform we report here would become a useful tool for the discovery of new natural products from transcriptionally silent biosynthetic gene clusters present in microbial genomes.
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Affiliation(s)
- Hiyoung Kim
- Department of Biomedical Science and Engineering , Konkuk University , Seoul 05029 , Korea
| | - Chang-Hun Ji
- Department of Biomedical Science and Engineering , Konkuk University , Seoul 05029 , Korea
| | - Hyun-Woo Je
- Department of Biomedical Science and Engineering , Konkuk University , Seoul 05029 , Korea
| | - Jong-Pyung Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju , Chungbuk 28116 , Korea
| | - Hahk-Soo Kang
- Department of Biomedical Science and Engineering , Konkuk University , Seoul 05029 , Korea
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29
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Wu R, Chen D, Cao S, Lu Z, Huang J, Lu Q, Chen Y, Chen X, Guan N, Wei Y, Huang R. Enhanced ethanol production from sugarcane molasses by industrially engineered Saccharomyces cerevisiae via replacement of the PHO4 gene. RSC Adv 2020; 10:2267-2276. [PMID: 35494577 PMCID: PMC9048610 DOI: 10.1039/c9ra08673k] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/27/2019] [Indexed: 11/21/2022] Open
Abstract
Replacement of a novel candidate ethanol fermentation-associated regulatory gene, PHO4, from a fast-growing strain MC15, as determined through comparative genomics analysis among three yeast strains with significant differences in ethanol yield, is hypothesised to shorten the fermentation time and enhance ethanol production from sugarcane molasses. This study sought to test this hypothesis through a novel strategy involving the transfer of the PHO4 gene from a low ethanol-producing, yet fast-growing strain MC15 to a high ethanol-producing industrial strain MF01 through homologous recombination. The results indicated that PHO4 in the industrially engineered strain MF01-PHO4 displayed genomic stability with a mean maximum ethanol yield that rose to 114.71 g L−1, accounting for a 5.30% increase in ethanol yield and 12.5% decrease in fermentation time in comparison with that in the original strain MF01, which was the current highest ethanol-producing strain in SCM fermentation in the reported literature. These results serve to advance our current understanding of the association between improving ethanol yield and replacement of PHO4, while providing a feasible strategy for industrially engineered yeast strains to improve ethanol production efficiently. Replacement of a novel candidate ethanol fermentation-associated regulatory gene, PHO4, from a fast-growing strain through a novel strategy (SHPERM-bCGHR), is hypothesised to shorten fermentation time and enhance ethanol yield from sugarcane molasses.![]()
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Kalkreuter E, Pan G, Cepeda AJ, Shen B. Targeting Bacterial Genomes for Natural Product Discovery. Trends Pharmacol Sci 2019; 41:13-26. [PMID: 31822352 DOI: 10.1016/j.tips.2019.11.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 11/19/2022]
Abstract
Bacterial natural products (NPs) and their analogs constitute more than half of the new small molecule drugs developed over the past few decades. Despite this success, interest in natural products from major pharmaceutical companies has decreased even as genomics has uncovered the large number of biosynthetic gene clusters (BGCs) that encode for novel natural products. To date, there is still a lack of universal strategies and enabling technologies to discover natural products at scale and speed. This review highlights several of the opportunities provided by genome sequencing and bioinformatics, challenges associated with translating genomes into natural products, and examples of successful strain prioritization and BGC activation strategies that have been used in the genomic era for natural product discovery from cultivatable bacteria.
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Affiliation(s)
- Edward Kalkreuter
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Guohui Pan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Alexis J Cepeda
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA; Natural Products Library Initiative at The Scripps Research Institute, The Scripps Research Institute, Jupiter, FL 33458, USA.
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31
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Xu W, Klumbys E, Ang EL, Zhao H. Emerging molecular biology tools and strategies for engineering natural product biosynthesis. Metab Eng Commun 2019; 10:e00108. [PMID: 32547925 PMCID: PMC7283510 DOI: 10.1016/j.mec.2019.e00108] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/05/2019] [Accepted: 11/05/2019] [Indexed: 02/08/2023] Open
Abstract
Natural products and their related derivatives play a significant role in drug discovery and have been the inspiration for the design of numerous synthetic bioactive compounds. With recent advances in molecular biology, numerous engineering tools and strategies were established to accelerate natural product synthesis in both academic and industrial settings. However, many obstacles in natural product biosynthesis still exist. For example, the native pathways are not appropriate for research or production; the key enzymes do not have enough activity; the native hosts are not suitable for high-level production. Emerging molecular biology tools and strategies have been developed to not only improve natural product titers but also generate novel bioactive compounds. In this review, we will discuss these emerging molecular biology tools and strategies at three main levels: enzyme level, pathway level, and genome level, and highlight their applications in natural product discovery and development.
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Affiliation(s)
- Wei Xu
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology, and Research, Singapore
| | - Evaldas Klumbys
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology, and Research, Singapore
| | - Ee Lui Ang
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology, and Research, Singapore
| | - Huimin Zhao
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology, and Research, Singapore.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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32
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Ke J, Yoshikuni Y. Multi-chassis engineering for heterologous production of microbial natural products. Curr Opin Biotechnol 2019; 62:88-97. [PMID: 31639618 DOI: 10.1016/j.copbio.2019.09.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/30/2019] [Accepted: 09/09/2019] [Indexed: 12/11/2022]
Abstract
Microbial genomes encode numerous biosynthetic gene clusters (BGCs) that may produce natural products with diverse applications in medicine, agriculture, the environment, and materials science. With the advent of genome sequencing and bioinformatics, heterologous expression of BGCs is of increasing interest in bioactive natural product (NP) discovery. However, this approach has had limited success because expression of BGCs relies heavily on the physiology of just a few commonly available host chassis. Expanding and diversifying the chassis portfolio for heterologous BGC expression may greatly increase the chances for successful NP production. In this review, we first discuss genetic and genome engineering technologies used to clone, modify, and transform BGCs into multiple strains and to engineer chassis strains. We then highlight studies that employed the multi-chassis approach successfully to optimize NP production, discover previously uncharacterized NPs, and better understand BGC function.
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Affiliation(s)
- Jing Ke
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA 94598, USA
| | - Yasuo Yoshikuni
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA 94598, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL 61801, USA; Global Institution for Collaborative Research and Education, Hokkaido University, Hokkaido, 060-8589, Japan.
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33
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Zhang JJ, Tang X, Moore BS. Genetic platforms for heterologous expression of microbial natural products. Nat Prod Rep 2019; 36:1313-1332. [PMID: 31197291 PMCID: PMC6750982 DOI: 10.1039/c9np00025a] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Covering: 2005 up to 2019Natural products are of paramount importance in human medicine. Not only are most antibacterial and anticancer drugs derived directly from or inspired by natural products, many other branches of medicine, such as immunology, neurology, and cardiology, have similarly benefited from natural product-based drugs. Typically, the genetic material required to synthesize a microbial specialized product is arranged in a multigene biosynthetic gene cluster (BGC), which codes for proteins associated with molecule construction, regulation, and transport. The ability to connect natural product compounds to BGCs and vice versa, along with ever-increasing knowledge of biosynthetic machineries, has spawned the field of genomics-guided natural product genome mining for the rational discovery of new chemical entities. One significant challenge in the field of natural product genome mining is how to rapidly link orphan biosynthetic genes to their associated chemical products. This review highlights state-of-the-art genetic platforms to identify, interrogate, and engineer BGCs from diverse microbial sources, which can be broken into three stages: (1) cloning and isolation of genomic loci, (2) heterologous expression in a host organism, and (3) genetic manipulation of cloned pathways. In the future, we envision natural product genome mining will be rapidly accelerated by de novo DNA synthesis and refactoring of whole biosynthetic pathways in combination with systematic heterologous expression methodologies.
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Affiliation(s)
- Jia Jia Zhang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA.
| | - Xiaoyu Tang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA.
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA. and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California, USA
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34
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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.
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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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35
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Weihmann R, Domröse A, Drepper T, Jaeger KE, Loeschcke A. Protocols for yTREX/Tn5-based gene cluster expression in Pseudomonas putida. Microb Biotechnol 2019; 13:250-262. [PMID: 31162833 PMCID: PMC6922528 DOI: 10.1111/1751-7915.13402] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/25/2019] [Accepted: 03/08/2019] [Indexed: 11/30/2022] Open
Abstract
Bacterial gene clusters, which represent a genetic treasure trove for secondary metabolite pathways, often need to be activated in a heterologous host to access the valuable biosynthetic products. We provide here a detailed protocol for the application of the yTREX ‘gene cluster transplantation tool’: Via yeast recombinational cloning, a gene cluster of interest can be cloned in the yTREX vector, which enables the robust conjugational transfer of the gene cluster to bacteria like Pseudomonas putida, and their subsequent transposon Tn5‐based insertion into the host chromosome. Depending on the gene cluster architecture and chromosomal insertion site, the respective pathway genes can be transcribed effectively from a chromosomal promoter, thereby enabling the biosynthesis of a natural product. We describe workflows for the design of a gene cluster expression cassette, cloning of the cassette in the yTREX vector by yeast recombineering, and subsequent transfer and expression in P. putida. As an example for yTREX‐based transplantation of a natural product biosynthesis, we provide details on the cloning and activation of the phenazine‐1‐carboxylic acid biosynthetic genes from Pseudomonas aeruginosa in P. putidaKT2440 as well as the use of β‐galactosidase‐encoding lacZ as a reporter of production levels.
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Affiliation(s)
- Robin Weihmann
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Andreas Domröse
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich-Heine-University, Düsseldorf, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
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36
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Bauman KD, Li J, Murata K, Mantovani SM, Dahesh S, Nizet V, Luhavaya H, Moore BS. Refactoring the Cryptic Streptophenazine Biosynthetic Gene Cluster Unites Phenazine, Polyketide, and Nonribosomal Peptide Biochemistry. Cell Chem Biol 2019; 26:724-736.e7. [PMID: 30853419 PMCID: PMC6525064 DOI: 10.1016/j.chembiol.2019.02.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/02/2019] [Accepted: 01/31/2019] [Indexed: 11/28/2022]
Abstract
The disconnect between the genomic prediction of secondary metabolite biosynthetic potential and the observed laboratory production profile of microorganisms is well documented. While heterologous expression of biosynthetic gene clusters (BGCs) is often seen as a potential solution to bridge this gap, it is not immune to many challenges including impaired regulation, the inability to recruit essential building blocks, and transcriptional and/or translational silence of the biosynthetic genes. Here we report the discovery, cloning, refactoring, and heterologous expression of a cryptic hybrid phenazine-type BGC (spz) from the marine actinomycete Streptomyces sp. CNB-091. Overexpression of the engineered spz pathway resulted in increased production and chemical diversity of phenazine natural products belonging to the streptophenazine family, including bioactive members containing an unprecedented N-formylglycine attachment. An atypical discrete adenylation enzyme in the spz cluster is required to introduce the formylglycine moiety and represents a phylogenetically distinct class of adenylation proteins.
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Affiliation(s)
- Katherine D Bauman
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - Jie Li
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - Kazuya Murata
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - Simone M Mantovani
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - Samira Dahesh
- Department of Pediatrics, University of California at San Diego, La Jolla, CA, USA
| | - Victor Nizet
- Department of Pediatrics, University of California at San Diego, La Jolla, CA, USA; Collaborative to Halt Antibiotic Resistant Microbes, University of California at San Diego, La Jolla, CA, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, USA
| | - Hanna Luhavaya
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA.
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, USA.
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37
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Ji CH, Kim H, Kang HS. Synthetic Inducible Regulatory Systems Optimized for the Modulation of Secondary Metabolite Production in Streptomyces. ACS Synth Biol 2019; 8:577-586. [PMID: 30807691 DOI: 10.1021/acssynbio.9b00001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Biosynthesis of secondary metabolites is a highly complex process that often requires tight control of their production, as overproduction of metabolites could be toxic and also may cause metabolic burden to their hosts. Tight control of metabolite production could be achieved by expressing key biosynthetic genes under control of an inducible regulatory system. In this study, we employed the modular design approach to build a high performance synthetic inducible regulatory system that displays a large dynamic range and thus is well-suited for the modulation of secondary metabolite production in Streptomyces. To this end, an inducible regulatory system was divided into three separate functional modules: (1) the induction module, (2) the target expression module, and (3) the repressor expression module. Then, these three separate modules were individually optimized in a stepwise manner and assembled to a new system. First, the cumate (CMT) induction module was chosen as the best performing induction module based on the large dynamic range and moderate inducer sensitivity. Then the CMT induction module maintained its performance when combined with diverse constitutive target expression modules, in which overall dynamic ranges varied depending on maximum promoter strengths. Lastly, the repressor expression module was optimized to achieve complete elimination of leaky expression, further increasing the dynamic range of the system. We also demonstrate that any strong constitutive regulatory system could be converted into an inducible regulatory system by simple CRISPR/Cas9-aided markerless insertion of an operator sequence whenever tight control of gene expression is required. We believe that the synthetic inducible regulatory system we report here would become a useful tool in modulating secondary metabolite production in Streptomyces.
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Affiliation(s)
- Chang-Hun Ji
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Hiyoung Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Hahk-Soo Kang
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
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38
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Zhou S, Lyu Y, Li H, Koffas MA, Zhou J. Fine‐tuning the (2
S
)‐naringenin synthetic pathway using an iterative high‐throughput balancing strategy. Biotechnol Bioeng 2019; 116:1392-1404. [DOI: 10.1002/bit.26941] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/15/2019] [Accepted: 01/22/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Shenghu Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of BiotechnologyJiangnan UniversityWuxi Jiangsu China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan UniversityWuxi Jiangsu China
- Jiangsu Provisional Research Center for Bioactive Product Processing TechnologyJiangnan University Wuxi Jiangsu China
| | - Yunbin Lyu
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of BiotechnologyJiangnan UniversityWuxi Jiangsu China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan UniversityWuxi Jiangsu China
- Jiangsu Provisional Research Center for Bioactive Product Processing TechnologyJiangnan University Wuxi Jiangsu China
| | - Huazhong Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of BiotechnologyJiangnan UniversityWuxi Jiangsu China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan UniversityWuxi Jiangsu China
| | - Mattheos A.G. Koffas
- Department of Chemical and Biological EngineeringRensselaer Polytechnic Institute Troy New York
- Department of Biological SciencesRensselaer Polytechnic Institute Troy New York
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of BiotechnologyJiangnan UniversityWuxi Jiangsu China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan UniversityWuxi Jiangsu China
- Jiangsu Provisional Research Center for Bioactive Product Processing TechnologyJiangnan University Wuxi Jiangsu China
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Kim SH, Lu W, Ahmadi MK, Montiel D, Ternei MA, Brady SF. Atolypenes, Tricyclic Bacterial Sesterterpenes Discovered Using a Multiplexed In Vitro Cas9-TAR Gene Cluster Refactoring Approach. ACS Synth Biol 2019; 8:109-118. [PMID: 30575381 DOI: 10.1021/acssynbio.8b00361] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Most natural product biosynthetic gene clusters identified in bacterial genomic and metagenomic sequencing efforts are silent under laboratory growth conditions. Here, we describe a scalable biosynthetic gene cluster activation method wherein the gene clusters are disassembled at interoperonic regions in vitro using CRISPR/Cas9 and then reassembled with PCR-amplified, short DNAs, carrying synthetic promoters, using transformation assisted recombination (TAR) in yeast. This simple, cost-effective, and scalable method allows for the simultaneous generation of combinatorial libraries of refactored gene clusters, eliminating the need to understand the transcriptional hierarchy of the silent genes. In two test cases, this in vitro disassembly-TAR reassembly method was used to create collections of promoter-replaced gene clusters that were tested in parallel to identify versions that enabled secondary metabolite production. Activation of the atolypene ( ato) gene cluster led to the characterization of two unprecedented bacterial cyclic sesterterpenes, atolypene A (1) and B (2), which are moderately cytotoxic to human cancer cell lines. This streamlined in vitro disassembly- in vivo reassembly method offers a simplified approach for silent gene cluster refactoring that should facilitate the discovery of natural products from silent gene clusters cloned from either metagenomes or cultured bacteria.
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Affiliation(s)
- Seong-Hwan Kim
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Wanli Lu
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Mahmoud Kamal Ahmadi
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Daniel Montiel
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Melinda A. Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Sean F. Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
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Song C, Luan J, Cui Q, Duan Q, Li Z, Gao Y, Li R, Li A, Shen Y, Li Y, Stewart AF, Zhang Y, Fu J, Wang H. Enhanced Heterologous Spinosad Production from a 79-kb Synthetic Multioperon Assembly. ACS Synth Biol 2019; 8:137-147. [PMID: 30590919 DOI: 10.1021/acssynbio.8b00402] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Refactoring biosynthetic pathways for enhanced secondary metabolite production is a central challenge for synthetic biology. Here we applied advanced DNA assembly methods and a uniform overexpression logic using constitutive promoters to achieve efficient heterologous production of the complex insecticidal macrolide spinosad. We constructed a 79-kb artificial gene cluster in which 23 biosynthetic genes were grouped into 7 operons, each with a strong constitutive promoter. Compared with the original gene cluster, the artificial gene cluster resulted in a 328-fold enhanced spinosad production in Streptomyces albus J1074. To achieve this goal, we applied the ExoCET DNA assembly method to build a plasmid from 13 GC-rich fragments with high efficiency in one step. Together with our previous direct cloning and recombineering tools, we present new synthetic biology options for refactoring large gene clusters for diverse applications.
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Affiliation(s)
- Chaoyi Song
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Ji Luan
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Qingwen Cui
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Qiuyue Duan
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Zhen Li
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Yunsheng Gao
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Ruijuan Li
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Aiying Li
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Yuemao Shen
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Yuezhong Li
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - A. Francis Stewart
- Genomics, Biotechnology Center, Technische Universität Dresden, Tatzberg 47-51, Dresden 01307, Germany
- GenArc GmbH, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Youming Zhang
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Jun Fu
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Hailong Wang
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
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Generation of a cluster-free Streptomyces albus chassis strains for improved heterologous expression of secondary metabolite clusters. Metab Eng 2018; 49:316-324. [DOI: 10.1016/j.ymben.2018.09.004] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/26/2018] [Accepted: 09/05/2018] [Indexed: 12/19/2022]
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Ji CH, Kim JP, Kang HS. Library of Synthetic Streptomyces Regulatory Sequences for Use in Promoter Engineering of Natural Product Biosynthetic Gene Clusters. ACS Synth Biol 2018; 7:1946-1955. [PMID: 29966097 DOI: 10.1021/acssynbio.8b00175] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Promoter engineering has emerged as a powerful tool to activate transcriptionally silent natural product biosynthetic gene clusters found in bacterial genomes. Since biosynthetic gene clusters are composed of multiple operons, their promoter engineering requires the use of a set of regulatory sequences with a similar level of activities. Although several successful examples of promoter engineering have been reported, its widespread use has been limited due to the lack of a library of regulatory sequences suitable for use in promoter engineering of large, multiple operon-containing biosynthetic gene clusters. Here, we present the construction of a library of constitutively active, synthetic Streptomyces regulatory sequences. The promoter assay system has been developed using a single-module nonribosomal peptide synthetase that produces the peptide blue pigment indigoidine, allowing for the rapid screening of a large pool of regulatory sequences. The highly randomized regulatory sequences in both promoter and ribosome binding site regions were screened for their ability to produce the blue pigment, and they are classified into the strong, medium, and weak regulatory sequences based on the strength of a blue color. We demonstrated the utility of our synthetic regulatory sequences for promoter engineering of natural product biosynthetic gene clusters using the actinorhodin gene cluster as a model cluster. We believe that the set of Streptomyces regulatory sequences we report here will facilitate the discovery of new natural products from silent, cryptic biosynthetic gene clusters found in sequenced Streptomyces genomes.
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Affiliation(s)
- Chang-Hun Ji
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea
| | - Jong-Pyung Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungbuk 28116, Korea
| | - Hahk-Soo Kang
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea
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Tao W, Yang A, Deng Z, Sun Y. CRISPR/Cas9-Based Editing of Streptomyces for Discovery, Characterization, and Production of Natural Products. Front Microbiol 2018; 9:1660. [PMID: 30087666 PMCID: PMC6066502 DOI: 10.3389/fmicb.2018.01660] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/04/2018] [Indexed: 12/21/2022] Open
Abstract
Microbial natural products (NPs) especially of the Streptomyces genus have been regarded as an unparalleled resource for pharmaceutical drugs discovery. Moreover, recent progress in sequencing technologies and computational resources further reinforces to identify numerous NP biosynthetic gene clusters (BGCs) from the genomes of Streptomyces. However, the majority of these BGCs are silent or poorly expressed in native strains and remain to be activated and investigated, which relies heavily on efficient genome editing approaches. Accordingly, numerous strategies are developed, especially, the most recently developed, namely, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated (Cas) system reveals remarkable higher accuracy and efficiency for genome editing in various model organisms including the Streptomyces. In this mini review, we highlight the application of CRISPR/Cas9-based approaches in Streptomyces, focus on the editing of BGCs either in vivo or in vitro, as well as target cloning of large-sized BGCs and heterologous expression in a genetically manipulatable host, for discovery, characterization, reengineering, and production of potential pharmaceutical drugs.
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Affiliation(s)
- Weixin Tao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University School of Pharmaceutical Sciences, Wuhan, China
| | - Anna Yang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University School of Pharmaceutical Sciences, Wuhan, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University School of Pharmaceutical Sciences, Wuhan, China
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University School of Pharmaceutical Sciences, Wuhan, China
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Whole-Genome Analysis of Bacillus thuringiensis Revealing Partial Genes as a Source of Novel Cry Toxins. Appl Environ Microbiol 2018; 84:AEM.00277-18. [PMID: 29752275 DOI: 10.1128/aem.00277-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 05/05/2018] [Indexed: 12/20/2022] Open
Abstract
Despite the successful application of crystal proteins (Cry) from Bacillus thuringiensis as biological control agents against insects, there is an increasing demand to identify new Cry toxins having higher toxicity and broad-spectrum activity against insects and plant-parasitic nematodes. To find novel Cry toxins, we screened 100 whole-genome sequences of B. thuringiensis Surprisingly, in addition to full Cry toxins, we found partial sequences, such as typical N-terminal or C-terminal regions with conserved domains, widely distributed among 20 strains of B. thuringiensis In order to further elucidate the functions of partial genes, here, we selected a partial sequence from strain C15, having 28% similarity with the N terminus of Cry5Ba and lacking a typical C terminus, and denoted it Cry5B-like N terminus. This fragment when coexpressed as a fusion protein with the C terminus of Cry5Ba (N-C fusion protein) produces pyramidal crystals. A recombinant N-C fusion protein having a 50% lethal concentration (LC50) of 23.7 μg/ml severely affected the life span, growth, and survival rate of nematodes. Light microscopy showed damage to the intestine of nematodes, confirming the pathogenicity of the N-C fusion protein. Last, the green fluorescent protein (GFP)-labeled mutant Caenorhabditis elegans FT63 showed significant damage to the intestine upon feeding N-C fusion toxin compared to the control. These results imply that partial genes can be a source of new Cry toxins, and further understanding about functions of partial cry genes can help in the study of the evolutionary strategy of B. thuringiensis to produce the multidomain toxins.IMPORTANCE Genomic analysis revealed that coding sequences for N termini and C termini of crystal proteins are widely distributed in B. thuringiensis We found Cry5B-like N terminus, lacking typical C terminus, was unable to be expressed in wild-type strain C15. However, its fusion with the C terminus of Cry5Ba not only was successfully expressed but also exhibited activity against the nematodes. This study provides insight into a potential source for novel Cry toxins.
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Hug JJ, Bader CD, Remškar M, Cirnski K, Müller R. Concepts and Methods to Access Novel Antibiotics from Actinomycetes. Antibiotics (Basel) 2018; 7:E44. [PMID: 29789481 PMCID: PMC6022970 DOI: 10.3390/antibiotics7020044] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 12/25/2022] Open
Abstract
Actinomycetes have been proven to be an excellent source of secondary metabolites for more than half a century. Exhibiting various bioactivities, they provide valuable approved drugs in clinical use. Most microorganisms are still untapped in terms of their capacity to produce secondary metabolites, since only a small fraction can be cultured in the laboratory. Thus, improving cultivation techniques to extend the range of secondary metabolite producers accessible under laboratory conditions is an important first step in prospecting underexplored sources for the isolation of novel antibiotics. Currently uncultured actinobacteria can be made available by bioprospecting extreme or simply habitats other than soil. Furthermore, bioinformatic analysis of genomes reveals most producers to harbour many more biosynthetic gene clusters than compounds identified from any single strain, which translates into a silent biosynthetic potential of the microbial world for the production of yet unknown natural products. This review covers discovery strategies and innovative methods recently employed to access the untapped reservoir of natural products. The focus is the order of actinomycetes although most approaches are similarly applicable to other microbes. Advanced cultivation methods, genomics- and metagenomics-based approaches, as well as modern metabolomics-inspired methods are highlighted to emphasise the interplay of different disciplines to improve access to novel natural products.
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Affiliation(s)
- Joachim J Hug
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Chantal D Bader
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Maja Remškar
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Katarina Cirnski
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
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Eyles TH, Vior NM, Truman AW. Rapid and Robust Yeast-Mediated Pathway Refactoring Generates Multiple New Bottromycin-Related Metabolites. ACS Synth Biol 2018; 7:1211-1218. [PMID: 29694038 DOI: 10.1021/acssynbio.8b00038] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Heterologous expression of biosynthetic gene clusters (BGCs) represents an attractive route to the production of new natural products, but is often hampered by poor yields. It is therefore important to develop tools that enable rapid refactoring, gene insertion/deletion, and targeted mutations in BGCs. Ideally, these tools should be highly efficient, affordable, accessible, marker free, and flexible for use with a wide range of BGCs. Here, we present a one-step yeast-based method that enables efficient, cheap, and flexible modifications to BGCs. Using the BGC for the antibiotic bottromycin, we showcase multiple modifications including refactoring, gene deletions and targeted mutations. This facilitated the construction of an inducible, riboswitch-controlled pathway that achieved a 120-fold increase in pathway productivity in a heterologous streptomycete host. Additionally, an unexpected biosynthetic bottleneck resulted in the production of a suite of new bottromycin-related metabolites.
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Affiliation(s)
- Tom H. Eyles
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, U.K
| | - Natalia M. Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, U.K
| | - Andrew W. Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, U.K
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Winn M, Francis D, Micklefield J. De novo Biosynthesis of “Non-Natural” Thaxtomin Phytotoxins. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801525] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Michael Winn
- School of Chemistry; Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Daniel Francis
- School of Chemistry; Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Jason Micklefield
- School of Chemistry; Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
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Winn M, Francis D, Micklefield J. De novo Biosynthesis of "Non-Natural" Thaxtomin Phytotoxins. Angew Chem Int Ed Engl 2018; 57:6830-6833. [PMID: 29603527 PMCID: PMC6001691 DOI: 10.1002/anie.201801525] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Indexed: 02/04/2023]
Abstract
Thaxtomins are diketopiperazine phytotoxins produced by Streptomyces scabies and other actinobacterial plant pathogens that inhibit cellulose biosynthesis in plants. Due to their potent bioactivity and novel mode of action there has been considerable interest in developing thaxtomins as herbicides for crop protection. To address the need for more stable derivatives, we have developed a new approach for structural diversification of thaxtomins. Genes encoding the thaxtomin NRPS from S. scabies, along with genes encoding a promiscuous tryptophan synthase (TrpS) from Salmonella typhimurium, were assembled in a heterologous host Streptomyces albus. Upon feeding indole derivatives to the engineered S. albus strain, tryptophan intermediates with alternative substituents are biosynthesized and incorporated by the NRPS to deliver a series of thaxtomins with different functionalities in place of the nitro group. The approach described herein, demonstrates how genes from different pathways and different bacterial origins can be combined in a heterologous host to create a de novo biosynthetic pathway to "non-natural" product target compounds.
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Affiliation(s)
- Michael Winn
- School of ChemistryManchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Daniel Francis
- School of ChemistryManchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Jason Micklefield
- School of ChemistryManchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
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Discovery of recombinases enables genome mining of cryptic biosynthetic gene clusters in Burkholderiales species. Proc Natl Acad Sci U S A 2018; 115:E4255-E4263. [PMID: 29666226 PMCID: PMC5939090 DOI: 10.1073/pnas.1720941115] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Natural products biosynthesized by cryptic gene clusters represent a largely untapped source for drug discovery. However, mining of these products by promoter engineering is restricted by the lack of streamlined genetic tools, especially in nonmodel biosynthetic gene cluster (BGC)-rich bacteria. Here, we describe the discovery of a pair of bacteriophage recombinases and application of recombinase-assisted promoter engineering to rapidly identify and activate several cryptic biosynthetic gene clusters in two Burkholderiales strains that currently lack effective genetic tools. Construction of an efficient genome engineering platform in a natural product producer expedites mining of cryptic BGCs in their native backgrounds, and host melioration for yield or structure optimization. This strategy enables potentially scalable discovery of novel metabolites with intriguing bioactivities from many other bacteria. Bacterial genomes encode numerous cryptic biosynthetic gene clusters (BGCs) that represent a largely untapped source of drugs or pesticides. Mining of the cryptic products is limited by the unavailability of streamlined genetic tools in native producers. Precise genome engineering using bacteriophage recombinases is particularly useful for genome mining. However, recombinases are usually host-specific. The genome-guided discovery of novel recombinases and their transient expression could boost cryptic BGC mining. Herein, we reported a genetic system employing Red recombinases from Burkholderiales strain DSM 7029 for efficient genome engineering in several Burkholderiales species that currently lack effective genetic tools. Using specialized recombinases-assisted in situ insertion of functional promoters, we successfully mined five cryptic nonribosomal peptide synthetase/polyketide synthase BGCs, two of which were silent. Two classes of lipopeptides, glidopeptins and rhizomides, were identified through extensive spectroscopic characterization. This recombinase expression strategy offers utility within other bacteria species, allowing bioprospecting for potentially scalable discovery of novel metabolites with attractive bioactivities.
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Choi SS, Katsuyama Y, Bai L, Deng Z, Ohnishi Y, Kim ES. Genome engineering for microbial natural product discovery. Curr Opin Microbiol 2018; 45:53-60. [PMID: 29510374 DOI: 10.1016/j.mib.2018.02.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 02/14/2018] [Accepted: 02/14/2018] [Indexed: 11/16/2022]
Abstract
The discovery and development of microbial natural products (MNPs) have played pivotal roles in the fields of human medicine and its related biotechnology sectors over the past several decades. The post-genomic era has witnessed the development of microbial genome mining approaches to isolate previously unsuspected MNP biosynthetic gene clusters (BGCs) hidden in the genome, followed by various BGC awakening techniques to visualize compound production. Additional microbial genome engineering techniques have allowed higher MNP production titers, which could complement a traditional culture-based MNP chasing approach. Here, we describe recent developments in the MNP research paradigm, including microbial genome mining, NP BGC activation, and NP overproducing cell factory design.
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Affiliation(s)
- Si-Sun Choi
- Department of Biological Engineering, Inha University, Incheon, Republic of Korea
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, China
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - Eung-Soo Kim
- Department of Biological Engineering, Inha University, Incheon, Republic of Korea.
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